**************************************************************************** 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/6jvz.pdb -o=6jvz.out --type=base File name: 6jvz.pdb no. of peptide chains: 2 [A=497,B=497] no. of DNA/RNA chains: 4 [C=17,D=17,I=17,J=17] no. of amino acids: 994 no. of nucleotides: 68 no. of atoms: 8705 no. of waters: 108 no. of metals: 0 **************************************************************************** List of 1 type of 2 modified nucleotides nt count list 1 5CM-c 2 I.5CM6,C.5CM6 **************************************************************************** List of 2 helices 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=16 strand-1 5'-TGTCCCTTcGCGTCTC-3' bp-type |||||||||||||||| strand-2 3'-ACAGGGAAGCGCAGAG-5' helix-form BBBBBBBB.B..BBB 1 I.DT-2 J.DA2 T-A WC 20-XX cWW cW-W 2 I.DG-1 J.DC1 G-C WC 19-XIX cWW cW-W 3 I.DT0 J.DA0 T-A WC 20-XX cWW cW-W 4 I.DC1 J.DG-1 C-G WC 19-XIX cWW cW-W 5 I.DC2 J.DG-2 C-G WC 19-XIX cWW cW-W 6 I.DC3 J.DG-3 C-G WC 19-XIX cWW cW-W 7 I.DT4 J.DA-4 T-A WC 20-XX cWW cW-W 8 I.DT5 J.DA-5 T-A WC 20-XX cWW cW-W 9 I.5CM6 J.DG-6 c-G WC 19-XIX cWW cW-W 10 I.DG7 J.DC-7 G-C WC 19-XIX cWW cW-W 11 I.DC8 J.DG-8 C-G WC 19-XIX cWW cW-W 12 I.DG9 J.DC-9 G-C WC 19-XIX cWW cW-W 13 I.DT10 J.DA-10 T-A WC 20-XX cWW cW-W 14 I.DC11 J.DG-11 C-G WC 19-XIX cWW cW-W 15 I.DT12 J.DA-12 T-A WC 20-XX cWW cW-W 16 I.DC13 J.DG-13 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=16 strand-1 5'-TGTCCCTTcGCGTCTC-3' bp-type |||||||||||||||| strand-2 3'-ACAGGGAAGCGCAGAG-5' helix-form BBBBBBBBBBBBBBB 1 C.DT-2 D.DA2 T-A WC 20-XX cWW cW-W 2 C.DG-1 D.DC1 G-C WC 19-XIX cWW cW-W 3 C.DT0 D.DA0 T-A WC 20-XX cWW cW-W 4 C.DC1 D.DG-1 C-G WC 19-XIX cWW cW-W 5 C.DC2 D.DG-2 C-G WC 19-XIX cWW cW-W 6 C.DC3 D.DG-3 C-G WC 19-XIX cWW cW-W 7 C.DT4 D.DA-4 T-A WC 20-XX cWW cW-W 8 C.DT5 D.DA-5 T-A WC 20-XX cWW cW-W 9 C.5CM6 D.DG-6 c-G WC 19-XIX cWW cW-W 10 C.DG7 D.DC-7 G-C WC 19-XIX cWW cW-W 11 C.DC8 D.DG-8 C-G WC 19-XIX cWW cW-W 12 C.DG9 D.DC-9 G-C WC 19-XIX cWW cW-W 13 C.DT10 D.DA-10 T-A WC 20-XX cWW cW-W 14 C.DC11 D.DG-11 C-G WC 19-XIX cWW cW-W 15 C.DT12 D.DA-12 T-A WC 20-XX cWW cW-W 16 C.DC13 D.DG-13 C-G WC 19-XIX cWW cW-W **************************************************************************** List of 80 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6jvz T-asp I.DT0 A.ASP301 8.86 -110.17 -3.25 7.87 2.43 38.81 -47.39 -96.61 2 6jvz C-asp I.DC1 A.ASP301 -8.74 -134.01 -3.56 7.98 0.01 25.44 -61.50 -124.28 3 6jvz C-arg I.DC2 A.ARG266 -11.38 101.14 7.01 -8.22 -3.57 25.89 -70.31 73.71 4 6jvz C-asp I.DC2 A.ASP301 -8.88 -165.33 -3.56 7.94 -1.75 9.84 -75.16 -161.38 5 6jvz C-asp I.DC2 A.ASP335 8.50 -140.81 -2.95 7.97 0.18 31.41 -69.02 -129.68 6 6jvz C-asp I.DC2 A.ASP369 8.93 -116.29 -3.01 8.01 2.54 48.25 -44.62 -102.15 7 6jvz C-asp I.DC3 A.ASP335 -8.96 -168.25 -3.39 8.12 -1.72 12.37 -77.98 -164.76 8 6jvz C-asp I.DC3 A.ASP369 8.37 -143.70 -3.17 7.75 0.17 35.10 -59.92 -135.46 9 6jvz T-asp I.DT4 A.ASP369 -9.29 -167.24 -3.65 8.30 -2.02 20.30 -73.84 -163.72 10 6jvz T-gly I.DT4 A.GLY403 8.78 -140.28 -3.37 8.10 -0.19 41.20 -64.45 -128.74 11 6jvz T-gly I.DT4 A.GLY404 -10.58 -174.41 -9.36 4.85 0.93 -7.90 -22.66 -174.28 12 6jvz T-gly I.DT5 A.GLY437 8.74 -134.55 -3.09 8.17 0.17 28.12 -66.98 -122.70 13 6jvz T-gly I.DT5 A.GLY438 -10.38 -173.63 -9.22 4.58 1.32 -15.05 -33.30 -173.29 14 6jvz T-ala I.DT5 A.ALA471 9.74 -105.39 -3.40 9.04 1.29 51.84 -40.89 -87.44 15 6jvz C-ala I.5CM6 A.ALA471 -9.17 -130.00 -3.04 8.51 -1.52 37.04 -55.02 -119.36 16 6jvz C-asn I.5CM6 A.ASN505 9.17 -114.39 -3.01 8.11 3.04 40.80 -48.48 -100.92 17 6jvz G-asn I.DG7 A.ASN505 8.19 -141.23 -3.42 7.39 0.79 24.98 -64.11 -132.56 18 6jvz C-asn I.DC8 A.ASN505 -8.86 -168.34 -3.67 7.91 -1.57 4.93 -73.65 -165.41 19 6jvz C-asp I.DC8 A.ASP539 8.34 -139.80 -2.82 7.83 0.54 21.59 -60.04 -132.24 20 6jvz C-asn I.DC8 A.ASN573 8.66 -119.80 -2.60 7.54 3.37 44.19 -48.51 -106.74 21 6jvz G-asp I.DG9 A.ASP539 -8.92 -167.77 -3.36 8.17 -1.23 10.38 -66.26 -165.31 22 6jvz G-asn I.DG9 A.ASN573 8.13 -146.22 -3.24 7.33 1.37 34.75 -62.18 -138.12 23 6jvz T-asn I.DT10 A.ASN573 -8.42 -174.86 -3.81 7.48 -0.69 13.22 -73.19 -173.55 24 6jvz T-gly I.DT10 A.GLY607 8.46 -144.64 -2.92 7.86 1.05 39.58 -64.04 -134.89 25 6jvz T-gly I.DT10 A.GLY608 -10.37 -177.19 -9.04 4.41 2.50 -14.38 -25.19 -177.09 26 6jvz T-asp I.DT10 A.ASP641 8.90 -119.57 -2.96 7.87 2.90 58.53 -47.05 -101.20 27 6jvz C-asp I.DC11 A.ASP641 8.19 -144.15 -2.70 7.73 0.22 38.22 -60.92 -135.30 28 6jvz T-gly I.DT12 A.GLY675 8.46 -140.20 -2.81 7.97 0.35 20.71 -48.25 -135.39 29 6jvz T-gly I.DT12 A.GLY676 -10.34 -174.98 -8.87 5.04 1.66 -27.59 -10.76 -174.80 30 6jvz T-leu I.DT14 A.LEU709 8.23 81.17 7.99 -0.51 1.91 14.44 -26.57 76.25 31 6jvz T-leu I.DT14 B.LEU721 8.73 52.72 -7.35 4.65 -0.67 -16.52 49.75 5.81 32 6jvz A-leu J.DA-14 B.LEU721 7.02 70.63 -3.50 -1.28 5.95 -61.74 -31.82 13.76 33 6jvz G-leu J.DG-13 B.LEU721 -7.26 -65.54 -6.39 -1.38 -3.15 -27.14 -45.39 -40.21 34 6jvz A-asn J.DA-10 A.ASN573 8.13 -179.64 3.25 7.44 -0.36 -23.82 -72.72 -179.55 35 6jvz A-arg J.DA-4 A.ARG266 11.69 -148.72 -7.75 8.36 -2.57 87.11 -15.23 -135.81 36 6jvz A-asp J.DA-4 A.ASP369 8.91 176.04 -2.91 -8.32 1.31 26.37 83.30 174.52 37 6jvz G-arg J.DG-3 A.ARG266 11.31 -95.27 3.24 9.84 4.54 -8.33 83.39 -50.27 38 6jvz G-asp J.DG-3 A.ASP335 9.04 175.36 -2.73 -8.57 0.89 19.63 86.74 173.50 39 6jvz G-arg J.DG-2 A.ARG266 -11.49 -107.54 7.48 8.37 2.46 19.99 74.37 -81.91 40 6jvz G-asp J.DG-2 A.ASP301 8.93 169.49 -3.31 -8.20 1.24 17.59 79.64 166.10 41 6jvz T-trp C.DT0 B.TRP232 -11.40 111.66 8.15 -6.66 -4.39 44.01 -47.65 96.57 42 6jvz T-asp C.DT0 B.ASP301 8.95 -110.70 -3.24 7.89 2.74 38.86 -50.37 -96.00 43 6jvz C-asp C.DC1 B.ASP301 8.72 -134.55 -3.47 8.00 0.25 24.74 -64.21 -124.16 44 6jvz C-asp C.DC2 B.ASP301 -8.92 -165.80 -3.51 8.08 -1.37 11.49 -77.02 -161.72 45 6jvz C-asp C.DC2 B.ASP335 8.77 -140.84 -2.96 8.24 0.49 32.80 -71.33 -128.71 46 6jvz C-asp C.DC3 B.ASP335 -8.99 -167.97 -3.16 8.31 -1.36 12.70 -81.34 -164.00 47 6jvz C-asp C.DC3 B.ASP369 8.60 -140.15 -2.89 8.09 0.49 31.95 -61.94 -130.94 48 6jvz T-asp C.DT4 B.ASP369 -9.36 -163.92 -3.46 8.54 -1.64 17.47 -73.04 -159.68 49 6jvz T-gly C.DT4 B.GLY403 9.09 -135.50 -3.14 8.53 -0.04 38.58 -62.60 -123.58 50 6jvz T-gly C.DT4 B.GLY404 -10.75 -174.50 -9.54 4.75 1.46 -9.83 -24.89 -174.35 51 6jvz T-gly C.DT5 B.GLY437 8.81 -132.22 -2.87 8.33 0.08 27.51 -66.14 -120.07 52 6jvz T-gly C.DT5 B.GLY438 -10.44 -173.85 -9.27 4.61 1.32 -15.62 -30.73 -173.56 53 6jvz T-ala C.DT5 B.ALA471 9.66 -105.47 -3.13 9.06 1.15 53.18 -39.48 -87.41 54 6jvz C-ala C.5CM6 B.ALA471 9.43 -128.73 -3.01 8.78 -1.63 39.94 -55.90 -116.79 55 6jvz C-asn C.5CM6 B.ASN505 8.98 -116.41 -3.07 7.79 3.24 40.92 -50.76 -102.57 56 6jvz G-asn C.DG7 B.ASN505 8.24 -145.16 -3.58 7.32 1.20 27.90 -66.25 -136.60 57 6jvz G-asp C.DG7 B.ASP539 8.79 -115.68 -3.00 7.52 3.42 43.30 -50.35 -100.99 58 6jvz C-asp C.DC8 B.ASP539 8.55 -140.27 -3.11 7.95 0.50 28.06 -61.31 -131.78 59 6jvz C-asn C.DC8 B.ASN573 8.71 -120.86 -3.05 7.43 3.37 48.78 -51.04 -105.59 60 6jvz G-asn C.DG9 B.ASN573 8.26 -145.47 -3.43 7.43 1.10 35.28 -65.95 -136.12 61 6jvz T-asn C.DT10 B.ASN573 -8.69 -172.75 -3.68 7.81 -1.00 14.09 -78.43 -170.55 62 6jvz T-gly C.DT10 B.GLY607 8.64 -140.24 -2.88 8.12 0.62 36.97 -66.82 -128.74 63 6jvz T-gly C.DT10 B.GLY608 -10.49 -177.73 -9.18 4.44 2.47 -18.90 -30.19 -177.62 64 6jvz T-asp C.DT10 B.ASP641 9.38 -133.47 -4.10 8.08 2.42 74.06 -49.80 -112.59 65 6jvz C-asp C.DC11 B.ASP641 8.65 -152.64 -3.99 7.67 -0.20 56.61 -68.06 -141.44 66 6jvz T-gly C.DT12 B.GLY676 -9.97 -161.42 -8.56 4.80 -1.74 57.70 -11.93 -158.63 67 6jvz C-his C.DC13 A.HIS724 5.68 167.52 4.68 -1.39 2.89 -43.96 -41.70 165.54 68 6jvz C-his C.DC13 A.HIS725 6.06 65.78 4.55 2.34 3.24 32.65 19.72 54.63 69 6jvz T-lys C.DT14 A.LYS720 -4.18 157.22 -0.61 -0.46 -4.11 36.67 -40.75 154.29 70 6jvz T-leu C.DT14 A.LEU721 -3.84 -97.35 1.71 0.81 -3.34 4.39 -25.73 -94.65 71 6jvz T-his C.DT14 A.HIS724 -7.29 131.18 4.11 -4.86 -3.55 37.49 -56.31 120.33 72 6jvz A-his D.DA-14 A.HIS723 7.32 -83.06 3.81 6.23 0.52 22.24 -15.46 -79.28 73 6jvz G-his D.DG-13 A.HIS724 -5.48 -178.58 4.68 0.96 -2.70 -56.53 43.06 -178.25 74 6jvz A-asp D.DA-12 B.ASP641 8.89 143.77 1.93 -8.66 -0.43 7.85 -79.42 132.17 75 6jvz C-asp D.DC-9 B.ASP539 8.53 170.46 -2.62 -8.11 0.30 19.90 66.76 168.37 76 6jvz A-arg D.DA-4 B.ARG266 11.54 -80.43 0.77 9.54 6.45 -23.29 76.18 -12.16 77 6jvz A-asp D.DA-4 B.ASP369 8.98 169.06 -2.83 -8.45 1.12 21.25 79.34 165.48 78 6jvz G-arg D.DG-3 B.ARG266 -11.38 -84.94 4.84 9.64 3.62 -6.61 74.85 -42.95 79 6jvz G-asp D.DG-3 B.ASP335 9.00 163.58 0.05 -8.96 0.92 -5.67 -86.59 157.33 80 6jvz G-asp D.DG-2 B.ASP301 8.78 168.94 -3.16 -8.11 1.13 16.77 83.62 164.95 **************************************************************************** List of 64 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 6jvz AT-ala J.DA-5 I.DT5 A.ALA471 -9.62 107.97 -3.44 -8.90 -1.19 54.38 45.86 87.42 2 6jvz AT-ala D.DA-5 C.DT5 B.ALA471 -9.57 107.97 -3.24 -8.91 -1.31 58.17 42.84 86.57 3 6jvz AT-arg J.DA-4 I.DT4 A.ARG266 11.70 -87.29 -1.07 8.98 7.42 -28.83 80.51 -19.45 4 6jvz AT-arg D.DA-4 C.DT4 B.ARG266 11.56 -76.72 0.70 9.24 6.90 -20.08 73.24 -11.83 5 6jvz AT-asn J.DA-10 I.DT10 A.ASN573 8.27 177.60 -3.53 -7.48 0.17 18.53 73.07 176.97 6 6jvz AT-asn D.DA-10 C.DT10 B.ASN573 8.68 173.69 -3.50 -7.91 0.73 16.41 77.21 171.83 7 6jvz AT-asp J.DA0 I.DT0 A.ASP301 -8.88 111.37 -3.30 -7.88 -2.42 41.77 52.10 95.07 8 6jvz AT-asp J.DA-4 I.DT4 A.ASP369 9.10 171.69 -3.27 -8.32 1.67 23.40 78.55 168.99 9 6jvz AT-asp J.DA-10 I.DT10 A.ASP641 -8.86 121.77 -2.95 -7.68 -3.30 63.40 49.90 100.66 10 6jvz AT-asp D.DA0 C.DT0 B.ASP301 -8.99 111.82 -3.52 -7.76 -2.88 43.73 55.42 93.26 11 6jvz AT-asp D.DA-4 C.DT4 B.ASP369 9.17 166.51 -3.14 -8.50 1.39 19.38 76.18 162.53 12 6jvz AT-asp D.DA-10 C.DT10 B.ASP641 -9.37 106.14 -6.47 -4.94 -4.65 -48.76 -74.02 65.77 13 6jvz AT-asp D.DA-12 C.DT12 B.ASP641 9.02 146.98 1.92 -8.80 0.37 0.42 -83.91 135.06 14 6jvz AT-gly J.DA-4 I.DT4 A.GLY403 -8.61 143.79 -3.19 -7.99 0.01 43.50 70.77 130.95 15 6jvz AT-gly J.DA-4 I.DT4 A.GLY404 10.43 177.83 -9.19 -4.85 -0.85 -3.00 26.22 177.78 16 6jvz AT-gly J.DA-5 I.DT5 A.GLY437 -8.68 138.33 -3.03 -8.13 -0.25 31.23 70.89 125.75 17 6jvz AT-gly J.DA-5 I.DT5 A.GLY438 10.37 176.41 -9.17 -4.69 -1.22 -10.33 34.47 176.22 18 6jvz AT-gly J.DA-10 I.DT10 A.GLY607 -8.35 147.25 -2.72 -7.74 -1.54 44.89 65.77 136.93 19 6jvz AT-gly J.DA-10 I.DT10 A.GLY608 -10.21 177.59 -8.87 -4.18 -2.85 -8.70 24.95 177.52 20 6jvz AT-gly J.DA-12 I.DT12 A.GLY675 -8.26 145.78 -2.45 -7.86 -0.66 24.42 58.45 139.55 21 6jvz AT-gly J.DA-12 I.DT12 A.GLY676 10.13 -179.26 8.62 5.08 -1.58 19.75 -16.90 -179.24 22 6jvz AT-gly D.DA-4 C.DT4 B.GLY403 -8.94 137.45 -2.97 -8.43 -0.13 39.89 66.63 124.48 23 6jvz AT-gly D.DA-4 C.DT4 B.GLY404 10.59 176.53 -9.38 -4.68 -1.47 -6.85 27.28 176.42 24 6jvz AT-gly D.DA-5 C.DT5 B.GLY437 -8.78 135.45 -2.86 -8.29 -0.40 33.00 68.37 122.54 25 6jvz AT-gly D.DA-5 C.DT5 B.GLY438 10.42 174.64 -9.26 -4.56 -1.48 -9.58 30.21 174.43 26 6jvz AT-gly D.DA-10 C.DT10 B.GLY607 -8.63 141.36 -2.69 -8.15 -0.89 39.58 66.43 129.87 27 6jvz AT-gly D.DA-10 C.DT10 B.GLY608 10.42 177.38 -9.03 -4.40 -2.77 -16.60 28.96 177.26 28 6jvz AT-gly D.DA-12 C.DT12 B.GLY676 -9.86 164.26 -8.33 -5.05 1.50 64.85 15.89 161.12 29 6jvz AT-trp D.DA0 C.DT0 B.TRP232 11.39 -115.93 8.56 6.58 3.62 39.18 49.32 -103.07 30 6jvz GC-ala J.DG-6 I.5CM6 A.ALA471 -9.15 134.10 -2.71 -8.60 1.53 37.67 60.53 122.65 31 6jvz GC-ala D.DG-6 C.5CM6 B.ALA471 -9.42 131.79 -2.86 -8.86 1.40 43.68 59.03 118.74 32 6jvz GC-arg J.DG-2 I.DC2 A.ARG266 -11.43 -104.29 7.25 8.31 3.02 22.95 72.37 -77.78 33 6jvz GC-arg J.DG-3 I.DC3 A.ARG266 11.25 -90.63 2.87 9.50 5.30 -3.22 80.08 -46.44 34 6jvz GC-arg D.DG-3 C.DC3 B.ARG266 11.39 -80.95 4.61 9.45 4.38 -1.01 71.99 -39.81 35 6jvz GC-asn J.DG-6 I.5CM6 A.ASN505 -9.11 118.19 -2.89 -8.11 -2.95 40.99 54.35 103.39 36 6jvz GC-asn I.DG7 J.DC-7 A.ASN505 8.03 -142.76 -3.24 7.28 0.93 24.69 -65.74 -134.05 37 6jvz GC-asn J.DG-8 I.DC8 A.ASN505 8.83 169.56 -3.56 -7.97 1.28 7.23 72.03 167.06 38 6jvz GC-asn J.DG-8 I.DC8 A.ASN573 -8.65 121.46 -2.47 -7.45 -3.64 47.08 48.38 107.96 39 6jvz GC-asn I.DG9 J.DC-9 A.ASN573 8.13 -151.15 -2.89 7.28 2.17 41.54 -62.44 -143.40 40 6jvz GC-asn D.DG-6 C.5CM6 B.ASN505 -8.93 119.39 -3.08 -7.68 -3.37 44.41 54.35 103.85 41 6jvz GC-asn C.DG7 D.DC-7 B.ASN505 8.18 -146.48 -3.53 7.31 0.97 28.12 -70.30 -137.15 42 6jvz GC-asn D.DG-8 C.DC8 B.ASN573 -8.73 120.79 -3.16 -7.42 -3.36 49.77 53.66 104.05 43 6jvz GC-asn C.DG9 D.DC-9 B.ASN573 8.10 -147.61 -3.10 7.27 1.78 38.94 -65.41 -138.50 44 6jvz GC-asp J.DG-1 I.DC1 A.ASP301 -8.67 137.40 -3.29 -8.01 -0.18 27.77 64.14 127.39 45 6jvz GC-asp J.DG-2 I.DC2 A.ASP301 8.90 167.39 -3.44 -8.07 1.51 13.69 77.46 163.68 46 6jvz GC-asp J.DG-2 I.DC2 A.ASP335 -8.49 142.51 -2.90 -7.97 -0.30 34.78 72.25 130.32 47 6jvz GC-asp J.DG-2 I.DC2 A.ASP369 -8.89 116.99 -3.11 -7.93 -2.54 50.91 48.24 100.65 48 6jvz GC-asp J.DG-3 I.DC3 A.ASP335 9.00 171.82 -3.06 -8.36 1.33 16.00 82.39 168.99 49 6jvz GC-asp J.DG-3 I.DC3 A.ASP369 -8.42 145.99 -3.00 -7.86 -0.32 38.20 65.52 136.48 50 6jvz GC-asp J.DG-8 I.DC8 A.ASP539 -8.32 141.14 -2.69 -7.83 -0.82 24.29 59.24 133.80 51 6jvz GC-asp I.DG9 J.DC-9 A.ASP539 -8.83 -172.19 -3.01 8.29 -0.34 16.80 -64.34 -170.66 52 6jvz GC-asp J.DG-11 I.DC11 A.ASP641 -8.20 144.32 -2.77 -7.72 -0.26 40.39 65.47 133.94 53 6jvz GC-asp D.DG-1 C.DC1 B.ASP301 -8.69 136.99 -3.29 -8.03 -0.43 27.89 66.86 125.94 54 6jvz GC-asp D.DG-2 C.DC2 B.ASP301 8.85 167.36 -3.34 -8.10 1.26 14.11 80.34 163.28 55 6jvz GC-asp D.DG-2 C.DC2 B.ASP335 -8.67 141.84 -2.90 -8.16 -0.50 34.71 75.20 128.32 56 6jvz GC-asp D.DG-3 C.DC3 B.ASP335 9.00 171.43 -2.91 -8.45 1.02 15.53 86.38 168.10 57 6jvz GC-asp D.DG-3 C.DC3 B.ASP369 -8.64 142.41 -2.82 -8.15 -0.58 34.00 68.07 131.71 58 6jvz GC-asp C.DG7 D.DC-7 B.ASP539 8.66 -116.23 -3.05 7.48 3.13 42.61 -54.43 -100.20 59 6jvz GC-asp D.DG-8 C.DC8 B.ASP539 -8.55 140.71 -3.09 -7.95 -0.56 29.59 63.91 131.41 60 6jvz GC-asp C.DG9 D.DC-9 B.ASP539 -8.84 -168.68 -2.98 8.27 -0.92 16.54 -68.38 -166.14 61 6jvz GC-asp D.DG-11 C.DC11 B.ASP641 -8.57 125.14 -2.63 -7.87 -2.14 -25.63 -83.55 100.84 62 6jvz GC-his D.DG-13 C.DC13 A.HIS724 -5.58 -173.10 4.68 1.17 -2.80 -50.27 42.30 -171.78 63 6jvz GC-his D.DG-13 C.DC13 A.HIS725 -6.09 -65.13 4.45 -2.44 -3.37 27.14 -14.63 -58.09 64 6jvz GC-leu J.DG-13 I.DC13 B.LEU721 -7.50 -66.31 -6.52 -1.36 -3.44 -18.16 -49.25 -42.06 **************************************************************************** List of 32 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 6jvz OP1@I.DG-1 N@A.THR270 3.74 po4:backbone 2 6jvz OP1@I.DT0 NE2@A.GLN305 2.75 po4:sidechain 3 6jvz OP2@I.DT0 OG1@A.THR270 3.48 po4:sidechain 4 6jvz OP1@I.DC1 NE2@A.GLN339 2.71 po4:sidechain 5 6jvz OP1@I.DC2 NE2@A.GLN373 2.90 po4:sidechain 6 6jvz OP1@I.DC3 NE2@A.GLN407 2.75 po4:sidechain 7 6jvz OP1@I.DT4 NE2@A.GLN441 2.79 po4:sidechain 8 6jvz OP1@I.DT5 NE2@A.GLN475 2.77 po4:sidechain 9 6jvz OP1@I.5CM6 NE2@A.GLN509 2.98 po4:sidechain 10 6jvz OP1@I.DG7 NE2@A.GLN543 3.06 po4:sidechain 11 6jvz OP1@I.DC8 NE2@A.GLN577 2.61 po4:sidechain 12 6jvz OP1@I.DG9 NE2@A.GLN611 2.72 po4:sidechain 13 6jvz OP1@I.DT10 NE2@A.GLN645 3.02 po4:sidechain 14 6jvz OP1@I.DC11 NE@A.ARG678 3.76 po4:sidechain:salt-bridge 15 6jvz OP1@I.DT12 NE@A.ARG712 2.82 po4:sidechain:salt-bridge 16 6jvz OP1@I.DT12 NH2@A.ARG712 3.22 po4:sidechain:salt-bridge 17 6jvz O3'@I.DC11 NH2@A.ARG712 3.21 po4:sidechain 18 6jvz OP2@J.DG-3 NZ@A.LYS265 3.62 po4:sidechain:salt-bridge 19 6jvz OP1@C.DT0 NE2@B.GLN305 2.52 po4:sidechain 20 6jvz OP2@C.DT0 OG1@B.THR270 3.06 po4:sidechain 21 6jvz OP1@C.DC1 NE2@B.GLN339 2.68 po4:sidechain 22 6jvz OP1@C.DC2 NE2@B.GLN373 2.85 po4:sidechain 23 6jvz OP1@C.DC3 NE2@B.GLN407 2.81 po4:sidechain 24 6jvz OP1@C.DT4 NE2@B.GLN441 2.91 po4:sidechain 25 6jvz OP1@C.DT5 NE2@B.GLN475 2.71 po4:sidechain 26 6jvz OP1@C.5CM6 NE2@B.GLN509 2.82 po4:sidechain 27 6jvz OP1@C.DG7 NE2@B.GLN543 3.03 po4:sidechain 28 6jvz OP1@C.DC8 NE2@B.GLN577 2.84 po4:sidechain 29 6jvz OP1@C.DG9 NE2@B.GLN611 2.78 po4:sidechain 30 6jvz OP1@C.DT10 NZ@B.LYS644 3.07 po4:sidechain:salt-bridge 31 6jvz OP2@C.DT10 N@B.GLY643 3.79 po4:backbone 32 6jvz O5'@D.DA-14 O@A.HIS726 2.67 po4:backbone **************************************************************************** List of 23 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 6jvz N4@I.DC1 OD2@A.ASP301 3.07 base:sidechain 2 6jvz N4@I.DC2 OD2@A.ASP301 3.94 base:sidechain 3 6jvz N4@I.DC2 OD2@A.ASP335 2.86 base:sidechain 4 6jvz N4@I.DC3 OD2@A.ASP369 3.00 base:sidechain 5 6jvz N7@I.DG7 ND2@A.ASN505 3.01 base:sidechain 6 6jvz O6@I.DG7 ND2@A.ASN505 2.91 base:sidechain 7 6jvz N4@I.DC8 OD2@A.ASP539 2.65 base:sidechain 8 6jvz N7@I.DG9 ND2@A.ASN573 3.14 base:sidechain 9 6jvz O6@I.DG9 ND2@A.ASN573 2.98 base:sidechain 10 6jvz N4@I.DC11 OD2@A.ASP641 2.98 base:sidechain 11 6jvz N7@J.DG-3 NH1@A.ARG266 3.07 base:sidechain 12 6jvz O6@J.DG-3 NH2@A.ARG266 2.97 base:sidechain 13 6jvz N4@C.DC1 OD2@B.ASP301 2.78 base:sidechain 14 6jvz N4@C.DC2 OD2@B.ASP335 3.09 base:sidechain 15 6jvz N4@C.DC3 OD2@B.ASP369 3.02 base:sidechain 16 6jvz N7@C.DG7 ND2@B.ASN505 2.81 base:sidechain 17 6jvz O6@C.DG7 ND2@B.ASN505 2.89 base:sidechain 18 6jvz N4@C.DC8 OD2@B.ASP539 2.77 base:sidechain 19 6jvz N7@C.DG9 ND2@B.ASN573 3.14 base:sidechain 20 6jvz O6@C.DG9 ND2@B.ASN573 3.09 base:sidechain 21 6jvz N4@C.DC11 OD2@B.ASP641 3.13 base:sidechain 22 6jvz N6@D.DA-14 O@A.HIS723 3.84 base:backbone 23 6jvz O6@D.DG-3 NH2@B.ARG266 3.28 base:sidechain **************************************************************************** List of 16 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 6jvz C-asp I.DC1 A.ASP301 0.88 20 2 6jvz C-asp I.DC2 A.ASP301 1.99 17 3 6jvz C-asp I.DC2 A.ASP335 0.54 10 4 6jvz C-asp I.DC3 A.ASP369 1.04 11 5 6jvz G-asn I.DG7 A.ASN505 0.26 4 6 6jvz C-asp I.DC8 A.ASP539 1.03 13 7 6jvz G-asn I.DG9 A.ASN573 0.49 19 8 6jvz C-asp I.DC11 A.ASP641 0.52 35 9 6jvz G-arg J.DG-3 A.ARG266 0.12 9 10 6jvz C-asp C.DC1 B.ASP301 0.47 7 11 6jvz C-asp C.DC2 B.ASP335 0.35 14 12 6jvz C-asp C.DC3 B.ASP369 0.83 3 13 6jvz G-asn C.DG7 B.ASN505 0.09 12 14 6jvz C-asp C.DC8 B.ASP539 0.73 8 15 6jvz G-asn C.DG9 B.ASN573 0.21 16 16 6jvz C-asp C.DC11 B.ASP641 0.14 16 **************************************************************************** List of 6 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 6jvz T-asp I.DT0 A.ASP301 3.90 19 2 6jvz C-asn I.5CM6 A.ASN505 3.92 6 3 6jvz T-asp C.DT0 B.ASP301 3.75 7 4 6jvz C-asn C.5CM6 B.ASN505 3.73 10 5 6jvz C-asn C.DC8 B.ASN573 3.79 18 6 6jvz C-his C.DC13 A.HIS724 3.85 21 **************************************************************************** List of 3 additional files 1 -- 6jvz-baseAA-pairs.pdb 2 -- 6jvz-baseAA-stacks.pdb 3 -- 6jvz-pairs.pdb