Документ взят из кэша поисковой машины. Адрес оригинального документа : http://kodomo.cmm.msu.ru/~lu.andreeva/2DLC_old.out Дата изменения: Mon Sep 21 22:17:02 2009 Дата индексирования: Tue Oct 2 03:30:37 2012 Кодировка:

****************************************************************************
This structure has broken O3'[i] to P[i+1] linkages
****************************************************************************
3DNA (v1.5, Nov. 2002) by Xiang-Jun Lu at Wilma K. Olson's Lab.
****************************************************************************
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: 2DLC_old.pdb
Date and time: Mon Sep 21 22:17:01 2009

Number of base-pairs: 20
Number of atoms: 1264
****************************************************************************
HEADER LIGASE/TRNA 18-APR-06 2DLC
COMPND TYROSYL-TRNA SYNTHETASE, CYTOPLASMIC;
EXPDTA X-RAY DIFFRACTION
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)

Strand I Strand II Helix
1 (0.007) Y:.501_:[..C]C-----G[..G]:.572_:Y (0.014) |
2 (0.009) Y:.502_:[..U]U-----A[..A]:.571_:Y (0.007) |
3 (0.007) Y:.503_:[..C]C-----G[..G]:.570_:Y (0.009) |
4 (0.010) Y:.504_:[..U]U-*---G[..G]:.569_:Y (0.008) |
5 (0.007) Y:.505_:[..C]C-----G[..G]:.568_:Y (0.009) |
6 (0.008) Y:.506_:[..G]G-----C[..C]:.567_:Y (0.012) |
7 (0.013) Y:.507_:[..G]Gx----C[..C]:.566_:Y (0.014) |
8 (0.010) Y:.549_:[..G]G-----C[..C]:.565_:Y (0.011) |
9 (0.009) Y:.550_:[..G]G-----C[..C]:.564_:Y (0.007) |
10 (0.008) Y:.551_:[..G]G-----C[..C]:.563_:Y (0.009) |
11 (0.008) Y:.552_:[..C]C-----G[..G]:.562_:Y (0.009) |
12 (0.010) Y:.553_:[..G]Gx---xC[..C]:.561_:Y (0.008) x
13 (0.009) Y:.508_:[..U]Ux**--A[..A]:.514_:Y (0.007) |
14 (0.008) Y:.522_:[..A]A-*---A[..A]:.513_:Y (0.008) |
15 (0.010) Y:.523_:[..G]G-----C[..C]:.512_:Y (0.007) |
16 (0.012) Y:.524_:[..G]G----xC[..C]:.511_:Y (0.007) |
17 (0.007) Y:.525_:[..C]Cx*--xG[..G]:.545_:Y (0.014) |
18 (0.007) Y:.527_:[..C]C-----G[..G]:.543_:Y (0.011) |
19 (0.009) Y:.528_:[..A]Ax*--xU[..U]:.542_:Y (0.011) x
20 (0.010) Y:.519_:[..G]G-----C[..C]:.556_:Y (0.007) +

Note: This structure contains 5[1] non-Watson-Crick base-pairs.
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 C-----G [3] O2 - N2 2.76 N3 - N1 2.83 N4 - O6 3.06
2 U-----A [2] N3 - N1 2.73 O4 - N6 2.92
3 C-----G [3] O2 - N2 2.77 N3 - N1 2.94 N4 - O6 3.05
4 U-*---G [2] O2 - N1 2.66 N3 - O6 2.92
5 C-----G [3] O2 - N2 2.85 N3 - N1 2.80 N4 - O6 2.64
6 G-----C [3] O6 - N4 2.92 N1 - N3 2.85 N2 - O2 2.69
7 G-----C [3] O6 - N4 3.57 N1 - N3 3.21 N2 - O2 2.75
8 G-----C [3] O6 - N4 3.04 N1 - N3 2.94 N2 - O2 2.76
9 G-----C [3] O6 - N4 2.77 N1 - N3 2.76 N2 - O2 2.65
10 G-----C [3] O6 - N4 2.67 N1 - N3 2.74 N2 - O2 2.79
11 C-----G [3] O2 - N2 2.66 N3 - N1 2.97 N4 - O6 3.21
12 G-----C [3] O6 - N4 2.78 N1 - N3 2.82 N2 - O2 2.78
13 U-**--A [3] O2 - N6 2.87 N3 - N7 3.19 O4 * O2P 3.40
14 A-*---A [1] N6 - O2' 2.95
15 G-----C [3] O6 - N4 3.23 N1 - N3 3.01 N2 - O2 2.72
16 G-----C [3] O6 - N4 3.48 N1 - N3 3.20 N2 - O2 2.82
17 C-*---G [1] N4 * N2 3.72
18 C-----G [3] O2 - N2 3.02 N3 - N1 3.10 N4 - O6 3.41
19 A-*---U [2] N6 * N3 3.16 N1 * O2 3.10
20 G-----C [3] O6 - N4 3.65 N1 - N3 3.27 N2 - O2 3.12
****************************************************************************
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 CU/AG 0.00( 0.00) 0.00( 0.00) 0.54( 0.00) 1.83( 1.76) 2.37( 1.76)
2 UC/GA 0.70( 0.00) 0.00( 0.00) 0.00( 0.00) 4.10( 2.87) 4.79( 2.88)
3 CU/GG 3.25( 1.18) 0.00( 0.00) 0.00( 0.00) 3.87( 2.45) 7.12( 3.63)
4 UC/GG 0.29( 0.00) 0.00( 0.00) 0.21( 0.00) 2.07( 0.63) 2.58( 0.63)
5 CG/CG 0.02( 0.00) 0.00( 0.00) 4.74( 1.89) 0.00( 0.00) 4.76( 1.89)
6 GG/CC 3.33( 1.80) 0.00( 0.00) 0.18( 0.00) 0.18( 0.00) 3.69( 1.80)
7 GG/CC 1.99( 0.56) 0.00( 0.00) 0.99( 0.00) 0.00( 0.00) 2.98( 0.56)
8 GG/CC 2.69( 1.16) 0.00( 0.00) 0.74( 0.00) 0.16( 0.04) 3.59( 1.20)
9 GG/CC 3.83( 2.61) 0.00( 0.00) 0.18( 0.00) 0.58( 0.00) 4.59( 2.61)
10 GC/GC 6.99( 4.11) 0.00( 0.00) 0.00( 0.00) 5.96( 2.87) 12.95( 6.98)
11 CG/CG 0.00( 0.00) 0.00( 0.00) 4.73( 1.84) 0.00( 0.00) 4.73( 1.84)
12 GU/AC 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00)
13 UA/AA 0.00( 0.00) 3.18( 0.46) 0.25( 0.04) 0.00( 0.00) 3.42( 0.50)
14 AG/CA 2.83( 0.81) 0.00( 0.00) 0.00( 0.00) 2.37( 0.38) 5.20( 1.20)
15 GG/CC 2.70( 1.20) 0.00( 0.00) 0.98( 0.00) 0.00( 0.00) 3.68( 1.20)
16 GC/GC 5.74( 2.68) 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.74( 2.68)
17 CC/GG 0.00( 0.00) 0.00( 0.00) 0.06( 0.00) 2.38( 0.14) 2.44( 0.14)
18 CA/UG 0.00( 0.00) 0.00( 0.00) 3.13( 0.52) 0.03( 0.00) 3.16( 0.52)
19 AG/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 C-G 23.50 -1.25 157.25 -0.48 -0.35 -0.81
2 U-A 20.34 -2.60 154.97 -0.44 -0.14 -0.89
3 C-G 17.70 -2.35 152.82 -0.44 -0.10 -0.89
4 U-G 16.19 -1.21 149.90 -0.40 -0.01 -0.92
5 C-G 15.10 0.86 147.13 -0.29 0.04 -0.96
6 G-C 16.31 2.17 143.24 -0.09 -0.00 -1.00
7 G-C 17.59 2.50 139.86 0.02 -0.16 -0.99
8 G-C 19.71 2.01 136.77 0.02 -0.22 -0.97
9 G-C 21.79 0.41 133.95 0.04 -0.26 -0.97
10 G-C 22.11 -1.97 131.42 -0.07 -0.37 -0.93
11 C-G 21.13 -4.17 129.07 -0.12 -0.32 -0.94
12 G-C 18.49 -6.12 126.55 -0.29 -0.25 -0.92
13 U-A 0.94 0.72 133.69 -0.60 0.80 0.08
14 A-A -1.28 2.70 136.29 -0.60 0.80 0.07
15 G-C -2.37 5.73 137.56 -0.62 0.79 -0.01
16 G-C -2.94 9.70 138.15 -0.48 0.85 -0.20
17 C-G -3.53 11.52 134.04 -0.62 0.79 0.00
18 C-G -8.53 15.48 131.17 -0.78 0.63 0.03
19 A-U -11.91 16.25 130.04 -0.82 0.38 0.42
20 G-C 9.16 -10.75 116.30 -0.44 -0.37 -0.82
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 C-G 0.02 -0.07 -0.10 22.20 -27.16 1.56
2 U-A -0.21 -0.19 0.32 -4.59 -15.57 0.46
3 C-G 0.31 -0.08 0.14 0.95 -13.34 1.52
4 U-G 2.48 -0.53 -0.02 0.89 -13.65 4.15
5 C-G 0.03 -0.24 -0.05 2.89 -8.81 -4.35
6 G-C -0.33 -0.17 -0.43 -9.17 -10.63 2.77
7 G-C -0.20 0.32 -0.31 -10.32 -5.50 8.13
8 G-C -0.82 -0.22 0.07 -8.75 -8.41 1.44
9 G-C -0.23 -0.27 0.04 -8.23 -9.14 -0.80
10 G-C -0.45 -0.39 -0.22 -6.29 -15.68 -2.48
11 C-G 0.58 -0.06 0.04 2.08 -11.97 5.67
12 G-C -0.19 -0.21 -0.03 -13.54 -11.29 -2.49
13 U-A 4.15 -1.65 0.48 -7.89 15.66 -92.95
14 A-A -7.04 -4.29 -0.13 0.73 -11.52 -14.08
15 G-C -0.86 -0.10 0.26 12.76 -6.94 4.73
16 G-C -0.21 0.22 -0.60 -3.66 -8.92 7.97
17 C-G -6.13 0.96 1.26 27.20 7.16 -22.69
18 C-G 0.05 0.09 0.53 15.11 -30.84 -1.48
19 A-U -3.06 -0.38 -0.42 10.30 1.94 -3.09
20 G-C -0.57 0.30 0.24 -27.30 -32.39 1.94
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.63 -0.35 0.05 -0.23 -10.85 -5.20
s.d. 2.45 1.04 0.41 12.86 11.34 21.86
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 CU/AG -0.33 -1.72 3.73 -4.84 11.90 37.30
2 UC/GA -0.17 -1.54 3.05 1.07 2.46 31.24
3 CU/GG 0.40 -1.26 3.21 3.38 4.35 40.98
4 UC/GG -0.30 -2.00 3.01 3.69 6.14 20.63
5 CG/CG 1.03 -2.07 3.61 3.84 11.36 27.59
6 GG/CC 0.15 -1.52 3.29 1.01 11.05 32.18
7 GG/CC -0.23 -2.04 3.17 0.52 3.60 32.31
8 GG/CC -0.44 -2.12 3.18 1.64 1.10 33.14
9 GG/CC 0.22 -1.50 3.14 3.74 8.25 30.26
10 GC/GC 0.45 -1.36 3.05 -1.99 3.15 36.57
11 CG/CG 0.67 -2.18 3.46 4.08 9.83 27.57
12 GU/AC ---- ---- ---- ---- ---- ----
13 UA/AA 0.63 -2.37 3.10 -0.84 -0.65 47.48
14 AG/CA 0.55 -1.43 3.10 -4.48 0.25 47.10
15 GG/CC 0.02 -1.99 3.54 2.07 13.94 36.96
16 GC/GC 3.69 -1.38 2.25 -11.10 -9.48 48.66
17 CC/GG 1.28 -2.81 6.27 -4.01 12.45 86.08
18 CA/UG -0.44 -2.14 2.91 -7.16 25.73 22.34
19 AG/CU ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. 0.42 -1.85 3.36 -0.55 6.79 37.55
s.d. 0.99 0.43 0.82 4.43 7.75 14.93
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 CU/AG -4.07 -0.12 3.08 17.96 7.31 39.38
2 UC/GA -3.27 0.50 2.92 4.55 -1.99 31.35
3 CU/GG -2.24 -0.22 3.09 6.18 -4.81 41.33
4 UC/GG -7.25 2.00 2.24 16.51 -9.93 21.82
5 CG/CG -6.33 -1.19 2.68 22.53 -7.61 30.04
6 GG/CC -4.26 -0.11 2.64 19.23 -1.76 33.99
7 GG/CC -4.24 0.49 2.93 6.44 -0.93 32.51
8 GG/CC -3.89 1.03 3.09 1.93 -2.87 33.20
9 GG/CC -4.15 0.23 2.66 15.37 -6.98 31.56
10 GC/GC -2.55 -0.95 2.90 5.00 3.16 36.75
11 CG/CG -6.29 -0.48 2.61 19.73 -8.18 29.52
12 GU/AC ---- ---- ---- ---- ---- ----
13 UA/AA -2.89 -0.85 3.12 -0.80 1.04 47.49
14 AG/CA -1.80 -1.03 3.03 0.31 5.60 47.30
15 GG/CC -4.55 0.21 2.64 21.07 -3.13 39.46
16 GC/GC -1.20 -4.79 1.65 -11.21 13.13 50.68
17 CC/GG -2.56 -1.09 5.85 9.08 2.93 86.88
18 CA/UG -6.07 0.05 0.42 48.93 13.62 34.69
19 AG/CU ---- ---- ---- ---- ---- ----
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -3.98 -0.37 2.80 11.93 -0.08 39.29
s.d. 1.73 1.41 1.04 13.36 7.00 14.31
****************************************************************************
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 C-G 50.9 54.5 10.7 8.9 9.8
2 U-A 51.7 54.6 10.6 8.8 9.8
3 C-G 55.3 53.0 10.7 9.0 9.9
4 U-G 68.9 42.5 10.4 8.8 9.8
5 C-G 50.8 51.9 10.8 9.0 9.8
6 G-C 54.5 55.5 10.6 8.9 9.8
7 G-C 56.9 56.5 10.9 9.2 10.3
8 G-C 51.5 56.6 10.6 8.9 9.8
9 G-C 52.9 52.9 10.6 8.8 9.7
10 G-C 50.6 52.4 10.6 8.8 9.6
11 C-G 58.1 54.5 10.6 8.9 10.0
12 G-C 52.5 51.3 10.7 8.9 9.7
13 U-A 30.4 17.4 10.2 7.6 6.7
14 A-A 1.7 91.1 9.9 8.6 8.9
15 G-C 51.1 59.6 10.6 8.9 9.9
16 G-C 56.0 57.0 10.8 9.2 10.2
17 C-G 16.7 69.5 13.8 11.9 12.2
18 C-G 49.4 53.8 11.0 9.2 10.0
19 A-U 38.0 67.1 10.9 9.2 10.0
20 G-C 55.5 53.3 10.9 9.1 10.1
****************************************************************************
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 CU/AG -2.01 8.02 2.71 -5.78 6.88 4.92 A
2 UC/GA -1.52 8.41 2.56 -4.66 8.19 3.18 A
3 CU/GG -1.74 8.28 2.51 -3.82 7.98 3.38 A
4 UC/GG -1.50 8.17 2.56 -8.55 7.11 4.80 A
5 CG/CG -1.94 8.63 2.42 -8.00 7.13 5.37 A
6 GG/CC -2.13 8.33 2.31 -6.18 7.17 4.81 A
7 GG/CC -1.68 7.53 3.45 -5.76 7.11 4.24 A
8 GG/CC -1.42 7.99 2.86 -5.12 7.90 3.09 A
9 GG/CC -1.24 8.32 2.48 -5.17 7.41 4.47 A
10 GC/GC -1.46 8.31 2.35 -3.89 8.09 3.03 A
11 CG/CG -1.82 8.28 2.76 -7.82 6.92 5.32 A
12 GU/AC --- --- --- --- --- --- ---
13 UA/AA -0.77 5.34 2.57 -3.41 5.37 2.56
14 AG/CA -1.44 8.24 2.39 -3.03 8.23 2.58 A
15 GG/CC -2.24 8.20 2.78 -6.54 6.77 5.39 A
16 GC/GC -3.69 7.84 3.13 -4.61 8.24 1.32
17 CC/GG -3.55 7.66 4.52 -5.34 7.09 5.39
18 CA/UG -2.27 8.22 2.24 -7.95 3.77 7.78
19 AG/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 CU/AG --- --- --- ---
2 UC/GA --- --- --- ---
3 CU/GG 16.6 --- 16.2 ---
4 UC/GG 16.7 15.3 17.4 14.0
5 CG/CG 17.5 15.6 17.8 14.2
6 GG/CC 17.6 15.7 17.6 15.1
7 GG/CC 16.5 14.9 18.7 17.0
8 GG/CC 16.3 14.9 17.7 17.1
9 GG/CC 16.7 --- 15.2 ---
10 GC/GC --- --- --- ---
11 CG/CG --- --- --- ---
12 GU/AC --- --- --- ---
13 UA/AA --- --- --- ---
14 AG/CA --- --- --- ---
15 GG/CC 18.2 --- 12.7 ---
16 GC/GC 20.0 --- 11.7 ---
17 CC/GG --- --- --- ---
18 CA/UG --- --- --- ---
19 AG/CU --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.19(2.81)
****************************************************************************
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 C --- -174.0 43.7 83.1 -144.3 -72.5 -160.8
2 U -70.4 -176.0 50.5 83.2 -149.5 -68.7 -165.0
3 C -78.3 167.7 67.9 80.2 -150.0 -68.6 -164.0
4 U -67.6 167.9 58.7 80.7 -139.9 -91.7 -158.5
5 C -56.6 149.4 63.0 79.1 -152.5 -80.5 -162.4
6 G 117.9 -162.1 -151.7 92.3 -144.2 -71.5 -174.0
7 G -64.0 176.1 67.5 134.8 --- --- -139.9
8 G --- 167.6 36.2 83.2 -144.4 -70.8 -179.8
9 G -68.7 176.5 58.2 77.6 -141.3 -77.3 -167.9
10 G -65.5 160.1 66.6 77.7 -149.2 -71.2 -166.8
11 C -66.4 172.0 53.2 78.8 -141.0 -92.0 -159.7
12 G 106.2 -146.6 -139.0 96.7 --- --- -178.8
13 U --- -145.9 53.7 81.1 --- --- -164.3
14 A --- 157.5 24.5 73.8 -150.1 -78.2 -159.2
15 G 137.8 -144.6 -178.6 93.1 -115.9 -80.2 -178.5
16 G -61.3 163.1 47.9 75.4 -147.8 -69.5 -171.4
17 C -67.4 172.4 59.8 77.0 --- --- -166.3
18 C --- 172.2 49.0 79.9 -172.3 -71.5 -164.7
19 A -135.0 -105.6 76.8 126.6 --- --- -126.2
20 G --- 162.8 36.9 139.6 --- --- -77.2

Strand II
base alpha beta gamma delta epsilon zeta chi
1 G -60.4 166.6 59.3 82.3 --- --- -168.1
2 A -59.1 152.2 64.9 78.3 -151.8 -70.6 -170.4
3 G -61.3 170.8 50.5 79.8 -137.8 -80.3 -166.0
4 G -59.8 171.5 55.9 77.5 -144.7 -74.8 -172.2
5 G -65.8 168.3 55.6 73.2 -155.1 -75.0 -172.1
6 C -65.8 170.1 56.1 80.2 -145.0 -83.3 -162.3
7 C -62.5 175.4 47.1 81.7 -146.6 -76.2 -160.7
8 C -66.1 163.0 70.6 78.9 -145.8 -76.9 -171.0
9 C -66.6 167.8 52.5 78.9 -147.3 -72.5 -164.1
10 C -62.2 164.1 61.2 80.5 -144.6 -77.4 -158.4
11 G -72.6 -171.1 46.6 80.9 -142.4 -78.9 -167.5
12 C --- -176.2 35.4 81.7 -154.6 -71.7 -169.4
13 A -82.1 -177.0 56.7 79.2 --- --- -166.1
14 A -145.2 105.5 164.7 95.0 -142.8 -87.6 -171.1
15 C -76.2 -173.7 53.8 79.0 -153.8 -7.3 -165.9
16 C --- 169.9 59.2 81.8 -148.9 -66.5 -166.9
17 G --- 172.1 60.7 82.0 --- --- -158.6
18 G -91.1 167.3 79.9 76.6 --- --- -164.9
19 U --- 129.7 64.6 82.3 -147.5 -71.8 -164.7
20 C --- 137.2 44.1 88.0 --- --- -157.2
****************************************************************************
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 C 7.2 -29.1 39.0 -35.8 18.2 39.5 8.4 C3'-endo
2 U 5.6 -28.7 39.6 -37.2 20.1 40.3 10.7 C3'-endo
3 C 0.8 -26.4 40.5 -40.8 25.3 42.4 17.3 C3'-endo
4 U 4.1 -28.4 40.9 -39.3 22.3 41.9 13.0 C3'-endo
5 C -8.4 -18.6 36.6 -42.4 32.1 42.1 29.7 C3'-endo
6 G 14.8 -31.9 35.9 -28.4 8.8 36.0 355.1 C2'-exo
7 G -20.2 30.3 -28.4 17.6 1.5 30.6 158.5 C2'-endo
8 G 14.3 -36.6 43.8 -36.8 14.3 43.8 0.1 C3'-endo
9 G 6.3 -32.1 44.4 -41.9 22.5 45.2 10.8 C3'-endo
10 G 0.6 -26.9 41.3 -42.2 26.3 43.4 17.9 C3'-endo
11 C 6.1 -31.0 43.0 -40.5 21.8 43.7 10.8 C3'-endo
12 G 20.7 -34.0 34.0 -22.9 1.7 35.4 344.0 C2'-exo
13 U 4.8 -28.1 39.5 -37.7 20.7 40.3 11.8 C3'-endo
14 A -3.3 -24.2 40.8 -43.9 29.8 44.2 22.8 C3'-endo
15 G 20.1 -34.8 36.1 -25.4 3.4 37.1 346.8 C2'-exo
16 G 5.4 -31.6 44.1 -42.0 23.3 45.1 11.8 C3'-endo
17 C 1.5 -27.7 42.1 -42.2 25.6 43.9 16.6 C3'-endo
18 C 5.5 -29.1 40.5 -38.3 20.9 41.3 11.1 C3'-endo
19 A -37.5 42.1 -30.0 8.9 17.8 41.5 136.2 C1'-exo
20 G -23.1 35.7 -34.4 21.9 0.5 36.5 160.5 C2'-endo

Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 G 2.1 -24.6 36.6 -36.4 21.7 38.0 15.6 C3'-endo
2 A 6.8 -33.0 44.8 -41.7 22.2 45.5 9.9 C3'-endo
3 G 8.6 -33.7 44.5 -40.7 20.3 44.9 7.8 C3'-endo
4 G 0.9 -27.0 41.4 -42.0 26.0 43.4 17.5 C3'-endo
5 G 0.5 -29.0 44.4 -45.1 28.6 46.7 17.9 C3'-endo
6 C 1.9 -27.3 40.4 -40.4 24.3 42.0 15.9 C3'-endo
7 C 7.8 -30.5 40.5 -36.8 18.5 40.9 7.8 C3'-endo
8 C 4.8 -29.2 41.2 -39.3 22.0 42.2 12.2 C3'-endo
9 C 5.4 -30.8 43.2 -41.0 22.6 44.1 11.7 C3'-endo
10 C 6.0 -29.5 40.5 -38.1 20.3 41.2 10.4 C3'-endo
11 G 10.3 -33.4 42.7 -37.9 17.5 42.9 5.1 C3'-endo
12 C 5.5 -28.6 39.4 -37.1 20.2 40.1 10.8 C3'-endo
13 A -1.1 -24.9 39.7 -41.3 27.0 42.3 20.0 C3'-endo
14 A 16.3 -30.5 32.8 -24.2 5.2 33.3 350.3 C2'-exo
15 C 3.3 -28.3 40.9 -40.0 23.3 42.2 14.2 C3'-endo
16 C 5.9 -29.9 41.2 -38.7 20.8 41.9 10.5 C3'-endo
17 G -2.4 -20.8 34.6 -36.9 24.9 37.4 22.2 C3'-endo
18 G -2.2 -24.1 39.5 -41.6 27.9 42.4 21.4 C3'-endo
19 U 5.5 -28.7 39.7 -37.3 20.2 40.4 10.8 C3'-endo
20 C 5.9 -25.6 34.8 -32.2 16.6 35.3 9.1 C3'-endo
****************************************************************************
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 C/U 5.3 5.9 1 G/A 6.3 5.3
2 U/C 5.6 5.3 2 A/G 5.5 5.1
3 C/U 6.1 5.2 3 G/G 5.6 5.5
4 U/C 5.7 5.3 4 G/G 5.8 5.5
5 C/G 6.2 5.4 5 G/C 5.8 5.8
6 G/G 6.7 5.9 6 C/C 5.6 5.5
7 G/G 7.8 6.2 7 C/C 6.1 5.7
8 G/G 5.5 5.8 8 C/C 5.7 5.2
9 G/G 5.7 5.3 9 C/C 5.9 5.4
10 G/C 6.2 5.4 10 C/G 5.2 5.5
11 C/G 5.5 5.2 11 G/C 5.5 6.0
12 G/U --- --- 12 C/A --- ---
13 U/A 15.2 12.5 13 A/A 6.6 6.6
14 A/G 5.3 4.8 14 A/C 5.7 5.0
15 G/G 6.4 5.9 15 C/C 6.0 6.0
16 G/C 5.8 5.6 16 C/G 17.5 13.1
17 C/C 10.9 10.3 17 G/G 12.4 10.0
18 C/A 6.0 6.3 18 G/U 6.4 5.7
19 A/G --- --- 19 U/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 CU/AG 8.5 8.8 8.2 9.5 9.0 8.4
2 UC/GA 10.1 9.0 8.2 8.7 8.2 7.5
3 CU/GG 8.6 7.4 6.5 9.1 8.5 7.8
4 UC/GG 12.8 12.2 11.6 9.8 10.8 10.7
5 CG/CG 11.1 10.0 9.7 10.5 11.1 10.5
6 GG/CC 10.0 9.4 8.8 8.9 9.2 8.6
7 GG/CC 9.3 9.9 9.3 9.0 8.9 8.3
8 GG/CC 10.6 9.9 9.1 8.2 8.0 7.5
9 GG/CC 9.8 9.3 8.7 8.3 8.6 8.0
10 GC/GC 8.2 7.4 6.7 9.8 9.0 8.1
11 CG/CG 10.9 10.4 10.0 10.0 10.8 10.3
12 GU/AC ---- ---- ---- ---- ---- ----
13 UA/AA 8.1 6.8 6.3 6.5 6.0 5.3
14 AG/CA 8.3 7.4 7.0 9.6 7.1 6.0
15 GG/CC 9.7 9.8 9.3 9.1 9.2 8.6
16 GC/GC 4.8 4.9 4.9 14.1 11.7 10.7
17 CC/GG 7.2 7.9 7.4 11.1 8.7 7.8
18 CA/UG 8.7 9.3 9.1 9.0 9.2 9.0
19 AG/CU ---- ---- ---- ---- ---- ----
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step

bp Px Py Pz Hx Hy Hz
1 CU/AG 21.21 1.66 154.97 -0.16 -0.33 -0.93
2 UC/GA 19.93 0.47 153.13 -0.36 -0.13 -0.92
3 CU/GG 18.82 -1.10 150.66 -0.31 -0.11 -0.94
4 UC/GG 22.68 1.04 146.63 -0.20 -0.28 -0.94
5 CG/CG 20.53 -2.40 145.38 -0.26 -0.37 -0.89
6 GG/CC 18.88 -1.23 141.93 -0.30 -0.26 -0.92
7 GG/CC 18.92 -1.75 139.13 -0.09 -0.20 -0.98
8 GG/CC 19.38 -2.27 136.33 -0.02 -0.26 -0.97
9 GG/CC 18.40 -2.33 133.68 -0.22 -0.12 -0.97
10 GC/GC 19.42 -1.75 129.93 -0.03 -0.28 -0.96
11 CG/CG 15.93 -0.46 128.26 -0.07 0.04 -1.00
12 GU/AC ---- ---- ---- ---- ---- ----
13 UA/AA 1.98 3.33 135.59 -0.61 0.79 0.08
14 AG/CA -0.94 5.12 135.52 -0.67 0.74 0.05
15 GG/CC -0.42 8.56 134.29 -0.73 0.61 -0.31
16 GC/GC -7.40 9.01 135.99 -0.36 0.93 0.06
17 CC/GG -7.41 12.10 133.08 -0.68 0.72 0.14
18 CA/UG -12.38 12.79 135.01 -0.11 0.84 0.53
19 AG/CU ---- ---- ---- ---- ---- ----