**************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. For example, B.DA1689 means adenosine #1689 on chain B, and C.ARG49 denotes arginine #49 on chain C. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-dssr snap -i=/data/pdb/pdbfiles/3vxx.pdb -o=3vxx.out --type=base File name: 3vxx.pdb no. of peptide chains: 1 [A=63] no. of DNA/RNA chains: 2 [B=14,C=14] no. of amino acids: 63 no. of nucleotides: 28 no. of atoms: 1240 no. of waters: 123 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 B.5CM9,C.5CM4 **************************************************************************** List of 1 helix Note: a helix is defined by base-stacking interactions, regardless of bp type and backbone connectivity, and may contain more than one stem. helix#number[stems-contained] bps=number-of-base-pairs in the helix bp-type: '|' for a canonical WC/wobble pair, '.' otherwise helix-form: classification of a dinucleotide step comprising the bp above the given designation and the bp that follows it. Types include 'A', 'B' or 'Z' for the common A-, B- and Z-form helices, '.' for an unclassified step, and 'x' for a step without a continuous backbone. -------------------------------------------------------------------- helix#1[0] bps=13 strand-1 5'-GTCACTACcGGAC-3' bp-type ||||||||||||| strand-2 3'-CAGTGATGGcCTG-5' helix-form .BBBBBBB..B. 1 B.DG1 C.DC13 G-C WC 19-XIX cWW cW-W 2 B.DT2 C.DA12 T-A WC 20-XX cWW cW-W 3 B.DC3 C.DG11 C-G WC 19-XIX cWW cW-W 4 B.DA4 C.DT10 A-T WC 20-XX cWW cW-W 5 B.DC5 C.DG9 C-G WC 19-XIX cWW cW-W 6 B.DT6 C.DA8 T-A WC 20-XX cWW cW-W 7 B.DA7 C.DT7 A-T WC 20-XX cWW cW-W 8 B.DC8 C.DG6 C-G WC 19-XIX cWW cW-W 9 B.5CM9 C.DG5 c-G WC 19-XIX cWW cW-W 10 B.DG10 C.5CM4 G-c WC 19-XIX cWW cW-W 11 B.DG11 C.DC3 G-C WC 19-XIX cWW cW-W 12 B.DA12 C.DT2 A-T WC 20-XX cWW cW-W 13 B.DC13 C.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 12 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3vxx T-lys B.DT6 A.LYS92 12.85 -95.49 -4.12 10.95 5.31 5.20 5.70 -95.25 2 3vxx C-arg B.5CM9 A.ARG84 11.51 165.88 -4.75 -10.22 -2.32 -33.48 48.61 163.77 3 3vxx C-arg B.5CM9 A.ARG106 10.11 -147.88 -6.64 7.14 2.69 -39.05 21.87 -145.18 4 3vxx G-arg B.DG10 A.ARG106 -10.53 -178.96 -3.35 9.97 -0.33 -27.71 34.53 -178.87 5 3vxx G-arg B.DG11 A.ARG106 -11.38 149.72 -1.02 -10.89 -3.12 14.10 -38.86 147.59 6 3vxx T-lys C.DT2 A.LYS104 14.39 -157.05 -3.90 13.65 -2.39 1.38 87.03 -148.15 7 3vxx C-arg C.DC3 A.ARG106 11.29 -154.96 -0.22 10.82 3.21 16.68 58.34 -150.91 8 3vxx C-arg C.5CM4 A.ARG84 11.24 -131.54 -6.04 7.22 6.15 -9.65 -53.92 -124.94 9 3vxx C-asp C.5CM4 A.ASP94 10.05 -159.20 -3.40 9.46 -0.08 51.17 11.02 -156.80 10 3vxx C-arg C.5CM4 A.ARG106 10.28 -174.66 2.63 9.90 0.94 32.06 39.22 -174.09 11 3vxx G-arg C.DG5 A.ARG84 -11.69 -161.10 -4.94 10.35 2.24 -37.96 -44.41 -158.32 12 3vxx G-thr C.DG5 A.THR89 10.11 -116.87 -4.30 9.11 0.89 17.09 -8.15 -115.89 **************************************************************************** List of 9 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 3vxx AT-lys C.DA8 B.DT6 A.LYS92 -12.79 95.00 -4.30 -10.75 -5.43 7.75 -1.07 94.76 2 3vxx AT-lys B.DA12 C.DT2 A.LYS104 -14.37 148.85 -4.16 -13.66 1.64 5.80 -74.96 140.39 3 3vxx GC-arg C.DG5 B.5CM9 A.ARG84 -11.59 -163.49 -4.84 10.28 2.28 -35.73 -46.51 -161.04 4 3vxx GC-arg C.DG5 B.5CM9 A.ARG106 -10.10 147.18 -6.50 -7.15 -2.94 -35.40 -22.96 144.74 5 3vxx GC-arg B.DG10 C.5CM4 A.ARG84 -11.21 132.67 -5.83 -7.62 -5.80 -14.25 53.77 126.02 6 3vxx GC-arg B.DG10 C.5CM4 A.ARG106 -10.41 177.82 2.99 -9.95 -0.64 29.93 -36.82 177.62 7 3vxx GC-arg B.DG11 C.DC3 A.ARG106 -11.33 152.27 -0.62 -10.86 -3.19 15.36 -48.61 149.21 8 3vxx GC-asp B.DG10 C.5CM4 A.ASP94 -10.10 161.33 -3.07 -9.61 0.48 48.06 -8.73 159.48 9 3vxx GC-thr C.DG5 B.5CM9 A.THR89 9.99 -117.44 -4.30 8.98 0.83 18.66 -11.59 -116.14 **************************************************************************** List of 10 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 3vxx OP1@B.DC8 N@A.ARG109 2.76 po4:backbone 2 3vxx OP2@B.DC8 N@A.LYS108 3.19 po4:backbone 3 3vxx OP1@B.5CM9 OG@A.SER107 2.49 po4:sidechain 4 3vxx OP2@C.DC3 NZ@A.LYS82 2.86 po4:sidechain:salt-bridge 5 3vxx OP1@C.5CM4 N@A.LEU85 2.73 po4:backbone 6 3vxx OP1@C.5CM4 N@A.SER86 3.06 po4:backbone 7 3vxx OP1@C.DG5 N@A.LYS88 2.97 po4:backbone 8 3vxx OP2@C.DG5 N@A.THR89 2.99 po4:backbone 9 3vxx OP2@C.DG5 OG1@A.THR89 2.73 po4:sidechain 10 3vxx OP2@C.DG6 NZ@A.LYS88 2.60 po4:sidechain:salt-bridge **************************************************************************** List of 4 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 3vxx N7@B.DG10 NH2@A.ARG106 3.21 base:sidechain 2 3vxx O6@B.DG10 NH1@A.ARG106 2.61 base:sidechain 3 3vxx N7@C.DG5 NH1@A.ARG84 2.80 base:sidechain 4 3vxx O6@C.DG5 NH2@A.ARG84 2.86 base:sidechain **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 3vxx G-arg B.DG10 A.ARG106 0.19 14 2 3vxx G-arg C.DG5 A.ARG84 0.08 25 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 3vxx C-arg B.5CM9 A.ARG106 3.49 10 2 3vxx C-arg C.5CM4 A.ARG84 3.70 14 **************************************************************************** List of 3 additional files 1 -- 3vxx-baseAA-pairs.pdb 2 -- 3vxx-baseAA-stacks.pdb 3 -- 3vxx-pairs.pdb