****************************************************************************
****************************************************************************
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: dna33.pdb
Date and time: Thu Nov 2 18:17:41 2006
Number of base-pairs: 12
Number of atoms: 486
****************************************************************************
****************************************************************************
RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change)
Strand I Strand II Helix
1 (0.010) A:...1_:[..C]C-----G[..G]:..24_:B (0.010) |
2 (0.007) A:...2_:[..G]G-----C[..C]:..23_:B (0.012) |
3 (0.010) A:...3_:[..C]C-----G[..G]:..22_:B (0.006) |
4 (0.008) A:...4_:[..G]G-----C[..C]:..21_:B (0.010) |
5 (0.004) A:...5_:[..A]A-----T[..T]:..20_:B (0.014) |
6 (0.012) A:...6_:[..A]A-----T[..T]:..19_:B (0.008) |
7 (0.007) A:...7_:[..T]T-----A[..A]:..18_:B (0.006) |
8 (0.010) A:...8_:[..T]T-----A[..A]:..17_:B (0.011) |
9 (0.010) A:...9_:[..C]C-----G[..G]:..16_:B (0.009) |
10 (0.012) A:..10_:[..G]G-----C[..C]:..15_:B (0.006) |
11 (0.012) A:..11_:[..C]C-----G[..G]:..14_:B (0.009) |
12 (0.010) A:..12_:[..G]G-----C[..C]:..13_:B (0.009) |
****************************************************************************
Detailed H-bond information: atom-name pair and length [ON]
1 C-----G [3] O2 - N2 2.83 N3 - N1 2.90 N4 - O6 2.98
2 G-----C [3] O6 - N4 2.91 N1 - N3 2.88 N2 - O2 2.88
3 C-----G [3] O2 - N2 2.71 N3 - N1 2.87 N4 - O6 2.85
4 G-----C [3] O6 - N4 2.93 N1 - N3 2.91 N2 - O2 2.83
5 A-----T [2] N6 - O4 3.01 N1 - N3 2.83
6 A-----T [2] N6 - O4 3.19 N1 - N3 2.83
7 T-----A [2] N3 - N1 2.81 O4 - N6 3.08
8 T-----A [2] N3 - N1 2.77 O4 - N6 3.11
9 C-----G [3] O2 - N2 2.90 N3 - N1 2.92 N4 - O6 2.84
10 G-----C [3] O6 - N4 3.08 N1 - N3 2.94 N2 - O2 2.69
11 C-----G [3] O2 - N2 2.87 N3 - N1 2.92 N4 - O6 2.92
12 G-----C [3] O6 - N4 2.93 N1 - N3 2.98 N2 - O2 2.90
****************************************************************************
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 CG/CG 1.48( 0.00) 0.00( 0.00) 0.97( 0.00) 0.94( 0.00) 3.39( 0.00)
2 GC/GC 2.95( 0.63) 0.00( 0.00) 0.00( 0.00) 0.96( 0.04) 3.91( 0.68)
3 CG/CG 2.66( 0.00) 0.00( 0.00) 0.15( 0.00) 3.44( 0.21) 6.25( 0.21)
4 GA/TC 3.94( 1.11) 0.00( 0.00) 0.00( 0.00) 4.17( 0.78) 8.11( 1.88)
5 AA/TT 3.51( 2.16) 0.00( 0.00) 0.00( 0.00) 5.09( 0.08) 8.60( 2.24)
6 AT/AT 5.91( 2.14) 0.00( 0.00) 0.00( 0.00) 5.65( 1.89) 11.56( 4.03)
7 TT/AA 5.08( 0.11) 0.00( 0.00) 0.00( 0.00) 3.68( 2.39) 8.76( 2.51)
8 TC/GA 2.20( 0.00) 0.00( 0.00) 0.00( 0.00) 4.98( 2.19) 7.18( 2.19)
9 CG/CG 5.50( 1.17) 0.00( 0.00) 0.01( 0.00) 1.56( 0.00) 7.06( 1.17)
10 GC/GC 0.57( 0.00) 0.00( 0.00) 0.00( 0.00) 5.32( 2.35) 5.89( 2.35)
11 CG/CG 0.73( 0.00) 0.00( 0.00) 0.54( 0.00) 1.98( 0.03) 3.25( 0.03)
****************************************************************************
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 17.13 25.96 25.88 -0.10 -0.44 -0.89
2 G-C 16.56 24.81 22.95 -0.21 -0.33 -0.92
3 C-G 16.16 23.97 19.28 -0.18 -0.48 -0.86
4 G-C 16.18 22.58 16.55 -0.18 -0.30 -0.94
5 A-T 15.25 21.34 13.51 -0.14 -0.30 -0.94
6 A-T 14.88 20.69 10.27 -0.13 -0.30 -0.94
7 T-A 14.58 20.27 7.04 -0.18 -0.29 -0.94
8 T-A 14.30 19.66 3.87 -0.16 -0.26 -0.95
9 C-G 13.99 19.06 0.45 -0.15 -0.23 -0.96
10 G-C 12.36 18.29 -2.24 -0.24 -0.25 -0.94
11 C-G 12.88 18.31 -5.84 -0.11 -0.15 -0.98
12 G-C 12.73 17.99 -9.02 -0.21 -0.10 -0.97
****************************************************************************
Local base-pair parameters
bp Shear Stretch Stagger Buckle Propeller Opening
1 C-G 0.28 -0.14 0.07 6.93 -17.31 -0.61
2 G-C -0.24 -0.18 0.49 9.34 -14.30 -2.08
3 C-G 0.24 -0.17 0.16 -4.43 -5.40 0.43
4 G-C -0.26 -0.11 0.01 10.81 -9.45 1.01
5 A-T -0.04 -0.11 0.01 4.72 -15.31 1.60
6 A-T 0.05 -0.05 0.07 0.44 -15.00 6.23
7 T-A -0.04 -0.12 0.17 -0.26 -16.74 3.93
8 T-A -0.11 -0.12 -0.00 -1.56 -16.36 5.12
9 C-G 0.21 -0.13 0.00 -12.41 -10.27 -1.22
10 G-C -0.11 -0.05 0.24 4.21 -9.60 3.21
11 C-G 0.16 -0.13 0.21 0.28 -17.42 -1.75
12 G-C -0.24 -0.07 0.25 4.67 -4.95 -1.62
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.01 -0.12 0.14 1.89 -12.68 1.19
s.d. 0.19 0.04 0.15 6.38 4.54 2.85
****************************************************************************
Local base-pair step parameters
step Shift Slide Rise Tilt Roll Twist
1 CG/CG 0.09 0.04 3.20 -3.22 8.52 32.73
2 GC/GC 0.50 0.67 3.69 2.85 -9.06 43.88
3 CG/CG -0.14 0.59 3.00 0.97 11.30 25.11
4 GA/TC -0.45 -0.14 3.39 -1.59 1.37 37.50
5 AA/TT 0.17 -0.33 3.30 -0.33 0.46 37.52
6 AT/AT -0.01 -0.60 3.22 -0.31 -2.67 32.40
7 TT/AA -0.08 -0.40 3.22 1.68 -0.97 33.74
8 TC/GA -0.27 -0.23 3.47 0.68 -1.69 42.14
9 CG/CG 0.70 0.78 3.07 -3.66 4.18 26.58
10 GC/GC -1.31 0.36 3.37 -2.85 -9.37 41.60
11 CG/CG -0.31 0.21 3.17 -0.68 6.69 33.31
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.10 0.09 3.28 -0.59 0.80 35.14
s.d. 0.53 0.47 0.19 2.09 6.62 6.09
****************************************************************************
Local base-pair helical parameters
step X-disp Y-disp h-Rise Incl. Tip h-Twist
1 CG/CG -1.27 -0.65 3.09 14.77 5.57 33.94
2 GC/GC 1.79 -0.36 3.52 -11.95 -3.76 44.84
3 CG/CG -1.40 0.52 2.98 24.46 -2.09 27.52
4 GA/TC -0.40 0.49 3.40 2.13 2.46 37.56
5 AA/TT -0.57 -0.31 3.29 0.71 0.51 37.52
6 AT/AT -0.61 -0.03 3.26 -4.78 0.56 32.51
7 TT/AA -0.53 0.41 3.22 -1.68 -2.89 33.80
8 TC/GA -0.13 0.45 3.47 -2.34 -0.95 42.17
9 CG/CG 0.66 -2.36 3.03 8.97 7.84 27.14
10 GC/GC 1.47 1.50 3.30 -12.97 3.95 42.69
11 CG/CG -0.69 0.42 3.16 11.53 1.17 33.96
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ave. -0.15 0.01 3.25 2.62 1.12 35.79
s.d. 1.04 0.98 0.17 11.41 3.61 5.84
****************************************************************************
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 C-G 53.5 52.7 10.7 9.0 9.9
2 G-C 53.4 55.4 10.6 8.9 9.8
3 C-G 55.8 53.9 10.6 8.9 9.9
4 G-C 54.6 56.9 10.6 8.9 9.9
5 A-T 54.3 55.1 10.6 8.9 9.8
6 A-T 56.4 56.6 10.4 8.8 9.9
7 T-A 56.2 56.1 10.4 8.8 9.8
8 T-A 55.3 55.6 10.4 8.8 9.8
9 C-G 54.9 53.6 10.7 8.9 9.9
10 G-C 58.1 56.9 10.5 8.9 10.0
11 C-G 52.9 51.2 10.8 9.0 9.9
12 G-C 54.0 53.9 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 CG/CG -2.24 8.78 0.37 -3.51 8.41 2.60 B
2 GC/GC -2.27 8.89 0.20 -0.59 8.76 -1.53 B
3 CG/CG -3.22 9.14 -0.51 -4.60 8.57 3.24 B
4 GA/TC -3.17 8.84 -0.33 -3.50 8.85 -0.03 B
5 AA/TT -3.43 8.95 -0.40 -3.97 8.95 -0.30 B
6 AT/AT -3.45 9.06 -0.20 -4.03 9.01 -0.92 B
7 TT/AA -3.53 9.07 -0.65 -4.04 9.05 -0.91 B
8 TC/GA -2.74 8.65 0.14 -2.85 8.65 -0.19 B
9 CG/CG -2.88 8.85 -0.43 -2.37 8.81 1.05 B
10 GC/GC -2.59 9.03 -0.04 -1.21 8.82 -1.93 B
11 CG/CG -2.96 8.99 -0.97 -3.62 9.01 0.77 B
****************************************************************************
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 CG/CG --- --- --- ---
2 GC/GC --- --- --- ---
3 CG/CG 14.3 --- 18.2 ---
4 GA/TC 12.0 11.9 17.3 17.3
5 AA/TT 9.7 9.6 19.1 19.0
6 AT/AT 9.1 9.1 16.4 16.0
7 TT/AA 9.1 9.1 17.8 17.7
8 TC/GA 9.6 9.6 18.6 18.6
9 CG/CG 10.4 --- 19.0 ---
10 GC/GC --- --- --- ---
11 CG/CG --- --- --- ---
****************************************************************************
Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs
Deviation from regular linear helix: 3.30(0.52)
Helix: -0.127 -0.275 -0.953
HETATM 9998 XS X X 999 17.536 25.713 25.665
HETATM 9999 XE X X 999 12.911 15.677 -9.080
Average and standard deviation of helix radius:
P: 9.42(0.82), O4': 6.37(0.85), C1': 5.85(0.86)
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 C-G 1.95 5.18 36.25 3.50
2 G-C 2.04 4.65 40.52 2.43
3 C-G 2.26 4.02 28.36 4.27
4 G-C 3.04 -0.22 36.02 3.07
5 A-T 3.53 -5.05 36.82 3.14
6 A-T 3.32 -5.83 32.80 3.09
7 T-A 2.98 -6.44 34.14 3.23
8 T-A 2.99 -7.13 39.93 2.82
9 C-G 2.88 -4.95 29.46 4.19
10 G-C 2.34 -6.66 39.85 2.81
11 C-G 2.37 -10.68 35.99 3.90
12 G-C 1.85 -4.90 --- ---
****************************************************************************
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 --- --- -70.0 144.7 -171.8 -98.4 -105.9
2 G -69.8 -172.2 43.0 148.1 -151.3 -157.0 -85.4
3 C -39.4 130.5 50.1 93.3 -165.4 -81.2 -132.4
4 G -64.8 174.4 50.1 145.0 -167.3 -144.6 -93.7
5 A -47.1 156.2 53.7 133.0 -177.5 -90.7 -118.6
6 A -64.2 -173.0 46.3 128.0 176.9 -95.8 -109.2
7 T -49.0 172.9 48.6 112.7 -176.6 -95.6 -119.6
8 T -54.1 168.3 53.4 114.0 171.5 -95.0 -119.9
9 C -53.3 -173.2 50.8 138.3 -155.9 -96.3 -112.3
10 G -60.3 163.2 39.5 143.2 -100.0 146.3 -83.6
11 C -73.1 144.3 50.8 143.5 -164.4 -126.1 -112.8
12 G 52.9 144.1 -65.6 147.9 --- --- -79.3
Strand II
base alpha beta gamma delta epsilon zeta chi
1 G -62.1 169.8 52.8 87.7 --- --- -141.3
2 C -57.2 129.7 51.4 83.8 -161.3 -77.6 -150.3
3 G -67.1 177.0 45.3 143.5 -148.6 -173.0 -86.2
4 C -58.1 159.5 51.3 95.5 -170.1 -81.3 -124.4
5 T -44.5 171.8 43.4 135.3 -164.1 -106.8 -110.1
6 T -49.1 178.5 51.6 127.6 -172.8 -106.8 -115.9
7 A -61.5 175.7 45.3 113.1 166.4 -91.2 -112.4
8 A -56.3 -160.2 54.1 145.8 -178.3 -91.9 -108.3
9 G -61.6 175.5 62.1 140.9 150.8 -89.6 -101.7
10 C -56.8 160.1 56.8 82.1 -174.4 -84.7 -137.2
11 G -58.3 166.6 49.5 115.0 178.2 -94.3 -110.2
12 C --- --- 58.5 138.1 -169.0 -104.8 -106.9
****************************************************************************
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 -20.3 33.1 -33.1 22.1 -1.2 34.5 163.5 C2'-endo
2 G -23.9 36.6 -34.9 22.3 0.8 37.1 160.0 C2'-endo
3 C -24.8 5.6 13.9 -28.7 33.8 33.3 65.3 C4'-exo
4 G -25.7 37.1 -33.9 20.1 3.4 37.1 156.2 C2'-endo
5 A -20.9 31.2 -29.3 17.7 2.0 31.6 158.0 C2'-endo
6 A -22.6 30.8 -27.2 14.8 4.8 30.6 152.6 C2'-endo
7 T -34.2 33.1 -20.1 0.8 20.9 34.8 125.2 C1'-exo
8 T -35.8 35.4 -22.0 1.8 21.1 36.7 126.9 C1'-exo
9 C -21.5 31.7 -29.8 18.0 2.0 32.2 157.9 C2'-endo
10 G -36.1 45.1 -36.0 16.8 11.4 43.6 145.6 C2'-endo
11 C -21.3 35.1 -35.2 23.4 -1.5 36.6 163.8 C2'-endo
12 G 4.1 12.3 -22.5 25.4 -18.8 25.4 207.4 C3'-exo
Strand II
base v0 v1 v2 v3 v4 tm P Puckering
1 G 2.9 -23.2 33.3 -32.7 18.6 34.3 13.7 C3'-endo
2 C 0.6 -22.5 34.5 -35.1 21.6 36.2 17.5 C3'-endo
3 G -30.7 41.1 -35.3 19.0 6.9 40.3 151.2 C2'-endo
4 C -40.0 25.4 -2.4 -21.1 38.2 40.6 93.3 O4'-endo
5 T -28.0 37.2 -32.5 17.2 6.6 37.1 151.4 C2'-endo
6 T -28.9 34.5 -27.4 11.1 11.1 34.2 143.0 C1'-exo
7 A -31.3 31.1 -19.7 1.9 18.6 32.4 127.5 C1'-exo
8 A -13.5 27.8 -31.1 23.6 -6.5 31.4 173.3 C2'-endo
9 G -15.6 28.7 -30.2 21.8 -4.0 30.8 168.8 C2'-endo
10 C -15.4 -9.0 28.1 -37.8 33.6 37.8 42.0 C4'-exo
11 G -31.7 32.2 -21.1 3.2 17.9 33.1 129.6 C1'-exo
12 C -18.0 29.3 -29.4 19.4 -1.0 30.7 163.5 C2'-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/G --- 5.0 1 G/C 6.3 5.2
2 G/C 6.5 4.5 2 C/G 6.7 4.8
3 C/G 6.5 5.1 3 G/C 6.4 5.1
4 G/A 6.8 5.0 4 C/T 6.8 4.7
5 A/A 7.0 5.0 5 T/T 6.7 4.9
6 A/T 6.7 4.7 6 T/A 6.7 4.8
7 T/T 6.6 4.9 7 A/A 6.7 4.7
8 T/C 6.8 5.1 8 A/G 7.1 4.8
9 C/G 6.7 4.6 9 G/C 6.3 5.4
10 G/C 6.4 5.3 10 C/G 6.7 4.3
11 C/G 7.1 5.6 11 G/C --- 4.7
****************************************************************************
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 CG/CG 9.1 6.4 5.7 9.3 7.9 7.0
2 GC/GC 8.5 5.2 4.8 9.1 6.1 5.6
3 CG/CG 9.9 7.6 6.7 9.5 6.7 5.9
4 GA/TC 9.7 7.2 6.5 9.4 6.0 5.5
5 AA/TT 9.5 6.4 5.9 10.1 6.9 6.4
6 AT/AT 9.9 6.5 6.1 9.8 6.6 6.1
7 TT/AA 10.3 6.9 6.4 9.5 6.2 5.7
8 TC/GA 9.7 6.6 6.2 8.5 6.0 5.5
9 CG/CG 7.4 4.0 3.4 11.1 8.8 7.9
10 GC/GC 10.1 6.9 6.7 7.7 4.2 3.7
11 CG/CG 10.0 7.1 6.5 9.4 6.4 5.8
****************************************************************************
Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz)
for each dinucleotide step
bp Px Py Pz Hx Hy Hz
1 CG/CG 15.99 26.43 24.17 0.03 -0.21 -0.98
2 GC/GC 17.37 23.05 21.31 -0.39 -0.41 -0.82
3 CG/CG 15.84 24.53 17.27 0.23 -0.39 -0.89
4 GA/TC 15.59 22.51 14.84 -0.16 -0.35 -0.92
5 AA/TT 15.65 20.84 11.86 -0.14 -0.31 -0.94
6 AT/AT 15.26 20.22 8.64 -0.14 -0.22 -0.97
7 TT/AA 15.05 19.77 5.44 -0.12 -0.30 -0.95
8 TC/GA 14.55 19.21 2.15 -0.12 -0.26 -0.96
9 CG/CG 11.86 20.64 -0.66 -0.23 -0.04 -0.97
10 GC/GC 14.37 17.46 -3.79 -0.05 -0.38 -0.93
11 CG/CG 12.05 18.00 -7.38 -0.08 0.04 -1.00