**************************************************************************** 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/4x9j.pdb -o=4x9j.out --type=base File name: 4x9j.pdb no. of peptide chains: 1 [A=86] no. of DNA/RNA chains: 2 [B=11,C=11] no. of amino acids: 86 no. of nucleotides: 22 no. of atoms: 2344 no. of waters: 208 no. of metals: 3 [Zn=3] **************************************************************************** List of 1 type of 4 modified nucleotides nt count list 1 5CM-c 4 B.5CM3,B.5CM9,C.5CM53,C.5CM59 **************************************************************************** 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=10 strand-1 5'-GcGTGGGcGT-3' bp-type |||||||||| strand-2 3'-CGcACCCGcA-5' helix-form ..BB.BBBB 1 B.DG2 C.DC61 G-C WC 19-XIX cWW cW-W 2 B.5CM3 C.DG60 c-G WC 19-XIX cWW cW-W 3 B.DG4 C.5CM59 G-c WC 19-XIX cWW cW-W 4 B.DT5 C.DA58 T-A WC 20-XX cWW cW-W 5 B.DG6 C.DC57 G-C WC 19-XIX cWW cW-W 6 B.DG7 C.DC56 G-C WC 19-XIX cWW cW-W 7 B.DG8 C.DC55 G-C WC 19-XIX cWW cW-W 8 B.5CM9 C.DG54 c-G WC 19-XIX cWW cW-W 9 B.DG10 C.5CM53 G-c WC 19-XIX cWW cW-W 10 B.DT11 C.DA52 T-A WC 20-XX cWW cW-W **************************************************************************** List of 41 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4x9j A-arg B.DA1 A.ARG180 -7.61 81.59 -6.41 -0.03 -4.10 -62.17 -32.11 44.94 2 4x9j G-glu B.DG2 A.GLU177 9.82 157.39 3.26 -2.69 8.87 13.75 79.94 150.10 3 4x9j G-arg B.DG2 A.ARG180 11.16 -154.03 -3.20 10.58 1.59 -7.76 58.45 -150.09 4 4x9j C-arg B.5CM3 A.ARG174 11.13 -139.04 -4.16 9.33 4.43 23.52 -50.60 -133.36 5 4x9j C-glu B.5CM3 A.GLU177 8.68 137.50 5.26 -2.57 6.40 26.71 81.42 120.75 6 4x9j C-arg B.5CM3 A.ARG180 -10.19 -174.03 -0.27 10.08 -1.46 4.71 51.08 -173.37 7 4x9j G-arg B.DG4 A.ARG174 11.17 -171.79 -2.67 10.65 2.06 16.93 -51.98 -170.76 8 4x9j T-his B.DT5 A.HIS149 9.15 164.89 3.65 -2.89 7.88 -10.65 88.63 158.71 9 4x9j T-thr B.DT5 A.THR152 10.86 -133.12 -2.75 10.23 2.42 -22.81 51.66 -126.31 10 4x9j T-arg B.DT5 A.ARG174 9.94 158.76 1.73 -9.78 0.51 -9.48 63.08 154.93 11 4x9j G-arg B.DG6 A.ARG146 10.77 -148.13 -3.87 9.56 3.11 33.36 -39.99 -144.42 12 4x9j G-his B.DG6 A.HIS149 9.06 139.92 4.88 -5.10 5.68 15.51 79.16 126.57 13 4x9j G-arg B.DG7 A.ARG124 12.61 -123.54 -7.07 9.32 4.71 -22.54 57.82 -112.99 14 4x9j G-arg B.DG7 A.ARG146 11.09 178.97 3.29 -10.57 0.68 -22.06 46.05 178.85 15 4x9j G-glu B.DG8 A.GLU121 9.72 154.56 3.80 -2.71 8.53 -0.82 83.45 145.68 16 4x9j G-arg B.DG8 A.ARG124 11.28 -149.23 -3.35 10.69 1.34 -5.90 57.37 -144.74 17 4x9j G-arg B.DG8 A.ARG146 -10.46 150.33 1.99 -10.11 -1.83 -11.11 53.96 146.43 18 4x9j C-arg B.5CM9 A.ARG118 10.84 -145.32 -4.75 8.89 3.96 24.10 -50.25 -140.59 19 4x9j C-asp B.5CM9 A.ASP120 9.25 -155.70 -2.84 7.10 5.21 -27.56 23.67 -154.40 20 4x9j C-glu B.5CM9 A.GLU121 8.53 130.65 5.50 -2.52 6.02 20.37 85.79 108.93 21 4x9j C-arg B.5CM9 A.ARG124 -10.02 -177.43 0.28 9.84 -1.85 9.61 50.29 -177.15 22 4x9j G-arg B.DG10 A.ARG118 11.13 -173.57 -3.36 10.57 0.92 12.47 -56.84 -172.64 23 4x9j T-arg B.DT11 A.ARG118 -10.41 157.01 2.34 -10.07 -1.24 1.74 62.54 153.03 24 4x9j T-ser C.DT51 A.SER119 10.70 -160.44 -7.21 6.18 -4.94 68.47 32.60 -155.14 25 4x9j T-asp C.DT51 A.ASP120 8.82 -114.75 -5.73 5.92 3.16 -22.07 34.83 -109.65 26 4x9j A-arg C.DA52 A.ARG118 10.40 -153.56 2.23 10.15 0.39 -7.77 -57.86 -149.63 27 4x9j A-asp C.DA52 A.ASP120 8.41 -149.18 -3.00 7.86 -0.06 -2.54 33.07 -147.81 28 4x9j C-arg C.5CM53 A.ARG118 -10.84 178.67 -2.94 -10.29 -1.74 19.78 58.54 178.45 29 4x9j C-asp C.5CM53 A.ASP120 -9.29 -176.35 -0.41 8.71 -3.22 8.52 27.87 -176.22 30 4x9j G-arg C.DG54 A.ARG124 -10.20 175.36 0.36 -10.13 1.18 15.93 -47.44 174.87 31 4x9j G-ser C.DG54 A.SER147 10.27 -158.59 -7.50 5.56 -4.30 69.16 25.87 -153.13 32 4x9j G-asp C.DG54 A.ASP148 8.88 -119.55 -6.80 5.00 2.75 -21.93 30.53 -115.75 33 4x9j C-arg C.DC55 A.ARG146 -10.52 -143.98 1.49 10.40 0.51 -21.71 -54.44 -138.47 34 4x9j C-asp C.DC55 A.ASP148 -8.92 -150.51 -4.11 7.90 -0.45 -14.18 36.58 -148.64 35 4x9j C-arg C.DC56 A.ARG146 -10.93 -174.49 2.92 10.45 -1.33 -30.05 -54.96 -173.54 36 4x9j C-asp C.DC56 A.ASP148 -9.38 -176.63 -1.03 8.78 -3.13 1.57 30.95 -176.51 37 4x9j A-arg C.DA58 A.ARG174 -9.95 -159.66 1.90 9.75 -0.54 -11.20 -50.84 -157.34 38 4x9j A-asp C.DA58 A.ASP176 8.03 -157.93 -2.71 7.55 -0.48 -3.85 44.19 -156.14 39 4x9j C-arg C.5CM59 A.ARG174 -10.90 174.35 -2.47 -10.29 -2.63 22.36 54.11 173.53 40 4x9j C-asp C.5CM59 A.ASP176 -9.27 177.49 0.21 -8.51 -3.67 -7.14 -36.41 177.35 41 4x9j G-arg C.DG60 A.ARG180 -10.51 172.13 -0.24 -10.47 0.97 9.96 -57.22 171.00 **************************************************************************** List of 30 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4x9j AT-arg C.DA58 B.DT5 A.ARG174 -9.94 -159.14 1.81 9.76 -0.53 -10.45 -56.97 -156.11 2 4x9j AT-arg C.DA52 B.DT11 A.ARG118 10.40 -155.26 2.29 10.12 0.81 -3.05 -60.28 -151.30 3 4x9j AT-asp C.DA58 B.DT5 A.ASP176 -7.99 -156.02 -2.71 7.49 -0.68 -4.57 38.15 -154.58 4 4x9j AT-asp C.DA52 B.DT11 A.ASP120 8.37 -146.72 -3.01 7.81 0.17 1.57 30.50 -145.46 5 4x9j AT-his C.DA58 B.DT5 A.HIS149 -9.07 -164.74 3.27 2.81 -7.98 -12.09 -82.52 -159.52 6 4x9j AT-thr C.DA58 B.DT5 A.THR152 -10.82 129.75 -2.83 -10.03 -2.90 -20.14 -55.63 121.55 7 4x9j GC-arg B.DG2 C.DC61 A.ARG180 11.06 -152.90 -3.24 10.42 1.79 -6.17 57.14 -149.00 8 4x9j GC-arg C.DG60 B.5CM3 A.ARG174 -11.13 140.93 -3.91 -9.31 -4.70 26.84 48.78 135.57 9 4x9j GC-arg C.DG60 B.5CM3 A.ARG180 10.35 173.07 -0.25 -10.28 1.22 7.32 -54.16 172.20 10 4x9j GC-arg B.DG4 C.5CM59 A.ARG174 11.03 -173.07 -2.57 10.47 2.35 19.64 -53.06 -172.13 11 4x9j GC-arg B.DG6 C.DC57 A.ARG146 10.63 -149.98 -3.69 9.28 3.63 38.25 -40.49 -145.94 12 4x9j GC-arg B.DG7 C.DC56 A.ARG124 12.53 -123.07 -7.17 9.28 4.43 -20.17 52.06 -114.72 13 4x9j GC-arg B.DG7 C.DC56 A.ARG146 11.01 176.69 3.10 -10.52 1.00 -26.09 50.47 176.23 14 4x9j GC-arg B.DG8 C.DC55 A.ARG124 11.30 -147.16 -3.43 10.61 1.83 -0.93 53.73 -143.05 15 4x9j GC-arg B.DG8 C.DC55 A.ARG146 -10.49 147.11 1.75 -10.28 -1.18 -16.41 54.22 142.48 16 4x9j GC-arg C.DG54 B.5CM9 A.ARG118 -10.85 146.89 -4.70 -8.90 -4.05 26.39 52.71 141.80 17 4x9j GC-arg C.DG54 B.5CM9 A.ARG124 10.11 176.39 0.32 -9.99 1.51 12.78 -48.89 176.01 18 4x9j GC-arg B.DG10 C.5CM53 A.ARG118 10.98 -176.12 -3.15 10.44 1.33 16.13 -57.70 -175.52 19 4x9j GC-asp B.DG4 C.5CM59 A.ASP176 9.38 -178.30 0.21 8.73 3.42 -10.05 37.26 -178.20 20 4x9j GC-asp B.DG7 C.DC56 A.ASP148 9.43 176.79 -1.01 -8.97 2.73 6.56 -35.04 176.63 21 4x9j GC-asp B.DG8 C.DC55 A.ASP148 -8.88 149.17 -4.13 -7.87 -0.08 -8.00 -36.92 147.37 22 4x9j GC-asp C.DG54 B.5CM9 A.ASP120 -9.32 155.81 -2.85 -7.06 -5.38 -24.62 -21.79 154.76 23 4x9j GC-asp C.DG54 B.5CM9 A.ASP148 8.83 -118.76 -6.82 4.81 2.86 -18.45 29.98 -115.40 24 4x9j GC-asp B.DG10 C.5CM53 A.ASP120 9.40 175.93 -0.33 -8.95 2.88 12.95 -28.21 175.78 25 4x9j GC-glu B.DG2 C.DC61 A.GLU177 9.73 156.06 3.17 -2.41 8.88 11.80 80.08 148.36 26 4x9j GC-glu C.DG60 B.5CM3 A.GLU177 -8.77 -136.45 5.08 2.72 -6.61 25.96 -77.37 -121.31 27 4x9j GC-glu B.DG8 C.DC55 A.GLU121 9.73 150.02 3.66 -2.23 8.74 -5.25 83.46 139.39 28 4x9j GC-glu C.DG54 B.5CM9 A.GLU121 -8.59 -127.72 5.43 2.47 -6.18 17.97 -84.71 -105.49 29 4x9j GC-his B.DG6 C.DC57 A.HIS149 8.89 136.96 4.48 -4.85 5.95 12.03 75.87 124.17 30 4x9j GC-ser C.DG54 B.5CM9 A.SER147 10.19 -159.05 -7.49 5.63 -4.02 72.67 26.22 -153.09 **************************************************************************** List of 8 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4x9j OP1@B.DG4 ND1@A.HIS153 2.71 po4:sidechain:salt-bridge 2 4x9j OP1@B.DT5 NH2@A.ARG142 3.71 po4:sidechain:salt-bridge 3 4x9j OP2@B.DG6 OG@A.SER145 2.80 po4:sidechain 4 4x9j OP1@B.DG7 NH1@A.ARG114 2.85 po4:sidechain:salt-bridge 5 4x9j OP1@B.DG7 NH2@A.ARG114 3.12 po4:sidechain:salt-bridge 6 4x9j OP1@C.DA52 NH2@A.ARG127 3.11 po4:sidechain:salt-bridge 7 4x9j OP2@C.DC57 NZ@A.LYS179 2.64 po4:sidechain:salt-bridge 8 4x9j O5'@C.DC57 NZ@A.LYS179 3.08 po4:sidechain **************************************************************************** List of 12 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4x9j N7@B.DG2 NH2@A.ARG180 2.88 base:sidechain 2 4x9j O6@B.DG2 NH1@A.ARG180 2.91 base:sidechain 3 4x9j N7@B.DG4 NH1@A.ARG174 2.92 base:sidechain 4 4x9j O6@B.DG4 NH2@A.ARG174 2.90 base:sidechain 5 4x9j N7@B.DG6 NE2@A.HIS149 2.71 base:sidechain 6 4x9j N7@B.DG7 NH1@A.ARG146 3.07 base:sidechain 7 4x9j O6@B.DG7 NH2@A.ARG146 2.84 base:sidechain 8 4x9j N7@B.DG8 NH2@A.ARG124 2.85 base:sidechain 9 4x9j O6@B.DG8 NH1@A.ARG124 3.05 base:sidechain 10 4x9j N7@B.DG10 NH1@A.ARG118 2.93 base:sidechain 11 4x9j O6@B.DG10 NH2@A.ARG118 2.87 base:sidechain 12 4x9j N4.A@C.DC55 OD2@A.ASP148 3.01 base:sidechain **************************************************************************** List of 7 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4x9j G-arg B.DG2 A.ARG180 0.04 14 2 4x9j G-arg B.DG4 A.ARG174 0.01 24 3 4x9j G-his B.DG6 A.HIS149 0.51 3 4 4x9j G-arg B.DG7 A.ARG146 0.29 8 5 4x9j G-arg B.DG8 A.ARG124 0.07 17 6 4x9j G-arg B.DG10 A.ARG118 0.09 8 7 4x9j C-asp C.DC55 A.ASP148 1.77 34 **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4x9j A-arg B.DA1 A.ARG180 3.37 3 2 4x9j C-arg B.5CM3 A.ARG174 3.50 14 3 4x9j T-his B.DT5 A.HIS149 3.49 11 4 4x9j G-arg B.DG6 A.ARG146 3.53 9 5 4x9j C-arg B.5CM9 A.ARG118 3.59 5 6 4x9j T-asp C.DT51 A.ASP120 4.76 51 **************************************************************************** List of 3 additional files 1 -- 4x9j-baseAA-pairs.pdb 2 -- 4x9j-baseAA-stacks.pdb 3 -- 4x9j-pairs.pdb