**************************************************************************** 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/1bsu.pdb -o=1bsu.out --type=base File name: 1bsu.pdb no. of peptide chains: 2 [A=236,B=229] no. of DNA/RNA chains: 2 [C=10,D=11] no. of amino acids: 465 no. of nucleotides: 21 no. of atoms: 4281 no. of waters: 218 no. of metals: 2 [Ca=2] **************************************************************************** List of 2 types of 4 modified nucleotides nt count list 1 DI-g 2 C.DI907,D.DI807 2 5CM-c 2 C.5CM906,D.5CM806 **************************************************************************** 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'-AAGAcgTCTT-3' bp-type |||||||||| strand-2 3'-TTCTgcAGAA-5' helix-form BBB...BBB 1 C.DA902 D.DT811 A-T WC 20-XX cWW cW-W 2 C.DA903 D.DT810 A-T WC 20-XX cWW cW-W 3 C.DG904 D.DC809 G-C WC 19-XIX cWW cW-W 4 C.DA905 D.DT808 A-T WC 20-XX cWW cW-W 5 C.5CM906 D.DI807 c-g WC 19-XIX cWW cW-W 6 C.DI907 D.5CM806 g-c WC 19-XIX cWW cW-W 7 C.DT908 D.DA805 T-A WC 20-XX cWW cW-W 8 C.DC909 D.DG804 C-G WC 19-XIX cWW cW-W 9 C.DT910 D.DA803 T-A WC 20-XX cWW cW-W 10 C.DT911 D.DA802 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 1bsu A-gly C.DA903 B.GLY182 7.83 -52.95 7.14 3.16 -0.68 -15.65 -38.92 -33.07 2 1bsu A-ser C.DA903 B.SER183 6.02 -118.31 2.75 2.78 4.57 -62.18 -44.82 -98.38 3 1bsu A-gly C.DA903 B.GLY184 6.35 -173.88 -5.18 2.88 2.28 22.09 -0.13 -173.76 4 1bsu G-ser C.DG904 B.SER183 -4.65 -142.44 2.15 3.73 1.77 -75.27 -30.49 -129.83 5 1bsu G-gly C.DG904 B.GLY184 -5.55 157.83 4.53 -2.97 -1.20 -20.62 10.66 157.37 6 1bsu G-asn C.DG904 B.ASN185 7.23 153.09 6.94 -1.99 -0.40 15.54 -47.91 150.20 7 1bsu A-asn C.DA905 A.ASN70 8.16 -60.71 -7.94 1.35 -1.30 46.62 35.29 -17.08 8 1bsu A-asn C.DA905 B.ASN185 -7.56 118.63 4.78 -4.22 -4.06 5.04 -52.49 110.56 9 1bsu A-thr C.DA905 B.THR186 6.94 -151.63 2.53 6.46 0.34 -18.30 -36.97 -149.64 10 1bsu C-thr C.5CM906 A.THR186 7.41 -151.90 -1.08 6.62 3.16 -26.03 -33.55 -149.81 11 1bsu G-thr C.DI907 A.THR186 7.17 -178.89 -2.43 6.42 2.06 17.70 -31.39 -178.84 12 1bsu G-thr C.DI907 B.THR186 -7.47 144.70 -0.98 -6.68 -3.19 -14.26 25.21 143.50 13 1bsu T-thr C.DT908 A.THR106 9.98 -103.34 -6.00 7.96 0.44 25.65 22.76 -99.06 14 1bsu T-ser C.DT908 A.SER183 6.28 170.37 2.61 -5.56 1.29 -76.34 -0.87 167.74 15 1bsu T-thr C.DT908 A.THR186 -6.80 150.62 2.62 -6.26 -0.47 -18.09 36.28 148.64 16 1bsu T-asn C.DT908 A.ASN188 9.52 173.04 6.27 -7.06 1.21 -22.54 -5.86 172.89 17 1bsu C-gly C.DC909 A.GLY182 7.59 76.68 6.69 -2.14 2.88 -14.01 37.67 66.73 18 1bsu C-ser C.DC909 A.SER183 -4.85 139.62 2.07 -3.71 -2.35 -53.79 22.63 133.43 19 1bsu C-asn C.DC909 B.ASN70 -9.35 -52.50 -9.17 1.35 -1.19 35.82 -27.35 -27.67 20 1bsu T-lys C.DT910 A.LYS104 12.65 -144.10 -2.64 11.30 5.04 -44.13 19.31 -140.54 21 1bsu A-gly D.DA803 A.GLY182 -7.81 -43.12 6.83 3.43 -1.59 -18.70 -24.28 -30.71 22 1bsu A-ser D.DA803 A.SER183 5.96 -113.61 2.34 3.77 3.98 -66.78 -32.10 -93.38 23 1bsu A-gly D.DA803 A.GLY184 6.71 -177.96 -5.77 3.04 1.56 10.17 3.92 -177.95 24 1bsu G-ser D.DG804 A.SER183 -4.68 -143.96 1.87 3.79 2.00 -67.09 -29.74 -134.61 25 1bsu G-gly D.DG804 A.GLY184 -5.78 156.15 4.81 -3.02 -1.08 -26.30 7.98 155.44 26 1bsu G-asn D.DG804 A.ASN185 7.38 159.01 7.08 -2.07 -0.27 16.22 -50.16 156.54 27 1bsu G-asn D.DG804 B.ASN70 9.51 51.06 -9.19 -0.90 2.25 26.73 38.33 21.18 28 1bsu A-asn D.DA805 A.ASN185 -7.43 123.83 4.64 -4.42 -3.75 1.85 -59.39 114.35 29 1bsu A-thr D.DA805 A.THR186 6.79 -152.92 2.68 6.19 0.73 -14.84 -36.54 -151.20 30 1bsu A-asn D.DA805 B.ASN70 7.95 -56.35 -7.78 1.22 -1.12 45.90 28.17 -17.26 31 1bsu C-asn D.5CM806 B.ASN70 -8.71 -64.79 -7.00 2.54 -4.52 39.20 11.67 -51.38 32 1bsu C-thr D.5CM806 B.THR186 7.54 -150.11 -1.13 6.76 3.15 -27.90 -33.72 -147.73 33 1bsu G-thr D.DI807 A.THR186 -7.56 144.68 -0.62 -6.91 -3.01 -23.69 15.25 143.55 34 1bsu G-thr D.DI807 B.THR186 7.19 179.86 2.37 -6.27 2.60 -29.34 26.18 179.85 35 1bsu T-thr D.DT808 B.THR106 10.12 -105.23 -6.25 7.95 0.34 21.67 24.81 -101.44 36 1bsu T-ser D.DT808 B.SER183 6.34 167.53 2.94 -5.56 0.85 -82.13 0.82 163.43 37 1bsu T-thr D.DT808 B.THR186 -6.93 153.11 2.69 -6.36 -0.54 -16.92 37.90 151.20 38 1bsu T-asn D.DT808 B.ASN188 9.64 177.21 6.14 -7.34 1.18 -18.45 -5.04 177.18 39 1bsu C-asn D.DC809 A.ASN70 -9.73 -53.76 -9.63 1.35 -0.47 34.45 -29.86 -29.29 40 1bsu C-gly D.DC809 B.GLY182 7.62 77.07 6.64 -2.15 3.06 -15.57 41.03 65.01 41 1bsu C-ser D.DC809 B.SER183 -4.76 138.49 2.31 -3.46 -2.33 -59.60 29.14 129.90 42 1bsu T-lys D.DT810 B.LYS104 -12.43 -149.13 -2.10 11.22 4.90 -51.99 19.04 -145.02 **************************************************************************** List of 35 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 1bsu AT-asn C.DA905 D.DT808 A.ASN70 8.17 -60.01 -7.95 1.35 -1.31 46.55 34.17 -17.08 2 1bsu AT-asn C.DA905 D.DT808 B.ASN185 -7.53 118.78 4.77 -4.28 -3.95 3.95 -52.80 110.66 3 1bsu AT-asn C.DA905 D.DT808 B.ASN188 -9.65 -176.81 6.08 7.37 -1.31 -19.43 5.32 -176.76 4 1bsu AT-asn D.DA805 C.DT908 A.ASN185 -7.43 123.28 4.59 -4.37 -3.87 3.49 -58.16 114.11 5 1bsu AT-asn D.DA805 C.DT908 A.ASN188 -9.50 -173.50 6.28 7.04 -1.09 -20.61 6.11 -173.38 6 1bsu AT-asn D.DA805 C.DT908 B.ASN70 7.94 -56.96 -7.79 1.18 -0.99 45.29 30.14 -17.58 7 1bsu AT-gly C.DA903 D.DT810 B.GLY182 7.69 -54.04 6.88 3.39 -0.60 -15.86 -42.66 -29.95 8 1bsu AT-gly C.DA903 D.DT810 B.GLY184 6.31 -170.42 -5.38 2.52 2.11 24.79 -1.82 -170.19 9 1bsu AT-gly D.DA803 C.DT910 A.GLY182 7.88 -47.61 7.04 3.38 -1.06 -15.97 -31.97 -31.98 10 1bsu AT-gly D.DA803 C.DT910 A.GLY184 6.66 -177.13 -5.68 2.98 1.79 18.30 4.37 -177.09 11 1bsu AT-lys C.DA903 D.DT810 B.LYS104 -12.56 145.03 -2.39 -11.19 -5.19 -49.13 -18.49 140.85 12 1bsu AT-lys D.DA803 C.DT910 A.LYS104 -12.53 142.49 -2.79 -10.82 -5.67 -36.78 -15.73 139.98 13 1bsu AT-ser C.DA903 D.DT810 B.SER183 5.87 -118.68 2.34 2.79 4.61 -60.49 -49.57 -97.84 14 1bsu AT-ser C.DA905 D.DT808 B.SER183 -6.38 -167.01 2.88 5.61 -0.94 -83.04 -0.74 -162.63 15 1bsu AT-ser D.DA805 C.DT908 A.SER183 -6.26 -170.68 2.62 5.56 -1.19 -74.43 1.32 -168.29 16 1bsu AT-ser D.DA803 C.DT910 A.SER183 5.99 -115.55 2.30 3.48 4.31 -60.68 -36.59 -98.25 17 1bsu AT-thr C.DA905 D.DT808 B.THR106 -10.10 105.42 -6.21 -7.96 -0.45 22.69 -24.38 101.55 18 1bsu AT-thr C.DA905 D.DT808 B.THR186 6.94 -152.37 2.61 6.41 0.44 -17.61 -37.43 -150.42 19 1bsu AT-thr D.DA805 C.DT908 A.THR106 -9.96 103.33 -6.01 -7.93 -0.43 24.29 -24.28 99.03 20 1bsu AT-thr D.DA805 C.DT908 A.THR186 6.80 -151.77 2.65 6.23 0.60 -16.46 -36.40 -149.92 21 1bsu GC-asn C.DG904 D.DC809 A.ASN70 9.74 54.22 -9.62 -1.05 1.05 32.31 36.30 24.81 22 1bsu GC-asn C.DG904 D.DC809 B.ASN185 7.24 157.63 6.99 -1.88 0.14 11.42 -53.29 154.79 23 1bsu GC-asn C.DI907 D.5CM806 B.ASN70 8.62 66.11 -6.78 -2.40 4.75 46.46 -11.30 47.08 24 1bsu GC-asn D.DG804 C.DC909 A.ASN185 7.42 161.96 7.12 -2.07 0.22 13.25 -56.79 159.31 25 1bsu GC-asn D.DG804 C.DC909 B.ASN70 9.43 51.26 -9.20 -1.14 1.73 31.32 32.88 24.44 26 1bsu GC-gly C.DG904 D.DC809 B.GLY182 -7.57 -75.95 6.46 1.97 -3.42 -22.80 -37.99 -63.33 27 1bsu GC-gly C.DG904 D.DC809 B.GLY184 -5.55 157.89 4.56 -3.07 -0.79 -26.10 5.04 157.27 28 1bsu GC-gly D.DG804 C.DC909 A.GLY182 -7.51 -75.83 6.58 1.95 -3.05 -21.29 -37.12 -64.15 29 1bsu GC-gly D.DG804 C.DC909 A.GLY184 5.84 154.58 4.86 -3.16 -0.72 -29.49 1.26 153.70 30 1bsu GC-ser C.DG904 D.DC809 B.SER183 4.71 -140.43 2.22 3.60 2.06 -67.42 -29.94 -129.93 31 1bsu GC-ser D.DG804 C.DC909 A.SER183 4.77 -141.71 1.97 3.76 2.17 -60.44 -26.18 -134.00 32 1bsu GC-thr D.DI807 C.5CM906 A.THR186 -7.48 148.21 -0.84 -6.76 -3.09 -24.82 24.41 146.64 33 1bsu GC-thr D.DI807 C.5CM906 B.THR186 6.95 -176.24 -2.69 6.06 2.08 27.68 -34.96 -175.93 34 1bsu GC-thr C.DI907 D.5CM806 A.THR186 6.86 -176.36 -2.68 6.06 1.78 22.71 -37.44 -176.08 35 1bsu GC-thr C.DI907 D.5CM806 B.THR186 -7.49 147.39 -1.05 -6.71 -3.18 -20.96 29.64 145.63 **************************************************************************** List of 31 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 1bsu OP1@C.DA902 NH2@B.ARG226 3.24 po4:sidechain:salt-bridge 2 1bsu OP2@C.DA902 NH2@B.ARG226 3.31 po4:sidechain:salt-bridge 3 1bsu OP2@C.DA902 OD1@B.ASN231 2.80 po4:sidechain 4 1bsu OP2@C.DA903 N@B.SER223 3.11 po4:backbone 5 1bsu O3'@C.DA902 OG@B.SER223 3.26 po4:sidechain 6 1bsu OP1@C.DA905 NZ@A.LYS119 2.65 po4:sidechain:salt-bridge 7 1bsu OP2@C.DA905 OG1@A.THR111 2.45 po4:sidechain 8 1bsu OP2@C.DA905 NH2@A.ARG221 3.22 po4:sidechain:salt-bridge 9 1bsu OP1@C.5CM906 OG@A.SER112 2.74 po4:sidechain 10 1bsu OP2@C.5CM906 N@A.GLY109 3.53 po4:backbone 11 1bsu OP1@C.DI907 OD2@A.ASP90 2.87 po4:sidechain 12 1bsu OP1@C.DI907 NZ@A.LYS92 3.00 po4:sidechain:salt-bridge 13 1bsu OP1@C.DT908 N@A.THR93 2.69 po4:backbone 14 1bsu OP2@C.DT908 OG1@A.THR106 2.78 po4:sidechain 15 1bsu OP1@C.DC909 OG1@A.THR37 2.64 po4:sidechain 16 1bsu OP2@C.DC909 OG1@A.THR94 3.01 po4:sidechain 17 1bsu OP1@C.DT910 N@B.GLN69 3.35 po4:backbone 18 1bsu OP2@C.DT910 OH@A.TYR95 2.88 po4:sidechain 19 1bsu O5'@D.DA802 NH2@A.ARG226 3.58 po4:sidechain 20 1bsu OP2@D.DA803 N@A.SER223 3.25 po4:backbone 21 1bsu OP2@D.DA805 OG1@B.THR111 2.70 po4:sidechain 22 1bsu OP1@D.5CM806 OG@B.SER112 2.99 po4:sidechain 23 1bsu OP2@D.5CM806 N@B.GLY109 3.50 po4:backbone 24 1bsu OP1@D.DI807 OD2@B.ASP90 2.99 po4:sidechain 25 1bsu OP1@D.DI807 NZ@B.LYS92 3.26 po4:sidechain:salt-bridge 26 1bsu OP1@D.DT808 N@B.THR93 2.80 po4:backbone 27 1bsu OP2@D.DT808 OG1@B.THR106 2.94 po4:sidechain 28 1bsu OP1@D.DC809 OG1@B.THR37 2.75 po4:sidechain 29 1bsu OP2@D.DC809 OG1@B.THR94 2.91 po4:sidechain 30 1bsu OP1@D.DT810 N@A.GLN69 3.90 po4:backbone 31 1bsu OP2@D.DT810 OH@B.TYR95 2.53 po4:sidechain **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 1bsu O4'@C.DT910 ND2@B.ASN70 3.27 sugar:sidechain **************************************************************************** List of 14 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 1bsu N7@C.DG904 N@B.ASN185 2.93 base:backbone 2 1bsu O6@C.DG904 N@B.GLY184 2.78 base:backbone 3 1bsu N7@C.DA905 ND2@B.ASN185 3.24 base:sidechain 4 1bsu N6@C.DA905 OD1@B.ASN185 3.05 base:sidechain 5 1bsu O4@C.DT908 OG1@A.THR186 2.63 base:sidechain 6 1bsu O2@C.DC909 ND2@B.ASN70 2.88 base:sidechain 7 1bsu N4@C.DC909 O@A.GLY182 2.94 base:backbone 8 1bsu N7@D.DA803 N@A.GLY184 3.21 base:backbone 9 1bsu N7@D.DG804 N@A.ASN185 3.03 base:backbone 10 1bsu O6@D.DG804 N@A.GLY184 2.92 base:backbone 11 1bsu N7@D.DA805 ND2@A.ASN185 3.01 base:sidechain 12 1bsu N6@D.DA805 OD1@A.ASN185 2.89 base:sidechain 13 1bsu O4@D.DT808 OG1@B.THR186 2.66 base:sidechain 14 1bsu N4@D.DC809 O@B.GLY182 3.05 base:backbone **************************************************************************** List of 2 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 1bsu A-asn C.DA905 B.ASN185 0.38 32 2 1bsu A-asn D.DA805 A.ASN185 0.30 29 **************************************************************************** List of 2 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 1bsu G-asn C.DG904 B.ASN185 3.50 26 2 1bsu G-asn D.DG804 A.ASN185 3.43 22 **************************************************************************** List of 3 additional files 1 -- 1bsu-baseAA-pairs.pdb 2 -- 1bsu-baseAA-stacks.pdb 3 -- 1bsu-pairs.pdb