**************************************************************************** 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/5kl7.pdb -o=5kl7.out --type=base File name: 5kl7.pdb no. of peptide chains: 1 [A=87] no. of DNA/RNA chains: 2 [B=11,C=11] no. of amino acids: 87 no. of nucleotides: 22 no. of atoms: 2323 no. of waters: 126 no. of metals: 3 [Zn=3] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 1CC-c 1 B.1CC9 2 5CM-c 1 C.5CM3 **************************************************************************** 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 BBBBB...B 1 B.DG2 C.DC11 G-C WC 19-XIX cWW cW-W 2 B.DC3 C.DG10 C-G WC 19-XIX cWW cW-W 3 B.DG4 C.DC9 G-C WC 19-XIX cWW cW-W 4 B.DT5 C.DA8 T-A WC 20-XX cWW cW-W 5 B.DG6 C.DC7 G-C WC 19-XIX cWW cW-W 6 B.DG7 C.DC6 G-C WC 19-XIX cWW cW-W 7 B.DG8 C.DC5 G-C WC 19-XIX cWW cW-W 8 B.1CC9 C.DG4 c-G WC 19-XIX cWW cW-W 9 B.DG10 C.5CM3 G-c WC 19-XIX cWW cW-W 10 B.DT11 C.DA2 T-A WC 20-XX cWW cW-W **************************************************************************** List of 42 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5kl7 A-arg B.DA1 A.ARG430 -8.13 77.42 -6.92 0.90 -4.17 -60.49 -35.13 35.52 2 5kl7 G-glu B.DG2 A.GLU427 9.80 151.02 3.72 -1.58 8.93 3.31 79.20 142.09 3 5kl7 G-arg B.DG2 A.ARG430 11.19 -147.52 -3.70 10.43 1.67 -3.07 57.68 -142.74 4 5kl7 C-arg B.DC3 A.ARG424 11.37 -136.27 -3.99 9.35 5.09 15.84 -57.73 -129.09 5 5kl7 C-glu B.DC3 A.GLU427 8.76 130.50 5.64 -2.08 6.37 19.45 83.95 110.04 6 5kl7 C-arg B.DC3 A.ARG430 -10.38 -171.36 -0.12 10.30 -1.32 8.38 48.36 -170.50 7 5kl7 G-arg B.DG4 A.ARG424 10.96 -173.21 -1.85 10.40 2.93 7.68 -55.22 -172.32 8 5kl7 G-asp B.DG4 A.ASP426 9.19 175.46 -0.37 -8.61 3.20 10.58 -34.97 175.22 9 5kl7 T-his B.DT5 A.HIS397 9.40 -172.21 -7.38 4.80 -3.30 16.08 86.54 -169.15 10 5kl7 T-thr B.DT5 A.THR400 11.01 -134.45 -2.80 10.33 2.59 -24.10 48.72 -128.41 11 5kl7 T-arg B.DT5 A.ARG424 9.81 158.61 1.13 -9.69 1.05 0.93 61.42 155.07 12 5kl7 G-arg B.DG6 A.ARG394 11.53 -147.78 -3.52 10.22 3.99 23.56 -48.38 -143.74 13 5kl7 G-his B.DG6 A.HIS397 9.13 136.93 4.54 -4.87 6.25 15.96 84.44 119.78 14 5kl7 G-arg B.DG7 A.ARG372 11.69 -131.78 -7.82 7.56 4.27 -40.10 55.07 -120.91 15 5kl7 G-arg B.DG7 A.ARG394 11.03 -176.14 -2.93 10.46 1.92 15.24 -54.61 -175.61 16 5kl7 G-his B.DG7 A.HIS397 -9.30 113.65 5.53 -6.02 4.43 32.74 74.69 87.46 17 5kl7 G-arg B.DG8 A.ARG372 11.28 -159.07 -3.66 10.47 2.04 -13.15 65.09 -154.92 18 5kl7 G-arg B.DG8 A.ARG394 -11.17 146.54 1.32 -11.09 -0.07 -2.10 52.98 142.46 19 5kl7 C-arg B.1CC9 A.ARG369 8.47 135.93 3.19 -3.56 7.00 35.36 73.00 120.82 20 5kl7 C-arg B.1CC9 A.ARG372 9.95 173.71 -0.38 -9.93 -0.63 -10.18 -61.32 172.66 21 5kl7 G-arg B.DG10 A.ARG366 10.80 -171.74 -1.97 10.01 3.54 3.66 -37.06 -171.29 22 5kl7 G-asp B.DG10 A.ASP368 9.24 -174.27 0.91 8.56 3.36 -20.17 53.70 -173.47 23 5kl7 G-arg B.DG10 A.ARG369 -9.44 124.16 5.69 -5.88 4.70 53.90 60.10 104.17 24 5kl7 T-arg B.DT11 A.ARG366 10.78 161.08 1.32 -10.65 1.10 4.42 45.85 159.42 25 5kl7 T-arg C.DT1 A.ARG366 -10.28 -120.65 -0.44 10.27 0.32 -2.84 -30.66 -118.20 26 5kl7 T-ser C.DT1 A.SER367 10.91 175.57 8.42 -5.01 -4.79 -48.57 -32.07 174.93 27 5kl7 T-asp C.DT1 A.ASP368 9.45 -140.52 -6.62 6.48 1.88 -30.33 58.18 -132.62 28 5kl7 A-arg C.DA2 A.ARG366 -10.84 -161.82 1.38 10.71 -0.93 2.82 -39.49 -160.67 29 5kl7 A-asp C.DA2 A.ASP368 9.45 -162.73 -3.65 8.71 -0.39 4.75 54.33 -160.56 30 5kl7 C-arg C.5CM3 A.ARG366 -10.46 170.05 -2.37 -9.55 -3.55 8.31 44.88 169.20 31 5kl7 C-asp C.5CM3 A.ASP368 -8.97 170.98 0.62 -8.21 -3.57 -17.74 -45.27 170.10 32 5kl7 G-arg C.DG4 A.ARG372 -10.04 -176.64 -0.27 10.01 0.78 -10.25 66.04 -175.97 33 5kl7 G-asp C.DG4 A.ASP396 8.50 -109.59 -5.83 5.36 3.10 -18.55 36.83 -103.96 34 5kl7 C-arg C.DC5 A.ARG372 -11.01 152.81 -3.72 -9.81 -3.35 -3.34 -66.14 147.41 35 5kl7 C-arg C.DC5 A.ARG394 -11.07 -141.86 0.84 11.01 -0.75 -10.14 -45.74 -138.28 36 5kl7 C-asp C.DC5 A.ASP396 -8.82 -141.63 -3.31 8.16 -0.48 -12.16 44.19 -138.20 37 5kl7 C-asp C.DC7 A.ASP426 8.88 -115.75 -5.71 6.15 2.93 -17.80 37.19 -110.76 38 5kl7 A-arg C.DA8 A.ARG424 -9.80 -155.84 0.91 9.65 -1.44 -3.59 -54.97 -152.70 39 5kl7 A-asp C.DA8 A.ASP426 -7.87 -151.36 -2.96 7.25 -0.78 -9.13 37.67 -149.59 40 5kl7 C-arg C.DC9 A.ARG424 -10.67 177.23 -1.55 -9.96 -3.51 13.41 57.70 176.81 41 5kl7 C-asp C.DC9 A.ASP426 -8.98 -176.34 -0.50 8.14 -3.75 3.50 33.30 -176.18 42 5kl7 G-arg C.DG10 A.ARG430 -10.58 168.86 -0.11 -10.56 0.68 15.94 -55.78 167.26 **************************************************************************** List of 28 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5kl7 AT-arg C.DA8 B.DT5 A.ARG424 -9.80 -157.21 1.02 9.67 -1.25 -1.35 -58.21 -153.86 2 5kl7 AT-arg C.DA2 B.DT11 A.ARG366 -10.81 -161.43 1.35 10.68 -1.01 3.60 -42.67 -160.04 3 5kl7 AT-asp C.DA8 B.DT5 A.ASP426 -7.84 -150.40 -2.89 7.25 -0.73 -6.99 34.32 -148.93 4 5kl7 AT-asp C.DA2 B.DT11 A.ASP368 9.36 -161.47 -3.58 8.63 -0.56 4.88 51.16 -159.42 5 5kl7 AT-his C.DA8 B.DT5 A.HIS397 -9.33 -163.17 3.32 2.81 -8.26 -10.72 -88.47 -156.29 6 5kl7 AT-thr C.DA8 B.DT5 A.THR400 -10.97 132.39 -2.81 -10.17 -2.99 -20.56 -49.54 126.22 7 5kl7 GC-arg B.DG2 C.DC11 A.ARG430 11.04 -146.72 -3.73 10.24 1.79 -1.50 56.09 -142.13 8 5kl7 GC-arg C.DG10 B.DC3 A.ARG424 -11.33 138.72 -3.74 -9.18 -5.49 20.40 55.75 132.13 9 5kl7 GC-arg C.DG10 B.DC3 A.ARG430 -10.48 170.10 -0.11 -10.43 1.01 12.15 -52.09 168.91 10 5kl7 GC-arg B.DG4 C.DC9 A.ARG424 10.81 -175.22 -1.70 10.18 3.22 10.55 -56.46 -174.55 11 5kl7 GC-arg B.DG6 C.DC7 A.ARG394 11.47 -148.97 -3.35 10.14 4.20 24.42 -47.00 -145.22 12 5kl7 GC-arg B.DG7 C.DC6 A.ARG372 11.58 -129.82 -7.76 7.16 4.75 -36.59 57.29 -118.48 13 5kl7 GC-arg B.DG7 C.DC6 A.ARG394 10.89 -178.01 -2.64 10.32 2.27 16.89 -50.94 -177.77 14 5kl7 GC-arg B.DG8 C.DC5 A.ARG372 11.15 -155.92 -3.69 10.16 2.71 -8.26 65.68 -151.16 15 5kl7 GC-arg B.DG8 C.DC5 A.ARG394 11.12 144.16 1.08 -11.06 0.36 -6.14 49.40 140.35 16 5kl7 GC-arg C.DG4 B.1CC9 A.ARG369 -8.46 -136.96 3.20 3.62 -6.94 34.53 -71.12 -123.20 17 5kl7 GC-arg C.DG4 B.1CC9 A.ARG372 -10.00 -175.19 -0.33 9.97 0.71 -10.24 63.67 -174.31 18 5kl7 GC-arg B.DG10 C.5CM3 A.ARG366 10.63 -170.87 -2.18 9.78 3.55 5.93 -41.00 -170.24 19 5kl7 GC-arg B.DG10 C.5CM3 A.ARG369 -9.31 122.20 5.71 -5.66 4.68 49.59 62.02 102.17 20 5kl7 GC-asp B.DG4 C.DC9 A.ASP426 9.08 175.90 -0.44 -8.38 3.48 7.03 -34.16 175.70 21 5kl7 GC-asp B.DG6 C.DC7 A.ASP426 -8.88 116.35 -5.66 -6.22 -2.85 -18.04 -35.37 111.80 22 5kl7 GC-asp B.DG8 C.DC5 A.ASP396 -8.78 139.72 -3.19 -8.18 0.24 -8.16 -40.38 136.83 23 5kl7 GC-asp C.DG4 B.1CC9 A.ASP396 8.42 -108.45 -5.92 5.31 2.77 -19.54 34.34 -103.20 24 5kl7 GC-asp B.DG10 C.5CM3 A.ASP368 9.11 -172.64 0.76 8.39 3.47 -19.01 49.47 -171.78 25 5kl7 GC-glu B.DG2 C.DC11 A.GLU427 9.69 149.51 3.64 -1.28 8.89 1.59 79.44 140.01 26 5kl7 GC-glu C.DG10 B.DC3 A.GLU427 -8.80 -128.59 5.42 2.17 -6.59 18.60 -78.59 -110.59 27 5kl7 GC-his B.DG6 C.DC7 A.HIS397 9.06 136.31 4.36 -4.88 6.28 16.59 82.43 119.86 28 5kl7 GC-his B.DG7 C.DC6 A.HIS397 -9.16 113.16 5.23 -6.05 4.46 33.99 70.60 89.44 **************************************************************************** List of 8 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5kl7 OP1@B.DG4 ND1@A.HIS401 2.75 po4:sidechain:salt-bridge 2 5kl7 OP1@B.DT5 NH2@A.ARG390 3.94 po4:sidechain:salt-bridge 3 5kl7 OP1@B.DG7 NE@A.ARG362 2.76 po4:sidechain:salt-bridge 4 5kl7 OP1@B.DG7 NH2@A.ARG362 3.22 po4:sidechain:salt-bridge 5 5kl7 OP1@B.DG7 NH1@A.ARG376 3.72 po4:sidechain:salt-bridge 6 5kl7 OP2@B.DG7 ND1@A.HIS373 2.81 po4:sidechain:salt-bridge 7 5kl7 OP1.A@C.DC5 NZ@A.LYS399 2.72 po4:sidechain:salt-bridge 8 5kl7 OP2@C.DC6 OG@A.SER425 3.14 po4:sidechain **************************************************************************** List of 15 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5kl7 N7@B.DG2 NH2@A.ARG430 2.75 base:sidechain 2 5kl7 O6@B.DG2 NH1@A.ARG430 2.95 base:sidechain 3 5kl7 N7@B.DG4 NH1@A.ARG424 2.96 base:sidechain 4 5kl7 O6@B.DG4 NH2@A.ARG424 2.85 base:sidechain 5 5kl7 N7@B.DG6 NE2@A.HIS397 2.88 base:sidechain 6 5kl7 N7@B.DG7 NH1@A.ARG394 2.89 base:sidechain 7 5kl7 O6@B.DG7 NH2@A.ARG394 2.84 base:sidechain 8 5kl7 N7@B.DG8 NH2@A.ARG372 2.93 base:sidechain 9 5kl7 O6@B.DG8 NH1@A.ARG372 2.91 base:sidechain 10 5kl7 N7@B.DG10 NH1@A.ARG369 3.06 base:sidechain 11 5kl7 O6@B.DG10 NH2@A.ARG366 2.93 base:sidechain 12 5kl7 O4@B.DT11 NH1@A.ARG366 2.86 base:sidechain 13 5kl7 O4@B.DT11 NH2@A.ARG366 3.23 base:sidechain 14 5kl7 N4.A@C.DC5 OD2@A.ASP396 2.84 base:sidechain 15 5kl7 N6@C.DA8 OD2@A.ASP426 3.17 base:sidechain **************************************************************************** List of 8 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5kl7 G-arg B.DG2 A.ARG430 0.12 21 2 5kl7 G-arg B.DG4 A.ARG424 0.05 29 3 5kl7 G-his B.DG6 A.HIS397 0.65 4 4 5kl7 G-arg B.DG7 A.ARG394 0.04 25 5 5kl7 G-arg B.DG8 A.ARG372 0.15 14 6 5kl7 G-arg B.DG10 A.ARG369 0.08 25 7 5kl7 T-arg B.DT11 A.ARG366 0.60 39 8 5kl7 C-asp C.DC5 A.ASP396 0.39 6 **************************************************************************** List of 7 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5kl7 A-arg B.DA1 A.ARG430 3.50 10 2 5kl7 C-arg B.DC3 A.ARG424 3.38 17 3 5kl7 T-his B.DT5 A.HIS397 3.52 10 4 5kl7 G-arg B.DG7 A.ARG372 3.34 7 5 5kl7 C-arg B.1CC9 A.ARG369 3.65 18 6 5kl7 T-asp C.DT1 A.ASP368 4.27 33 7 5kl7 G-asp C.DG4 A.ASP396 3.42 12 **************************************************************************** List of 3 additional files 1 -- 5kl7-baseAA-pairs.pdb 2 -- 5kl7-baseAA-stacks.pdb 3 -- 5kl7-pairs.pdb