**************************************************************************** 3DNA v2.4.3-2019apr06, created and maintained by xiangjun@x3dna.org **************************************************************************** 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: coor_7972_9.pdb Date and time: Wed Apr 16 17:39:23 2025 Number of base-pairs: 20 Number of atoms: 1265 **************************************************************************** **************************************************************************** RMSD of the bases (----- for WC bp, + for isolated bp, x for helix change) Strand I Strand II Helix 1 (0.053) ....>-:...1_:[CYT]C-----G[GUA]:..40_:-<.... (0.078) | 2 (0.097) ....>-:...2_:[GUA]G-----C[CYT]:..39_:-<.... (0.042) | 3 (0.083) ....>-:...3_:[ADE]A-----T[THY]:..38_:-<.... (0.074) | 4 (0.066) ....>-:...4_:[CYT]C-----G[GUA]:..37_:-<.... (0.057) | 5 (0.102) ....>-:...5_:[THY]T-----A[ADE]:..36_:-<.... (0.061) | 6 (0.035) ....>-:...6_:[CYT]C-----G[GUA]:..35_:-<.... (0.091) | 7 (0.056) ....>-:...7_:[THY]T-----A[ADE]:..34_:-<.... (0.095) | 8 (0.054) ....>-:...8_:[ADE]A-----T[THY]:..33_:-<.... (0.065) | 9 (0.067) ....>-:...9_:[CYT]C-----G[GUA]:..32_:-<.... (0.058) | 10 (0.071) ....>-:..10_:[GUA]G-----C[CYT]:..31_:-<.... (0.048) | 11 (0.065) ....>-:..11_:[GUA]G-----C[CYT]:..30_:-<.... (0.032) | 12 (0.049) ....>-:..12_:[CYT]C-----G[GUA]:..29_:-<.... (0.102) | 13 (0.037) ....>-:..13_:[ADE]A-----T[THY]:..28_:-<.... (0.056) | 14 (0.072) ....>-:..14_:[THY]T-----A[ADE]:..27_:-<.... (0.068) | 15 (0.049) ....>-:..15_:[CYT]C-----G[GUA]:..26_:-<.... (0.065) | 16 (0.055) ....>-:..16_:[THY]T-----A[ADE]:..25_:-<.... (0.051) | 17 (0.061) ....>-:..17_:[GUA]G-----C[CYT]:..24_:-<.... (0.051) | 18 (0.052) ....>-:..18_:[CYT]C-----G[GUA]:..23_:-<.... (0.071) | 19 (0.061) ....>-:..19_:[GUA]G-----C[CYT]:..22_:-<.... (0.038) | 20 (0.053) ....>-:..20_:[CYT]C-----G[GUA]:..21_:-<.... (0.054) | **************************************************************************** Detailed H-bond information: atom-name pair and length [ O N] 1 C-----G [3] O2 - N2 3.12 N3 - N1 2.88 N4 - O6 2.63 2 G-----C [3] N1 - N3 2.74 N2 - O2 2.79 O6 - N4 2.58 3 A-----T [2] N1 - N3 2.87 N6 - O4 2.73 4 C-----G [3] O2 - N2 2.80 N3 - N1 2.84 N4 - O6 2.64 5 T-----A [2] N3 - N1 2.82 O4 - N6 2.69 6 C-----G [3] O2 - N2 2.79 N3 - N1 2.83 N4 - O6 2.83 7 T-----A [2] N3 - N1 2.86 O4 - N6 2.91 8 A-----T [2] N1 - N3 2.98 N6 - O4 2.71 9 C-----G [3] O2 - N2 2.88 N3 - N1 2.79 N4 - O6 2.62 10 G-----C [3] N1 - N3 2.89 N2 - O2 2.94 O6 - N4 2.69 11 G-----C [3] N1 - N3 2.86 N2 - O2 2.79 O6 - N4 2.89 12 C-----G [3] O2 - N2 2.70 N3 - N1 2.76 N4 - O6 2.80 13 A-----T [2] N1 - N3 2.89 N6 - O4 2.70 14 T-----A [2] N3 - N1 3.03 O4 - N6 2.83 15 C-----G [3] O2 - N2 2.84 N3 - N1 2.74 N4 - O6 2.72 16 T-----A [2] N3 - N1 3.01 O4 - N6 2.76 17 G-----C [3] N1 - N3 2.85 N2 - O2 3.03 O6 - N4 2.72 18 C-----G [3] O2 - N2 2.64 N3 - N1 2.74 N4 - O6 2.70 19 G-----C [3] N1 - N3 2.81 N2 - O2 2.78 O6 - N4 2.73 20 C-----G [3] O2 - N2 2.90 N3 - N1 2.93 N4 - O6 2.91 **************************************************************************** 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 3.88( 1.34) 0.00( 0.00) 0.37( 0.00) 1.55( 0.00) 5.80( 1.34) 2 GA/TC 3.94( 0.98) 0.00( 0.00) 0.00( 0.00) 3.17( 0.11) 7.10( 1.09) 3 AC/GT 3.38( 1.82) 0.00( 0.00) 0.00( 0.00) 6.79( 2.33) 10.17( 4.16) 4 CT/AG 3.99( 0.00) 0.00( 0.00) 0.00( 0.00) 4.92( 3.53) 8.91( 3.53) 5 TC/GA 3.44( 0.00) 0.00( 0.00) 0.00( 0.00) 2.36( 0.44) 5.80( 0.44) 6 CT/AG 6.07( 0.64) 0.00( 0.00) 0.00( 0.00) 7.35( 4.69) 13.42( 5.33) 7 TA/TA 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 5.58( 1.21) 5.58( 1.21) 8 AC/GT 3.10( 0.48) 0.23( 0.00) 0.00( 0.00) 0.00( 0.00) 3.33( 0.48) 9 CG/CG 2.14( 0.37) 0.00( 0.00) 0.58( 0.00) 3.07( 0.88) 5.78( 1.25) 10 GG/CC 2.91( 0.21) 0.00( 0.00) 0.00( 0.00) 4.77( 0.99) 7.68( 1.20) 11 GC/GC 4.86( 2.04) 0.00( 0.00) 0.00( 0.00) 0.41( 0.00) 5.27( 2.04) 12 CA/TG 0.00( 0.00) 0.00( 0.00) 0.00( 0.00) 8.35( 3.88) 8.35( 3.88) 13 AT/AT 6.37( 2.55) 0.00( 0.00) 0.00( 0.00) 5.99( 2.24) 12.36( 4.79) 14 TC/GA 1.74( 0.11) 0.00( 0.00) 0.00( 0.00) 3.62( 1.14) 5.36( 1.25) 15 CT/AG 4.09( 0.00) 0.00( 0.00) 0.00( 0.00) 6.25( 4.50) 10.34( 4.50) 16 TG/CA 0.52( 0.00) 0.00( 0.00) 0.00( 0.00) 3.77( 0.02) 4.29( 0.02) 17 GC/GC 2.14( 0.60) 0.00( 0.00) 0.00( 0.00) 3.16( 1.12) 5.30( 1.71) 18 CG/CG 1.39( 0.00) 0.00( 0.00) 0.42( 0.00) 3.10( 0.33) 4.92( 0.33) 19 GC/GC 5.77( 3.42) 0.00( 0.00) 0.00( 0.00) 1.89( 0.17) 7.66( 3.58) **************************************************************************** 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 45.098 61.731 50.768 0.913 -0.233 -0.335 2 G-C 47.974 61.072 50.390 0.933 -0.168 -0.318 3 A-T 50.931 60.582 49.246 0.927 -0.280 -0.251 4 C-G 54.286 59.906 48.986 0.960 -0.164 -0.225 5 T-A 58.239 59.797 48.648 0.935 -0.150 -0.322 6 C-G 60.871 60.031 46.498 0.916 -0.235 -0.325 7 T-A 63.994 60.340 45.729 0.875 -0.098 -0.474 8 A-T 67.844 59.407 46.262 0.956 -0.040 -0.291 9 C-G 71.543 60.098 46.079 0.887 -0.335 -0.319 10 G-C 74.313 59.310 44.963 0.951 -0.202 -0.233 11 G-C 77.526 58.231 43.878 0.977 -0.201 -0.074 12 C-G 80.112 56.724 44.731 0.949 -0.313 0.041 13 A-T 83.645 56.457 42.517 0.947 -0.317 -0.061 14 T-A 86.506 55.408 42.913 0.911 -0.407 -0.068 15 C-G 89.352 53.230 42.982 0.863 -0.480 -0.160 16 T-A 92.651 51.403 43.457 0.849 -0.476 -0.230 17 G-C 95.857 50.666 43.147 0.871 -0.450 -0.197 18 C-G 98.789 49.136 42.899 0.901 -0.401 -0.166 19 G-C 101.673 47.917 42.819 0.953 -0.275 -0.129 20 C-G 104.804 48.258 42.453 0.952 -0.223 -0.211 **************************************************************************** Local base-pair parameters bp Shear Stretch Stagger Buckle Propeller Opening 1 C-G -0.19 -0.15 0.10 -2.34 -6.10 -12.21 2 G-C 0.14 -0.29 -0.15 11.56 -2.02 -9.05 3 A-T -0.27 -0.23 -0.08 11.97 -9.97 -8.54 4 C-G -0.06 -0.25 -0.49 8.30 -21.81 -2.65 5 T-A 0.13 -0.23 0.38 -12.90 -22.30 -14.40 6 C-G -0.06 -0.15 -0.17 -9.09 -8.26 -2.70 7 T-A 0.65 -0.26 0.21 5.36 -14.64 -1.79 8 A-T -0.29 -0.17 0.59 -2.89 -36.86 -15.62 9 C-G -0.53 -0.22 0.11 -5.93 -2.20 -6.67 10 G-C -0.14 -0.23 -0.12 -2.55 -12.68 -5.15 11 G-C -0.32 -0.18 -0.48 -16.45 -13.10 0.25 12 C-G -0.22 -0.20 -0.17 0.96 -3.93 1.89 13 A-T 0.01 -0.09 -0.22 -2.78 -14.75 -6.75 14 T-A 0.11 0.02 -0.33 7.25 -16.07 -9.99 15 C-G -0.12 -0.24 0.12 -6.10 -19.43 -3.28 16 T-A 0.36 -0.13 0.54 -7.30 -11.01 -12.10 17 G-C 0.10 -0.15 0.01 -5.39 -24.12 -2.98 18 C-G -0.09 -0.30 -0.13 -6.74 -10.47 -5.25 19 G-C 0.06 -0.19 -0.01 0.97 -5.52 -3.77 20 C-G 0.03 -0.08 -0.60 12.96 -7.96 -4.39 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.04 -0.19 -0.04 -1.06 -13.16 -6.26 s.d. 0.26 0.08 0.32 8.34 8.60 4.79 **************************************************************************** Local base-pair step parameters step Shift Slide Rise Tilt Roll Twist 1 CG/CG 0.61 -0.03 2.91 3.97 0.58 28.99 2 GA/TC -0.33 -0.01 3.19 -2.33 7.13 38.55 3 AC/GT 0.01 -0.57 3.38 2.93 -6.40 38.23 4 CT/AG -0.83 -0.41 3.86 -5.33 2.22 40.66 5 TC/GA 0.83 1.17 3.09 4.54 2.10 39.70 6 CT/AG -0.33 0.96 3.07 -5.41 10.57 26.63 7 TA/TA -1.85 0.99 3.40 -10.70 -5.27 37.35 8 AC/GT 1.32 1.03 3.37 3.26 -17.24 44.42 9 CG/CG -0.12 -0.25 3.08 -0.34 9.84 27.92 10 GG/CC -0.67 0.12 3.49 -3.66 8.50 40.31 11 GC/GC 1.06 0.56 2.87 -4.95 7.91 37.59 12 CA/TG -2.07 1.10 3.46 -4.59 -3.60 34.57 13 AT/AT 0.02 -0.60 3.01 -1.15 5.47 31.78 14 TC/GA 0.40 -0.72 3.49 -2.58 6.75 35.92 15 CT/AG -1.05 -0.58 3.61 -1.81 3.69 34.29 16 TG/CA -0.29 0.90 3.17 -2.11 -1.71 35.51 17 GC/GC -0.34 0.16 3.29 -3.61 0.83 35.99 18 CG/CG -0.24 0.34 3.11 -3.79 7.19 33.45 19 GC/GC 1.08 -0.32 2.96 5.49 0.75 36.31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.15 0.20 3.25 -1.69 2.07 35.69 s.d. 0.92 0.66 0.26 4.16 6.86 4.54 **************************************************************************** Local base-pair helical parameters step X-disp Y-disp h-Rise Incl. Tip h-Twist 1 CG/CG -0.17 -0.43 2.97 1.15 -7.88 29.26 2 GA/TC -0.85 0.21 3.15 10.68 3.49 39.24 3 AC/GT -0.05 0.36 3.42 -9.67 -4.43 38.85 4 CT/AG -0.87 0.49 3.91 3.18 7.62 41.05 5 TC/GA 1.48 -0.71 3.22 3.08 -6.65 40.00 6 CT/AG -0.42 -0.54 3.21 21.63 11.07 29.11 7 TA/TA 2.17 1.35 3.61 -7.99 16.21 39.14 8 AC/GT 2.65 -1.38 2.89 -21.82 -4.13 47.60 9 CG/CG -2.43 0.16 2.83 19.64 0.69 29.57 10 GG/CC -0.81 0.53 3.49 12.15 5.22 41.32 11 GC/GC -0.00 -2.13 2.77 12.05 7.54 38.69 12 CA/TG 2.41 2.69 3.57 -6.01 7.66 35.05 13 AT/AT -1.95 -0.22 2.87 9.90 2.08 32.25 14 TC/GA -2.11 -1.01 3.27 10.81 4.13 36.62 15 CT/AG -1.60 1.47 3.58 6.22 3.06 34.53 16 TG/CA 1.72 0.17 3.13 -2.80 3.46 35.61 17 GC/GC 0.14 0.03 3.31 1.34 5.83 36.18 18 CG/CG -0.50 -0.17 3.12 12.27 6.46 34.40 19 GC/GC -0.60 -1.02 3.08 1.20 -8.75 36.72 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.10 -0.01 3.23 4.05 2.77 36.59 s.d. 1.53 1.09 0.31 10.68 6.63 4.65 **************************************************************************** The 'simple' parameters are intuitive for non-Watson-Crick base pairs and associated base-pair steps (where the above corresponding 3DNA parameters often appear cryptic). Note that they are for structural *description* only, not to be fed into the 'rebuild' program. See URL http://x3dna.org/highlights/details-on-the-simple-base-pair-parameters and related blogposts on the 3DNA home page for details. This structure contains 0 non-Watson-Crick (with leading *) base pair(s) ---------------------------------------------------------------------------- Simple base-pair parameters based on RC8--YC6 vectors bp Shear Stretch Stagger Buckle Propeller Opening 1 C-G -0.19 -0.15 0.10 -2.48 -6.04 -12.20 2 G-C 0.14 -0.28 -0.15 11.60 -1.81 -9.10 3 A-T -0.27 -0.22 -0.08 11.69 -10.30 -8.55 4 C-G -0.07 -0.25 -0.49 7.94 -21.95 -2.61 5 T-A 0.13 -0.23 0.38 -12.46 -22.55 -14.21 6 C-G -0.06 -0.15 -0.17 -9.14 -8.20 -2.70 7 T-A 0.66 -0.22 0.21 6.18 -14.31 -1.78 8 A-T -0.29 -0.16 0.59 -3.92 -36.77 -14.83 9 C-G -0.54 -0.19 0.11 -6.05 -1.86 -6.67 10 G-C -0.15 -0.23 -0.12 -2.66 -12.66 -5.12 11 G-C -0.33 -0.17 -0.48 -16.71 -12.75 0.26 12 C-G -0.23 -0.20 -0.17 0.87 -3.95 1.88 13 A-T 0.01 -0.09 -0.22 -2.72 -14.76 -6.69 14 T-A 0.11 0.02 -0.33 7.39 -16.01 -9.91 15 C-G -0.12 -0.24 0.12 -6.24 -19.39 -3.24 16 T-A 0.36 -0.12 0.54 -6.99 -11.21 -12.07 17 G-C 0.10 -0.15 0.01 -5.03 -24.20 -2.91 18 C-G -0.09 -0.30 -0.13 -6.83 -10.41 -5.24 19 G-C 0.06 -0.19 -0.01 1.00 -5.51 -3.77 20 C-G 0.03 -0.08 -0.60 12.90 -8.05 -4.41 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.04 -0.18 -0.04 -1.08 -13.14 -6.19 s.d. 0.26 0.07 0.32 8.34 8.63 4.70 ---------------------------------------------------------------------------- Simple base-pair step parameters based on consecutive C1'-C1' vectors step Shift Slide Rise Tilt Roll Twist 1 CG/CG 0.61 -0.03 2.91 3.97 0.57 27.69 2 GA/TC -0.33 -0.01 3.19 -2.23 7.16 41.02 3 AC/GT 0.00 -0.57 3.38 2.80 -6.46 36.50 4 CT/AG -0.82 -0.42 3.86 -5.36 2.15 38.54 5 TC/GA 0.80 1.19 3.09 4.49 2.20 40.79 6 CT/AG -0.37 0.94 3.07 -5.85 10.33 23.21 7 TA/TA -1.87 0.94 3.40 -10.57 -5.53 42.86 8 AC/GT 1.36 0.99 3.37 2.74 -17.33 45.19 9 CG/CG -0.12 -0.25 3.08 -0.07 9.84 26.88 10 GG/CC -0.67 0.14 3.49 -3.46 8.59 40.79 11 GC/GC 1.06 0.56 2.87 -4.92 7.93 34.93 12 CA/TG -2.08 1.08 3.46 -4.56 -3.64 35.83 13 AT/AT 0.02 -0.60 3.01 -1.14 5.47 31.68 14 TC/GA 0.40 -0.72 3.49 -2.54 6.76 36.36 15 CT/AG -1.04 -0.60 3.61 -1.90 3.64 30.49 16 TG/CA -0.31 0.89 3.17 -2.06 -1.77 38.52 17 GC/GC -0.34 0.16 3.29 -3.61 0.83 36.53 18 CG/CG -0.23 0.34 3.11 -3.78 7.20 33.14 19 GC/GC 1.09 -0.31 2.96 5.49 0.79 35.60 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ave. -0.15 0.20 3.25 -1.71 2.04 35.61 s.d. 0.93 0.66 0.26 4.12 6.89 5.71 **************************************************************************** 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 44.7 46.5 11.3 9.2 9.8 2 G-C 54.1 46.1 10.9 8.9 9.6 3 A-T 44.8 45.5 11.1 8.9 9.7 4 C-G 47.6 48.7 10.9 9.0 9.7 5 T-A 45.6 46.4 11.0 9.0 9.7 6 C-G 53.4 55.4 10.8 9.1 9.8 7 T-A 58.8 52.2 10.6 8.9 9.7 8 A-T 45.3 49.5 11.1 9.1 9.8 9 C-G 41.2 55.1 11.1 9.1 9.8 10 G-C 50.3 47.3 11.0 9.0 9.7 11 G-C 47.0 50.8 10.9 8.9 9.7 12 C-G 48.5 61.7 10.6 8.9 9.8 13 A-T 51.6 48.0 10.9 9.0 9.9 14 T-A 50.1 45.3 11.2 9.2 10.0 15 C-G 48.2 52.1 10.9 9.0 9.8 16 T-A 50.1 47.9 11.1 9.1 9.8 17 G-C 48.8 43.5 11.1 9.1 9.8 18 C-G 50.4 49.4 10.8 8.9 9.7 19 G-C 49.8 47.3 11.0 9.0 9.9 20 C-G 48.7 51.6 11.1 9.1 9.9 **************************************************************************** Classification of each dinucleotide step in a right-handed nucleic acid structure: A-like; B-like; TA-like, or other cases. step Xp Yp Zp XpH YpH ZpH Form 1 CG/CG -2.05 9.33 0.06 -2.23 9.33 0.21 2 GA/TC -1.71 8.84 0.77 -2.45 8.57 2.30 3 AC/GT -2.09 9.10 0.22 -2.18 9.02 -1.23 B 4 CT/AG -2.20 9.07 -0.20 -3.01 9.07 0.26 B 5 TC/GA -1.77 8.84 -0.54 -0.23 8.85 -0.08 B 6 CT/AG -2.92 8.99 -1.35 -3.34 8.89 1.90 B 7 TA/TA -2.07 8.74 -0.90 0.21 8.54 -2.09 B 8 AC/GT -1.64 8.88 -0.75 0.85 8.08 -3.77 9 CG/CG -2.57 9.32 0.08 -4.91 8.78 3.12 B 10 GG/CC -2.31 8.78 0.09 -3.09 8.59 1.84 B 11 GC/GC -2.67 8.85 -0.19 -2.76 8.71 1.62 B 12 CA/TG -2.77 8.95 -0.70 -0.42 8.83 -1.67 B 13 AT/AT -2.54 9.24 -0.45 -4.41 9.18 1.09 B 14 TC/GA -2.36 9.23 0.49 -4.35 8.99 2.14 B 15 CT/AG -2.36 9.34 0.29 -3.91 9.26 1.24 B 16 TG/CA -1.90 8.99 -0.41 -0.26 8.96 -0.84 B 17 GC/GC -2.42 9.32 -0.99 -2.32 9.34 -0.76 B 18 CG/CG -2.05 9.30 -0.41 -2.55 9.19 1.52 B 19 GC/GC -2.89 8.97 -0.63 -3.43 8.98 -0.48 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 GA/TC --- --- --- --- 3 AC/GT 10.4 --- 16.0 --- 4 CT/AG 10.8 10.7 15.5 15.2 5 TC/GA 12.6 12.5 16.2 16.2 6 CT/AG 13.5 13.3 14.6 14.6 7 TA/TA 12.9 12.8 17.0 16.8 8 AC/GT 11.3 11.2 17.0 16.9 9 CG/CG 11.3 11.2 14.7 14.6 10 GG/CC 12.8 12.7 17.4 17.4 11 GC/GC 13.4 13.3 15.6 15.4 12 CA/TG 14.0 13.9 15.2 14.7 13 AT/AT 13.5 13.4 17.2 16.9 14 TC/GA 12.4 12.4 17.1 16.9 15 CT/AG 12.3 12.3 18.3 18.2 16 TG/CA 12.7 12.7 16.5 16.5 17 GC/GC 13.0 --- 15.4 --- 18 CG/CG --- --- --- --- 19 GC/GC --- --- --- --- **************************************************************************** Global linear helical axis defined by equivalent C1' and RN9/YN1 atom pairs Deviation from regular linear helix: 3.29(0.53) Helix: 0.9372 -0.2834 -0.2031 HETATM 9998 XS X X 999 45.862 65.053 51.814 HETATM 9999 XE X X 999 104.681 47.264 39.065 Average and standard deviation of helix radius: P: 9.42(1.82), O4': 6.65(1.83), C1': 6.08(1.79) 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 4.63 4.01 27.89 3.73 2 G-C 3.63 3.18 40.58 3.29 3 A-T 2.60 -4.66 35.82 2.87 4 C-G 0.63 -8.96 39.12 3.18 5 T-A 0.92 -12.60 41.04 3.25 6 C-G 0.54 -5.80 24.28 4.20 7 T-A 0.11 -5.70 44.05 3.03 8 A-T 0.49 -4.27 43.49 2.71 9 C-G 0.99 5.62 26.98 3.45 10 G-C 2.67 1.16 41.51 3.03 11 G-C 4.39 -0.35 34.79 3.58 12 C-G 3.81 5.26 36.57 3.47 13 A-T 5.10 1.85 31.90 3.40 14 T-A 4.41 4.96 36.83 2.80 15 C-G 3.60 7.30 30.62 3.15 16 T-A 3.74 12.61 38.75 3.04 17 G-C 4.03 2.82 35.98 3.17 18 C-G 3.94 -3.33 33.45 3.56 19 G-C 3.80 -5.97 35.56 3.84 20 C-G 1.95 -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 --- --- 61.2 140.4 -171.4 -96.4 -113.7 2 G -68.6 171.3 57.2 134.7 -166.3 -153.8 -99.2 3 A -46.1 143.7 53.9 142.5 179.4 -107.0 -130.6 4 C -52.3 -179.8 50.3 139.3 168.2 -92.9 -114.4 5 T -63.9 -159.6 52.9 135.8 -177.8 -97.1 -118.0 6 C -58.1 -171.7 48.4 137.2 -176.0 -98.4 -85.3 7 T -65.2 175.5 48.1 148.3 -103.6 155.3 -89.2 8 A -60.5 129.0 42.1 140.8 -170.1 -106.9 -101.5 9 C -62.4 168.4 52.6 137.0 172.7 -111.1 -105.6 10 G -55.3 176.3 50.3 149.7 -156.7 -147.9 -104.7 11 G -58.2 171.1 45.9 148.0 -177.3 -85.2 -110.6 12 C -65.7 172.1 53.0 145.2 -128.9 -179.8 -86.0 13 A -61.1 137.2 55.7 140.2 -174.2 -97.4 -112.1 14 T -66.2 173.4 54.5 127.1 178.9 -104.4 -95.7 15 C -66.6 -179.9 53.3 130.1 -174.0 -96.2 -119.0 16 T -51.0 -166.8 41.0 154.7 -151.4 -162.4 -95.2 17 G -51.0 128.7 61.4 125.9 -172.5 -94.6 -122.7 18 C -63.6 170.0 51.8 125.2 -177.4 -107.6 -114.1 19 G -65.5 169.2 65.7 143.2 179.2 -97.1 -100.2 20 C -56.4 -170.0 30.7 140.1 --- --- -88.2 Strand II base alpha beta gamma delta epsilon zeta chi 1 G -53.6 -179.4 41.0 147.5 --- --- -97.5 2 C -61.8 -156.3 37.0 139.6 177.3 -102.8 -108.6 3 T -39.9 168.7 49.3 118.2 171.3 -84.8 -142.7 4 G -62.1 177.5 54.9 128.7 -180.0 -109.9 -109.4 5 A -47.0 120.6 54.9 135.4 -176.1 -99.6 -106.4 6 G -52.9 167.7 53.5 149.4 -142.8 168.4 -75.8 7 A -59.6 -178.2 43.4 135.3 -173.7 -105.5 -95.3 8 T -63.0 145.4 42.4 145.2 -176.3 -98.7 -96.8 9 G -61.4 165.9 43.8 146.6 -93.2 147.9 -99.2 10 C -57.4 178.3 48.0 141.5 -165.3 -100.6 -106.1 11 C -48.8 154.3 35.0 138.8 177.9 -94.8 -94.1 12 G -60.9 151.5 54.5 141.1 -142.2 -175.2 -93.7 13 T -47.0 179.1 38.8 133.3 -160.7 -103.7 -89.5 14 A -43.9 179.0 38.1 142.7 -174.5 -111.3 -113.4 15 G -46.1 157.9 57.7 95.7 -175.1 -94.3 -131.8 16 A -60.2 174.5 55.1 139.2 179.9 -103.2 -99.0 17 C -43.9 173.7 43.7 127.4 -172.7 -108.0 -96.3 18 G -35.4 175.3 36.7 139.4 178.4 -106.5 -102.3 19 C -60.5 -142.3 16.4 148.9 -179.4 -104.6 -98.9 20 G --- --- 56.9 142.2 -167.9 -95.2 -137.2 **************************************************************************** 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: the amplitude of pucker P: the phase angle of pseudorotation Strand I base v0 v1 v2 v3 v4 tm P Puckering 1 C -13.0 28.9 -31.6 24.8 -7.8 31.8 174.5 C2'-endo 2 G -32.1 38.3 -26.7 9.1 14.8 36.4 137.2 C1'-exo 3 A -28.9 34.5 -28.7 12.4 10.3 34.9 145.3 C2'-endo 4 C -22.2 30.8 -28.2 15.1 4.7 31.4 153.9 C2'-endo 5 T -29.2 38.3 -32.9 15.1 8.9 38.5 148.8 C2'-endo 6 C -9.7 25.4 -30.9 26.6 -10.7 30.9 181.3 C3'-exo 7 T -26.4 40.4 -38.2 22.6 1.1 40.9 158.9 C2'-endo 8 A -22.8 31.9 -28.0 14.7 4.9 31.6 152.5 C2'-endo 9 C -27.2 33.7 -26.7 11.2 10.3 33.1 143.9 C1'-exo 10 G -31.9 46.4 -41.4 23.4 3.5 45.5 155.4 C2'-endo 11 G -19.4 34.1 -32.2 21.4 -0.9 33.8 162.5 C2'-endo 12 C -25.6 37.2 -33.4 19.8 3.1 36.6 155.9 C2'-endo 13 A -16.6 31.0 -30.2 22.1 -2.8 31.1 166.3 C2'-endo 14 T -28.9 36.4 -30.5 16.0 7.7 35.7 148.7 C2'-endo 15 C -24.8 28.8 -23.2 9.1 8.8 28.9 143.2 C1'-exo 16 T -15.8 33.2 -35.0 27.6 -7.8 35.3 172.8 C2'-endo 17 G -34.2 33.0 -22.3 3.3 18.8 34.9 129.7 C1'-exo 18 C -31.5 35.6 -26.2 6.8 16.2 36.1 136.5 C1'-exo 19 G -28.2 36.6 -34.7 19.2 4.7 38.4 154.7 C2'-endo 20 C -28.2 36.0 -31.7 16.2 7.0 36.4 150.6 C2'-endo Strand II base v0 v1 v2 v3 v4 tm P Puckering 1 G -24.9 36.3 -35.2 22.6 1.2 37.5 159.8 C2'-endo 2 C -12.4 25.9 -27.1 19.3 -4.1 27.6 169.9 C2'-endo 3 T -34.6 34.0 -21.1 0.6 22.7 36.2 125.6 C1'-exo 4 G -27.3 36.1 -31.5 15.8 6.3 36.0 151.0 C2'-endo 5 A -28.0 34.6 -27.0 10.6 10.9 33.9 142.9 C1'-exo 6 G -23.7 34.2 -31.6 20.1 1.5 34.1 158.0 C2'-endo 7 A -33.0 37.8 -29.5 8.8 15.7 38.8 139.4 C1'-exo 8 T -22.2 36.4 -35.2 22.4 0.5 37.1 161.3 C2'-endo 9 G -28.0 41.3 -38.2 22.0 3.9 41.6 156.5 C2'-endo 10 C -25.3 29.5 -21.8 8.9 9.8 28.4 140.3 C1'-exo 11 C -8.9 22.4 -26.7 22.3 -7.2 26.7 178.8 C2'-endo 12 G -38.3 47.1 -36.7 15.0 15.7 46.1 142.7 C1'-exo 13 T -32.2 37.0 -28.6 11.4 12.4 36.6 141.4 C1'-exo 14 A -24.2 38.6 -37.6 25.7 -1.4 39.3 162.8 C2'-endo 15 G -30.6 20.1 -3.3 -14.7 28.7 30.7 96.2 O4'-endo 16 A -18.2 28.3 -28.0 17.4 0.5 29.6 161.0 C2'-endo 17 C -34.9 39.7 -29.6 9.9 15.0 39.3 138.8 C1'-exo 18 G -24.2 31.0 -27.2 12.9 7.3 31.6 149.4 C2'-endo 19 C 0.7 17.1 -27.3 27.8 -18.1 28.9 199.4 C3'-exo 20 G -26.1 35.0 -29.7 15.7 6.1 34.1 150.5 C2'-endo **************************************************************************** Same strand P--P and C1'--C1' virtual bond distances Strand I Strand II step P--P C1'--C1' step P--P C1'--C1' 1 C/G --- 4.82 1 G/C 6.55 4.74 2 G/A 6.67 5.12 2 C/T 6.76 5.37 3 A/C 6.93 5.01 3 T/G 6.79 4.69 4 C/T 6.86 5.18 4 G/A 6.92 4.88 5 T/C 6.46 5.19 5 A/G 6.67 4.88 6 C/T 6.65 4.56 6 G/A 6.69 5.01 7 T/A 6.56 5.36 7 A/T 6.99 4.79 8 A/C 6.77 4.72 8 T/G 6.59 5.60 9 C/G 7.11 4.58 9 G/C 6.68 4.74 10 G/G 6.82 5.67 10 C/C 6.86 4.74 11 G/C 6.72 4.69 11 C/G 6.77 5.70 12 C/A 6.43 5.52 12 G/T 6.56 4.54 13 A/T 7.08 4.91 13 T/A 6.79 5.23 14 T/C 6.79 5.00 14 A/G 6.74 5.20 15 C/T 6.54 5.47 15 G/A 6.98 4.39 16 T/G 6.59 4.75 16 A/C 6.74 5.20 17 G/C 6.92 5.12 17 C/G 6.84 4.82 18 C/G 6.67 4.99 18 G/C 6.24 4.69 19 G/C 6.94 4.90 19 C/G --- 6.09 **************************************************************************** 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 9.12 6.19 5.52 10.09 7.00 6.38 2 GA/TC 8.61 7.13 6.17 9.22 6.76 6.03 3 AC/GT 9.45 6.69 6.14 9.10 5.85 5.38 4 CT/AG 9.86 7.24 6.64 9.26 6.23 5.73 5 TC/GA 8.28 5.19 4.84 9.44 6.70 6.12 6 CT/AG 8.93 5.91 5.14 10.07 7.12 6.46 7 TA/TA 9.90 6.91 6.73 7.19 4.16 3.95 8 AC/GT 6.72 3.80 3.74 9.53 6.52 6.56 9 CG/CG 9.98 8.05 7.23 10.15 7.51 6.71 10 GG/CC 9.38 7.55 6.83 8.88 6.47 5.74 11 GC/GC 7.72 4.79 4.16 10.63 8.61 7.75 12 CA/TG 11.41 8.40 8.02 6.32 2.99 2.62 13 AT/AT 10.11 7.28 6.58 10.27 7.61 7.05 14 TC/GA 8.98 6.89 6.14 11.02 8.55 7.78 15 CT/AG 11.10 8.51 7.87 9.07 6.19 5.52 16 TG/CA 9.03 6.14 5.67 8.90 5.82 5.38 17 GC/GC 9.70 6.42 5.86 9.56 6.27 5.85 18 CG/CG 9.31 6.59 5.89 9.76 6.91 6.21 19 GC/GC 8.84 5.69 5.29 10.40 7.90 7.16 **************************************************************************** Position (Px, Py, Pz) and local helical axis vector (Hx, Hy, Hz) for each dinucleotide step step Px Py Pz Hx Hy Hz 1 CG/CG 46.46 60.98 50.70 0.95 -0.24 -0.20 2 GA/TC 49.65 60.41 50.50 0.85 -0.31 -0.43 3 AC/GT 52.64 60.27 49.45 0.96 -0.26 -0.07 4 CT/AG 56.24 58.92 48.80 0.97 -0.02 -0.26 5 TC/GA 60.22 60.95 48.50 0.88 -0.18 -0.43 6 CT/AG 62.31 60.79 45.87 0.98 0.14 -0.14 7 TA/TA 65.29 57.66 46.71 0.89 -0.35 -0.28 8 AC/GT 70.21 57.31 47.30 0.77 -0.12 -0.62 9 CG/CG 73.87 61.64 46.48 0.90 -0.44 0.01 10 GG/CC 76.30 59.46 44.87 0.90 -0.41 -0.14 11 GC/GC 77.93 55.72 43.88 0.89 -0.41 -0.18 12 CA/TG 82.43 59.96 44.09 0.99 -0.16 -0.02 13 AT/AT 84.42 54.16 42.75 0.91 -0.34 -0.23 14 TC/GA 87.10 53.18 41.23 0.92 -0.30 -0.24 15 CT/AG 90.13 50.56 42.54 0.91 -0.37 -0.20 16 TG/CA 94.32 50.63 44.90 0.84 -0.51 -0.16 17 GC/GC 97.28 49.80 43.10 0.88 -0.47 -0.10 18 CG/CG 100.43 48.99 42.92 0.91 -0.40 0.07 19 GC/GC 103.36 48.19 43.75 0.99 -0.13 -0.09