****************************************************************************
****************************************************************************
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: gatc-a.pdb
Date and time: Thu Nov 2 19:20:32 2006
Number of base-pairs: 16
Number of atoms: 656
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.008) A:...1_:[..G]G-----C[..C]:..32_:B (0.008) |
2 (0.009) A:...2_:[..A]A-----T[..T]:..31_:B (0.018) |
3 (0.018) A:...3_:[..T]T-----A[..A]:..30_:B (0.009) |
4 (0.008) A:...4_:[..C]C-----G[..G]:..29_:B (0.008) |
5 (0.008) A:...5_:[..G]G-----C[..C]:..28_:B (0.008) |
6 (0.009) A:...6_:[..A]A-----T[..T]:..27_:B (0.018) |
7 (0.018) A:...7_:[..T]T-----A[..A]:..26_:B (0.009) |
8 (0.008) A:...8_:[..C]C-----G[..G]:..25_:B (0.008) |
9 (0.008) A:...9_:[..G]G-----C[..C]:..24_:B (0.008) |
10 (0.009) A:..10_:[..A]A-----T[..T]:..23_:B (0.018) |
11 (0.018) A:..11_:[..T]T-----A[..A]:..22_:B (0.009) |
12 (0.009) A:..12_:[..C]C-----G[..G]:..21_:B (0.008) |
13 (0.008) A:..13_:[..G]G-----C[..C]:..20_:B (0.008) |
14 (0.009) A:..14_:[..A]A-----T[..T]:..19_:B (0.018) |
15 (0.018) A:..15_:[..T]T-----A[..A]:..18_:B (0.009) |
16 (0.008) A:..16_:[..C]C-----G[..G]:..17_:B (0.008) |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 G-----C [3] O6 - N4 2.83 N1 - N3 2.85 N2 - O2 2.81
2 A-----T [2] N6 - O4 2.90 N1 - N3 2.88
3 T-----A [2] N3 - N1 2.88 O4 - N6 2.90
4 C-----G [3] O2 - N2 2.81 N3 - N1 2.85 N4 - O6 2.83
5 G-----C [3] O6 - N4 2.83 N1 - N3 2.85 N2 - O2 2.81
6 A-----T [2] N6 - O4 2.90 N1 - N3 2.88
7 T-----A [2] N3 - N1 2.88 O4 - N6 2.90
8 C-----G [3] O2 - N2 2.81 N3 - N1 2.85 N4 - O6 2.83
9 G-----C [3] O6 - N4 2.83 N1 - N3 2.85 N2 - O2 2.81
10 A-----T [2] N6 - O4 2.90 N1 - N3 2.88
11 T-----A [2] N3 - N1 2.88 O4 - N6 2.90
12 C-----G [3] O2 - N2 2.81 N3 - N1 2.85 N4 - O6 2.83
13 G-----C [3] O6 - N4 2.83 N1 - N3 2.85 N2 - O2 2.81
14 A-----T [2] N6 - O4 2.90 N1 - N3 2.88
15 T-----A [2] N3 - N1 2.88 O4 - N6 2.90
16 C-----G [3] O2 - N2 2.81 N3 - N1 2.85 N4 - O6 2.83
****************************************************************************
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 GA/TC 3.83( 2.42) 0.00( 0.00) 0.00( 0.00) 0.91( 0.04) 4.74( 2.46)
2 AT/AT 6.62( 3.14) 0.00( 0.00) 0.00( 0.00) 6.62( 3.14) 13.25( 6.28)
3 TC/GA 0.91( 0.04) 0.00( 0.00) 0.00( 0.00) 3.83( 2.42) 4.74( 2.46)
4 CG/CG 0.36( 0.00) 0.00( 0.00) 3.70( 0.98) 0.36( 0.00) 4.43( 0.98)
5 GA/TC 3.83( 2.42) 0.00( 0.00) 0.00( 0.00) 0.91( 0.04) 4.74( 2.46)
6 AT/AT 6.62( 3.14) 0.00( 0.00) 0.00( 0.00) 6.62( 3.14) 13.25( 6.28)
7 TC/GA 0.91( 0.04) 0.00( 0.00) 0.00( 0.00) 3.83( 2.42) 4.74( 2.46)
8 CG/CG 0.36( 0.00) 0.00( 0.00) 3.70( 0.98) 0.36( 0.00) 4.42( 0.98)
9 GA/TC 3.83( 2.42) 0.00( 0.00) 0.00( 0.00) 0.91( 0.04) 4.74( 2.46)
10 AT/AT 6.62( 3.14) 0.00( 0.00) 0.00( 0.00) 6.62( 3.14) 13.25( 6.28)
11 TC/GA 0.91( 0.04) 0.00( 0.00) 0.00( 0.00) 3.83( 2.42) 4.74( 2.46)
12 CG/CG 0.37( 0.00) 0.00( 0.00) 3.70( 0.98) 0.36( 0.00) 4.43( 0.98)
13 GA/TC 3.83( 2.42) 0.00( 0.00) 0.00( 0.00) 0.91( 0.04) 4.74( 2.46)
14 AT/AT 6.62( 3.14) 0.00( 0.00) 0.00( 0.00) 6.62( 3.14) 13.25( 6.28)
15 TC/GA 0.91( 0.04) 0.00( 0.00) 0.00( 0.00) 3.83( 2.42) 4.74( 2.46)
****************************************************************************
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 4.43 -0.03 0.02 -0.00 -0.38 -0.92
2 A-T 3.77 -2.42 -2.55 -0.21 -0.32 -0.92
3 T-A 1.86 -4.07 -5.09 -0.35 -0.16 -0.92
4 C-G -0.60 -4.39 -7.66 -0.38 0.05 -0.92
5 G-C -2.92 -3.34 -10.17 -0.29 0.25 -0.92
6 A-T -4.29 -1.28 -12.74 -0.11 0.37 -0.92
7 T-A -4.30 1.25 -15.29 0.11 0.37 -0.92
8 C-G -2.93 3.32 -17.85 0.29 0.25 -0.92
9 G-C -0.62 4.39 -20.37 0.38 0.06 -0.92
10 A-T 1.84 4.08 -22.93 0.35 -0.16 -0.92
11 T-A 3.76 2.44 -25.48 0.21 -0.32 -0.92
12 C-G 4.43 0.05 -28.05 0.00 -0.38 -0.92
13 G-C 3.73 -2.40 -30.56 -0.21 -0.32 -0.92
14 A-T 1.89 -4.06 -33.13 -0.35 -0.16 -0.92
15 T-A -0.61 -4.44 -35.67 -0.38 0.05 -0.92
16 C-G -2.86 -3.39 -38.24 -0.29 0.25 -0.92
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 G-C -0.14 -0.18 0.07 0.19 -10.52 -1.29
2 A-T 0.01 -0.10 0.06 0.03 -10.51 -2.33
3 T-A -0.01 -0.11 0.06 -0.02 -10.51 -2.33
4 C-G 0.14 -0.18 0.07 -0.19 -10.52 -1.30
5 G-C -0.14 -0.18 0.07 0.19 -10.52 -1.30
6 A-T 0.01 -0.11 0.06 0.03 -10.51 -2.35
7 T-A -0.01 -0.11 0.06 -0.03 -10.51 -2.35
8 C-G 0.14 -0.18 0.07 -0.19 -10.52 -1.29
9 G-C -0.14 -0.18 0.07 0.19 -10.51 -1.27
10 A-T 0.01 -0.11 0.06 0.03 -10.51 -2.33
11 T-A -0.01 -0.11 0.06 -0.02 -10.50 -2.32
12 C-G 0.14 -0.18 0.07 -0.19 -10.52 -1.29
13 G-C -0.14 -0.18 0.07 0.19 -10.52 -1.29
14 A-T 0.01 -0.11 0.06 0.03 -10.51 -2.34
15 T-A -0.01 -0.11 0.06 -0.03 -10.51 -2.33
16 C-G 0.14 -0.18 0.07 -0.19 -10.52 -1.30
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.00 -0.14 0.06 0.00 -10.51 -1.81
s.d. 0.11 0.04 0.00 0.14 0.01 0.54
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 GA/TC -0.02 -1.35 3.31 -0.13 12.43 31.24
2 AT/AT 0.00 -1.40 3.30 0.00 12.43 30.47
3 TC/GA 0.02 -1.35 3.31 0.13 12.44 31.25
4 CG/CG 0.00 -1.43 3.28 -0.00 12.44 28.26
5 GA/TC -0.03 -1.35 3.31 -0.13 12.43 31.25
6 AT/AT 0.00 -1.40 3.30 -0.00 12.43 30.47
7 TC/GA 0.03 -1.35 3.31 0.13 12.43 31.25
8 CG/CG 0.00 -1.43 3.28 -0.00 12.44 28.25
9 GA/TC -0.03 -1.35 3.31 -0.13 12.43 31.25
10 AT/AT -0.00 -1.40 3.30 -0.00 12.44 30.48
11 TC/GA 0.02 -1.35 3.31 0.12 12.43 31.24
12 CG/CG 0.00 -1.43 3.28 -0.00 12.44 28.26
13 GA/TC -0.03 -1.35 3.31 -0.13 12.43 31.25
14 AT/AT 0.00 -1.40 3.30 0.00 12.43 30.47
15 TC/GA 0.02 -1.35 3.31 0.13 12.43 31.24
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.00 -1.38 3.30 0.00 12.43 30.44
s.d. 0.02 0.04 0.01 0.10 0.00 1.18
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 GA/TC -4.24 0.02 2.60 22.02 0.22 33.56
2 AT/AT -4.46 -0.00 2.55 22.51 -0.00 32.85
3 TC/GA -4.24 -0.02 2.60 22.02 -0.23 33.57
4 CG/CG -4.91 -0.00 2.44 24.06 0.00 30.82
5 GA/TC -4.24 0.02 2.60 22.02 0.23 33.57
6 AT/AT -4.46 -0.00 2.55 22.51 0.00 32.85
7 TC/GA -4.24 -0.02 2.60 22.02 -0.23 33.57
8 CG/CG -4.91 -0.00 2.44 24.06 0.00 30.82
9 GA/TC -4.24 0.02 2.60 22.02 0.23 33.57
10 AT/AT -4.46 -0.00 2.55 22.52 0.00 32.86
11 TC/GA -4.24 -0.02 2.60 22.02 -0.22 33.56
12 CG/CG -4.91 -0.00 2.44 24.06 0.00 30.83
13 GA/TC -4.24 0.02 2.60 22.02 0.22 33.57
14 AT/AT -4.46 0.00 2.55 22.52 -0.00 32.85
15 TC/GA -4.24 -0.02 2.60 22.02 -0.22 33.57
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -4.44 0.00 2.55 22.56 -0.00 32.83
s.d. 0.27 0.02 0.06 0.81 0.17 1.08
****************************************************************************
Structure classification:
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 54.3 54.3 10.7 8.9 9.8
2 A-T 54.3 54.3 10.7 8.9 9.9
3 T-A 54.3 54.3 10.7 8.9 9.9
4 C-G 54.3 54.3 10.7 8.9 9.8
5 G-C 54.3 54.3 10.7 8.9 9.8
6 A-T 54.3 54.3 10.7 8.9 9.9
7 T-A 54.3 54.3 10.7 8.9 9.9
8 C-G 54.3 54.3 10.7 8.9 9.8
9 G-C 54.3 54.3 10.7 8.9 9.8
10 A-T 54.3 54.3 10.7 8.9 9.9
11 T-A 54.3 54.3 10.7 8.9 9.9
12 C-G 54.3 54.3 10.7 8.9 9.8
13 G-C 54.3 54.3 10.7 8.9 9.8
14 A-T 54.3 54.3 10.7 8.9 9.9
15 T-A 54.3 54.3 10.7 8.9 9.9
16 C-G 54.3 54.3 10.7 8.9 9.8
****************************************************************************
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 GA/TC -0.92 8.36 2.48 -4.98 6.90 5.33 A
2 AT/AT -0.90 8.36 2.48 -5.18 6.85 5.40 A
3 TC/GA -0.92 8.36 2.48 -4.98 6.90 5.33 A
4 CG/CG -0.95 8.36 2.48 -5.69 6.70 5.58 A
5 GA/TC -0.92 8.36 2.48 -4.98 6.90 5.33 A
6 AT/AT -0.90 8.36 2.48 -5.18 6.85 5.40 A
7 TC/GA -0.92 8.36 2.48 -4.98 6.90 5.33 A
8 CG/CG -0.95 8.36 2.48 -5.69 6.70 5.58 A
9 GA/TC -0.92 8.36 2.48 -4.98 6.90 5.33 A
10 AT/AT -0.90 8.36 2.48 -5.18 6.85 5.40 A
11 TC/GA -0.92 8.36 2.48 -4.98 6.90 5.33 A
12 CG/CG -0.95 8.36 2.48 -5.69 6.70 5.58 A
13 GA/TC -0.92 8.36 2.48 -4.98 6.90 5.33 A
14 AT/AT -0.90 8.36 2.48 -5.18 6.85 5.40 A
15 TC/GA -0.92 8.36 2.48 -4.98 6.90 5.33 A
****************************************************************************
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 GA/TC --- --- --- ---
2 AT/AT --- --- --- ---
3 TC/GA 18.5 --- 15.2 ---
4 CG/CG 18.5 16.7 15.2 11.1
5 GA/TC 18.5 16.7 15.2 11.1
6 AT/AT 18.5 16.7 15.2 11.1
7 TC/GA 18.5 16.7 15.2 11.1
8 CG/CG 18.5 16.7 15.2 11.1
9 GA/TC 18.5 16.7 15.2 11.1
10 AT/AT 18.5 16.7 15.2 11.1
11 TC/GA 18.5 16.7 15.2 11.1
12 CG/CG 18.5 16.7 15.2 11.1
13 GA/TC 18.5 --- 15.2 ---
14 AT/AT --- --- --- ---
15 TC/GA --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 2.55(0.00)
Helix: -0.000 -0.000 -1.000
HETATM 9998 XS X X 999 0.000 -0.000 0.000
HETATM 9999 XE X X 999 0.000 -0.000 -38.220
Average and standard deviation of helix radius:
P: 8.59(0.00), O4': 9.09(0.00), C1': 8.50(0.00)
Global parameters based on C1'-C1' vectors:
disp.: displacement of the middle C1'-C1' point from the helix
angle: inclination between C1'-C1' vector and helix (subtracted from 90)
twist: helical twist angle between consecutive C1'-C1' vectors
rise: helical rise by projection of the vector connecting consecutive
C1'-C1' middle points onto the helical axis
bp disp. angle twist rise
1 G-C 6.87 20.58 32.70 2.55
2 A-T 6.87 20.58 32.70 2.55
3 T-A 6.87 20.58 32.70 2.55
4 C-G 6.87 20.58 32.70 2.55
5 G-C 6.87 20.58 32.70 2.55
6 A-T 6.87 20.58 32.70 2.55
7 T-A 6.87 20.58 32.69 2.55
8 C-G 6.87 20.58 32.70 2.55
9 G-C 6.87 20.58 32.70 2.55
10 A-T 6.87 20.58 32.71 2.55
11 T-A 6.87 20.58 32.70 2.55
12 C-G 6.87 20.58 32.70 2.55
13 G-C 6.87 20.58 32.70 2.55
14 A-T 6.87 20.58 32.70 2.55
15 T-A 6.87 20.58 32.70 2.55
16 C-G 6.87 20.58 --- ---
****************************************************************************
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 --- 174.8 41.7 79.0 -147.8 -75.1 -157.2
2 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
3 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
4 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
5 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
6 A -51.7 174.8 41.7 79.0 -147.8 -75.1 -157.2
7 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
8 C -51.7 174.8 41.7 79.0 -147.8 -75.0 -157.2
9 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
10 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
11 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
12 C -51.7 174.8 41.7 79.1 -147.7 -75.1 -157.2
13 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
14 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
15 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
16 C -51.7 174.8 41.7 79.1 --- --- -157.2
Strand II
base alpha beta gamma delta epsilon zeta chi
1 C -51.7 174.8 41.7 79.0 --- --- -157.2
2 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
3 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
4 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
5 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
6 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
7 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
8 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
9 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
10 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
11 A -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
12 G -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
13 C -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
14 T -51.7 174.8 41.7 79.1 -147.8 -75.1 -157.2
15 A -51.7 174.8 41.7 79.0 -147.8 -75.1 -157.2
16 G --- 174.8 41.7 79.1 -147.7 -75.1 -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 G 8.2 -33.5 44.0 -40.1 20.5 44.5 7.9 C3'-endo
2 A 8.2 -33.5 44.0 -40.1 20.6 44.5 8.0 C3'-endo
3 T 8.2 -33.5 44.1 -40.2 20.6 44.5 8.0 C3'-endo
4 C 8.2 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
5 G 8.2 -33.5 44.1 -40.1 20.6 44.5 7.9 C3'-endo
6 A 8.2 -33.5 44.0 -40.1 20.5 44.4 7.9 C3'-endo
7 T 8.2 -33.5 44.1 -40.1 20.5 44.5 7.9 C3'-endo
8 C 8.3 -33.6 44.0 -40.1 20.5 44.5 7.9 C3'-endo
9 G 8.2 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
10 A 8.3 -33.6 44.1 -40.2 20.5 44.5 7.9 C3'-endo
11 T 8.3 -33.6 44.1 -40.2 20.5 44.5 7.9 C3'-endo
12 C 8.2 -33.5 44.1 -40.1 20.5 44.5 7.9 C3'-endo
13 G 8.3 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
14 A 8.2 -33.5 44.0 -40.1 20.6 44.5 8.0 C3'-endo
15 T 8.3 -33.6 44.1 -40.1 20.5 44.5 7.9 C3'-endo
16 C 8.2 -33.6 44.1 -40.2 20.5 44.5 7.9 C3'-endo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 C 8.2 -33.5 44.0 -40.1 20.5 44.5 7.9 C3'-endo
2 T 8.3 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
3 A 8.2 -33.6 44.1 -40.2 20.6 44.5 8.0 C3'-endo
4 G 8.2 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
5 C 8.3 -33.6 44.1 -40.2 20.5 44.5 7.9 C3'-endo
6 T 8.2 -33.6 44.1 -40.1 20.5 44.5 7.9 C3'-endo
7 A 8.2 -33.5 44.1 -40.2 20.6 44.5 8.0 C3'-endo
8 G 8.2 -33.5 44.0 -40.1 20.6 44.5 8.0 C3'-endo
9 C 8.2 -33.5 44.1 -40.2 20.6 44.5 8.0 C3'-endo
10 T 8.2 -33.5 44.1 -40.2 20.6 44.5 8.0 C3'-endo
11 A 8.2 -33.6 44.1 -40.2 20.6 44.5 8.0 C3'-endo
12 G 8.2 -33.5 44.1 -40.2 20.6 44.5 8.0 C3'-endo
13 C 8.2 -33.6 44.1 -40.2 20.6 44.5 7.9 C3'-endo
14 T 8.2 -33.6 44.1 -40.2 20.6 44.5 8.0 C3'-endo
15 A 8.3 -33.5 44.1 -40.1 20.5 44.5 7.9 C3'-endo
16 G 8.3 -33.6 44.1 -40.1 20.5 44.5 7.9 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 G/A 5.5 5.4 1 C/T 5.5 5.4
2 A/T 5.5 5.4 2 T/A 5.5 5.4
3 T/C 5.5 5.4 3 A/G 5.5 5.4
4 C/G 5.5 5.4 4 G/C 5.5 5.4
5 G/A 5.5 5.4 5 C/T 5.5 5.4
6 A/T 5.5 5.4 6 T/A 5.5 5.4
7 T/C 5.5 5.4 7 A/G 5.5 5.4
8 C/G 5.5 5.4 8 G/C 5.5 5.4
9 G/A 5.5 5.4 9 C/T 5.5 5.4
10 A/T 5.5 5.4 10 T/A 5.5 5.4
11 T/C 5.5 5.4 11 A/G 5.5 5.4
12 C/G 5.5 5.4 12 G/C 5.5 5.4
13 G/A 5.5 5.4 13 C/T 5.5 5.4
14 A/T 5.5 5.4 14 T/A 5.5 5.4
15 T/C 5.5 5.4 15 A/G 5.5 5.4
****************************************************************************
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 GA/TC 8.6 9.0 8.4 8.4 8.9 8.3
2 AT/AT 8.6 9.1 8.5 8.6 9.1 8.5
3 TC/GA 8.4 8.9 8.3 8.6 9.0 8.4
4 CG/CG 8.8 9.4 8.9 8.8 9.4 8.9
5 GA/TC 8.6 9.0 8.4 8.4 8.9 8.3
6 AT/AT 8.6 9.1 8.5 8.6 9.1 8.5
7 TC/GA 8.4 8.9 8.3 8.6 9.0 8.4
8 CG/CG 8.8 9.4 8.9 8.8 9.4 8.9
9 GA/TC 8.6 9.0 8.4 8.4 8.9 8.3
10 AT/AT 8.6 9.1 8.5 8.6 9.1 8.5
11 TC/GA 8.4 8.9 8.3 8.6 9.0 8.4
12 CG/CG 8.8 9.4 8.9 8.8 9.4 8.9
13 GA/TC 8.6 9.0 8.4 8.4 8.9 8.3
14 AT/AT 8.6 9.1 8.5 8.6 9.1 8.5
15 TC/GA 8.4 8.9 8.3 8.6 9.0 8.4
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 GA/TC 0.19 -0.14 -1.27 -0.00 -0.01 -1.00
2 AT/AT 0.01 -0.01 -3.82 -0.00 -0.00 -1.00
3 TC/GA 0.11 -0.21 -6.38 -0.01 -0.00 -1.00
4 CG/CG 0.20 0.45 -8.92 0.02 -0.01 -1.00
5 GA/TC -0.23 -0.05 -11.46 -0.01 0.01 -1.00
6 AT/AT -0.01 -0.00 -14.01 -0.00 0.00 -1.00
7 TC/GA -0.23 0.05 -16.57 0.01 0.01 -1.00
8 CG/CG 0.21 -0.45 -19.11 -0.02 -0.01 -1.00
9 GA/TC 0.11 0.21 -21.65 0.01 -0.00 -1.00
10 AT/AT 0.01 0.01 -24.21 0.00 -0.00 -1.00
11 TC/GA 0.19 0.14 -26.76 0.00 -0.01 -1.00
12 CG/CG -0.47 0.14 -29.30 0.01 0.02 -1.00
13 GA/TC 0.08 -0.22 -31.84 -0.01 -0.01 -1.00
14 AT/AT 0.00 -0.01 -34.40 -0.00 -0.00 -1.00
15 TC/GA -0.02 -0.23 -36.95 -0.01 0.00 -1.00