Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~julia_p/projects/1G59_old.out Дата изменения: Sun Sep 27 23:59:54 2009 Дата индексирования: Tue Oct 2 12:23:32 2012 Кодировка:

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This structure has broken O3'[i] to P[i+1] linkages
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3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
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1. The list of the parameters given below correspond to the 5' to 3' direction
of strand I and 3' to 5' direction of strand II.

2. All angular parameters, except for the phase angle of sugar pseudo-
rotation, are measured in degrees in the range of [-180, +180], and all
displacements are measured in Angstrom units.
****************************************************************************
File name: 1G59_old.pdb
Date and time: Sun Sep 27 23:59:54 2009

Number of base-pairs: 56
Number of atoms: 11092
****************************************************************************
HEADER LIGASE/RNA 31-OCT-00 1G59
TITLE GLUTAMYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(GLU).
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRNA(GLU);
COMPND 3 CHAIN: B, D;
COMPND 4 ENGINEERED: YES;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: GLUTAMYL-TRNA SYNTHETASE;
COMPND 7 CHAIN: A, C;
COMPND 8 EC: 6.1.1.17;
COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 SYNTHETIC: YES;
SOURCE 3 MOL_ID: 2;
SOURCE 4 ORGANISM_SCIENTIFIC: THERMUS THERMOPHILUS;
SOURCE 5 ORGANISM_TAXID: 274;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PK7
KEYWDS AMINOACYL-TRNA SYNTHETASE, PROTEIN-RNA COMPLEX, TRANSFER
KEYWDS 2 RNA, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI,
KEYWDS 3 STRUCTURAL GENOMICS, LIGASE/RNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR S.SEKINE,O.NUREKI,A.SHIMADA,D.G.VASSYLYEV,S.YOKOYAMA,RIKEN
AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 1G59 1 VERSN
REVDAT 1 01-SEP-01 1G59 0
JRNL AUTH S.SEKINE,O.NUREKI,A.SHIMADA,D.G.VASSYLYEV,
JRNL AUTH 2 S.YOKOYAMA
JRNL TITL STRUCTURAL BASIS FOR ANTICODON RECOGNITION BY
JRNL TITL 2 DISCRIMINATING GLUTAMYL-TRNA SYNTHETASE.
JRNL REF NAT.STRUCT.BIOL. V. 8 203 2001
JRNL REFN ISSN 1072-8368
JRNL PMID 11224561
JRNL DOI 10.1038/84927
HELIX 1 1 HIS A 15 ASN A 32 1 18
HELIX 2 2 GLY A 51 LEU A 63 1 13
HELIX 3 3 GLN A 82 GLU A 84 5 3
HELIX 4 4 ARG A 85 LYS A 98 1 14
HELIX 5 5 THR A 108 LYS A 119 1 12
HELIX 6 6 GLY A 124 ILE A 129 5 6
HELIX 7 7 PRO A 130 ARG A 140 1 11
HELIX 8 8 GLN A 171 ILE A 173 5 3
HELIX 9 9 THR A 186 MET A 198 1 13
HELIX 10 10 GLU A 208 LEU A 210 5 3
HELIX 11 11 SER A 212 PHE A 223 1 12
HELIX 12 12 SER A 252 GLU A 259 1 8
HELIX 13 13 LEU A 262 MET A 273 1 12
HELIX 14 14 THR A 285 PHE A 293 1 9
HELIX 15 15 THR A 294 ARG A 297 5 4
HELIX 16 16 ASP A 306 VAL A 321 1 16
HELIX 17 17 SER A 323 ALA A 338 1 16
HELIX 18 18 SER A 344 ARG A 356 1 13
HELIX 19 19 PRO A 357 PHE A 359 5 3
HELIX 20 20 LYS A 363 ALA A 369 1 7
HELIX 21 21 ARG A 370 PHE A 373 5 4
HELIX 22 22 SER A 380 LEU A 391 1 12
HELIX 23 23 GLY A 390 GLU A 396 1 7
HELIX 24 24 LEU A 397 GLN A 404 1 8
HELIX 25 25 THR A 408 LYS A 423 1 16
HELIX 26 26 LEU A 427 THR A 439 1 13
HELIX 27 27 GLY A 446 GLY A 455 1 10
HELIX 28 28 GLY A 455 ALA A 468 1 14
HELIX 29 29 HIS C 15 ASN C 32 1 18
HELIX 30 30 ASP C 44 TYR C 48 5 5
HELIX 31 31 ALA C 52 LEU C 63 1 12
HELIX 32 32 ARG C 85 LYS C 98 1 14
HELIX 33 33 THR C 108 LYS C 119 1 12
HELIX 34 34 GLY C 124 ILE C 129 5 6
HELIX 35 35 PRO C 130 ARG C 140 1 11
HELIX 36 36 GLN C 171 ILE C 173 5 3
HELIX 37 37 THR C 186 MET C 198 1 13
HELIX 38 38 GLU C 208 LEU C 210 5 3
HELIX 39 39 SER C 212 PHE C 223 1 12
HELIX 40 40 SER C 252 GLU C 259 1 8
HELIX 41 41 LEU C 262 MET C 273 1 12
HELIX 42 42 THR C 285 PHE C 293 1 9
HELIX 43 43 THR C 294 ARG C 297 5 4
HELIX 44 44 ASP C 306 VAL C 321 1 16
HELIX 45 45 SER C 323 ALA C 338 1 16
HELIX 46 46 SER C 344 ARG C 356 1 13
HELIX 47 47 PRO C 357 PHE C 359 5 3
HELIX 48 48 LYS C 363 ALA C 369 1 7
HELIX 49 49 ARG C 370 PHE C 373 5 4
HELIX 50 50 SER C 380 LEU C 391 1 12
HELIX 51 51 GLY C 390 GLU C 396 1 7
HELIX 52 52 LEU C 397 GLN C 404 1 8
HELIX 53 53 THR C 408 LYS C 423 1 16
HELIX 54 54 LYS C 426 THR C 439 1 14
HELIX 55 55 GLY C 446 GLY C 455 1 10
HELIX 56 56 GLY C 455 ALA C 468 1 14
SHEET 1 A 2 VAL A 3 ILE A 6 0
SHEET 2 A 2 ARG A 35 VAL A 38 1 O ARG A 35 N THR A 4
SHEET 1 B 3 ALA A 102 ALA A 105 0
SHEET 2 B 3 VAL A 145 LEU A 148 -1 N VAL A 145 O ALA A 105
SHEET 3 B 3 VAL A 177 LEU A 179 -1 N LEU A 178 O ILE A 146
SHEET 1 C 2 THR A 155 ASP A 160 0
SHEET 2 C 2 GLY A 164 ASP A 169 -1 N GLY A 164 O ASP A 160
SHEET 1 D 2 ASP A 202 ALA A 206 0
SHEET 2 D 2 ARG A 229 MET A 233 1 O ARG A 229 N VAL A 203
SHEET 1 E 2 VAL C 3 ILE C 6 0
SHEET 2 E 2 ARG C 35 VAL C 38 1 O ARG C 35 N THR C 4
SHEET 1 F 3 ALA C 102 ALA C 105 0
SHEET 2 F 3 VAL C 145 LEU C 148 -1 N VAL C 145 O ALA C 105
SHEET 3 F 3 VAL C 177 LEU C 179 -1 N LEU C 178 O ILE C 146
SHEET 1 G 2 THR C 155 ASP C 160 0
SHEET 2 G 2 GLY C 164 ASP C 169 -1 O GLY C 164 N ASP C 160
SHEET 1 H 2 ASP C 202 ALA C 206 0
SHEET 2 H 2 ARG C 229 MET C 233 1 O ARG C 229 N VAL C 203
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.011) B:.501_:[..G]G-----C[..C]:.572_:B (0.010) |
2 (0.008) B:.502_:[..G]G-*---U[..U]:.571_:B (0.015) |
3 (0.011) B:.503_:[..C]C-----G[..G]:.570_:B (0.007) |
4 (0.010) B:.504_:[..C]C-----G[..G]:.569_:B (0.008) |
5 (0.010) B:.505_:[..C]C-----G[..G]:.568_:B (0.007) |
6 (0.011) B:.506_:[..C]C-----G[..G]:.567_:B (0.007) |
7 (0.012) B:.507_:[..A]Ax----U[..U]:.566_:B (0.014) |
8 (0.007) B:.549_:[..G]G-----C[..C]:.565_:B (0.010) |
9 (0.006) B:.550_:[..G]G-----C[..C]:.564_:B (0.011) |
10 (0.007) B:.551_:[..G]G-----C[..C]:.563_:B (0.010) |
11 (0.007) B:.552_:[..G]G-----C[..C]:.562_:B (0.010) |
12 (0.009) B:.553_:[..G]G----xC[..C]:.561_:B (0.010) |
13 (0.016) B:.554_:[..U]U-*--xA[..A]:.558_:B (0.008) |
14 (0.017) B:.555_:[..U]Ux**+xG[..G]:.517_:B (0.015) x
15 (0.008) B:.538_:[..A]A-*---C[..C]:.532_:B (0.012) |
16 (0.009) B:.539_:[..G]G-----C[..C]:.531_:B (0.010) |
17 (0.012) B:.540_:[..G]G-----C[..C]:.530_:B (0.010) |
18 (0.012) B:.541_:[..C]C-----G[..G]:.529_:B (0.011) |
19 (0.011) B:.542_:[..C]C-----G[..G]:.528_:B (0.006) |
20 (0.008) B:.543_:[..G]G-----C[..C]:.527_:B (0.010) |
21 (0.007) B:.544_:[..A]Ax*---G[..G]:.526_:B (0.006) |
22 (0.010) B:.510_:[..G]G-----C[..C]:.525_:B (0.010) |
23 (0.015) B:.511_:[..U]U-----A[..A]:.524_:B (0.013) |
24 (0.012) B:.512_:[..C]C----xG[..G]:.523_:B (0.007) |
25 (0.017) B:.513_:[..U]U-**+xA[..A]:.546_:B (0.008) |
26 (0.009) B:.514_:[..A]A-**-xU[..U]:.508_:B (0.014) |
27 (0.008) B:.515_:[..G]Gx**+xC[..C]:.548_:B (0.009) x
28 (0.008) B:.518_:[..G]Gx---xC[..C]:.556_:B (0.015) +
29 (0.009) D:.501_:[..G]G-----C[..C]:.572_:D (0.010) |
30 (0.010) D:.502_:[..G]G-*---U[..U]:.571_:D (0.016) |
31 (0.010) D:.503_:[..C]C-----G[..G]:.570_:D (0.008) |
32 (0.009) D:.504_:[..C]C-----G[..G]:.569_:D (0.006) |
33 (0.009) D:.505_:[..C]C-----G[..G]:.568_:D (0.009) |
34 (0.008) D:.506_:[..C]C-----G[..G]:.567_:D (0.008) |
35 (0.009) D:.507_:[..A]Ax----U[..U]:.566_:D (0.015) |
36 (0.011) D:.549_:[..G]G-----C[..C]:.565_:D (0.012) |
37 (0.008) D:.550_:[..G]G-----C[..C]:.564_:D (0.010) |
38 (0.009) D:.551_:[..G]G-----C[..C]:.563_:D (0.014) |
39 (0.007) D:.552_:[..G]G-----C[..C]:.562_:D (0.011) |
40 (0.011) D:.553_:[..G]G----xC[..C]:.561_:D (0.009) |
41 (0.017) D:.554_:[..U]U-*--xA[..A]:.558_:D (0.008) |
42 (0.019) D:.555_:[..U]Ux**+xG[..G]:.517_:D (0.022) x
43 (0.011) D:.538_:[..A]A-*---C[..C]:.532_:D (0.013) |
44 (0.013) D:.539_:[..G]G-----C[..C]:.531_:D (0.008) |
45 (0.008) D:.540_:[..G]G-----C[..C]:.530_:D (0.009) |
46 (0.010) D:.541_:[..C]C-----G[..G]:.529_:D (0.008) |
47 (0.010) D:.542_:[..C]C-----G[..G]:.528_:D (0.006) |
48 (0.009) D:.543_:[..G]G-----C[..C]:.527_:D (0.012) |
49 (0.009) D:.544_:[..A]Ax*---G[..G]:.526_:D (0.009) |
50 (0.010) D:.510_:[..G]G-----C[..C]:.525_:D (0.012) |
51 (0.018) D:.511_:[..U]U-----A[..A]:.524_:D (0.009) |
52 (0.011) D:.512_:[..C]C-----G[..G]:.523_:D (0.008) |
53 (0.016) D:.513_:[..U]U-*--xG[..G]:.522_:D (0.007) |
54 (0.010) D:.514_:[..A]A-**-xU[..U]:.508_:D (0.015) |
55 (0.010) D:.515_:[..G]Gx**+xC[..C]:.548_:D (0.008) x
56 (0.012) D:.518_:[..G]G-----C[..C]:.556_:D (0.032) +

Note: This structure contains 16[7] non-Watson-Crick base-pairs.
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 3.13 N1 - N3 3.08 N2 - O2 3.00
2 G-*---U [2] O6 - N3 3.11 N1 - O2 2.97
3 C-----G [3] O2 - N2 2.89 N3 - N1 2.93 N4 - O6 2.88
4 C-----G [3] O2 - N2 2.70 N3 - N1 2.89 N4 - O6 2.95
5 C-----G [3] O2 - N2 2.98 N3 - N1 2.93 N4 - O6 2.75
6 C-----G [3] O2 - N2 2.64 N3 - N1 2.97 N4 - O6 3.19
7 A-----U [2] N6 - O4 3.40 N1 - N3 3.14
8 G-----C [3] O6 - N4 3.31 N1 - N3 2.97 N2 - O2 2.52
9 G-----C [3] O6 - N4 3.34 N1 - N3 3.16 N2 - O2 2.90
10 G-----C [3] O6 - N4 2.87 N1 - N3 2.75 N2 - O2 2.51
11 G-----C [3] O6 - N4 3.48 N1 - N3 3.05 N2 - O2 2.53
12 G-----C [3] O6 - N4 3.25 N1 - N3 3.12 N2 - O2 2.93
13 U-*---A [3] O2 - N6 2.73 N3 - N7 3.09 O4 * O2P 3.99
14 U-**+-G [2] O2'- O6 3.53 O2 - N1 2.34
15 A-*---C [1] N6 - O2 3.05
16 G-----C [3] O6 - N4 3.09 N1 - N3 2.88 N2 - O2 2.58
17 G-----C [3] O6 - N4 3.25 N1 - N3 2.92 N2 - O2 2.52
18 C-----G [3] O2 - N2 2.52 N3 - N1 2.63 N4 - O6 2.63
19 C-----G [3] O2 - N2 2.52 N3 - N1 2.66 N4 - O6 2.69
20 G-----C [3] O6 - N4 2.79 N1 - N3 2.74 N2 - O2 2.63
21 A-*---G [2] N6 - O6 3.15 N1 - N1 2.72
22 G-----C [3] O6 - N4 3.08 N1 - N3 2.98 N2 - O2 2.76
23 U-----A [2] N3 - N1 2.78 O4 - N6 3.39
24 C-----G [3] O2 - N2 2.68 N3 - N1 2.91 N4 - O6 3.02
25 U-**+-A [1] O4 * N3 3.49
26 A-**--U [3] O2P* O4 3.35 N7 - N3 2.61 N6 - O2 2.49
27 G-**+-C [2] N1 - O2 3.03 N2 - N3 2.84
28 G-----C [3] O6 - N4 2.92 N1 - N3 3.02 N2 - O2 2.98
29 G-----C [3] O6 - N4 2.86 N1 - N3 2.86 N2 - O2 2.78
30 G-*---U [2] O6 - N3 2.79 N1 - O2 2.80
31 C-----G [3] O2 - N2 2.80 N3 - N1 2.92 N4 - O6 2.90
32 C-----G [3] O2 - N2 2.74 N3 - N1 2.92 N4 - O6 2.97
33 C-----G [3] O2 - N2 2.99 N3 - N1 2.92 N4 - O6 2.75
34 C-----G [3] O2 - N2 2.64 N3 - N1 2.97 N4 - O6 3.17
35 A-----U [2] N6 - O4 3.35 N1 - N3 3.12
36 G-----C [3] O6 - N4 3.29 N1 - N3 2.99 N2 - O2 2.58
37 G-----C [3] O6 - N4 3.31 N1 - N3 3.13 N2 - O2 2.89
38 G-----C [3] O6 - N4 2.94 N1 - N3 2.84 N2 - O2 2.63
39 G-----C [3] O6 - N4 3.74 N1 - N3 3.28 N2 - O2 2.78
40 G-----C [3] O6 - N4 3.45 N1 - N3 3.29 N2 - O2 3.06
41 U-*---A [3] O2 - N6 2.50 N3 - N7 2.89 O4 * O2P 3.94
42 U-**+-G [2] O2'- O6 3.74 O2 - N1 2.74
43 A-*---C [1] N6 - O2 3.09
44 G-----C [3] O6 - N4 3.05 N1 - N3 2.83 N2 - O2 2.59
45 G-----C [3] O6 - N4 3.26 N1 - N3 2.97 N2 - O2 2.61
46 C-----G [3] O2 - N2 2.53 N3 - N1 2.63 N4 - O6 2.59
47 C-----G [3] O2 - N2 2.48 N3 - N1 2.62 N4 - O6 2.64
48 G-----C [3] O6 - N4 2.77 N1 - N3 2.76 N2 - O2 2.67
49 A-*---G [2] N6 - O6 3.11 N1 - N1 2.75
50 G-----C [3] O6 - N4 3.12 N1 - N3 2.98 N2 - O2 2.73
51 U-----A [2] N3 - N1 2.78 O4 - N6 3.36
52 C-----G [3] O2 - N2 2.67 N3 - N1 2.93 N4 - O6 3.04
53 U-*---G [2] O2 - N1 2.52 N3 - O6 2.87
54 A-**--U [3] O2P* O4 3.46 N7 - N3 2.62 N6 - O2 2.53
55 G-**+-C [2] N1 - O2 2.97 N2 - N3 2.84
56 G-----C [3] O6 - N4 3.02 N1 - N3 3.02 N2 - O2 2.86
****************************************************************************
Overlap area in Angstrom^2 between polygons defined by atoms on successive
bases. Polygons projected in the mean plane of the designed base-pair step.

Values in parentheses measure the overlap of base ring atoms only. Those
outside parentheses include exocyclic atoms on the ring. Intra- and
inter-strand overlap is designated according to the following diagram:

i2 3' 5' j2
/|\ |
| |
Strand I | | II
| |
| |
| \|/
i1 5' 3' j1

step i1-i2 i1-j2 j1-i2 j1-j2 sum
1 GG/UC 0.56( 0.00) 0.00( 0.00) 0.00( 0.00) 1.94( 0.01) 2.50( 0.01)
2 GC/GU 6.79( 3.91) 0.00( 0.00) 0.00( 0.00) 6.51( 3.94) 13.30( 7.85)
3 CC/GG 0.62( 0.13) 0.00( 0.00) 0.16( 0.00) 2.69( 1.22) 3.47( 1.35)
4 CC/GG 0.54( 0.00) 0.00( 0.00) 0.07( 0.00) 3.98( 2.71) 4.58( 2.71)
5 CC/GG 0.48( 0.11) 0.00( 0.00) 0.24( 0.00) 2.71( 1.24) 3.42( 1.35)
6 CA/UG 0.53( 0.00) 0.00( 0.00) 1.42( 0.65) 0.01( 0.00) 1.97( 0.65)
7 AG/CU 0.00( 0.00) 0.00( 0.00) 0.06( 0.00) 2.17( 0.70) 2.23( 0.70)
8 GG/CC 2.57( 1.11) 0.00( 0.00) 0.40( 0.00) 0.09( 0.00) 3.05( 1.11)
9 GG/CC 3.48( 2.05) 0.00( 0.00) 0.31( 0.00) 0.65( 0.00) 4.43( 2.05)
10 GG/CC 5.06( 3.70) 0.00( 0.00) 0.03( 0.00) 0.48( 0.00) 5.57( 3.70)
11 GG/CC 4.16( 2.48) 0.00( 0.00) 0.41( 0.00) 0.00( 0.00) 4.57( 2.48)
12 GU/AC 7.21( 4.53) 0.00( 0.00) 0.00( 0.00) 3.33( 0.90) 10.54( 5.43)
13 UU/GA 6.59( 3.44) 0.00( 0.00) 0.00( 0.00) 5.87( 3.11) 12.47( 6.55)
14 UA/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
15 AG/CC 4.15( 2.41) 0.00( 0.00) 0.00( 0.00) 5.74( 2.74) 9.90( 5.15)
16 GG/CC 2.50( 0.99) 0.00( 0.00) 0.36( 0.00) 0.82( 0.04) 3.68( 1.03)
17 GC/GC 5.87( 2.73) 0.00( 0.00) 0.00( 0.00) 6.00( 2.98) 11.87( 5.71)
18 CC/GG 0.06( 0.00) 0.00( 0.00) 0.89( 0.00) 3.33( 1.87) 4.28( 1.87)
19 CG/CG 0.01( 0.00) 0.00( 0.00) 5.08( 2.30) 0.00( 0.00) 5.09( 2.30)
20 GA/GC 2.45( 0.34) 0.00( 0.00) 0.00( 0.00) 4.31( 1.92) 6.76( 2.26)
21 AG/CG 0.00( 0.00) 0.00( 0.00) 0.70( 0.00) 1.52( 0.95) 2.21( 0.95)
22 GU/AC 4.88( 2.17) 0.00( 0.00) 0.00( 0.00) 3.05( 1.73) 7.93( 3.90)
23 UC/GA 0.11( 0.00) 0.00( 0.00) 0.00( 0.00) 3.89( 2.45) 4.00( 2.45)
24 CU/AG 1.74( 0.16) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 1.74( 0.16)
25 UA/UA 0.00( 0.00) 2.97( 0.39) 0.00( 0.00) 0.00( 0.00) 2.97( 0.39)
26 AG/CU 4.83( 2.31) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.83( 2.31)
27 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
28 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
29 GG/UC 0.90( 0.00) 0.00( 0.00) 0.02( 0.00) 1.32( 0.00) 2.24( 0.00)
30 GC/GU 6.86( 4.14) 0.00( 0.00) 0.00( 0.00) 6.65( 4.06) 13.51( 8.20)
31 CC/GG 0.74( 0.16) 0.00( 0.00) 0.19( 0.00) 2.64( 1.17) 3.57( 1.33)
32 CC/GG 0.40( 0.00) 0.00( 0.00) 0.07( 0.00) 4.01( 2.73) 4.48( 2.73)
33 CC/GG 0.65( 0.17) 0.00( 0.00) 0.17( 0.00) 2.62( 1.17) 3.44( 1.34)
34 CA/UG 0.59( 0.00) 0.00( 0.00) 1.37( 0.63) 0.00( 0.00) 1.96( 0.63)
35 AG/CU 0.00( 0.00) 0.00( 0.00) 0.14( 0.00) 1.67( 0.48) 1.81( 0.48)
36 GG/CC 2.59( 1.07) 0.00( 0.00) 0.75( 0.00) 0.00( 0.00) 3.34( 1.07)
37 GG/CC 3.42( 1.95) 0.00( 0.00) 0.45( 0.00) 0.60( 0.00) 4.47( 1.95)
38 GG/CC 5.04( 3.70) 0.00( 0.00) 0.01( 0.00) 0.42( 0.00) 5.46( 3.70)
39 GG/CC 4.11( 2.49) 0.00( 0.00) 0.20( 0.00) 0.00( 0.00) 4.31( 2.49)
40 GU/AC 7.24( 4.67) 0.00( 0.00) 0.00( 0.00) 3.97( 1.25) 11.21( 5.92)
41 UU/GA 7.23( 4.29) 0.00( 0.00) 0.00( 0.00) 5.20( 2.93) 12.43( 7.22)
42 UA/CG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
43 AG/CC 4.07( 2.23) 0.00( 0.00) 0.00( 0.00) 5.64( 2.61) 9.71( 4.84)
44 GG/CC 2.76( 1.22) 0.00( 0.00) 0.34( 0.00) 0.60( 0.01) 3.70( 1.22)
45 GC/GC 5.91( 2.77) 0.00( 0.00) 0.00( 0.00) 5.69( 2.76) 11.59( 5.53)
46 CC/GG 0.11( 0.00) 0.00( 0.00) 0.81( 0.00) 3.36( 1.93) 4.28( 1.93)
47 CG/CG 0.03( 0.00) 0.00( 0.00) 5.06( 2.27) 0.00( 0.00) 5.09( 2.27)
48 GA/GC 2.60( 0.44) 0.00( 0.00) 0.00( 0.00) 4.42( 1.97) 7.02( 2.41)
49 AG/CG 0.00( 0.00) 0.00( 0.00) 0.81( 0.00) 1.37( 0.85) 2.17( 0.85)
50 GU/AC 5.14( 2.34) 0.00( 0.00) 0.00( 0.00) 3.26( 1.87) 8.40( 4.21)
51 UC/GA 0.28( 0.00) 0.00( 0.00) 0.00( 0.00) 3.76( 2.35) 4.04( 2.35)
52 CU/GG 1.38( 0.05) 0.00( 0.00) 0.00( 0.00) 2.90( 1.40) 4.27( 1.45)
53 UA/UG 0.00( 0.00) 2.56( 0.19) 6.17( 4.48) 0.00( 0.00) 8.73( 4.67)
54 AG/CU 4.86( 2.31) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.86( 2.31)
55 GG/CC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
****************************************************************************
Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in
the coordinate system of the given structure

bp Ox Oy Oz Nx Ny Nz
1 G-C 25.81 89.06 67.58 -0.60 -0.20 -0.77
2 G-U 24.97 88.71 65.09 -0.73 -0.29 -0.62
3 C-G 23.22 87.20 62.67 -0.70 -0.33 -0.63
4 C-G 20.82 84.48 61.42 -0.77 -0.38 -0.52
5 C-G 18.28 81.78 60.29 -0.77 -0.37 -0.52
6 C-G 14.33 80.71 60.10 -0.85 -0.22 -0.49
7 A-U 11.17 80.36 59.90 -0.88 -0.05 -0.46
8 G-C 7.42 79.86 60.75 -0.89 -0.04 -0.45
9 G-C 4.21 81.68 59.34 -0.87 0.03 -0.49
10 G-C 2.05 82.91 56.41 -0.74 -0.04 -0.67
11 G-C 0.78 82.63 53.38 -0.76 -0.11 -0.64
12 G-C 0.03 80.96 50.28 -0.80 -0.15 -0.58
13 U-A -1.14 78.75 46.80 -0.81 -0.28 -0.52
14 U+G -4.79 78.10 47.22 -0.85 -0.33 -0.41
15 A-C 21.07 36.78 54.32 -0.53 0.80 -0.28
16 G-C 18.48 38.84 53.48 -0.60 0.79 -0.10
17 G-C 15.38 41.06 54.10 -0.55 0.84 0.05
18 C-G 13.29 43.30 55.17 -0.48 0.88 -0.00
19 C-G 12.45 46.48 56.99 -0.37 0.93 0.01
20 G-C 12.77 50.64 57.94 -0.17 0.98 -0.14
21 A-G 13.63 53.98 58.44 -0.11 0.97 -0.23
22 G-C 16.60 57.66 58.60 -0.02 0.83 -0.56
23 U-A 16.35 59.76 55.01 -0.13 0.84 -0.53
24 C-G 15.76 61.25 52.04 -0.26 0.79 -0.55
25 U+A 10.48 62.76 52.10 -0.46 0.79 -0.41
26 A-U 10.03 64.80 48.99 -0.37 0.80 -0.47
27 G+C 6.72 68.09 50.06 -0.31 0.94 -0.13
28 G-C -7.00 73.26 40.43 -0.69 -0.55 -0.47
29 G-C 85.13 89.55 129.73 -0.74 -0.08 -0.66
30 G-U 83.52 89.17 127.06 -0.79 -0.27 -0.56
31 C-G 81.68 87.43 125.09 -0.76 -0.36 -0.54
32 C-G 79.16 84.64 124.11 -0.83 -0.39 -0.40
33 C-G 76.54 81.87 123.45 -0.85 -0.37 -0.38
34 C-G 72.60 80.81 123.92 -0.91 -0.25 -0.33
35 A-U 69.45 80.41 124.16 -0.93 -0.10 -0.34
36 G-C 65.91 79.94 125.57 -0.95 -0.09 -0.29
37 G-C 62.56 81.87 124.59 -0.94 0.01 -0.35
38 G-C 59.94 83.11 122.03 -0.83 -0.04 -0.55
39 G-C 58.27 82.86 119.26 -0.85 -0.13 -0.50
40 G-C 56.81 81.15 116.20 -0.86 -0.17 -0.48
41 U-A 55.03 78.94 113.23 -0.87 -0.33 -0.36
42 U+G 51.61 78.21 114.52 -0.89 -0.39 -0.23
43 A-C 78.61 36.99 116.99 -0.56 0.80 -0.19
44 G-C 75.85 39.06 116.58 -0.62 0.78 -0.03
45 G-C 72.90 41.27 117.73 -0.54 0.83 0.14
46 C-G 71.09 43.40 119.10 -0.48 0.87 0.11
47 C-G 70.51 46.60 121.08 -0.35 0.93 0.09
48 G-C 70.96 50.67 122.03 -0.19 0.97 -0.11
49 A-G 71.84 54.12 122.37 -0.15 0.97 -0.19
50 G-C 74.77 57.78 122.04 -0.12 0.83 -0.54
51 U-A 73.99 59.73 118.66 -0.21 0.82 -0.53
52 C-G 72.87 61.36 115.75 -0.36 0.78 -0.52
53 U-G 69.28 63.20 115.17 -0.41 0.83 -0.38
54 A-U 66.73 64.82 113.63 -0.43 0.81 -0.40
55 G+C 63.55 68.11 115.20 -0.33 0.94 -0.09
56 G-C 48.90 73.59 108.09 -0.67 -0.71 -0.21
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.39 0.01 0.06 -2.50 -15.51 -0.44
2 G-U -2.08 -0.21 0.22 15.58 -8.70 1.87
3 C-G 0.17 -0.09 -0.48 17.84 -7.11 -1.36
4 C-G 0.33 -0.19 -0.65 9.98 -0.77 1.23
5 C-G 0.18 -0.20 -0.52 4.47 4.43 -5.50
6 C-G 0.78 -0.14 -0.12 -13.65 3.32 5.13
7 A-U 0.86 0.21 -0.01 -10.57 -2.51 3.71
8 G-C -0.43 -0.03 -0.48 -4.25 2.72 7.59
9 G-C -0.65 0.00 -0.80 -9.56 7.25 2.08
10 G-C -0.30 -0.39 -1.16 -19.20 3.11 0.76
11 G-C 0.02 0.12 -0.68 -8.36 7.67 9.14
12 G-C -1.03 -0.13 0.09 -1.16 11.65 3.26
13 U-A 4.58 -2.70 0.37 -4.61 10.13 -85.28
14 U+G 0.52 -5.03 0.37 17.31 5.01 -93.99
15 A-C -5.03 -0.81 1.23 16.40 13.14 5.57
16 G-C -0.19 -0.08 0.12 12.65 -8.06 5.05
17 G-C -0.36 -0.07 -0.53 -2.66 -8.06 8.56
18 C-G -0.03 -0.37 -0.21 7.77 -5.23 0.28
19 C-G 0.44 -0.46 -0.47 4.28 -4.25 1.18
20 G-C -0.09 -0.23 -0.22 -19.94 -15.65 0.26
21 A-G 0.19 1.45 -0.06 -18.46 -17.13 -7.53
22 G-C -0.31 -0.04 0.01 7.41 3.40 2.10
23 U-A -0.24 -0.03 0.35 -7.68 -4.03 12.34
24 C-G -0.01 -0.10 -0.40 0.44 0.87 2.75
25 U+A -2.31 1.08 -0.28 -2.70 -9.93 109.21
26 A-U -3.74 -1.95 0.88 6.14 20.12 -95.41
27 G+C 0.09 3.74 -0.67 -2.63 1.10 162.66
28 G-C 0.65 0.01 0.03 -13.40 -10.96 -2.59
29 G-C 0.30 -0.19 0.67 9.31 -6.31 -2.78
30 G-U -1.62 -0.53 0.09 12.42 -1.55 -1.94
31 C-G 0.09 -0.07 -0.68 21.45 -5.13 -0.63
32 C-G 0.35 -0.19 -0.74 9.70 1.88 0.39
33 C-G 0.17 -0.22 -0.64 4.59 6.85 -6.15
34 C-G 0.72 -0.14 -0.27 -12.21 3.59 5.02
35 A-U 0.84 0.18 0.14 -8.33 0.92 3.37
36 G-C -0.70 -0.06 -0.31 -2.83 2.41 6.78
37 G-C -0.89 -0.13 -0.89 -10.71 8.02 1.70
38 G-C -0.57 -0.41 -1.31 -21.56 3.49 -0.19
39 G-C -0.15 0.31 -0.87 -9.52 13.37 8.00
40 G-C -0.98 0.06 -0.48 -7.67 13.30 2.09
41 U-A 4.16 -2.60 -0.42 -9.89 10.54 -85.32
42 U+G 0.86 -5.57 0.04 20.06 4.98 -92.44
43 A-C -5.01 -0.82 1.40 16.47 11.78 4.86
44 G-C -0.27 -0.14 0.32 12.29 -9.05 3.63
45 G-C -0.32 -0.03 -0.55 -4.73 -9.06 8.21
46 C-G -0.01 -0.40 -0.41 8.73 -5.62 -0.28
47 C-G 0.35 -0.49 -0.51 3.59 -5.35 1.14
48 G-C -0.09 -0.25 -0.10 -17.40 -16.47 -0.97
49 A-G 0.30 1.45 -0.04 -19.15 -17.23 -8.62
50 G-C -0.27 -0.02 0.05 8.61 5.63 3.30
51 U-A -0.13 -0.02 0.04 -0.65 -4.40 12.53
52 C-G -0.06 -0.08 -0.52 2.23 1.13 2.89
53 U-G 2.44 -0.59 -0.15 2.21 4.16 7.18
54 A-U -3.78 -1.99 1.01 8.03 20.40 -95.39
55 G+C 0.09 3.70 -0.61 0.10 2.13 162.21
56 G-C 0.68 -0.16 1.23 7.12 0.37 -0.01
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.21 -0.29 -0.15 0.02 0.19 -0.16
s.d. 1.61 1.42 0.57 11.38 9.01 45.93
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/UC -0.53 -1.01 2.40 -9.39 8.25 34.26
2 GC/GU -0.23 -0.82 3.23 2.88 0.24 41.83
3 CC/GG 0.42 -1.62 3.46 3.32 7.07 32.38
4 CC/GG -0.47 -1.48 3.55 -0.20 0.73 30.82
5 CC/GG 0.67 -1.79 3.62 0.17 9.95 34.50
6 CA/UG -0.27 -1.32 2.88 4.27 8.64 32.41
7 AG/CU -2.20 -1.20 2.96 1.25 0.05 45.91
8 GG/CC -0.31 -1.82 3.48 3.70 2.22 30.97
9 GG/CC 0.26 -1.65 3.47 3.91 12.90 32.50
10 GG/CC 0.69 -1.27 2.97 -3.43 2.88 29.34
11 GG/CC 1.29 -2.01 2.69 -4.63 2.42 25.53
12 GU/AC -1.37 -2.34 3.32 5.49 6.04 100.11
13 UU/GA 1.66 -1.39 3.04 7.09 1.64 43.13
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC -0.15 -0.92 3.28 2.61 10.46 50.92
16 GG/CC -0.21 -1.44 3.58 2.15 9.49 32.26
17 GC/GC -0.28 -1.16 3.01 -4.43 3.37 34.54
18 CC/GG 0.10 -1.89 3.25 2.63 6.33 33.18
19 CG/CG 0.14 -1.86 3.85 2.46 14.57 28.63
20 GA/GC -0.75 -1.52 3.04 2.14 5.74 36.35
21 AG/CG -3.02 -1.88 3.12 15.07 15.05 56.38
22 GU/AC 0.40 -1.84 3.72 -3.15 5.74 36.26
23 UC/GA -0.61 -1.54 2.94 5.74 6.41 34.56
24 CU/AG 4.33 -1.36 3.09 -0.47 13.62 -24.23
25 UA/UA -1.90 0.54 3.18 -4.82 -3.52 120.26
26 AG/CU 1.56 -2.55 3.74 1.17 21.18 -76.11
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC -0.43 -1.00 2.94 -2.97 12.62 35.30
30 GC/GU 0.03 -0.99 3.06 4.20 3.23 38.88
31 CC/GG 0.38 -1.59 3.52 2.48 8.48 33.32
32 CC/GG -0.50 -1.55 3.51 0.14 2.14 30.29
33 CC/GG 0.75 -1.75 3.64 0.82 8.25 34.27
34 CA/UG -0.19 -1.30 2.91 1.77 8.61 32.86
35 AG/CU -2.08 -1.35 2.93 2.55 -1.90 45.17
36 GG/CC -0.17 -2.06 3.42 5.47 2.95 31.31
37 GG/CC 0.23 -1.70 3.46 4.56 12.76 32.83
38 GG/CC 0.65 -1.31 2.89 -4.72 3.03 28.81
39 GG/CC 1.22 -1.97 3.01 -1.49 2.34 26.82
40 GU/AC -1.12 -2.08 3.36 6.30 9.53 98.48
41 UU/GA 1.78 -1.52 2.91 8.32 2.47 44.47
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC -0.09 -0.97 3.33 3.85 8.82 50.64
44 GG/CC -0.10 -1.47 3.57 2.96 10.63 33.05
45 GC/GC -0.25 -1.08 2.91 -2.20 3.42 34.54
46 CC/GG 0.11 -1.85 3.32 2.12 8.30 32.19
47 CG/CG 0.10 -1.84 3.77 1.05 14.63 28.86
48 GA/GC -0.74 -1.50 3.16 2.40 5.14 36.76
49 AG/CG -2.98 -1.91 3.09 14.80 15.35 56.47
50 GU/AC 0.35 -1.75 3.56 -0.15 5.51 36.14
51 UC/GA -0.56 -1.44 3.16 4.68 7.31 33.55
52 CU/GG 1.57 -2.09 3.12 -1.29 8.86 27.73
53 UA/UG -1.16 -1.08 3.00 0.45 -2.04 68.83
54 AG/CU 1.53 -2.63 3.75 1.88 20.09 -75.84
55 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.05 -1.54 3.24 1.87 7.04 35.05
s.d. 1.25 0.51 0.32 4.41 5.49 31.03
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/UC -2.45 -0.09 2.18 13.47 15.33 36.41
2 GC/GU -1.17 0.62 3.21 0.33 -4.03 41.92
3 CC/GG -4.02 -0.17 3.07 12.46 -5.84 33.28
4 CC/GG -2.94 0.85 3.51 1.37 0.37 30.83
5 CC/GG -4.39 -1.06 3.01 16.36 -0.28 35.86
6 CA/UG -3.42 1.04 2.41 15.07 -7.45 33.77
7 AG/CU -1.55 2.91 2.90 0.06 -1.61 45.93
8 GG/CC -3.82 1.31 3.29 4.13 -6.88 31.26
9 GG/CC -4.62 0.14 2.65 21.91 -6.64 35.11
10 GG/CC -3.02 -1.97 2.73 5.64 6.72 29.67
11 GG/CC -4.97 -3.82 2.23 5.41 10.34 26.05
12 GU/AC -1.61 0.98 3.16 3.93 -3.57 100.35
13 UU/GA -2.02 -1.58 3.21 2.22 -9.57 43.71
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC -1.73 0.34 3.04 12.01 -3.00 51.97
16 GG/CC -4.08 0.72 3.03 16.61 -3.77 33.65
17 GC/GC -2.39 -0.14 2.90 5.62 7.40 34.97
18 CC/GG -4.20 0.22 2.85 10.94 -4.54 33.86
19 CG/CG -6.11 0.20 2.63 27.28 -4.60 32.15
20 GA/GC -3.09 1.45 2.73 9.12 -3.40 36.84
21 AG/CG -2.47 3.61 1.82 15.33 -15.36 59.96
22 GU/AC -3.76 -1.10 3.35 9.14 5.01 36.83
23 UC/GA -3.30 1.70 2.50 10.59 -9.48 35.58
24 CU/AG -0.67 8.91 3.44 -29.64 -1.03 -27.75
25 UA/UA 0.34 1.05 3.21 -2.03 2.78 120.35
26 AG/CU 1.29 1.27 4.20 -16.88 0.93 -78.58
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC -2.97 0.33 2.48 19.99 4.70 37.54
30 GC/GU -1.84 0.41 2.95 4.82 -6.27 39.23
31 CC/GG -4.03 -0.25 3.06 14.47 -4.23 34.43
32 CC/GG -3.41 0.99 3.39 4.09 -0.27 30.37
33 CC/GG -4.19 -1.12 3.16 13.75 -1.36 35.23
34 CA/UG -3.38 0.56 2.48 14.90 -3.07 33.98
35 AG/CU -1.60 2.90 2.86 -2.47 -3.32 45.28
36 GG/CC -4.28 1.32 3.14 5.40 -10.02 31.90
37 GG/CC -4.61 0.28 2.65 21.48 -7.67 35.45
38 GG/CC -3.13 -2.14 2.60 6.01 9.38 29.34
39 GG/CC -4.75 -2.96 2.76 5.02 3.19 26.96
40 GU/AC -1.52 0.84 3.15 6.28 -4.15 98.97
41 UU/GA -2.17 -1.63 3.09 3.22 -10.87 45.27
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC -1.72 0.37 3.12 10.21 -4.45 51.49
44 GG/CC -4.11 0.62 2.96 18.06 -5.04 34.79
45 GC/GC -2.27 0.12 2.81 5.74 3.68 34.77
46 CC/GG -4.55 0.15 2.77 14.65 -3.74 33.28
47 CG/CG -5.98 0.01 2.57 27.25 -1.95 32.31
48 GA/GC -2.99 1.46 2.88 8.10 -3.77 37.18
49 AG/CG -2.50 3.55 1.80 15.62 -15.06 60.05
50 GU/AC -3.59 -0.58 3.26 8.82 0.24 36.54
51 UC/GA -3.44 1.59 2.69 12.41 -7.94 34.63
52 CU/GG -5.81 -3.37 2.29 17.90 2.61 29.11
53 UA/UG -0.89 1.04 3.02 -1.81 -0.40 68.86
54 AG/CU 1.39 1.28 4.21 -16.08 1.50 -78.09
55 GG/CC ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -2.97 0.46 2.91 8.17 -2.21 35.86
s.d. 1.64 1.96 0.46 10.39 6.10 31.63
****************************************************************************
Structure classification:

This structure contains more than one helical regions
This is a right-handed nucleic acid structure
****************************************************************************
lambda: virtual angle between C1'-YN1 or C1'-RN9 glycosidic bonds and the
base-pair C1'-C1' line

C1'-C1': distance between C1' atoms for each base-pair
RN9-YN1: distance between RN9-YN1 atoms for each base-pair
RC8-YC6: distance between RC8-YC6 atoms for each base-pair

bp lambda(I) lambda(II) C1'-C1' RN9-YN1 RC8-YC6
1 G-C 52.8 55.4 10.9 9.1 10.0
2 G-U 44.7 68.5 10.6 9.0 9.9
3 C-G 55.4 54.6 10.6 8.9 9.8
4 C-G 57.6 54.4 10.5 8.9 9.8
5 C-G 53.1 52.1 10.8 9.0 9.8
6 C-G 61.5 54.6 10.4 8.8 9.8
7 A-U 62.9 52.7 10.7 9.1 10.2
8 G-C 57.3 60.7 10.4 8.9 10.0
9 G-C 53.2 59.6 10.7 9.1 10.0
10 G-C 54.1 58.2 10.3 8.6 9.6
11 G-C 60.1 59.2 10.5 9.0 10.1
12 G-C 50.2 61.5 10.6 9.0 9.9
13 U-A 41.1 15.3 9.7 7.3 6.6
14 U+G 105.6 24.2 8.7 8.0 9.3
15 A-C 30.8 84.1 10.9 9.5 10.4
16 G-C 57.1 58.2 10.4 8.8 9.9
17 G-C 57.3 60.4 10.4 8.8 9.9
18 C-G 55.3 57.3 10.3 8.7 9.6
19 C-G 57.9 54.6 10.3 8.6 9.6
20 G-C 55.9 55.4 10.4 8.7 9.6
21 A-G 53.8 51.1 12.3 10.5 11.2
22 G-C 54.7 57.0 10.7 9.0 10.0
23 U-A 60.7 64.1 10.0 8.6 9.9
24 C-G 56.0 57.9 10.5 8.9 9.9
25 U+A 5.3 75.4 11.4 9.7 10.5
26 A-U 15.2 30.2 9.7 7.1 6.1
27 G+C 41.4 56.6 10.7 9.0 10.5
28 G-C 59.6 49.1 10.9 9.1 10.0
29 G-C 54.9 51.9 10.7 9.0 9.8
30 G-U 45.0 64.3 10.3 8.7 9.6
31 C-G 55.4 55.4 10.6 8.9 9.8
32 C-G 57.2 54.3 10.6 8.9 9.8
33 C-G 52.7 51.8 10.8 9.0 9.8
34 C-G 60.8 55.4 10.4 8.8 9.8
35 A-U 62.6 52.9 10.7 9.1 10.2
36 G-C 55.3 61.5 10.5 8.9 10.0
37 G-C 51.7 61.1 10.6 9.0 9.9
38 G-C 52.3 59.9 10.3 8.6 9.6
39 G-C 58.6 60.1 10.7 9.2 10.3
40 G-C 49.8 60.8 10.8 9.2 10.1
41 U-A 38.5 16.8 9.6 7.1 6.4
42 U+G 109.5 26.6 9.0 8.4 9.8
43 A-C 31.0 83.4 11.0 9.6 10.4
44 G-C 55.8 57.8 10.5 8.8 9.8
45 G-C 57.8 60.3 10.4 8.9 10.0
46 C-G 55.2 56.5 10.3 8.7 9.6
47 C-G 57.3 54.5 10.2 8.6 9.5
48 G-C 55.3 54.4 10.5 8.8 9.6
49 A-G 54.1 50.2 12.3 10.5 11.1
50 G-C 55.8 57.7 10.6 9.0 10.0
51 U-A 61.6 62.8 10.0 8.6 9.9
52 C-G 55.8 57.8 10.6 9.0 10.0
53 U-G 73.7 45.6 10.1 8.6 9.7
54 A-U 15.5 30.8 9.7 7.0 6.1
55 G+C 40.9 56.6 10.7 9.0 10.5
56 G-C 60.2 50.1 10.8 9.1 10.0
****************************************************************************
Classification of each dinucleotide step in a right-handed nucleic acid
structure: A-like; B-like; TA-like; intermediate of A and B, or other cases

step Xp Yp Zp XpH YpH ZpH Form
1 GG/UC -1.73 8.16 2.22 -3.78 7.45 4.02
2 GC/GU -1.44 8.43 2.30 -2.60 8.42 2.33 A
3 CC/GG -1.52 8.30 2.41 -5.41 7.61 4.11 A
4 CC/GG -1.08 8.24 2.47 -3.91 8.18 2.66 A
5 CC/GG -1.44 8.14 2.91 -5.62 7.06 4.99 A
6 CA/UG -2.00 8.35 2.64 -5.15 7.42 4.65 A
7 AG/CU -2.75 7.45 3.07 -4.17 7.44 3.05
8 GG/CC -1.72 8.05 2.73 -5.32 7.85 3.22 A
9 GG/CC -1.64 8.44 2.34 -5.96 7.06 5.13 A
10 GG/CC -1.67 8.60 2.09 -4.67 8.37 2.92 A
11 GG/CC -2.24 7.80 3.17 -7.08 7.47 3.95 A
12 GU/AC -1.00 6.97 4.07 -1.99 6.78 4.49
13 UU/GA 3.83 4.45 0.04 1.59 4.43 0.69
14 UA/CG --- --- --- --- --- --- ---
15 AG/CC -1.96 8.38 3.14 -3.57 7.65 4.59 A
16 GG/CC -2.01 8.26 2.51 -5.93 7.25 4.65 A
17 GC/GC -1.77 8.35 2.17 -4.02 8.11 2.94 A
18 CC/GG -1.80 8.25 2.52 -5.83 7.65 3.99 A
19 CG/CG -1.79 8.26 2.49 -7.62 6.29 5.90 A
20 GA/GC -1.42 8.63 2.25 -4.27 8.19 3.52 A
21 AG/CG -2.54 7.09 4.50 -4.82 5.90 5.59
22 GU/AC -1.94 7.76 3.05 -5.47 7.21 4.20 A
23 UC/GA -1.87 8.04 2.76 -4.93 7.44 4.08 A
24 CU/AG -3.07 7.79 2.14 -3.72 7.84 -1.95
25 UA/UA 2.99 6.66 3.64 3.14 6.73 3.65
26 AG/CU 2.22 1.79 0.67 3.22 1.91 0.32
27 GG/CC --- --- --- --- --- --- ---
28 GG/CC --- --- --- --- --- --- ---
29 GG/UC -1.47 7.95 2.70 -4.19 6.64 5.13 A
30 GC/GU -1.38 8.42 2.30 -3.20 8.21 2.95 A
31 CC/GG -1.59 8.33 2.41 -5.48 7.51 4.37 A
32 CC/GG -1.09 8.27 2.47 -4.39 8.08 3.04 A
33 CC/GG -1.46 8.17 2.82 -5.45 7.31 4.61 A
34 CA/UG -1.98 8.30 2.69 -5.17 7.38 4.67 A
35 AG/CU -2.71 7.29 3.28 -4.18 7.41 2.93
36 GG/CC -1.67 7.90 2.90 -5.68 7.61 3.50 A
37 GG/CC -1.65 8.36 2.36 -5.92 7.02 5.03 A
38 GG/CC -1.56 8.56 2.12 -4.72 8.30 3.03 A
39 GG/CC -2.13 7.91 3.04 -6.77 7.63 3.74 A
40 GU/AC -0.98 7.20 3.74 -1.91 6.91 4.38
41 UU/GA 3.94 4.38 -0.22 1.59 4.37 0.55
42 UA/CG --- --- --- --- --- --- ---
43 AG/CC -1.92 8.39 3.14 -3.54 7.79 4.33 A
44 GG/CC -1.96 8.29 2.60 -5.90 7.15 4.91 A
45 GC/GC -1.73 8.37 2.05 -3.89 8.14 2.83 A
46 CC/GG -1.74 8.27 2.39 -6.11 7.44 4.34 A
47 CG/CG -1.71 8.33 2.46 -7.44 6.38 5.90 A
48 GA/GC -1.38 8.69 2.24 -4.12 8.31 3.38 A
49 AG/CG -2.53 7.06 4.50 -4.81 5.84 5.63
50 GU/AC -2.00 7.74 2.98 -5.40 7.22 4.08 A
51 UC/GA -1.91 8.17 2.54 -5.14 7.47 4.14 A
52 CU/GG -1.88 8.50 2.57 -7.51 7.35 4.99 A
53 UA/UG -1.44 6.36 2.72 -2.17 6.43 2.57
54 AG/CU 2.22 1.75 0.77 3.32 1.89 0.50
55 GG/CC --- --- --- --- --- --- ---
****************************************************************************
Minor and major groove widths: direct P-P distances and refined P-P distances
which take into account the directions of the sugar-phosphate backbones

(Subtract 5.8 Angstrom from the values to take account of the vdw radii
of the phosphate groups, and for comparison with FreeHelix and Curves.)

Ref: M. A. El Hassan and C. R. Calladine (1998). ``Two Distinct Modes of
Protein-induced Bending in DNA.'' J. Mol. Biol., v282, pp331-343.

Minor Groove Major Groove
P-P Refined P-P Refined
1 GG/UC --- --- --- ---
2 GC/GU --- --- --- ---
3 CC/GG 16.1 --- 14.6 ---
4 CC/GG 16.0 15.3 16.1 13.1
5 CC/GG 16.6 15.0 15.4 12.7
6 CA/UG 16.6 14.5 13.6 11.4
7 AG/CU 16.1 14.4 13.4 11.6
8 GG/CC 16.1 14.9 13.5 12.3
9 GG/CC 16.8 15.7 15.0 11.3
10 GG/CC 16.9 15.7 15.7 13.1
11 GG/CC 16.6 --- 13.3 ---
12 GU/AC --- --- --- ---
13 UU/GA --- --- --- ---
14 UA/CG --- --- --- ---
15 AG/CC --- --- --- ---
16 GG/CC --- --- --- ---
17 GC/GC 16.6 --- 15.8 ---
18 CC/GG 16.4 15.2 16.1 10.0
19 CG/CG 18.5 15.1 15.7 10.3
20 GA/GC 19.7 15.5 13.7 10.0
21 AG/CG 18.1 15.3 12.1 9.7
22 GU/AC 17.3 15.2 11.5 10.6
23 UC/GA 17.1 15.4 6.9 4.2
24 CU/AG 16.7 --- 8.7 ---
25 UA/UA --- --- --- ---
26 AG/CU --- --- --- ---
27 GG/CC --- --- --- ---
28 GG/CC --- --- --- ---
29 GG/UC --- --- --- ---
30 GC/GU --- --- --- ---
31 CC/GG 16.3 --- 14.5 ---
32 CC/GG 16.0 15.3 15.9 12.8
33 CC/GG 16.6 15.0 15.3 12.4
34 CA/UG 16.6 14.5 13.6 11.3
35 AG/CU 15.9 14.2 13.2 11.3
36 GG/CC 15.8 14.5 13.4 12.2
37 GG/CC 16.5 15.5 15.1 11.4
38 GG/CC 16.8 15.7 15.5 12.8
39 GG/CC 16.5 --- 12.9 ---
40 GU/AC --- --- --- ---
41 UU/GA --- --- --- ---
42 UA/CG --- --- --- ---
43 AG/CC --- --- --- ---
44 GG/CC --- --- --- ---
45 GC/GC 16.6 --- 15.8 ---
46 CC/GG 16.5 15.3 16.1 10.0
47 CG/CG 18.4 15.1 15.6 10.2
48 GA/GC 19.7 15.4 13.8 10.0
49 AG/CG 18.1 15.3 12.0 9.5
50 GU/AC 17.3 15.2 11.5 11.2
51 UC/GA 17.1 15.4 14.6 10.3
52 CU/GG 16.7 --- 8.5 ---
53 UA/UG --- --- --- ---
54 AG/CU --- --- --- ---
55 GG/CC --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 0.41(3.58)
****************************************************************************
Main chain and chi torsion angles:

Note: alpha: O3'(i-1)-P-O5'-C5'
beta: P-O5'-C5'-C4'
gamma: O5'-C5'-C4'-C3'
delta: C5'-C4'-C3'-O3'
epsilon: C4'-C3'-O3'-P(i+1)
zeta: C3'-O3'-P(i+1)-O5'(i+1)

chi for pyrimidines(Y): O4'-C1'-N1-C2
chi for purines(R): O4'-C1'-N9-C4

Strand I
base alpha beta gamma delta epsilon zeta chi
1 G --- -157.0 59.6 98.9 -153.8 -79.8 -171.3
2 G -84.9 -162.0 51.6 96.1 -155.3 -68.9 -154.4
3 C -69.6 -179.4 51.3 92.5 -152.5 -74.0 -148.7
4 C -60.1 176.5 47.0 90.4 -161.9 -83.7 -149.4
5 C -60.4 168.9 51.9 89.1 -157.7 -69.5 -161.6
6 C -66.0 -176.8 55.6 96.2 -161.6 -76.4 -165.7
7 A -73.5 174.6 73.2 128.9 --- --- -144.7
8 G --- 151.9 31.3 97.1 -148.8 -79.0 -170.4
9 G -75.8 176.5 63.6 91.3 -160.6 -64.4 -165.4
10 G -63.8 -170.7 41.7 90.7 -162.9 -97.4 -156.2
11 G 130.2 -154.5 -168.9 104.6 -118.0 -26.4 -178.1
12 G -109.6 56.1 178.5 110.9 -115.0 -87.5 167.2
13 U 0.9 155.6 -12.8 97.3 -136.3 -77.9 -152.5
14 U -69.9 156.0 60.4 88.9 --- --- -153.1
15 A --- 173.1 54.9 94.0 -146.6 -61.6 -167.3
16 G -69.5 177.9 49.6 93.0 -157.1 -77.9 -156.7
17 G -61.8 178.8 44.4 93.8 -157.3 -74.7 -154.8
18 C -81.4 175.2 64.5 87.3 -159.0 -69.1 -157.2
19 C -70.5 -179.2 55.4 87.5 -157.7 -73.2 -154.6
20 G -66.2 172.9 62.0 87.9 -158.6 -79.5 -164.1
21 A -60.2 -176.6 42.0 88.8 --- --- -145.2
22 G --- 159.7 45.6 93.8 -144.5 -73.1 -175.6
23 U -68.1 -171.7 46.2 93.1 -153.8 -79.1 -166.8
24 C -59.7 -176.0 41.7 91.1 -151.4 -71.1 -147.9
25 U 120.0 -154.7 -146.4 92.3 -161.4 -79.7 -170.3
26 A -68.2 -169.7 52.4 91.3 -134.5 -68.0 -162.7
27 G -78.8 162.3 72.4 99.5 --- --- -147.4
28 G --- -111.4 52.7 121.2 --- --- -62.9
29 G --- -161.2 55.0 98.3 -155.1 -75.7 -163.9
30 G -78.8 -165.2 44.9 96.0 -151.7 -71.0 -155.8
31 C -65.5 174.8 48.7 92.0 -152.0 -75.1 -146.4
32 C -57.5 175.0 44.6 91.2 -159.7 -84.2 -151.5
33 C -64.4 170.1 55.5 88.1 -158.5 -69.8 -162.5
34 C -64.6 -177.7 55.1 96.5 -162.4 -76.1 -163.7
35 A -75.6 175.3 74.8 130.5 --- --- -145.1
36 G --- 151.0 30.0 93.2 -147.9 -78.5 -173.7
37 G -69.3 177.2 61.9 92.2 -158.5 -66.6 -166.9
38 G -61.2 -173.6 40.7 90.2 -159.8 -99.2 -157.4
39 G 126.3 -151.0 -166.9 104.6 -119.8 -27.5 179.1
40 G -110.5 56.4 178.7 112.4 -118.9 -89.0 166.5
41 U 9.3 148.6 -19.7 92.5 -131.1 -75.9 -152.2
42 U -71.9 158.4 68.3 89.9 --- --- -146.5
43 A --- 172.6 51.8 92.5 -147.5 -58.4 -167.8
44 G -79.3 -179.5 57.9 90.6 -156.5 -77.8 -157.2
45 G -60.6 177.9 43.0 92.2 -156.5 -75.3 -157.2
46 C -76.6 174.7 60.8 88.5 -159.3 -69.1 -153.4
47 C -68.9 -178.7 54.0 87.1 -156.5 -73.1 -153.3
48 G -64.2 171.0 62.2 89.1 -155.9 -81.0 -163.1
49 A -59.9 -178.7 41.1 87.0 --- --- -146.0
50 G --- 166.4 48.1 97.2 -147.7 -72.6 -174.0
51 U -66.5 -172.1 46.0 93.2 -153.5 -78.6 -159.6
52 C -61.7 -177.5 43.0 90.7 -152.1 -73.5 -146.3
53 U 118.5 -152.1 -146.8 91.1 -159.5 -80.7 -172.2
54 A -63.5 -171.1 49.9 92.5 -134.0 -68.6 -163.1
55 G -76.2 161.0 71.7 98.9 --- --- -147.0
56 G --- -109.6 52.4 121.6 --- --- -59.1

Strand II
base alpha beta gamma delta epsilon zeta chi
1 C 132.8 -141.0 176.7 99.8 --- --- -156.8
2 U -69.2 159.2 68.1 93.3 -141.6 -115.9 -164.2
3 G -54.1 172.8 47.2 92.3 -149.2 -74.3 -166.3
4 G -72.5 166.4 67.8 90.2 -154.2 -80.8 -170.1
5 G -54.2 170.4 43.5 90.1 -155.5 -75.9 -164.9
6 G -53.1 172.0 37.6 91.0 -154.2 -81.9 -154.6
7 U -57.0 173.5 46.0 94.3 -151.9 -77.8 -154.3
8 C -56.5 170.6 48.5 91.8 -149.6 -71.8 -164.7
9 C -64.8 169.0 50.2 91.8 -154.8 -80.0 -161.2
10 C -49.7 170.0 39.1 93.6 -153.5 -83.9 -144.1
11 C -72.1 -164.1 47.8 100.3 -154.0 -82.3 -154.5
12 C --- -175.6 25.8 99.1 -158.6 -83.8 179.9
13 A --- 157.8 128.4 108.5 --- --- -127.5
14 G --- -117.2 48.1 109.1 --- --- -99.4
15 C -50.4 166.6 40.6 95.9 --- --- -157.1
16 C -63.6 171.2 60.2 89.6 -135.6 -74.4 -164.2
17 C -67.4 167.8 56.9 89.9 -156.7 -74.5 -153.3
18 G -75.1 175.2 60.0 87.4 -150.0 -84.6 -166.5
19 G -68.0 174.3 54.1 88.4 -153.5 -72.4 -165.8
20 C -63.6 -169.0 43.0 90.0 -151.2 -76.6 -149.6
21 G -73.5 176.5 50.9 87.6 -150.7 -64.2 -161.7
22 C -71.5 -179.7 59.1 91.6 -147.2 -63.0 -160.4
23 A -65.3 -177.5 45.7 92.6 -159.9 -77.7 -158.9
24 G --- 173.0 52.4 91.5 -156.2 -74.3 -163.5
25 A --- -179.3 70.2 94.3 --- --- -123.6
26 U --- -148.7 56.4 96.3 --- --- -140.9
27 C --- 104.4 171.5 134.2 --- --- -136.0
28 C --- -159.5 167.7 104.6 --- --- 165.6
29 C 152.4 -141.2 163.0 105.5 --- --- -166.6
30 U -75.0 168.0 67.8 95.6 -153.5 -116.4 -161.1
31 G -57.7 175.8 44.9 94.5 -151.9 -73.1 -166.4
32 G -74.3 168.6 68.3 93.7 -155.8 -80.9 -169.3
33 G -55.1 174.2 40.2 90.2 -158.7 -73.3 -163.5
34 G -55.6 174.4 40.3 95.7 -158.1 -81.5 -153.4
35 U -60.5 176.0 48.0 94.3 -150.2 -77.8 -158.8
36 C -56.4 169.8 48.0 91.6 -150.4 -72.6 -168.6
37 C -60.8 167.2 47.2 92.9 -155.4 -81.0 -161.6
38 C -50.7 169.7 42.9 95.0 -152.6 -85.8 -144.8
39 C -72.7 -162.9 44.6 100.3 -153.9 -83.7 -156.3
40 C --- -166.4 35.7 100.6 -158.5 -83.2 -175.2
41 A --- 143.7 115.0 115.2 --- --- -133.9
42 G --- -116.2 50.9 109.8 --- --- -99.6
43 C -60.9 169.3 48.0 96.2 --- --- -159.1
44 C -61.3 171.1 58.6 89.4 -137.8 -71.2 -164.2
45 C -70.2 169.5 58.1 91.1 -156.2 -74.7 -152.3
46 G -72.1 173.9 59.9 88.2 -150.1 -84.4 -165.2
47 G -64.2 171.1 52.3 86.6 -152.4 -73.8 -164.9
48 C -67.2 -170.2 46.4 86.9 -148.6 -77.0 -151.6
49 G -67.9 175.9 46.3 87.4 -154.5 -62.7 -159.6
50 C -74.9 -174.3 59.6 92.0 -147.0 -65.1 -161.8
51 A -65.3 178.9 47.2 90.0 -162.6 -75.1 -161.8
52 G -52.3 170.8 52.0 91.7 -154.3 -76.0 -164.5
53 G --- 153.8 38.2 87.0 -150.3 -82.3 -166.4
54 U --- -150.8 52.9 96.0 --- --- -141.0
55 C --- 105.3 170.0 134.9 --- --- -134.4
56 C --- -151.0 -179.2 106.6 --- --- 143.6
****************************************************************************
Sugar conformational parameters:

Note: v0: C4'-O4'-C1'-C2'
v1: O4'-C1'-C2'-C3'
v2: C1'-C2'-C3'-C4'
v3: C2'-C3'-C4'-O4'
v4: C3'-C4'-O4'-C1'

tm: amplitude of pseudorotation of the sugar ring
P: phase angle of pseudorotation of the sugar ring

Strand I
base v0 v1 v2 v3 v4 tm P Puckering
1 G 10.4 -21.5 24.0 -18.0 4.6 24.2 352.8 C2'-exo
2 G 10.0 -23.0 27.0 -21.1 6.8 27.0 356.5 C2'-exo
3 C 5.4 -20.5 27.4 -24.4 11.6 27.6 6.9 C3'-endo
4 C -1.0 -15.7 25.7 -26.6 16.8 27.3 20.0 C3'-endo
5 C 4.7 -21.2 29.4 -26.9 13.6 29.8 9.2 C3'-endo
6 C 1.5 -14.2 21.2 -20.5 11.8 21.9 14.3 C3'-endo
7 A -12.7 17.4 -15.2 8.0 2.9 17.3 152.0 C2'-endo
8 G 8.7 -20.6 24.1 -19.2 6.2 24.2 357.0 C2'-exo
9 G -0.8 -14.9 24.4 -25.2 16.0 25.9 19.9 C3'-endo
10 G -5.7 -9.8 21.2 -25.1 19.1 24.9 31.5 C3'-endo
11 G 12.9 -20.1 19.4 -11.8 -0.8 20.7 339.8 C2'-exo
12 G 17.2 -20.3 15.8 -5.7 -7.3 20.3 321.1 C1'-endo
13 U 7.8 -20.0 24.3 -19.9 7.4 24.3 359.6 C2'-exo
14 U 3.3 -21.1 30.0 -28.2 15.1 30.6 11.6 C3'-endo
15 A 4.1 -18.6 25.5 -23.5 11.9 25.8 9.2 C3'-endo
16 G -1.2 -13.1 21.9 -23.0 14.9 23.5 21.1 C3'-endo
17 G -1.2 -12.8 21.4 -22.5 14.5 23.0 21.0 C3'-endo
18 C -3.0 -14.9 26.8 -29.0 19.7 29.3 24.0 C3'-endo
19 C -2.8 -14.4 25.9 -28.0 19.1 28.3 24.0 C3'-endo
20 G -5.1 -11.7 23.8 -27.3 20.2 27.2 29.2 C3'-endo
21 A 4.1 -20.2 28.6 -26.5 13.7 29.0 10.2 C3'-endo
22 G 6.7 -20.5 26.2 -22.4 9.6 26.2 3.4 C3'-endo
23 U 5.1 -20.0 26.6 -23.9 11.5 26.8 7.1 C3'-endo
24 C 2.7 -18.0 26.2 -24.9 13.7 26.9 12.5 C3'-endo
25 U 0.9 -16.5 25.2 -25.1 15.0 26.3 16.3 C3'-endo
26 A -7.0 -8.6 20.4 -25.0 19.8 24.7 34.6 C3'-endo
27 G -10.5 -0.8 11.1 -17.7 17.5 18.3 52.8 C4'-exo
28 G 0.5 3.2 -5.6 6.0 -4.1 6.1 203.1 C3'-exo
29 G 11.9 -23.1 25.5 -18.5 4.1 25.8 351.0 C2'-exo
30 G 10.1 -22.7 26.3 -20.5 6.3 26.4 355.8 C2'-exo
31 C 4.6 -19.5 26.7 -24.1 12.0 27.0 8.3 C3'-endo
32 C -0.5 -15.6 25.1 -25.8 16.0 26.6 19.1 C3'-endo
33 C 2.5 -19.7 29.3 -28.1 15.8 30.2 13.5 C3'-endo
34 C 1.2 -13.8 20.8 -20.4 11.8 21.6 15.0 C3'-endo
35 A -12.5 18.6 -17.4 10.3 1.3 18.8 157.5 C2'-endo
36 G 9.0 -23.1 27.9 -22.8 8.1 27.9 359.2 C2'-exo
37 G -0.3 -14.9 23.8 -24.3 15.1 25.1 18.7 C3'-endo
38 G -5.1 -10.3 21.5 -25.0 18.7 24.9 30.2 C3'-endo
39 G 9.9 -17.0 17.6 -11.8 1.0 18.1 345.3 C2'-exo
40 G 16.8 -18.5 13.3 -3.4 -8.5 18.7 315.4 C1'-endo
41 U 6.4 -20.8 27.0 -23.5 10.3 27.0 4.5 C3'-endo
42 U 1.2 -17.4 26.6 -26.1 15.1 27.6 15.5 C3'-endo
43 A 5.3 -20.4 27.2 -24.4 11.7 27.5 7.1 C3'-endo
44 G -2.5 -13.5 23.9 -25.8 17.5 26.1 23.7 C3'-endo
45 G -0.3 -13.9 22.5 -23.0 14.4 23.8 19.0 C3'-endo
46 C -2.2 -15.2 26.3 -27.9 18.5 28.4 22.4 C3'-endo
47 C -4.0 -13.8 25.9 -28.7 20.2 28.8 26.2 C3'-endo
48 G -7.2 -9.0 21.2 -26.1 20.8 25.8 34.6 C3'-endo
49 A 3.0 -20.4 29.6 -28.3 15.4 30.3 12.5 C3'-endo
50 G 10.1 -22.8 26.3 -20.5 6.2 26.4 355.6 C2'-exo
51 U 4.9 -19.2 25.9 -23.2 11.3 26.1 7.5 C3'-endo
52 C 1.1 -17.3 26.6 -26.2 15.4 27.6 15.8 C3'-endo
53 U 0.8 -16.9 25.9 -25.7 15.4 27.0 16.4 C3'-endo
54 A -6.9 -8.3 19.5 -24.2 19.1 23.8 34.9 C3'-endo
55 G -11.2 -0.2 10.9 -17.9 18.2 18.8 54.6 C4'-exo
56 G -1.9 5.9 -7.4 6.4 -2.8 7.4 183.3 C3'-exo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C 8.7 -19.1 22.0 -17.0 5.1 22.1 355.3 C2'-exo
2 U 0.5 -14.1 22.1 -22.1 13.3 23.1 17.1 C3'-endo
3 G -2.6 -12.3 22.2 -24.1 16.5 24.3 24.4 C3'-endo
4 G -3.0 -13.1 23.6 -26.0 17.8 26.0 25.0 C3'-endo
5 G -4.3 -11.4 22.3 -25.3 18.3 25.3 28.0 C3'-endo
6 G -4.6 -10.7 21.5 -24.6 18.1 24.6 28.9 C3'-endo
7 U 1.3 -14.9 22.4 -21.9 12.7 23.2 14.9 C3'-endo
8 C -0.1 -14.5 23.2 -23.6 14.6 24.4 18.5 C3'-endo
9 C -1.1 -13.9 23.1 -24.2 15.7 24.7 20.8 C3'-endo
10 C -2.7 -10.7 19.9 -21.8 15.2 22.0 25.3 C3'-endo
11 C 7.8 -17.8 20.7 -16.4 5.3 20.7 356.4 C2'-exo
12 C 8.8 -19.6 22.6 -17.6 5.3 22.7 355.4 C2'-exo
13 A 11.1 -15.8 14.2 -7.7 -2.1 15.8 334.0 C2'-exo
14 G -17.4 11.9 -2.4 -7.9 15.8 17.4 97.9 O4'-endo
15 C -0.3 -12.9 20.5 -21.1 13.1 21.6 18.8 C3'-endo
16 C -0.3 -15.4 25.1 -25.8 16.1 26.5 19.1 C3'-endo
17 C 2.9 -19.3 27.9 -26.5 14.5 28.6 12.3 C3'-endo
18 G -5.7 -11.8 24.3 -28.3 21.0 28.0 30.0 C3'-endo
19 G -2.6 -14.9 26.1 -28.1 18.9 28.5 23.3 C3'-endo
20 C 1.5 -17.7 26.7 -26.3 15.2 27.7 15.2 C3'-endo
21 G 4.5 -22.5 31.4 -29.2 14.8 31.9 9.9 C3'-endo
22 C 2.9 -18.1 26.2 -24.7 13.4 26.8 12.0 C3'-endo
23 A 4.5 -19.4 26.6 -24.1 12.0 26.8 8.5 C3'-endo
24 G 0.3 -16.3 25.3 -25.6 15.4 26.5 17.4 C3'-endo
25 A 0.2 -14.6 22.7 -23.0 14.0 23.9 17.7 C3'-endo
26 U 6.4 -19.6 24.7 -21.2 9.0 24.7 3.2 C3'-endo
27 C -11.3 19.5 -19.9 13.5 -1.4 20.6 165.5 C2'-endo
28 C 0.7 -8.3 12.8 -12.5 7.4 13.2 15.5 C3'-endo
29 C 0.5 -7.8 11.8 -11.7 6.9 12.3 15.8 C3'-endo
30 U -4.9 -8.6 18.2 -21.5 16.3 21.3 31.4 C3'-endo
31 G -2.5 -11.1 19.9 -21.7 14.9 21.9 24.6 C3'-endo
32 G -6.2 -7.6 18.0 -22.1 17.6 21.9 34.7 C3'-endo
33 G -4.5 -11.6 22.7 -25.9 18.7 25.8 28.2 C3'-endo
34 G -5.0 -7.5 16.8 -20.1 15.6 19.9 32.8 C3'-endo
35 U 2.1 -15.4 22.4 -21.5 11.8 22.9 12.9 C3'-endo
36 C -0.7 -13.9 22.9 -23.7 15.0 24.4 19.9 C3'-endo
37 C -2.5 -11.6 21.0 -22.8 15.8 23.0 24.6 C3'-endo
38 C -2.3 -10.6 19.2 -20.9 14.4 21.1 24.6 C3'-endo
39 C 9.0 -19.2 21.7 -16.6 4.6 21.8 354.0 C2'-exo
40 C 8.0 -18.0 20.8 -16.2 5.0 20.9 355.7 C2'-exo
41 A 9.4 -9.9 6.8 -1.3 -5.0 10.1 312.2 C1'-endo
42 G -18.3 13.3 -3.7 -7.1 15.9 18.1 101.9 O4'-endo
43 C -0.4 -12.5 20.1 -20.7 13.1 21.3 19.3 C3'-endo
44 C -1.9 -14.0 24.3 -26.0 17.2 26.3 22.5 C3'-endo
45 C 2.1 -17.6 26.1 -25.2 14.3 26.9 13.8 C3'-endo
46 G -5.8 -11.5 24.0 -28.0 20.8 27.8 30.2 C3'-endo
47 G -3.3 -15.0 27.4 -29.8 20.5 30.1 24.6 C3'-endo
48 C 1.0 -18.8 29.0 -28.8 17.0 30.2 16.2 C3'-endo
49 G 5.1 -22.9 31.7 -28.9 14.5 32.1 9.0 C3'-endo
50 C 2.0 -16.8 25.3 -24.3 13.9 26.0 14.0 C3'-endo
51 A 3.6 -19.3 27.7 -25.7 13.7 28.2 11.0 C3'-endo
52 G 0.5 -15.8 24.6 -24.6 14.8 25.7 17.0 C3'-endo
53 G 9.7 -26.9 33.7 -28.2 11.1 33.7 1.5 C3'-endo
54 U 6.5 -20.0 25.1 -21.5 9.1 25.2 3.0 C3'-endo
55 C -11.9 20.4 -20.9 14.1 -1.5 21.6 165.5 C2'-endo
56 C -5.4 -1.0 6.9 -10.2 9.8 10.5 49.1 C4'-exo
****************************************************************************
Same strand P--P and C1'--C1' virtual bond distances

Strand I Strand II
base P--P C1'--C1' base P--P C1'--C1'
1 G/G 5.7 6.3 1 C/U 6.2 5.6
2 G/C 5.6 5.2 2 U/G 5.7 4.9
3 C/C 5.7 5.4 3 G/G 6.2 5.4
4 C/C 5.9 5.3 4 G/G 5.8 5.1
5 C/C 6.0 5.4 5 G/G 5.5 5.3
6 C/A 6.0 5.4 6 G/U 5.8 5.2
7 A/G 10.5 8.5 7 U/C 5.8 5.2
8 G/G 5.6 5.7 8 C/C 6.0 5.3
9 G/G 6.2 5.7 9 C/C 5.7 5.3
10 G/G 5.6 5.0 10 C/C 5.6 5.3
11 G/G 6.5 4.8 11 C/C 5.5 6.2
12 G/U 5.8 5.8 12 C/A 13.6 8.5
13 U/U 4.8 5.1 13 A/G 13.8 6.0
14 U/A --- --- 14 G/C --- ---
15 A/G 5.8 5.4 15 C/C 5.6 5.3
16 G/G 5.9 5.5 16 C/C 6.0 5.2
17 G/C 5.8 5.3 17 C/G 5.8 5.4
18 C/C 6.0 5.5 18 G/G 5.9 5.5
19 C/G 5.8 5.3 19 G/C 5.4 5.5
20 G/A 6.0 5.7 20 C/G 5.6 5.8
21 A/G 14.7 12.2 21 G/C 5.7 5.1
22 G/U 5.7 6.0 22 C/A 5.7 5.6
23 U/C 5.6 5.8 23 A/G 5.9 5.5
24 C/U 5.4 5.0 24 G/A 13.8 13.6
25 U/A 7.0 6.3 25 A/U 14.0 5.2
26 A/G 5.3 5.3 26 U/C 11.0 4.0
27 G/G --- --- 27 C/C --- ---
28 G/G --- --- 28 C/C --- ---
29 G/G 5.6 6.1 29 C/U 6.3 5.7
30 G/C 5.5 5.2 30 U/G 5.8 5.2
31 C/C 5.8 5.3 31 G/G 6.3 5.5
32 C/C 5.8 5.3 32 G/G 5.7 5.2
33 C/C 6.0 5.4 33 G/G 5.7 5.3
34 C/A 6.0 5.4 34 G/U 5.7 5.3
35 A/G 10.4 8.4 35 U/C 5.8 5.2
36 G/G 5.5 5.8 36 C/C 5.9 5.3
37 G/G 6.2 5.7 37 C/C 5.7 5.2
38 G/G 5.6 5.0 38 C/C 5.5 5.2
39 G/G 6.5 4.8 39 C/C 5.5 6.2
40 G/U 5.9 5.7 40 C/A 13.6 8.7
41 U/U 4.4 5.3 41 A/G 14.1 6.3
42 U/A --- --- 42 G/C --- ---
43 A/G 5.8 5.4 43 C/C 5.7 5.2
44 G/G 5.9 5.5 44 C/C 6.0 5.2
45 G/C 5.7 5.4 45 C/G 5.8 5.4
46 C/C 6.0 5.5 46 G/G 5.8 5.5
47 C/G 5.7 5.3 47 G/C 5.4 5.5
48 G/A 6.1 5.6 48 C/G 5.6 5.7
49 A/G 14.7 12.3 49 G/C 5.6 5.1
50 G/U 5.9 5.9 50 C/A 5.8 5.7
51 U/C 5.5 5.7 51 A/G 5.9 5.5
52 C/U 5.5 5.0 52 G/G 5.6 5.5
53 U/A 7.0 6.3 53 G/U 16.1 11.3
54 A/G 5.3 5.2 54 U/C 11.0 4.1
55 G/G --- --- 55 C/C --- ---
****************************************************************************
Helix radius (radial displacement of P, O4', and C1' atoms in local helix
frame of each dimer)

Strand I Strand II
step P O4' C1' P O4' C1'
1 GG/UC 7.4 8.1 7.3 9.3 7.8 6.9
2 GC/GU 9.2 8.3 7.3 8.4 6.6 5.6
3 CC/GG 9.0 8.9 8.1 9.6 9.4 8.6
4 CC/GG 9.5 9.0 8.0 8.7 7.8 7.1
5 CC/GG 7.8 8.4 7.8 10.2 10.2 9.4
6 CA/UG 10.2 9.4 8.5 7.9 8.1 7.4
7 AG/CU 10.9 10.2 9.2 6.2 5.6 5.0
8 GG/CC 11.0 10.3 9.5 7.9 8.0 7.3
9 GG/CC 10.3 9.9 9.2 8.1 8.9 8.1
10 GG/CC 8.2 7.4 6.7 11.0 10.1 9.1
11 GG/CC 8.3 8.1 8.1 12.8 12.7 11.8
12 GU/AC 9.4 7.9 6.8 6.3 5.5 4.7
13 UU/GA 5.6 3.6 2.3 6.0 7.7 7.3
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC 8.9 8.6 7.8 8.3 6.7 5.7
16 GG/CC 10.2 9.9 9.1 8.5 8.7 8.0
17 GC/GC 8.9 8.1 7.2 9.2 8.2 7.3
18 CC/GG 9.7 9.3 8.5 9.5 9.2 8.4
19 CG/CG 10.5 10.6 10.0 9.3 10.2 9.7
20 GA/GC 11.2 9.8 9.0 7.3 7.5 6.8
21 AG/CG 10.7 11.5 10.5 4.6 5.3 4.9
22 GU/AC 8.0 8.4 7.7 10.2 9.9 9.0
23 UC/GA 10.8 10.2 9.2 7.1 7.5 6.8
24 CU/AG 17.8 14.1 13.2 0.5 9.1 9.4
25 UA/UA 8.6 7.5 6.3 9.9 7.3 6.4
26 AG/CU 9.3 6.3 5.2 10.7 7.3 6.5
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC 7.3 8.3 7.5 8.4 7.7 6.9
30 GC/GU 8.9 8.2 7.3 8.7 7.2 6.2
31 CC/GG 8.8 8.8 8.1 9.8 9.5 8.7
32 CC/GG 9.7 9.4 8.4 8.7 8.1 7.4
33 CC/GG 7.9 8.2 7.6 10.4 10.2 9.3
34 CA/UG 9.6 9.0 8.1 8.4 8.5 7.7
35 AG/CU 10.9 10.3 9.2 6.1 5.6 5.0
36 GG/CC 11.2 10.7 9.9 7.8 8.2 7.5
37 GG/CC 10.6 10.1 9.4 7.8 8.6 7.9
38 GG/CC 8.2 7.5 6.9 11.0 10.3 9.3
39 GG/CC 9.1 8.4 8.1 11.7 11.9 10.9
40 GU/AC 9.4 7.8 6.7 6.4 5.6 4.8
41 UU/GA 5.5 3.3 2.1 6.0 8.0 7.5
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC 9.1 8.7 7.8 8.3 6.7 5.6
44 GG/CC 10.1 9.8 9.0 8.5 8.7 8.0
45 GC/GC 9.2 8.2 7.3 8.9 7.9 7.0
46 CC/GG 9.6 9.4 8.7 9.6 9.4 8.7
47 CG/CG 10.1 10.3 9.7 9.5 10.2 9.7
48 GA/GC 11.3 9.7 8.9 7.3 7.4 6.7
49 AG/CG 10.5 11.5 10.5 4.7 5.4 4.9
50 GU/AC 8.5 8.7 7.9 9.6 9.4 8.5
51 UC/GA 10.8 10.2 9.2 7.4 7.8 7.1
52 CU/GG 8.7 8.2 8.0 12.6 13.3 12.4
53 UA/UG 7.7 7.0 6.0 7.1 6.4 5.5
54 AG/CU 9.3 6.3 5.2 10.9 7.4 6.6
55 GG/CC ---- ---- ---- ---- ---- ----
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step

bp Px Py Pz Hx Hy Hz
1 GG/UC 24.84 86.68 66.83 -0.79 0.06 -0.61
2 GC/GU 24.03 86.93 64.56 -0.74 -0.34 -0.57
3 CC/GG 19.87 86.27 65.22 -0.83 -0.15 -0.54
4 CC/GG 17.66 84.04 62.93 -0.76 -0.36 -0.54
5 CC/GG 15.18 85.39 60.17 -0.68 -0.19 -0.71
6 CA/UG 12.37 83.94 60.05 -0.71 -0.07 -0.70
7 AG/CU 8.98 83.11 60.71 -0.88 -0.03 -0.48
8 GG/CC 7.85 81.96 56.96 -0.82 -0.08 -0.57
9 GG/CC 5.70 80.09 55.06 -0.81 -0.36 -0.46
10 GG/CC 1.20 79.31 55.29 -0.83 -0.01 -0.55
11 GG/CC -1.90 77.08 54.94 -0.84 0.05 -0.54
12 GU/AC -0.74 78.87 49.22 -0.84 -0.19 -0.50
13 UU/GA -3.38 80.76 46.95 -0.90 -0.17 -0.41
14 UA/CG ---- ---- ---- ---- ---- ----
15 AG/CC 19.27 37.79 55.40 -0.42 0.90 -0.13
16 GG/CC 18.40 41.03 57.31 -0.34 0.93 -0.14
17 GC/GC 16.08 43.51 55.24 -0.58 0.81 -0.10
18 CC/GG 16.55 46.32 55.28 -0.39 0.90 -0.19
19 CG/CG 16.90 49.14 53.50 -0.49 0.76 -0.42
20 GA/GC 15.23 52.17 55.67 -0.27 0.93 -0.27
21 AG/CG 16.64 54.74 55.23 -0.37 0.82 -0.44
22 GU/AC 12.77 58.73 57.06 -0.02 0.92 -0.40
23 UC/GA 12.65 59.57 53.74 -0.27 0.90 -0.33
24 CU/AG 10.81 54.07 49.44 -0.54 0.40 -0.74
25 UA/UA 9.83 63.46 50.40 -0.42 0.78 -0.46
26 AG/CU 7.38 65.61 49.01 -0.55 0.80 -0.24
27 GG/CC ---- ---- ---- ---- ---- ----
28 GG/CC ---- ---- ---- ---- ---- ----
29 GG/UC 84.12 86.59 128.92 -0.93 -0.00 -0.37
30 GC/GU 82.38 87.08 127.35 -0.85 -0.31 -0.44
31 CC/GG 78.63 86.46 127.99 -0.88 -0.14 -0.45
32 CC/GG 76.05 84.31 126.50 -0.84 -0.33 -0.43
33 CC/GG 73.51 85.33 123.75 -0.81 -0.21 -0.55
34 CA/UG 70.59 83.83 123.65 -0.81 -0.18 -0.56
35 AG/CU 67.44 83.20 125.27 -0.94 -0.03 -0.34
36 GG/CC 66.04 82.17 121.38 -0.87 -0.13 -0.47
37 GG/CC 63.43 80.42 120.09 -0.86 -0.38 -0.34
38 GG/CC 58.87 79.35 121.12 -0.92 0.01 -0.39
39 GG/CC 56.63 77.52 120.68 -0.90 -0.09 -0.42
40 GU/AC 55.84 79.17 115.42 -0.91 -0.21 -0.36
41 UU/GA 52.80 81.03 113.88 -0.95 -0.20 -0.24
42 UA/CG ---- ---- ---- ---- ---- ----
43 AG/CC 76.95 37.96 118.34 -0.46 0.89 -0.05
44 GG/CC 76.45 41.26 120.36 -0.34 0.93 -0.10
45 GC/GC 73.75 43.49 118.95 -0.55 0.83 0.02
46 CC/GG 74.52 46.64 118.52 -0.45 0.88 -0.15
47 CG/CG 74.06 49.35 116.93 -0.57 0.76 -0.29
48 GA/GC 73.00 52.26 119.49 -0.29 0.93 -0.22
49 AG/CG 74.20 54.91 118.71 -0.45 0.82 -0.36
50 GU/AC 71.00 58.34 120.88 -0.17 0.90 -0.41
51 UC/GA 70.01 59.74 118.07 -0.29 0.91 -0.31
52 CU/GG 71.45 64.87 121.41 -0.10 0.91 -0.39
53 UA/UG 67.53 64.22 115.41 -0.44 0.82 -0.37
54 AG/CU 64.03 65.59 114.00 -0.57 0.80 -0.16
55 GG/CC ---- ---- ---- ---- ---- ----