Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~lesiad/Term3/rna.out Дата изменения: Sun Sep 14 23:15:32 2008 Дата индексирования: Tue Oct 2 06:35:27 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.
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File name: rna.pdb
Date and time: Sun Sep 14 23:28:38 2008

Number of base-pairs: 28
Number of atoms: 1556
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RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.010) B:.902_:[..G]G-----C[..C]:.971_:B (0.005) |
2 (0.012) B:.903_:[..G]G-----C[..C]:.970_:B (0.007) |
3 (0.011) B:.904_:[..G]G-----C[..C]:.969_:B (0.006) |
4 (0.012) B:.905_:[..G]G-----C[..C]:.968_:B (0.010) |
5 (0.010) B:.906_:[..U]U-----A[..A]:.967_:B (0.010) |
6 (0.013) B:.907_:[..A]Ax----U[..U]:.966_:B (0.004) |
7 (0.006) B:.949_:[..C]C-----G[..G]:.965_:B (0.011) |
8 (0.008) B:.950_:[..G]G-----C[..C]:.964_:B (0.004) |
9 (0.005) B:.951_:[..A]A-----U[..U]:.963_:B (0.004) |
10 (0.014) B:.952_:[..G]G-----C[..C]:.962_:B (0.005) |
11 (0.006) B:.953_:[..G]G----xC[..C]:.961_:B (0.005) |
12 (0.002) B:.954_:[..U]U-*--xA[..A]:.958_:B (0.008) |
13 (0.005) B:.955_:[..U]Ux**+xG[..G]:.918_:B (0.009) x
14 (0.007) B:.937_:[..A]A-*---U[..U]:.933_:B (0.003) |
15 (0.004) B:.938_:[..U]U-*---U[..U]:.932_:B (0.006) |
16 (0.006) B:.939_:[..U]U-----A[..A]:.931_:B (0.006) |
17 (0.005) B:.940_:[..C]C-*---G[..G]:.930_:B (0.012) |
18 (0.005) B:.941_:[..C]C-----G[..G]:.929_:B (0.007) |
19 (0.012) B:.942_:[..G]G-----C[..C]:.928_:B (0.010) |
20 (0.007) B:.943_:[..G]G-----C[..C]:.927_:B (0.003) |
21 (0.008) B:.944_:[..A]Ax*---A[..A]:.926_:B (0.015) |
22 (0.013) B:.910_:[..G]G-----C[..C]:.925_:B (0.006) |
23 (0.013) B:.911_:[..C]C-----G[..G]:.924_:B (0.006) |
24 (0.008) B:.912_:[..C]C----xG[..G]:.923_:B (0.007) |
25 (0.012) B:.913_:[..A]A-**+xG[..G]:.946_:B (0.008) |
26 (0.006) B:.914_:[..A]A-*--xA[..A]:.921_:B (0.008) |
27 (0.015) B:.915_:[..G]Gx**+xU[..U]:.948_:B (0.012) x
28 (0.029) B:.919_:[..G]G-----C[..C]:.956_:B (0.012) +

Note: This structure contains 9[3] non-Watson-Crick base-pairs.
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Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 2.58 N1 - N3 2.89 N2 - O2 3.12
2 G-----C [3] O6 - N4 2.58 N1 - N3 2.55 N2 - O2 2.48
3 G-----C [3] O6 - N4 2.63 N1 - N3 2.60 N2 - O2 2.53
4 G-----C [3] O6 - N4 2.65 N1 - N3 2.72 N2 - O2 2.74
5 U-----A [2] N3 - N1 2.58 O4 - N6 2.60
6 A-----U [2] N6 - O4 2.41 N1 - N3 2.70
7 C-----G [3] O2 - N2 2.60 N3 - N1 2.71 N4 - O6 2.76
8 G-----C [3] O6 - N4 2.69 N1 - N3 2.58 N2 - O2 2.50
9 A-----U [2] N6 - O4 2.69 N1 - N3 2.44
10 G-----C [3] O6 - N4 2.79 N1 - N3 2.67 N2 - O2 2.55
11 G-----C [3] O6 - N4 3.04 N1 - N3 2.95 N2 - O2 2.74
12 U-*---A [2] O2 - N6 2.57 N3 - N7 3.03
13 U-**+-G [3] O4'* O6 3.33 N1 * N1 3.97 O2 - N2 2.38
14 A-*---U [1] N6 - O2 2.80
15 U-*---U [1] O4 - N3 3.15
16 U-----A [2] N3 - N1 2.86 O4 - N6 3.28
17 C-*---G [2] O2 - N1 2.68 N3 * O6 3.20
18 C-----G [3] O2 - N2 3.11 N3 - N1 3.00 N4 - O6 2.76
19 G-----C [3] O6 - N4 2.74 N1 - N3 2.59 N2 - O2 2.35
20 G-----C [3] O6 - N4 2.77 N1 - N3 2.86 N2 - O2 2.84
21 A-*---A [1] N1 - N6 2.75
22 G-----C [3] O6 - N4 2.79 N1 - N3 2.79 N2 - O2 2.71
23 C-----G [3] O2 - N2 2.84 N3 - N1 2.82 N4 - O6 2.80
24 C-----G [3] O2 - N2 2.62 N3 - N1 2.90 N4 - O6 3.05
25 A-**+-G [1] N1 - N2 2.92
26 A-*---A [2] N6 - N3 3.03 N1 - O2' 2.90
27 G-**+-U [2] O6 - N3 2.78 N1 - O4 2.80
28 G-----C [3] O6 - N4 3.02 N1 - N3 2.61 N2 - O2 2.27
****************************************************************************
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/CC 3.66( 2.18) 0.00( 0.00) 0.39( 0.00) 1.01( 0.21) 5.06( 2.38)
2 GG/CC 3.51( 2.12) 0.00( 0.00) 0.80( 0.00) 0.00( 0.00) 4.31( 2.12)
3 GG/CC 4.30( 2.56) 0.00( 0.00) 0.83( 0.00) 0.00( 0.00) 5.13( 2.56)
4 GU/AC 6.59( 3.65) 0.00( 0.00) 0.00( 0.00) 4.43( 2.87) 11.02( 6.52)
5 UA/UA 0.56( 0.00) 0.00( 0.00) 2.46( 1.75) 0.00( 0.00) 3.02( 1.75)
6 AC/GU 2.36( 0.94) 0.00( 0.00) 0.00( 0.00) 7.15( 4.52) 9.51( 5.46)
7 CG/CG 0.00( 0.00) 0.00( 0.00) 5.78( 2.91) 0.00( 0.00) 5.78( 2.91)
8 GA/UC 4.36( 3.00) 0.00( 0.00) 0.00( 0.00) 0.24( 0.00) 4.60( 3.00)
9 AG/CU 4.26( 3.40) 0.00( 0.00) 0.45( 0.00) 0.00( 0.00) 4.71( 3.40)
10 GG/CC 3.05( 1.56) 0.00( 0.00) 1.34( 0.00) 0.00( 0.00) 4.40( 1.56)
11 GU/AC 7.23( 4.23) 0.00( 0.00) 0.00( 0.00) 5.31( 2.58) 12.53( 6.81)
12 UU/GA 4.75( 2.36) 0.00( 0.00) 0.00( 0.00) 5.39( 3.28) 10.14( 5.65)
13 UA/UG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
14 AU/UU 4.13( 0.55) 0.00( 0.00) 0.00( 0.00) 1.61( 0.50) 5.74( 1.04)
15 UU/AU 2.04( 0.73) 0.00( 0.00) 0.00( 0.00) 5.94( 4.50) 7.98( 5.23)
16 UC/GA 0.35( 0.08) 0.00( 0.00) 0.33( 0.00) 2.29( 0.88) 2.98( 0.96)
17 CC/GG 0.00( 0.00) 0.00( 0.00) 1.39( 0.02) 1.82( 0.45) 3.21( 0.47)
18 CG/CG 0.00( 0.00) 0.00( 0.00) 5.44( 2.67) 0.00( 0.00) 5.44( 2.67)
19 GG/CC 2.61( 1.11) 0.00( 0.00) 1.17( 0.00) 0.00( 0.00) 3.77( 1.11)
20 GA/AC 3.60( 1.16) 0.00( 0.00) 0.00( 0.00) 3.40( 1.70) 7.01( 2.86)
21 AG/CA 0.00( 0.00) 0.00( 0.00) 1.56( 0.39) 0.00( 0.00) 1.56( 0.39)
22 GC/GC 4.95( 2.09) 0.00( 0.00) 0.00( 0.00) 6.86( 3.65) 11.81( 5.74)
23 CC/GG 0.56( 0.16) 0.00( 0.00) 0.13( 0.00) 1.75( 0.45) 2.44( 0.62)
24 CA/GG 4.52( 2.04) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 4.52( 2.04)
25 AA/AG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 6.56( 4.29) 6.56( 4.29)
26 AG/UA 4.33( 3.52) 0.00( 0.00) 0.00( 0.00) 4.42( 3.38) 8.75( 6.90)
27 GG/CU 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 42.92 41.56 34.00 -0.97 -0.09 -0.24
2 G-C 40.03 39.76 32.67 -0.98 -0.10 -0.18
3 G-C 36.91 37.70 32.40 -0.98 -0.08 -0.17
4 G-C 33.41 36.12 34.17 -1.00 -0.06 0.06
5 U-A 30.18 35.62 35.88 -0.99 0.01 0.12
6 A-U 27.72 36.21 37.90 -0.96 0.19 0.19
7 C-G 25.20 37.21 39.81 -0.96 0.14 0.22
8 G-C 21.83 39.83 41.34 -0.97 0.20 0.10
9 A-U 18.91 41.30 40.22 -0.97 0.23 -0.08
10 G-C 16.19 42.51 38.10 -0.98 0.16 -0.13
11 G-C 13.41 42.65 35.28 -0.98 -0.00 -0.19
12 U-A 10.58 42.02 32.81 -0.99 0.07 -0.13
13 U+G 7.56 41.07 34.48 -0.97 -0.22 -0.05
14 A-U 19.04 -6.18 19.25 -0.46 0.89 0.05
15 U-U 15.58 -4.21 19.25 -0.29 0.93 0.23
16 U-A 14.03 -2.00 22.12 -0.17 0.97 0.18
17 C-G 13.23 1.03 24.58 -0.16 0.98 0.15
18 C-G 12.49 2.99 27.55 -0.02 0.97 0.23
19 G-C 14.05 6.11 29.62 0.04 1.00 0.07
20 G-C 16.14 9.64 30.86 0.10 0.99 0.04
21 A-A 18.23 12.75 31.05 0.07 0.99 -0.09
22 G-C 22.30 15.10 29.14 0.11 0.95 -0.28
23 C-G 22.51 17.63 26.53 0.09 0.96 -0.26
24 C-G 20.40 20.42 25.27 -0.01 0.98 -0.18
25 A+G 17.25 22.93 29.47 -0.25 0.97 -0.08
26 A-A 15.44 26.13 30.11 -0.19 0.98 0.06
27 G+U 14.03 29.57 28.96 -0.26 0.94 0.24
28 G-C 1.42 39.52 27.99 -0.93 -0.15 -0.32
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.76 -0.42 -0.33 -11.44 1.37 -9.18
2 G-C -0.11 -0.51 -0.39 -2.55 -5.91 0.32
3 G-C -0.13 -0.43 0.05 -1.91 -13.74 -0.33
4 G-C -0.19 -0.32 -0.13 -13.82 -14.60 -2.21
5 U-A 0.26 -0.41 0.09 -14.00 -11.55 -0.15
6 A-U 0.03 -0.35 -0.10 2.44 -8.19 -9.32
7 C-G 0.69 -0.43 -0.18 15.23 -10.36 0.04
8 G-C 0.43 -0.39 0.03 -11.45 -16.75 0.51
9 A-U -0.09 -0.47 -0.16 -10.10 -16.01 4.40
10 G-C 0.21 -0.30 -0.20 0.34 -12.67 3.33
11 G-C -0.31 -0.05 -0.03 -13.28 -7.60 2.12
12 U-A 4.48 -3.42 1.43 3.33 19.23 -74.48
13 U+G 0.03 -5.95 0.45 16.76 -3.67 -91.88
14 A-U -5.88 -4.98 0.43 -1.63 20.25 -31.48
15 U-U -3.66 -1.20 0.41 3.72 10.79 -28.94
16 U-A 0.08 -0.10 0.58 12.51 12.59 12.49
17 C-G 2.07 -0.23 0.35 -3.18 2.00 15.21
18 C-G -0.57 -0.04 -0.14 8.24 -9.04 -6.58
19 G-C -0.32 -0.42 -0.38 -9.47 -1.00 4.20
20 G-C 0.06 -0.11 -0.33 -19.57 -11.64 -2.07
21 A-A 1.68 1.41 0.04 -27.58 -19.68 -11.21
22 G-C -0.26 -0.28 -0.43 -6.75 -11.66 0.92
23 C-G 0.42 -0.29 -0.00 -2.51 -14.80 -0.79
24 C-G -0.14 -0.06 0.08 5.97 -1.93 4.06
25 A+G -3.01 4.38 0.46 8.02 2.79 116.12
26 A-A -6.58 -0.91 0.32 -1.06 -8.42 42.78
27 G+U 0.34 -0.93 -0.79 0.32 -11.28 161.43
28 G-C -0.20 -0.25 0.09 -21.82 -23.01 8.25
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.41 -0.62 0.04 -3.40 -5.87 3.84
s.d. 2.15 1.80 0.42 10.98 11.07 46.21
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GG/CC 0.18 -1.65 3.26 -1.32 3.51 34.69
2 GG/CC 0.17 -1.79 3.29 -0.98 0.77 33.76
3 GG/CC 0.85 -2.20 3.50 6.31 11.75 27.03
4 GU/AC 0.19 -1.46 3.38 1.18 4.73 34.79
5 UA/UA 0.08 -1.63 2.80 6.02 9.58 29.71
6 AC/GU -0.56 -1.32 2.99 -0.89 -2.87 43.77
7 CG/CG -0.63 -2.09 3.98 2.27 7.39 28.23
8 GA/UC 0.74 -1.19 3.16 5.26 9.13 32.95
9 AG/CU 0.57 -1.84 3.11 -0.29 4.37 26.47
10 GG/CC 0.38 -2.31 3.20 2.69 9.72 31.68
11 GU/AC -1.15 -1.76 3.16 -5.13 0.41 88.38
12 UU/GA 1.28 -1.63 2.93 16.89 -4.55 47.20
13 UA/UG ---- ---- ---- ---- ---- ----
14 AU/UU 0.68 -2.38 3.11 -13.34 5.49 50.65
15 UU/AU 1.70 -1.84 3.05 -8.34 0.13 45.58
16 UC/GA 0.44 -1.89 3.48 -1.55 0.09 41.63
17 CC/GG -1.02 -2.38 2.55 6.10 6.50 21.92
18 CG/CG 0.18 -2.19 3.41 -5.00 8.81 33.69
19 GG/CC -0.51 -2.04 3.73 2.81 2.47 35.74
20 GA/AC -0.94 -1.58 3.28 1.62 7.53 38.99
21 AG/CA -2.96 -2.78 3.03 11.18 2.19 49.82
22 GC/GC -0.54 -1.74 3.16 -0.55 1.57 35.22
23 CC/GG 0.99 -2.10 2.90 0.92 7.63 23.35
24 CA/GG 5.31 -0.52 2.33 9.80 11.12 3.07
25 AA/AG 0.79 -0.98 3.52 -4.42 7.64 34.38
26 AG/UA -1.69 -0.62 3.45 4.48 10.30 -21.27
27 GG/CU ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.18 -1.76 3.19 1.43 5.02 34.06
s.d. 1.47 0.54 0.35 6.35 4.49 18.72
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GG/CC -3.27 -0.50 3.08 5.87 2.20 34.89
2 GG/CC -3.20 -0.45 3.24 1.32 1.68 33.78
3 GG/CC -6.57 -0.40 2.48 23.42 -12.57 30.09
4 GU/AC -3.13 -0.14 3.17 7.86 -1.95 35.12
5 UA/UA -4.37 0.72 2.16 17.88 -11.24 31.74
6 AC/GU -1.51 0.67 3.07 -3.85 1.19 43.87
7 CG/CG -5.95 1.81 3.27 14.80 -4.55 29.25
8 GA/UC -3.33 -0.49 2.82 15.60 -8.99 34.55
9 AG/CU -4.98 -1.30 2.77 9.47 0.62 26.82
10 GG/CC -5.48 -0.27 2.43 17.28 -4.79 33.20
11 GU/AC -1.27 0.72 3.21 0.29 3.68 88.50
12 UU/GA -1.60 -0.31 3.31 -5.46 -20.30 50.16
13 UA/UG ---- ---- ---- ---- ---- ----
14 AU/UU -3.01 -1.55 2.61 6.27 15.24 52.53
15 UU/AU -2.34 -2.79 2.71 0.16 10.66 46.30
16 UC/GA -2.66 -0.80 3.46 0.12 2.18 41.66
17 CC/GG -7.19 3.78 1.46 16.25 -15.25 23.64
18 CG/CG -4.89 -1.02 2.72 14.79 8.40 35.14
19 GG/CC -3.71 1.27 3.53 4.02 -4.57 35.93
20 GA/AC -3.16 1.56 2.90 11.15 -2.40 39.72
21 AG/CA -3.35 4.07 2.25 2.56 -13.08 51.02
22 GC/GC -3.10 0.81 3.09 2.60 0.91 35.26
23 CC/GG -6.80 -2.11 2.15 18.22 -2.19 24.56
24 CA/GG -15.53 -8.18 3.53 58.79 -51.82 15.14
25 AA/AG -2.76 -1.96 3.11 12.67 7.33 35.46
26 AG/UA -2.33 -2.40 3.63 -25.73 11.20 -24.03
27 GG/CU ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -4.22 -0.37 2.89 9.05 -3.54 35.37
s.d. 2.87 2.35 0.52 14.57 13.32 18.47
****************************************************************************
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 44.6 52.8 10.8 8.9 9.6
2 G-C 54.5 54.1 10.3 8.6 9.5
3 G-C 52.4 53.5 10.4 8.7 9.6
4 G-C 53.5 52.8 10.5 8.8 9.6
5 U-A 57.8 52.8 10.2 8.5 9.5
6 A-U 50.7 49.6 10.7 8.8 9.6
7 C-G 56.2 49.5 10.4 8.6 9.5
8 G-C 57.9 51.1 10.3 8.7 9.6
9 A-U 56.9 57.0 10.0 8.4 9.4
10 G-C 57.6 54.3 10.3 8.7 9.7
11 G-C 54.5 57.0 10.6 9.0 9.9
12 U-A 46.2 12.0 9.3 7.0 6.4
13 U+G 113.9 32.4 8.2 7.9 9.4
14 A-U 1.9 79.9 8.9 7.4 7.5
15 U-U 21.2 58.8 11.1 8.9 9.3
16 U-A 62.0 59.9 10.0 8.6 9.8
17 C-G 73.6 51.7 10.0 8.7 9.9
18 C-G 46.4 53.5 11.1 9.2 10.0
19 G-C 56.7 58.8 10.1 8.5 9.6
20 G-C 54.7 52.6 10.7 8.9 9.8
21 A-A 59.0 41.8 12.3 10.5 11.0
22 G-C 53.9 56.4 10.5 8.8 9.7
23 C-G 56.0 51.7 10.5 8.8 9.7
24 C-G 54.9 57.5 10.5 8.9 9.9
25 A+G 25.0 86.1 12.2 10.9 12.2
26 A-A 33.2 117.1 9.8 9.3 10.5
27 G+U 15.2 37.0 11.7 9.2 9.6
28 G-C 62.8 56.0 9.9 8.5 9.6
****************************************************************************
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/CC -1.13 8.25 2.26 -4.25 7.99 3.07 A
2 GG/CC -1.43 8.05 2.39 -4.50 8.00 2.56 A
3 GG/CC -1.84 8.51 2.30 -7.99 6.99 5.25 A
4 GU/AC -1.48 8.31 2.22 -4.44 7.95 3.28 A
5 UA/UA -1.50 8.21 2.11 -5.51 7.23 4.36 A
6 AC/GU -1.70 7.65 3.25 -3.08 7.84 2.77 A
7 CG/CG -1.57 7.94 2.77 -7.32 7.00 4.65 A
8 GA/UC -1.80 8.36 1.98 -4.84 7.57 4.01 A
9 AG/CU -2.15 8.69 1.80 -7.00 8.29 3.17 A
10 GG/CC -1.92 7.84 2.98 -7.13 6.66 5.10 A
11 GU/AC -0.86 6.75 3.74 -1.83 6.74 3.58
12 UU/GA 3.24 4.56 0.45 0.84 4.62 1.04
13 UA/UG --- --- --- --- --- --- ---
14 AU/UU 0.95 6.49 3.37 -1.67 6.10 4.47
15 UU/AU -0.68 7.79 3.38 -2.67 7.78 3.59
16 UC/GA -2.25 7.13 3.71 -4.72 7.12 3.71
17 CC/GG -2.13 7.72 3.04 -9.08 6.59 4.97 A
18 CG/CG -1.86 7.90 2.93 -6.47 6.94 4.84 A
19 GG/CC -1.58 7.88 2.70 -5.05 7.68 3.20 A
20 GA/AC -1.28 8.75 2.03 -4.17 8.24 3.58 A
21 AG/CA -3.16 7.32 3.36 -6.06 7.19 3.23
22 GC/GC -1.76 8.29 2.29 -4.72 8.18 2.64 A
23 CC/GG -1.80 8.50 2.39 -8.43 7.36 4.87 A
24 CA/GG -3.96 7.91 2.35 -18.01 3.52 4.84
25 AA/AG 0.15 3.42 3.05 -2.56 2.59 4.79
26 AG/UA -4.24 5.91 0.69 -6.17 5.84 -0.99
27 GG/CU --- --- --- --- --- --- ---
****************************************************************************
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/CC --- --- --- ---
2 GG/CC --- --- --- ---
3 GG/CC 16.2 --- 16.3 ---
4 GU/AC 17.2 15.4 16.8 14.1
5 UA/UA 17.3 15.6 17.8 16.7
6 AC/GU 15.9 14.7 16.6 15.8
7 CG/CG 15.9 14.7 16.1 15.5
8 GA/UC 16.7 15.4 15.3 10.9
9 AG/CU 16.7 15.1 16.5 12.0
10 GG/CC 16.4 --- 14.8 ---
11 GU/AC --- --- --- ---
12 UU/GA --- --- --- ---
13 UA/UG --- --- --- ---
14 AU/UU --- --- --- ---
15 UU/AU --- --- --- ---
16 UC/GA 16.7 --- 14.4 ---
17 CC/GG 16.2 14.4 16.9 12.1
18 CG/CG 15.6 14.3 16.5 11.0
19 GG/CC 16.8 13.8 16.2 12.4
20 GA/AC 17.6 13.6 15.5 12.9
21 AG/CA 16.5 14.1 14.1 11.9
22 GC/GC 16.6 14.9 15.3 13.9
23 CC/GG 16.8 15.4 7.2 7.2
24 CA/GG 16.6 --- 22.1 ---
25 AA/AG --- --- --- ---
26 AG/UA --- --- --- ---
27 GG/CU --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 0.66(3.46)
****************************************************************************
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 --- --- 174.2 89.3 -134.7 -66.8 175.2
2 G -71.9 179.9 53.2 81.6 -166.3 -63.7 -165.0
3 G -61.8 -177.5 53.8 81.1 -156.4 -69.1 -159.3
4 G 145.5 -164.3 -172.8 79.2 -139.8 -68.6 -174.8
5 U -60.2 178.6 47.8 81.0 175.8 -82.7 -158.0
6 A -172.6 -130.2 164.7 112.4 --- --- -157.0
7 C --- -170.5 48.4 87.8 -144.1 -78.8 -166.8
8 G -49.6 169.2 46.1 84.8 -152.8 -63.9 -164.8
9 A -67.4 178.6 49.1 78.3 -175.7 -37.8 -149.7
10 G 178.4 148.9 160.4 84.0 -147.4 -68.6 -169.4
11 G -55.0 178.6 42.1 79.1 -155.7 -67.8 -168.1
12 U -63.9 -172.8 50.7 86.3 -140.0 -68.3 -165.1
13 U -59.3 170.3 49.0 83.1 --- --- -143.9
14 A --- -158.0 54.1 81.8 -143.6 -62.4 -170.2
15 U -51.6 163.3 56.3 82.8 -128.5 -59.9 170.1
16 U -68.4 176.4 48.2 86.2 -153.3 -70.8 -172.3
17 C -62.4 163.9 54.9 84.7 -108.8 -147.6 174.1
18 C 105.8 -105.2 179.1 82.6 -129.9 -69.1 173.8
19 G -67.4 179.4 41.9 78.4 -156.9 -77.9 -177.4
20 G -56.7 176.5 50.9 70.3 83.5 54.7 -168.3
21 A 96.2 -176.4 162.9 92.2 --- --- -168.0
22 G --- 151.2 52.5 79.1 -155.8 -67.4 -173.9
23 C -65.4 -172.3 49.2 80.7 -158.5 -72.0 -154.3
24 C 148.2 -165.2 178.3 85.3 -129.8 -63.5 -170.6
25 A -53.1 161.1 56.7 82.2 -176.3 -82.7 -146.5
26 A 157.2 175.0 178.0 87.5 -138.1 -80.2 -172.6
27 G -39.0 159.7 46.3 87.4 --- --- -150.5
28 G --- 150.0 55.3 97.7 --- --- -102.7

Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -75.6 -173.5 54.6 81.6 --- --- -146.6
2 C -69.6 -167.8 45.2 84.3 -164.4 -63.0 -153.6
3 C -64.1 -176.9 47.9 81.1 -162.6 -60.8 -166.1
4 C -59.5 170.8 51.0 81.6 -159.6 -68.1 -156.8
5 A -53.7 174.7 43.5 83.3 -152.7 -75.0 -155.1
6 U -48.3 142.3 57.3 77.0 -149.4 -79.7 -170.0
7 G 156.8 -149.0 174.8 84.1 -106.9 -88.5 166.1
8 C -71.0 -168.6 39.7 80.1 -172.7 -75.8 -150.5
9 U -55.9 175.6 48.3 79.5 -171.8 -69.5 -148.9
10 C -66.4 -171.6 44.6 80.6 -147.4 -74.7 -166.2
11 C --- -164.9 52.3 84.6 -158.9 -66.6 -169.7
12 A --- -166.1 60.5 101.3 --- --- -115.0
13 G --- -140.5 40.4 85.5 --- --- -120.1
14 U -72.6 -166.9 45.2 82.3 --- --- -155.0
15 U 157.4 -139.3 165.6 83.4 -135.8 -59.6 178.3
16 A -81.5 -141.1 47.9 82.8 -169.4 -91.7 -164.4
17 G -73.1 169.0 56.6 79.4 -176.5 -58.1 -177.5
18 G 149.1 -137.2 169.1 85.2 -118.7 -86.2 170.3
19 C -59.3 -178.5 42.3 78.8 -157.3 -103.7 -162.6
20 C -57.9 178.4 50.2 82.3 -148.5 -69.1 -163.7
21 A -68.3 -174.8 52.1 77.1 -149.3 -65.9 -158.7
22 C -63.3 161.8 57.7 74.3 -146.6 -64.4 -167.4
23 G -56.9 159.8 56.4 77.9 -140.8 -73.3 -170.2
24 G --- 164.7 40.6 82.2 -142.4 -87.1 -174.7
25 G --- -179.5 47.6 81.0 --- --- -121.2
26 A --- 101.0 154.6 87.5 --- --- -162.9
27 U --- 148.7 156.8 96.0 --- --- -166.6
28 C --- -167.8 50.2 86.3 --- --- -156.4
****************************************************************************
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 14.9 -32.7 37.6 -29.8 9.4 37.7 355.8 C2'-exo
2 G 0.9 -26.7 41.2 -41.7 25.6 43.1 17.4 C3'-endo
3 G 1.1 -26.3 40.6 -40.8 24.9 42.5 17.0 C3'-endo
4 G 4.9 -29.6 42.2 -40.3 22.2 43.2 12.2 C3'-endo
5 U -1.2 -25.1 40.6 -42.3 27.2 43.2 20.0 C3'-endo
6 A -26.1 16.4 -1.3 -13.7 24.8 26.4 92.7 O4'-endo
7 C 9.5 -29.4 37.2 -32.9 14.8 37.3 4.4 C3'-endo
8 G -2.0 -21.6 35.7 -37.9 25.0 38.4 21.5 C3'-endo
9 A -5.1 -21.0 37.8 -41.4 29.4 41.8 25.3 C3'-endo
10 G 9.7 -30.0 37.9 -33.6 15.1 38.0 4.4 C3'-endo
11 G 0.9 -26.6 41.3 -41.5 25.4 43.2 17.2 C3'-endo
12 U 11.7 -32.0 39.2 -33.5 13.8 39.2 1.7 C3'-endo
13 U 4.3 -27.6 39.3 -37.8 21.0 40.2 12.5 C3'-endo
14 A 5.3 -29.4 41.1 -39.1 21.3 42.0 11.5 C3'-endo
15 U 4.3 -27.7 39.1 -37.9 21.2 40.1 12.7 C3'-endo
16 U 3.5 -25.4 36.2 -35.3 20.0 37.2 13.4 C3'-endo
17 C 6.3 -28.3 38.4 -35.9 18.6 39.0 9.5 C3'-endo
18 C 2.8 -25.9 38.2 -37.7 21.8 39.5 14.7 C3'-endo
19 G -5.0 -21.1 37.4 -41.6 29.3 41.5 25.4 C3'-endo
20 G 6.2 -29.7 40.9 -38.3 20.3 41.6 10.2 C3'-endo
21 A 9.8 -28.7 35.4 -31.1 13.4 35.4 3.2 C3'-endo
22 G -5.2 -21.8 39.3 -43.4 30.5 43.5 25.3 C3'-endo
23 C -0.6 -25.2 39.8 -41.3 26.5 42.2 19.4 C3'-endo
24 C 4.7 -29.1 41.5 -39.6 22.0 42.5 12.3 C3'-endo
25 A -0.5 -22.1 35.1 -36.5 23.4 37.3 19.5 C3'-endo
26 A 9.8 -31.4 39.9 -35.4 16.2 40.0 4.8 C3'-endo
27 G -3.7 -17.8 31.1 -34.3 24.0 34.2 24.8 C3'-endo
28 G -12.2 -4.7 18.6 -26.6 24.2 26.5 45.6 C4'-exo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C -1.7 -23.7 38.9 -40.6 26.8 41.6 20.8 C3'-endo
2 C 3.3 -27.1 39.1 -38.4 22.1 40.3 14.0 C3'-endo
3 C 3.2 -28.6 41.7 -40.8 23.8 43.0 14.4 C3'-endo
4 C -0.7 -24.3 3