**************************************************************************** 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/7sfg.pdb -o=7sfg.out --type=base File name: 7sfg.pdb no. of peptide chains: 1 [A=818] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 818 no. of nucleotides: 25 no. of atoms: 7130 no. of waters: 287 no. of metals: 2 [Zn=2] **************************************************************************** List of 3 types of 3 modified nucleotides nt count list 1 5CM-c 1 C.5CM6 2 PYO-u 1 D.PYO18 3 SAM-a 1 A.SAM1703 **************************************************************************** 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=11 strand-1 5'-GAGGCcCCTGC-3' bp-type ||||||||||| strand-2 3'-CTCCGGGGACG-5' helix-form BBBBBxBB.B 1 C.DG1 D.DC24 G-C WC 19-XIX cWW cW-W 2 C.DA2 D.DT23 A-T WC 20-XX cWW cW-W 3 C.DG3 D.DC22 G-C WC 19-XIX cWW cW-W 4 C.DG4 D.DC21 G-C WC 19-XIX cWW cW-W 5 C.DC5 D.DG20 C-G WC 19-XIX cWW cW-W 6 C.5CM6 D.DG19 c-G WC 19-XIX cWW cW-W 7 C.DC8 D.DG17 C-G WC 19-XIX cWW cW-W 8 C.DC9 D.DG16 C-G WC 19-XIX cWW cW-W 9 C.DT10 D.DA15 T-A WC 20-XX cWW cW-W 10 C.DG11 D.DC14 G-C WC 19-XIX cWW cW-W 11 C.DC12 D.DG13 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 49 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7sfg G-met C.DG4 A.MET1533 9.90 150.77 4.86 -3.22 8.00 -27.93 62.31 144.50 2 7sfg C-arg C.DC5 A.ARG1234 9.19 91.02 -8.16 0.69 4.17 -2.12 37.43 84.53 3 7sfg C-met C.DC5 A.MET1533 8.55 124.84 5.82 -2.73 5.64 -15.13 74.22 108.18 4 7sfg C-arg C.5CM6 A.ARG1234 8.89 61.00 -8.03 3.78 0.46 -7.68 35.57 49.82 5 7sfg C-cys C.5CM6 A.CYS1499 -11.20 -115.54 -4.46 9.33 -4.31 -12.06 45.91 -108.73 6 7sfg C-leu C.5CM6 A.LEU1500 11.39 -95.52 1.48 7.86 8.12 -87.94 16.40 -37.75 7 7sfg C-trp C.5CM6 A.TRP1510 10.90 88.34 0.71 6.01 9.07 -0.66 87.22 15.70 8 7sfg C-leu C.5CM6 A.LEU1513 10.41 165.62 4.43 -8.95 -2.93 -49.87 -65.33 160.87 9 7sfg C-met C.5CM6 A.MET1533 -7.06 98.67 5.66 -2.80 3.16 -8.95 77.30 66.26 10 7sfg C-gly C.5CM6 A.GLY1534 4.45 -94.45 3.46 2.14 1.81 -22.32 18.68 -90.88 11 7sfg C-lys C.5CM6 A.LYS1535 5.04 178.96 2.41 -2.07 3.90 20.92 -68.16 178.73 12 7sfg G-gly C.DG7 A.GLY1231 4.13 65.71 -0.42 -3.87 1.38 16.99 -63.23 5.96 13 7sfg G-met C.DG7 A.MET1232 -3.41 -47.46 2.31 -1.55 -1.97 -21.38 38.65 -17.80 14 7sfg G-asn C.DG7 A.ASN1233 -5.14 -136.41 -0.11 -3.46 -3.80 27.73 -29.27 -133.40 15 7sfg G-arg C.DG7 A.ARG1234 -5.29 60.39 -1.02 2.35 -4.63 16.10 26.02 52.71 16 7sfg G-his C.DG7 A.HIS1507 10.44 86.76 2.89 5.55 8.35 -5.91 85.83 12.48 17 7sfg G-lys C.DG7 A.LYS1535 -8.77 -161.52 -0.82 8.01 -3.47 -0.84 -83.95 -155.05 18 7sfg C-gly C.DC8 A.GLY1231 -5.62 -73.79 -4.79 -2.93 -0.36 -8.45 -67.01 -31.67 19 7sfg G-gly D.DG17 A.GLY1231 5.70 88.32 -4.89 2.93 0.01 -25.96 81.59 24.12 20 7sfg G-met D.DG17 A.MET1232 5.82 73.97 1.67 2.70 4.88 -20.37 -22.70 68.23 21 7sfg G-lys D.DG17 A.LYS1535 8.65 -161.75 -6.34 5.85 0.57 -27.52 75.34 -156.07 22 7sfg G-gln D.DG17 A.GLN1536 10.87 152.25 9.43 -1.08 5.30 22.98 39.42 149.84 23 7sfg U-pro D.PYO18 A.PRO1224 6.44 -59.84 5.41 2.50 2.46 13.68 52.55 -26.16 24 7sfg U-pro D.PYO18 A.PRO1225 -7.19 49.55 6.86 2.05 -0.65 -10.98 -8.46 47.69 25 7sfg U-cys D.PYO18 A.CYS1226 -6.71 -158.28 -5.37 4.01 0.19 6.60 -80.40 -151.38 26 7sfg U-gln D.PYO18 A.GLN1227 -10.21 68.53 4.18 8.28 -4.26 -25.78 -51.88 38.32 27 7sfg U-glu D.PYO18 A.GLU1266 -4.40 -153.55 2.86 1.32 -3.08 -50.57 -56.32 -146.31 28 7sfg U-asn D.PYO18 A.ASN1267 -3.66 38.46 1.75 -0.38 -3.20 -10.29 34.13 14.66 29 7sfg U-val D.PYO18 A.VAL1268 -5.90 96.21 -0.90 3.42 -4.73 -26.67 -16.68 92.15 30 7sfg U-arg D.PYO18 A.ARG1310 -10.28 -109.75 -9.41 -3.94 -1.24 -66.98 -57.93 -73.03 31 7sfg U-arg D.PYO18 A.ARG1312 -6.85 -111.80 -4.07 -1.99 -5.14 -59.84 -53.65 -85.57 32 7sfg U-gly D.PYO18 A.GLY1577 9.63 127.92 4.83 4.02 7.30 -71.62 -50.17 105.19 33 7sfg U-asn D.PYO18 A.ASN1578 6.70 57.09 0.01 6.39 2.04 46.32 -21.16 26.71 34 7sfg G-met D.DG19 A.MET1232 -6.87 52.19 -3.68 5.26 -2.44 -32.49 -37.50 16.74 35 7sfg G-arg D.DG19 A.ARG1234 -8.22 -62.99 -7.58 -3.15 -0.44 6.86 -31.90 -54.64 36 7sfg G-met D.DG19 A.MET1533 7.65 -100.99 6.17 3.47 -2.89 3.08 -71.05 -77.12 37 7sfg G-gly D.DG19 A.GLY1534 5.02 91.92 4.19 -2.43 -1.32 -14.18 -31.39 86.59 38 7sfg G-lys D.DG19 A.LYS1535 -5.13 -179.91 1.58 2.80 -4.00 24.69 83.17 -179.88 39 7sfg G-arg D.DG20 A.ARG1234 -9.10 -90.35 -8.26 -0.31 -3.79 -6.42 -31.20 -85.71 40 7sfg G-phe D.DG20 A.PHE1235 -10.77 -134.11 -10.61 -0.18 -1.86 -82.99 -30.97 -114.00 41 7sfg A-phe A.SAM1703 A.PHE1145 -6.73 52.88 -2.78 3.05 -5.31 28.10 40.68 19.39 42 7sfg A-ile A.SAM1703 A.ILE1167 -7.15 -83.09 -5.75 -3.95 1.55 62.90 7.64 -56.83 43 7sfg A-glu A.SAM1703 A.GLU1168 6.53 142.76 0.19 6.32 1.60 -0.33 -17.55 142.30 44 7sfg A-met A.SAM1703 A.MET1169 5.45 81.91 -3.42 -0.69 4.18 -79.64 14.98 13.12 45 7sfg A-glu A.SAM1703 A.GLU1189 6.12 -103.41 -0.27 -3.78 4.81 11.18 10.55 -102.59 46 7sfg A-asp A.SAM1703 A.ASP1190 3.31 -79.36 0.54 -3.20 0.64 -75.05 -7.49 -26.78 47 7sfg A-cys A.SAM1703 A.CYS1191 -3.60 147.41 -3.57 0.28 -0.40 -70.60 -18.37 139.15 48 7sfg A-pro A.SAM1703 A.PRO1225 -9.52 -48.80 -2.09 7.99 -4.72 4.12 -46.71 -13.94 49 7sfg A-leu A.SAM1703 A.LEU1247 -7.58 128.08 1.94 -4.52 -5.77 30.32 -21.52 124.99 **************************************************************************** List of 17 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7sfg GC-met C.DG4 D.DC21 A.MET1533 9.79 148.73 4.73 -2.37 8.24 -36.48 63.58 140.75 2 7sfg GC-gly D.DG17 C.DC8 A.GLY1231 5.66 80.77 -4.83 2.94 0.21 -17.02 74.56 28.24 3 7sfg GC-met D.DG17 C.DC8 A.MET1232 5.91 71.79 1.52 2.39 5.19 -14.99 -31.93 63.56 4 7sfg GC-lys D.DG17 C.DC8 A.LYS1535 8.86 -157.84 -6.47 5.82 1.67 -20.90 84.06 -149.37 5 7sfg GC-gln D.DG17 C.DC8 A.GLN1536 11.07 151.28 8.97 -1.17 6.37 21.34 28.01 149.84 6 7sfg GC-met D.DG19 C.5CM6 A.MET1232 -7.12 56.14 -4.18 5.05 -2.77 -39.31 -35.01 20.28 7 7sfg GC-arg D.DG19 C.5CM6 A.ARG1234 -8.55 -61.56 -7.81 -3.46 -0.47 -0.40 -33.78 -52.24 8 7sfg GC-cys D.DG19 C.5CM6 A.CYS1499 11.26 115.44 -4.52 -9.60 3.78 -9.28 -52.92 106.45 9 7sfg GC-leu D.DG19 C.5CM6 A.LEU1500 -11.45 88.75 2.08 -7.49 -8.41 -81.46 -19.18 32.74 10 7sfg GC-trp D.DG19 C.5CM6 A.TRP1510 -10.90 -90.20 0.90 -5.02 -9.63 5.41 -87.62 -23.23 11 7sfg GC-leu D.DG19 C.5CM6 A.LEU1513 -10.59 -161.82 4.30 9.12 3.24 -47.72 71.78 -155.01 12 7sfg GC-met D.DG19 C.5CM6 A.MET1533 7.35 -99.61 5.92 3.15 -3.03 -2.91 -74.29 -71.81 13 7sfg GC-gly D.DG19 C.5CM6 A.GLY1534 -4.73 92.94 3.84 -2.28 -1.57 -18.28 -25.06 88.75 14 7sfg GC-lys D.DG19 C.5CM6 A.LYS1535 -5.07 -179.44 1.99 2.44 -3.97 22.80 75.67 -179.28 15 7sfg GC-arg D.DG20 C.DC5 A.ARG1234 -9.14 -90.62 -8.21 -0.50 -3.98 -4.31 -34.34 -85.11 16 7sfg GC-phe D.DG20 C.DC5 A.PHE1235 -10.82 -134.77 -10.57 -0.30 -2.31 -80.34 -33.78 -115.89 17 7sfg GC-met D.DG20 C.DC5 A.MET1533 -8.63 -123.31 5.71 2.75 -5.86 -17.95 -71.51 -107.20 **************************************************************************** List of 23 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7sfg OP1@C.DG3 N@A.SER1418 3.45 po4:backbone 2 7sfg OP1@C.DG4 NH1@A.ARG1424 2.95 po4:sidechain:salt-bridge 3 7sfg OP2@C.DC5 N@A.CYS1499 3.39 po4:backbone 4 7sfg OP2@C.5CM6 ND1@A.HIS1502 2.70 po4:sidechain:salt-bridge 5 7sfg OP1@C.DG7 NH2@A.ARG1506 3.38 po4:sidechain:salt-bridge 6 7sfg OP2@C.DG7 NE@A.ARG1506 3.13 po4:sidechain:salt-bridge 7 7sfg OP2@C.DG7 NE2@A.HIS1507 2.75 po4:sidechain:salt-bridge 8 7sfg OP1@C.DT10 NH1@A.ARG1276 2.77 po4:sidechain:salt-bridge 9 7sfg OP1@C.DG11 NH2@A.ARG1269 3.09 po4:sidechain:salt-bridge 10 7sfg OP1@C.DG11 N@A.VAL1344 3.53 po4:backbone 11 7sfg O3'@C.DT10 NH1@A.ARG1269 4.00 po4:sidechain 12 7sfg OP1@D.DC14 OH@A.TYR976 3.38 po4:sidechain 13 7sfg OP1@D.DA15 OG@A.SER977 3.16 po4:sidechain 14 7sfg OP2@D.DA15 ND2@A.ASN1508 3.21 po4:sidechain 15 7sfg OP1@D.DG16 OH@A.TYR979 2.90 po4:sidechain 16 7sfg OP2@D.DG16 NZ@A.LYS981 2.61 po4:sidechain:salt-bridge 17 7sfg OP1@D.DG17 NH1@A.ARG1311 2.83 po4:sidechain:salt-bridge 18 7sfg OP1@D.PYO18 OG@A.SER1230 2.75 po4:sidechain 19 7sfg OP2@D.PYO18 NH1@A.ARG1312 3.07 po4:sidechain:salt-bridge 20 7sfg O5'@D.PYO18 NH2@A.ARG1312 3.25 po4:sidechain 21 7sfg OP2@D.DG19 N@A.THR1528 3.23 po4:backbone 22 7sfg OP2@D.DG19 OG1@A.THR1528 2.69 po4:sidechain 23 7sfg OP1@D.DC22 NH1@A.ARG1238 3.27 po4:sidechain:salt-bridge **************************************************************************** List of 4 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 7sfg O4'@C.DG7 NE@A.ARG1234 3.63 sugar:sidechain 2 7sfg O4'@D.PYO18 NH2@A.ARG1312 2.85 sugar:sidechain 3 7sfg O2'@D.PYO18 OD1@A.ASN1578 3.74 sugar:sidechain 4 7sfg O2'@A.SAM1703 OE2@A.GLU1168 2.59 sugar:sidechain **************************************************************************** List of 11 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7sfg O2@C.5CM6 NH1@A.ARG1234 3.30 base:sidechain 2 7sfg N4@C.5CM6 O@A.MET1533 2.74 base:backbone 3 7sfg N1@C.DG7 O@A.GLY1231 2.42 base:backbone 4 7sfg N2@C.DG7 O@A.GLY1231 3.24 base:backbone 5 7sfg O2@D.PYO18 NH2@A.ARG1310 3.04 base:sidechain 6 7sfg O2@D.PYO18 NE@A.ARG1312 3.03 base:sidechain 7 7sfg O2@D.PYO18 NH2@A.ARG1312 3.04 base:sidechain 8 7sfg N3@D.PYO18 OE2@A.GLU1266 3.41 base:sidechain 9 7sfg O6@D.DG19 N@A.LYS1535 2.94 base:backbone 10 7sfg N6@A.SAM1703 OD1@A.ASP1190 3.30 base:sidechain 11 7sfg N1@A.SAM1703 N@A.CYS1191 2.98 base:backbone **************************************************************************** List of 3 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 7sfg U-glu D.PYO18 A.GLU1266 0.55 25 2 7sfg U-arg D.PYO18 A.ARG1310 1.71 23 3 7sfg U-arg D.PYO18 A.ARG1312 0.36 64 **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7sfg C-trp C.5CM6 A.TRP1510 3.22 28 **************************************************************************** List of 3 additional files 1 -- 7sfg-baseAA-pairs.pdb 2 -- 7sfg-baseAA-stacks.pdb 3 -- 7sfg-pairs.pdb