**************************************************************************** SNAP: a software tool for the characterization of 3D Structures of Nucleic Acid-Protein complexes v1.0.6-2019sep30, by xiangjun@x3dna.org SNAP has been made possible by the NIH grant R01GM096889 (to X.J.Lu). It is being actively maintained and developed. As always, I greatly appreciate your feedback. Please report all SNAP-related issues on the 3DNA Forum (forum.x3dna.org). I strive to respond promptly to any questions posted there. SNAP is free of charge for NON-COMMERCIAL purposes, and it comes with ABSOLUTELY NO WARRANTY. **************************************************************************** Note: By default, each nucleotide/amino-acid is identified by chainId.name#. So a common case would be B.DA1689, meaning adenosine #1689 on chain B. Use the --idstr=long option to get strictly delineated id strings. Command: x3dna-snap -i=6cnp.pdb -o=6cnp.out File name: 6cnp.pdb no. of peptide chains: 2 [A=68,B=58] no. of DNA/RNA chains: 4 [C=12,D=12,E=12,F=12] no. of amino acids: 126 no. of nucleotides: 48 no. of atoms: 1968 no. of waters: 34 no. of metals: 1 [Ca=1] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 C.5CM6,D.5CM6,E.5CM6,F.5CM6 **************************************************************************** List of 2 helices 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=12 strand-1 5'-GCCACcGGTGGC-3' bp-type |||||||||||| strand-2 3'-CGGTGGcCACCG-5' helix-form BB.BBBBB.BB 1 C.DG1 D.DC12 G-C WC 19-XIX cWW cW-W 2 C.DC2 D.DG11 C-G WC 19-XIX cWW cW-W 3 C.DC3 D.DG10 C-G WC 19-XIX cWW cW-W 4 C.DA4 D.DT9 A-T WC 20-XX cWW cW-W 5 C.DC5 D.DG8 C-G WC 19-XIX cWW cW-W 6 C.5CM6 D.DG7 c-G WC 19-XIX cWW cW-W 7 C.DG7 D.5CM6 G-c WC 19-XIX cWW cW-W 8 C.DG8 D.DC5 G-C WC 19-XIX cWW cW-W 9 C.DT9 D.DA4 T-A WC 20-XX cWW cW-W 10 C.DG10 D.DC3 G-C WC 19-XIX cWW cW-W 11 C.DG11 D.DC2 G-C WC 19-XIX cWW cW-W 12 C.DC12 D.DG1 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=12 strand-1 5'-GCCACcGGTGGC-3' bp-type |||||||||||| strand-2 3'-CGGTGGcCACCG-5' helix-form BB.BBBBB.BB 1 E.DG1 F.DC12 G-C WC 19-XIX cWW cW-W 2 E.DC2 F.DG11 C-G WC 19-XIX cWW cW-W 3 E.DC3 F.DG10 C-G WC 19-XIX cWW cW-W 4 E.DA4 F.DT9 A-T WC 20-XX cWW cW-W 5 E.DC5 F.DG8 C-G WC 19-XIX cWW cW-W 6 E.5CM6 F.DG7 c-G WC 19-XIX cWW cW-W 7 E.DG7 F.5CM6 G-c WC 19-XIX cWW cW-W 8 E.DG8 F.DC5 G-C WC 19-XIX cWW cW-W 9 E.DT9 F.DA4 T-A WC 20-XX cWW cW-W 10 E.DG10 F.DC3 G-C WC 19-XIX cWW cW-W 11 E.DG11 F.DC2 G-C WC 19-XIX cWW cW-W 12 E.DC12 F.DG1 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 24 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cnp A-lys C.DA4 A.LYS186 13.00 -155.13 -6.99 10.20 -4.04 -7.82 79.19 -147.45 2 6cnp C-tyr C.DC5 A.TYR178 13.39 -155.50 -5.36 11.13 -5.18 50.89 58.14 -148.48 3 6cnp C-arg C.DC5 A.ARG188 10.79 -145.92 -2.10 10.18 2.90 0.34 64.15 -139.53 4 6cnp C-arg C.5CM6 A.ARG166 11.54 -126.52 -6.14 7.77 5.92 -10.01 -62.51 -116.19 5 6cnp C-asp C.5CM6 A.ASP176 10.45 -149.54 -3.91 9.67 -0.56 46.53 10.06 -146.63 6 6cnp C-tyr C.5CM6 A.TYR178 12.94 -172.91 -1.02 10.59 -7.37 67.40 37.36 -170.93 7 6cnp C-arg C.5CM6 A.ARG188 10.02 -167.11 1.95 9.81 0.54 19.66 54.68 -165.24 8 6cnp G-arg C.DG7 A.ARG166 -11.46 -162.35 -4.51 10.16 2.78 -35.84 -54.44 -159.02 9 6cnp C-arg D.5CM6 A.ARG166 11.25 166.37 -4.71 -9.84 -2.72 -31.35 63.35 163.27 10 6cnp C-asp D.5CM6 A.ASP176 -9.18 -174.33 0.17 8.58 3.25 -50.75 -15.95 -173.66 11 6cnp C-arg D.5CM6 A.ARG188 9.76 -159.28 -6.72 6.94 1.40 -42.86 36.19 -156.49 12 6cnp G-arg D.DG7 A.ARG188 -10.34 170.89 2.44 -10.00 -1.00 23.82 -52.99 169.58 13 6cnp C-tyr E.DC5 B.TYR178 13.69 -155.64 -5.00 11.45 -5.58 53.92 57.30 -148.34 14 6cnp C-arg E.DC5 B.ARG188 11.02 -145.45 -1.72 10.52 2.80 -1.57 62.75 -139.29 15 6cnp C-arg E.5CM6 B.ARG166 11.57 -125.89 -6.12 7.79 5.97 -9.64 -59.53 -116.52 16 6cnp C-asp E.5CM6 B.ASP176 10.14 -151.12 -3.58 9.46 -0.61 47.22 10.64 -148.27 17 6cnp C-tyr E.5CM6 B.TYR178 12.75 -174.40 -0.68 10.34 -7.43 71.00 34.43 -172.75 18 6cnp C-arg E.5CM6 B.ARG188 9.82 -168.87 2.32 9.54 0.44 18.72 53.37 -167.35 19 6cnp G-arg E.DG7 B.ARG166 -11.66 -159.38 -4.60 10.37 2.68 -32.99 -54.77 -155.64 20 6cnp C-arg F.DC5 B.ARG166 12.51 -174.21 3.20 12.06 -0.99 34.95 -46.91 -173.36 21 6cnp C-arg F.5CM6 B.ARG166 11.21 162.20 -4.85 -9.75 -2.65 -28.30 62.02 158.46 22 6cnp C-asp F.5CM6 B.ASP176 -9.03 -177.10 0.12 8.39 3.34 -51.45 -13.88 -176.76 23 6cnp C-arg F.5CM6 B.ARG188 9.89 -160.89 -6.80 7.03 1.51 -39.51 36.50 -158.55 24 6cnp G-arg F.DG7 B.ARG188 -10.30 168.49 2.59 -9.92 -0.93 21.10 -48.61 167.14 **************************************************************************** List of 20 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6cnp AT-lys C.DA4 D.DT9 A.LYS186 12.89 -151.62 -7.09 10.08 -3.77 -6.55 75.88 -143.71 2 6cnp GC-arg D.DG8 C.DC5 A.ARG188 -11.04 141.45 -2.44 -10.20 -3.46 2.74 -60.50 135.05 3 6cnp GC-arg D.DG7 C.5CM6 A.ARG166 -11.51 129.27 -5.79 -7.94 -5.98 -10.90 62.94 119.37 4 6cnp GC-arg D.DG7 C.5CM6 A.ARG188 -10.18 169.00 2.19 -9.91 -0.77 21.75 -53.87 167.41 5 6cnp GC-arg C.DG7 D.5CM6 A.ARG166 -11.35 -164.34 -4.62 10.00 2.74 -33.66 -58.93 -161.10 6 6cnp GC-arg C.DG7 D.5CM6 A.ARG188 -9.80 156.25 -6.72 -6.89 -1.88 -39.52 -38.90 153.11 7 6cnp GC-arg F.DG8 E.DC5 B.ARG188 -11.22 142.19 -1.94 -10.57 -3.21 0.17 -58.75 136.34 8 6cnp GC-arg F.DG7 E.5CM6 B.ARG166 -11.50 127.43 -5.97 -7.95 -5.79 -10.17 61.94 117.50 9 6cnp GC-arg F.DG7 E.5CM6 B.ARG188 -10.06 168.67 2.46 -9.73 -0.68 19.93 -51.00 167.24 10 6cnp GC-arg E.DG7 F.5CM6 B.ARG166 -11.43 -160.77 -4.73 10.06 2.67 -30.70 -58.43 -157.03 11 6cnp GC-arg E.DG7 F.5CM6 B.ARG188 -10.01 158.13 -6.77 -7.10 -1.97 -36.57 -38.35 155.53 12 6cnp GC-arg E.DG8 F.DC5 B.ARG166 -12.76 173.05 3.05 -12.37 0.74 38.23 45.91 171.99 13 6cnp GC-asp D.DG7 C.5CM6 A.ASP176 -10.55 151.81 -3.58 -9.91 0.43 47.56 -8.49 149.04 14 6cnp GC-asp C.DG7 D.5CM6 A.ASP176 9.31 172.37 0.23 -8.64 -3.47 -47.31 12.61 171.62 15 6cnp GC-asp F.DG7 E.5CM6 B.ASP176 -10.24 150.84 -3.37 -9.66 0.63 47.84 -8.04 147.94 16 6cnp GC-asp E.DG7 F.5CM6 B.ASP176 9.29 175.29 0.17 -8.56 -3.61 -48.29 11.51 174.81 17 6cnp GC-tyr D.DG8 C.DC5 A.TYR178 -13.56 150.68 -5.48 -11.45 4.76 53.42 -56.24 142.11 18 6cnp GC-tyr D.DG7 C.5CM6 A.TYR178 -13.06 174.61 -0.70 -10.85 7.23 69.11 -35.54 173.07 19 6cnp GC-tyr F.DG8 E.DC5 B.TYR178 -13.81 151.50 -4.99 -11.74 5.30 55.70 -54.71 143.05 20 6cnp GC-tyr F.DG7 E.5CM6 B.TYR178 -12.94 173.43 -0.37 -10.64 7.35 72.13 -32.07 171.49 **************************************************************************** List of 22 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cnp OP2@C.DA4 NZ@A.LYS186 2.57 po4:sidechain:salt-bridge 2 6cnp OP1@C.5CM6 N@A.LYS167 2.86 po4:backbone 3 6cnp OP1@C.5CM6 N@A.SER168 2.77 po4:backbone 4 6cnp OP1@C.DG7 N@A.LEU170 2.80 po4:backbone 5 6cnp OP2@C.DG7 N@A.SER171 2.99 po4:backbone 6 6cnp OP2@C.DG7 OG@A.SER171 2.32 po4:sidechain 7 6cnp OP2@D.DA4 NE@A.ARG209 3.15 po4:sidechain:salt-bridge 8 6cnp OP2@D.DC5 N@A.LYS190 3.80 po4:backbone 9 6cnp OP2@D.5CM6 OG@A.SER189 2.39 po4:sidechain 10 6cnp OP2@E.DA4 NZ@B.LYS186 3.22 po4:sidechain:salt-bridge 11 6cnp OP1@E.5CM6 N@B.SER168 2.89 po4:backbone 12 6cnp OP1@E.5CM6 OG@B.SER168 2.92 po4:sidechain 13 6cnp OP2@E.5CM6 N@B.LYS167 3.14 po4:backbone 14 6cnp OP1@E.DG7 N@B.LEU170 2.94 po4:backbone 15 6cnp OP2@E.DG7 N@B.SER171 3.00 po4:backbone 16 6cnp OP2@E.DG7 OG@B.SER171 2.52 po4:sidechain 17 6cnp OP2@E.DG8 NZ@A.LYS185 2.95 po4:sidechain:salt-bridge 18 6cnp OP2@F.DA4 N@B.THR210 3.50 po4:backbone 19 6cnp OP2@F.DC5 N@B.LYS190 3.54 po4:backbone 20 6cnp OP1@F.5CM6 NH1@B.ARG195 2.80 po4:sidechain:salt-bridge 21 6cnp OP2@F.5CM6 OG@B.SER189 2.48 po4:sidechain 22 6cnp OP2@F.5CM6 NH2@B.ARG195 3.60 po4:sidechain:salt-bridge **************************************************************************** List of 8 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6cnp N7@C.DG7 NH1@A.ARG166 2.64 base:sidechain 2 6cnp O6@C.DG7 NH2@A.ARG166 2.73 base:sidechain 3 6cnp N7@D.DG7 NH2@A.ARG188 3.12 base:sidechain 4 6cnp O6@D.DG7 NH1@A.ARG188 2.68 base:sidechain 5 6cnp N7@E.DG7 NH1@B.ARG166 2.83 base:sidechain 6 6cnp O6@E.DG7 NH2@B.ARG166 2.82 base:sidechain 7 6cnp N7@F.DG7 NH2@B.ARG188 3.23 base:sidechain 8 6cnp O6@F.DG7 NH1@B.ARG188 2.75 base:sidechain **************************************************************************** List of 4 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6cnp G-arg C.DG7 A.ARG166 0.52 16 2 6cnp G-arg D.DG7 A.ARG188 0.08 8 3 6cnp G-arg E.DG7 B.ARG166 0.36 14 4 6cnp G-arg F.DG7 B.ARG188 0.24 9 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6cnp C-arg C.5CM6 A.ARG166 3.67 13 2 6cnp C-arg D.5CM6 A.ARG188 3.46 5 3 6cnp C-arg E.5CM6 B.ARG166 3.67 12 4 6cnp C-arg F.5CM6 B.ARG188 3.57 8