**************************************************************************** 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=6c1t.pdb -o=6c1t.out File name: 6c1t.pdb no. of peptide chains: 2 [A=68,D=66] no. of DNA/RNA chains: 2 [B=12,C=12] no. of amino acids: 134 no. of nucleotides: 24 no. of atoms: 1559 no. of waters: 41 no. of metals: 0 **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 B.5CM6 **************************************************************************** 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=12 strand-1 5'-GCCTAcACTCCG-3' bp-type |||||||||||| strand-2 3'-CGGATGTGAGGC-5' helix-form BBB.BBBB.BB 1 B.DG1 C.DC12 G-C WC 19-XIX cWW cW-W 2 B.DC2 C.DG11 C-G WC 19-XIX cWW cW-W 3 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 4 B.DT4 C.DA9 T-A WC 20-XX cWW cW-W 5 B.DA5 C.DT8 A-T WC 20-XX cWW cW-W 6 B.5CM6 C.DG7 c-G WC 19-XIX cWW cW-W 7 B.DA7 C.DT6 A-T WC 20-XX cWW cW-W 8 B.DC8 C.DG5 C-G WC 19-XIX cWW cW-W 9 B.DT9 C.DA4 T-A WC 20-XX cWW cW-W 10 B.DC10 C.DG3 C-G WC 19-XIX cWW cW-W 11 B.DC11 C.DG2 C-G WC 19-XIX cWW cW-W 12 B.DG12 C.DC1 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 23 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6c1t A-arg B.DA5 A.ARG166 12.28 -177.89 3.13 11.81 -1.25 38.22 -42.23 -177.60 2 6c1t C-arg B.5CM6 A.ARG166 11.43 163.84 -4.25 -10.18 -2.99 -33.77 57.52 160.63 3 6c1t C-arg B.5CM6 A.ARG188 9.82 -157.95 -6.91 6.77 1.65 -42.37 32.36 -155.29 4 6c1t A-arg B.DA7 A.ARG188 -10.01 166.22 2.38 -9.65 -1.14 25.99 -46.74 164.56 5 6c1t C-arg B.DC10 D.ARG166 11.90 178.50 -1.96 -11.72 -0.50 -44.85 42.16 178.25 6 6c1t C-arg B.DC11 D.ARG166 11.06 157.62 -3.88 -9.94 -2.89 -37.74 57.06 152.86 7 6c1t C-asp B.DC11 D.ASP176 -9.01 -177.65 -0.26 8.33 3.43 -49.12 -17.94 -177.38 8 6c1t C-arg B.DC11 D.ARG188 9.86 -161.81 -7.09 6.73 1.26 -39.73 26.60 -160.08 9 6c1t G-arg B.DG12 D.ARG188 -10.00 164.55 3.34 -9.32 -1.42 24.31 -36.23 163.35 10 6c1t C-arg C.DC1 D.ARG166 10.97 -123.78 -5.67 7.40 5.77 -17.26 -64.43 -111.32 11 6c1t C-asp C.DC1 D.ASP176 9.51 -146.87 -3.02 9.01 -0.52 50.14 1.54 -143.30 12 6c1t C-arg C.DC1 D.ARG188 9.70 -162.61 3.00 9.12 1.40 25.95 39.83 -160.98 13 6c1t G-arg C.DG2 D.ARG166 -11.49 -153.28 -4.13 10.40 2.61 -41.95 -54.87 -147.42 14 6c1t G-arg C.DG3 D.ARG166 -12.20 -179.49 -2.08 12.02 -0.23 -51.23 -49.22 -179.37 15 6c1t A-arg C.DA4 A.ARG188 13.11 -111.06 -5.76 9.84 6.46 -20.22 58.89 -97.22 16 6c1t G-tyr C.DG5 A.TYR178 13.13 -148.10 -4.91 11.48 -4.06 53.02 56.44 -138.75 17 6c1t G-arg C.DG5 A.ARG188 10.86 -137.59 -1.61 10.04 3.81 4.88 57.23 -131.29 18 6c1t T-arg C.DT6 A.ARG166 11.72 -122.94 -5.96 7.90 6.28 -14.04 -59.48 -112.63 19 6c1t T-asp C.DT6 A.ASP176 10.37 -150.58 -4.00 9.55 -0.47 47.36 7.67 -147.73 20 6c1t T-tyr C.DT6 A.TYR178 12.74 -172.20 -0.84 10.67 -6.91 66.24 35.25 -170.17 21 6c1t T-arg C.DT6 A.ARG188 9.90 -166.38 2.16 9.64 0.65 20.36 49.65 -164.73 22 6c1t G-arg C.DG7 A.ARG166 -11.66 -159.28 -4.02 10.41 3.38 -34.97 -46.36 -156.26 23 6c1t T-arg C.DT8 A.ARG166 -12.24 174.83 3.02 -11.82 1.07 41.27 45.24 173.99 **************************************************************************** List of 17 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6c1t AT-arg B.DA5 C.DT8 A.ARG166 12.26 -176.35 3.07 11.81 -1.16 39.73 -43.75 -175.80 2 6c1t AT-arg B.DA7 C.DT6 A.ARG166 -11.68 125.60 -5.91 -7.91 -6.24 -13.25 61.47 115.22 3 6c1t AT-arg B.DA7 C.DT6 A.ARG188 -9.95 166.30 2.28 -9.65 -0.89 23.20 -48.23 164.64 4 6c1t AT-arg C.DA4 B.DT9 A.ARG188 13.08 -107.17 -5.94 9.40 6.90 -12.56 53.83 -95.85 5 6c1t AT-asp B.DA7 C.DT6 A.ASP176 -10.36 151.23 -3.86 -9.61 0.39 49.67 -5.63 148.18 6 6c1t AT-tyr B.DA7 C.DT6 A.TYR178 -12.78 172.00 -0.63 -10.86 6.70 69.00 -33.63 169.79 7 6c1t GC-arg C.DG7 B.5CM6 A.ARG166 -11.54 -161.54 -4.14 10.29 3.18 -34.41 -51.95 -158.39 8 6c1t GC-arg C.DG7 B.5CM6 A.ARG188 -9.85 155.30 -6.84 -6.75 -2.19 -39.58 -36.87 152.21 9 6c1t GC-arg C.DG5 B.DC8 A.ARG188 10.79 -134.69 -1.87 9.75 4.23 9.10 53.74 -128.65 10 6c1t GC-arg C.DG3 B.DC10 D.ARG166 -12.05 -179.00 -2.03 11.88 0.14 -48.04 -45.69 -178.80 11 6c1t GC-arg C.DG2 B.DC11 D.ARG166 -11.28 -155.44 -4.00 10.17 2.75 -39.85 -55.97 -150.15 12 6c1t GC-arg C.DG2 B.DC11 D.ARG188 -9.90 161.41 -6.95 -6.87 -1.57 -36.55 -26.96 159.83 13 6c1t GC-arg B.DG12 C.DC1 D.ARG166 -10.90 124.38 -5.51 -7.58 -5.56 -19.48 65.20 111.49 14 6c1t GC-arg B.DG12 C.DC1 D.ARG188 -9.85 163.57 3.17 -9.22 -1.41 25.14 -38.02 162.17 15 6c1t GC-asp C.DG2 B.DC11 D.ASP176 -9.21 178.32 -0.08 -8.42 -3.73 -46.19 16.93 178.15 16 6c1t GC-asp B.DG12 C.DC1 D.ASP176 -9.57 147.13 -2.81 -9.12 0.66 48.73 0.21 143.81 17 6c1t GC-tyr C.DG5 B.DC8 A.TYR178 13.06 -144.90 -5.00 11.52 -3.59 57.20 53.80 -134.16 **************************************************************************** List of 17 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6c1t OP1@B.DT4 NE@A.ARG209 3.36 po4:sidechain:salt-bridge 2 6c1t OP2@B.DT4 NH2@A.ARG209 3.30 po4:sidechain:salt-bridge 3 6c1t OP2@B.DA5 N@A.LYS190 3.29 po4:backbone 4 6c1t OP2@B.5CM6 OG@A.SER189 2.48 po4:sidechain 5 6c1t OP1@B.DT9 NE@D.ARG209 3.01 po4:sidechain:salt-bridge 6 6c1t OP2@B.DT9 NH2@D.ARG209 3.00 po4:sidechain:salt-bridge 7 6c1t OP2@B.DC10 N@D.LYS190 3.26 po4:backbone 8 6c1t OP2@B.DC11 OG@D.SER189 2.62 po4:sidechain 9 6c1t OP1@C.DG2 N@D.LEU170 2.90 po4:backbone 10 6c1t OP2@C.DG2 N@D.SER171 2.83 po4:backbone 11 6c1t OP2@C.DG2 OG@D.SER171 2.73 po4:sidechain 12 6c1t OP2@C.DA4 NZ@A.LYS186 2.81 po4:sidechain:salt-bridge 13 6c1t OP1@C.DT6 N@A.SER168 3.19 po4:backbone 14 6c1t OP1@C.DT6 OG@A.SER168 2.74 po4:sidechain 15 6c1t OP2@C.DT6 N@A.LYS167 2.99 po4:backbone 16 6c1t OP2@C.DG7 N@A.LEU170 3.06 po4:backbone 17 6c1t OP2@C.DG7 N@A.SER171 3.76 po4:backbone **************************************************************************** List of 8 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6c1t N7@B.DG12 NH2@D.ARG188 2.95 base:sidechain 2 6c1t O6@B.DG12 NH1@D.ARG188 2.71 base:sidechain 3 6c1t N7@C.DG2 NH1@D.ARG166 2.75 base:sidechain 4 6c1t O6@C.DG2 NH2@D.ARG166 2.82 base:sidechain 5 6c1t N7@C.DA4 NH2@A.ARG188 3.14 base:sidechain 6 6c1t O6@C.DG5 NH1@A.ARG188 2.71 base:sidechain 7 6c1t N7@C.DG7 NH1@A.ARG166 2.90 base:sidechain 8 6c1t O6@C.DG7 NH2@A.ARG166 2.92 base:sidechain **************************************************************************** List of 3 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6c1t G-arg B.DG12 D.ARG188 0.03 8 2 6c1t G-arg C.DG2 D.ARG166 0.43 16 3 6c1t G-arg C.DG7 A.ARG166 0.47 7 **************************************************************************** List of 3 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6c1t C-arg B.DC11 D.ARG188 3.30 3 2 6c1t C-arg C.DC1 D.ARG166 3.53 12 3 6c1t T-arg C.DT6 A.ARG166 3.65 6