**************************************************************************** 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/7sfc.pdb -o=7sfc.out --type=base File name: 7sfc.pdb no. of peptide chains: 1 [A=842] no. of DNA/RNA chains: 2 [C=12,D=12] no. of amino acids: 842 no. of nucleotides: 24 no. of atoms: 7714 no. of waters: 508 no. of metals: 2 [Zn=2] **************************************************************************** List of 2 types of 2 modified nucleotides nt count list 1 5CM-c 1 C.5CM6 2 PYO-u 1 D.PYO18 **************************************************************************** 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'-GAGGCcGCCTGC-3' bp-type .|||||.||||| strand-2 3'-CTCCGGuGGACG-5' helix-form ..BBB.BBBBB 1 C.DG1 D.DC24 G-C -- -- 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.DG7 D.PYO18 G-u -- -- cWW cW-W 8 C.DC8 D.DG17 C-G WC 19-XIX cWW cW-W 9 C.DC9 D.DG16 C-G WC 19-XIX cWW cW-W 10 C.DT10 D.DA15 T-A WC 20-XX cWW cW-W 11 C.DG11 D.DC14 G-C WC 19-XIX cWW cW-W 12 C.DC12 D.DG13 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 15 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7sfc G-glu C.DG3 A.GLU1531 11.87 -92.52 -5.02 9.93 4.13 1.39 -7.90 -92.25 2 7sfc G-met C.DG4 A.MET1533 9.52 148.33 4.55 -3.20 7.73 -17.84 66.37 141.39 3 7sfc C-cys C.DC5 A.CYS1499 11.56 -96.03 -7.93 8.41 -0.06 -19.98 60.86 -75.80 4 7sfc C-met C.DC5 A.MET1533 8.46 121.22 5.62 -2.88 5.63 -8.11 68.21 107.07 5 7sfc C-cys C.5CM6 A.CYS1499 -11.12 -116.66 -4.47 9.27 -4.21 -9.64 47.46 -109.70 6 7sfc C-leu C.5CM6 A.LEU1500 11.18 -91.18 2.99 7.76 -7.47 84.51 -28.69 -21.04 7 7sfc C-trp C.5CM6 A.TRP1510 10.74 87.60 0.60 5.37 9.29 -1.66 86.39 16.04 8 7sfc C-met C.5CM6 A.MET1533 -7.04 95.95 5.53 -2.95 3.21 -4.90 74.28 65.58 9 7sfc C-gly C.5CM6 A.GLY1534 4.49 -98.70 3.34 2.08 2.16 -16.67 29.71 -94.10 10 7sfc G-his C.DG7 A.HIS1507 9.41 -178.85 -5.31 7.02 -3.33 83.36 3.69 -178.46 11 7sfc A-asn D.DA15 A.ASN1508 9.47 -164.63 -6.51 6.02 3.31 -1.62 -31.08 -164.04 12 7sfc G-lys D.DG17 A.LYS1535 9.66 -177.98 0.22 6.53 7.12 19.44 -80.23 -177.31 13 7sfc U-lys D.PYO18 A.LYS1535 8.34 166.85 0.97 -6.69 4.89 -5.13 89.74 161.38 14 7sfc G-gly D.DG19 A.GLY1534 5.41 101.11 4.53 -2.58 -1.45 -10.59 -52.95 89.04 15 7sfc G-lys D.DG19 A.LYS1535 -5.91 143.91 4.84 -3.34 0.60 2.24 78.23 132.92 **************************************************************************** List of 14 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 7sfc GC-glu C.DG3 D.DC22 A.GLU1531 12.00 -99.41 -4.30 9.83 5.38 16.40 -11.64 -97.89 2 7sfc GC-met C.DG4 D.DC21 A.MET1533 9.40 146.85 4.53 -2.31 7.90 -26.30 68.83 138.23 3 7sfc GU-his C.DG7 D.PYO18 A.HIS1507 9.42 -178.10 -5.05 7.18 -3.40 88.85 -3.57 -177.34 4 7sfc GU-lys C.DG7 D.PYO18 A.LYS1535 -8.31 -160.20 0.47 6.45 -5.21 -5.30 -83.42 -153.33 5 7sfc AT-asn D.DA15 C.DT10 A.ASN1508 9.42 -164.88 -6.46 5.89 3.52 3.86 -31.36 -164.29 6 7sfc GC-lys D.DG17 C.DC8 A.LYS1535 9.62 -177.50 0.31 6.29 7.27 22.12 -78.48 -176.70 7 7sfc GC-cys D.DG19 C.5CM6 A.CYS1499 11.21 118.94 -4.54 -9.62 3.54 -8.34 -59.50 108.14 8 7sfc GC-leu D.DG19 C.5CM6 A.LEU1500 -11.31 87.98 2.87 -6.76 -8.60 -81.06 -23.26 27.81 9 7sfc GC-trp D.DG19 C.5CM6 A.TRP1510 -10.86 -173.08 6.17 8.90 0.82 -87.00 20.87 -170.26 10 7sfc GC-met D.DG19 C.5CM6 A.MET1533 7.50 -100.49 5.95 3.52 -2.90 5.59 -72.93 -74.44 11 7sfc GC-gly D.DG19 C.5CM6 A.GLY1534 -4.94 99.38 3.96 -2.32 -1.84 -13.74 -41.36 91.67 12 7sfc GC-lys D.DG19 C.5CM6 A.LYS1535 -5.68 177.02 -1.39 -2.45 -4.94 -35.50 -82.27 175.80 13 7sfc GC-cys D.DG20 C.DC5 A.CYS1499 -11.57 96.53 -8.06 -8.29 0.00 -20.73 -60.67 76.48 14 7sfc GC-met D.DG20 C.DC5 A.MET1533 -8.39 -121.45 5.43 2.83 -5.73 -8.25 -69.11 -106.90 **************************************************************************** List of 18 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 7sfc OP1@C.DG3 N@A.SER1418 2.68 po4:backbone 2 7sfc OP1@C.DG4 NH1@A.ARG1424 3.34 po4:sidechain:salt-bridge 3 7sfc OP1@C.DC5 NE@A.ARG1490 2.74 po4:sidechain:salt-bridge 4 7sfc OP1@C.DC5 NH2@A.ARG1490 3.14 po4:sidechain:salt-bridge 5 7sfc OP2@C.DC5 N@A.CYS1499 3.69 po4:backbone 6 7sfc O3'@C.DG4 NH2@A.ARG1490 3.38 po4:sidechain 7 7sfc OP2@C.5CM6 ND1@A.HIS1502 2.72 po4:sidechain:salt-bridge 8 7sfc OP1@C.DG7 NH2@A.ARG1506 2.87 po4:sidechain:salt-bridge 9 7sfc OP2@C.DG7 NE@A.ARG1506 3.03 po4:sidechain:salt-bridge 10 7sfc OP2@C.DG7 NE2@A.HIS1507 2.66 po4:sidechain:salt-bridge 11 7sfc OP1@C.DT10 NH1@A.ARG1276 3.38 po4:sidechain:salt-bridge 12 7sfc OP1@C.DT10 NH2@A.ARG1276 3.09 po4:sidechain:salt-bridge 13 7sfc OP1@D.DC14 OH@A.TYR976 2.85 po4:sidechain 14 7sfc OP1@D.DA15 OG@A.SER977 2.61 po4:sidechain 15 7sfc OP2@D.DA15 ND2@A.ASN1508 3.22 po4:sidechain 16 7sfc OP1@D.DG16 OH@A.TYR979 2.64 po4:sidechain 17 7sfc OP2@D.DG16 NZ@A.LYS981 2.51 po4:sidechain:salt-bridge 18 7sfc OP1@D.DG17 NH2@A.ARG1311 3.51 po4:sidechain:salt-bridge **************************************************************************** List of 3 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 7sfc N4@C.5CM6 O@A.MET1533 2.78 base:backbone 2 7sfc O6@D.DG17 NZ@A.LYS1535 3.51 base:sidechain 3 7sfc O6@D.DG19 N@A.LYS1535 3.42 base:backbone **************************************************************************** List of 1 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 7sfc C-trp C.5CM6 A.TRP1510 3.38 25 **************************************************************************** List of 2 additional files 1 -- 7sfc-baseAA-stacks.pdb 2 -- 7sfc-pairs.pdb