**************************************************************************** File name: 5xus.pdb no. of peptide chains: 1 [A=1206] no. of DNA/RNA chains: 3 [B=40,C=29,D=9] no. of amino acids: 1206 no. of nucleotides: 78 no. of atoms: 11530 no. of waters: 135 no. of metals: 5 [Na=3,Mg=2] **************************************************************************** List of 3 helices Note: A helix is defined by base-stacking interactions, regardless of pair 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=7 strand-1 5'-AGUAGAU-3' bp-type .|||||. strand-2 3'-UCAUCUU-5' helix-form x.AAA. 1 B.A-19 B.U-11 A-U rHoogsteen 24-XXIV tHW tM-W 2 B.G-6 B.C-12 G-C WC 19-XIX cWW cW-W 3 B.U-5 B.A-13 U-A WC 20-XX cWW cW-W 4 B.A-4 B.U-14 A-U WC 20-XX cWW cW-W 5 B.G-3 B.C-15 G-C WC 19-XIX cWW cW-W 6 B.A-2 B.U-16 A-U WC 20-XX cWW cW-W 7 B.U-1 B.U-17 U-U -- 16-XVI cWW cW-W -------------------------------------------------------------------------- helix#2[0] bps=20 strand-1 5'-GGAAAUUAGGUGCGCUUGGC-3' bp-type |||||||||||||||||||| strand-2 3'-CCTTTAATCCACGCGAACCG-5' helix-form ........AAAAAAAA.AA 1 B.G0 C.DC0 G-C WC 19-XIX cWW cW-W 2 B.G1 C.DC-1 G-C WC 19-XIX cWW cW-W 3 B.A2 C.DT-2 A-T WC 20-XX cWW cW-W 4 B.A3 C.DT-3 A-T WC 20-XX cWW cW-W 5 B.A4 C.DT-4 A-T WC 20-XX cWW cW-W 6 B.U5 C.DA-5 U-A WC 20-XX cWW cW-W 7 B.U6 C.DA-6 U-A WC 20-XX cWW cW-W 8 B.A7 C.DT-7 A-T WC 20-XX cWW cW-W 9 B.G8 C.DC-8 G-C WC 19-XIX cWW cW-W 10 B.G9 C.DC-9 G-C WC 19-XIX cWW cW-W 11 B.U10 C.DA-10 U-A WC 20-XX cWW cW-W 12 B.G11 C.DC-11 G-C WC 19-XIX cWW cW-W 13 B.C12 C.DG-12 C-G WC 19-XIX cWW cW-W 14 B.G13 C.DC-13 G-C WC 19-XIX cWW cW-W 15 B.C14 C.DG-14 C-G WC 19-XIX cWW cW-W 16 B.U15 C.DA-15 U-A WC 20-XX cWW cW-W 17 B.U16 C.DA-16 U-A WC 20-XX cWW cW-W 18 B.G17 C.DC-17 G-C WC 19-XIX cWW cW-W 19 B.G18 C.DC-18 G-C WC 19-XIX cWW cW-W 20 B.C19 C.DG-19 C-G WC 19-XIX cWW cW-W -------------------------------------------------------------------------- helix#3[0] bps=9 strand-1 5'-TAAAGGACG-3' bp-type ||||||||| strand-2 3'-ATTTCCTGC-5' helix-form .BB.BBBB 1 C.DT1 D.DA-1 T-A WC 20-XX cWW cW-W 2 C.DA2 D.DT-2 A-T WC 20-XX cWW cW-W 3 C.DA3 D.DT-3 A-T WC 20-XX cWW cW-W 4 C.DA4 D.DT-4 A-T WC 20-XX cWW cW-W 5 C.DG5 D.DC-5 G-C WC 19-XIX cWW cW-W 6 C.DG6 D.DC-6 G-C WC 19-XIX cWW cW-W 7 C.DA7 D.DT-7 A-T WC 20-XX cWW cW-W 8 C.DC8 D.DG-8 C-G WC 19-XIX cWW cW-W 9 C.DG9 D.DC-9 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 96 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5xus A-his B.A-20 A.HIS759 -8.79 105.83 5.43 5.03 -4.74 -3.91 89.60 63.47 2 5xus A-ile B.A-20 A.ILE765 -5.19 155.86 -0.32 -3.27 -4.01 19.75 -30.81 154.56 3 5xus A-ala B.A-20 A.ALA766 -6.07 68.66 5.20 -0.28 -3.12 -50.65 -11.49 46.57 4 5xus A-asn B.A-20 A.ASN767 5.27 -130.27 1.62 2.54 4.33 -68.57 37.25 -114.47 5 5xus A-thr B.A-20 A.THR777 -4.77 -69.08 3.24 -3.50 -0.03 35.34 32.45 -51.26 6 5xus A-val B.A-20 A.VAL783 -8.87 172.92 1.95 8.34 -2.28 -51.75 -48.98 171.28 7 5xus A-leu B.A-19 A.LEU779 -7.37 -66.34 5.26 -1.65 -4.90 -2.51 34.56 -57.47 8 5xus A-tyr B.A-19 A.TYR781 -8.12 -154.00 -1.40 0.28 -7.99 -57.21 -42.32 -147.89 9 5xus A-val B.A-19 A.VAL783 -7.37 -176.33 -1.76 -3.24 -6.39 24.32 42.49 -175.97 10 5xus U-lys B.U-18 A.LYS707 -11.34 158.08 7.07 8.75 -1.43 13.03 69.71 153.01 11 5xus U-arg B.U-18 A.ARG788 12.54 -125.40 -11.19 5.43 1.65 -13.60 25.49 -123.46 12 5xus U-arg B.U-17 A.ARG18 -6.62 -151.83 -4.76 -0.22 -4.59 -54.33 -1.81 -148.25 13 5xus U-asn B.U-17 A.ASN706 -9.79 109.66 7.07 6.36 -2.35 -51.37 -60.54 83.05 14 5xus U-asn B.U-17 A.ASN718 -7.61 -23.10 7.03 2.75 -0.94 10.50 7.34 -19.26 15 5xus U-his B.U-17 A.HIS720 -6.40 -167.25 -2.38 5.13 -2.98 -32.60 -66.89 -163.97 16 5xus U-arg B.U-16 A.ARG18 -9.72 161.46 4.46 -1.58 -8.49 47.04 -13.55 159.61 17 5xus U-lys B.U-16 A.LYS707 -10.28 102.27 9.94 -2.04 1.64 -61.19 50.14 71.05 18 5xus U-asn B.U-16 A.ASN718 -6.61 -68.18 5.53 -0.59 -3.57 6.77 -3.62 -67.80 19 5xus A-phe B.A-10 A.PHE863 -5.63 -145.16 -2.84 1.44 -4.65 -54.00 -44.98 -137.04 20 5xus A-ile B.A-10 A.ILE866 -7.52 110.94 0.79 -1.74 -7.27 23.57 -62.20 94.65 21 5xus A-ile B.A-10 A.ILE868 -6.48 91.02 6.12 -1.89 -1.02 -73.76 45.18 31.64 22 5xus A-lys B.A-9 A.LYS774 9.29 -177.04 -4.88 7.62 2.10 19.36 4.75 -176.99 23 5xus A-asn B.A-9 A.ASN864 5.03 117.70 -4.14 -2.72 0.86 44.39 41.59 106.29 24 5xus A-ile B.A-9 A.ILE866 7.69 117.37 0.44 -6.85 3.47 -15.36 -46.73 110.28 25 5xus G-lys B.G-8 A.LYS774 -8.07 140.13 -4.78 -6.29 -1.60 -46.73 -39.91 133.26 26 5xus G-thr B.G-8 A.THR777 4.67 -176.31 1.92 2.10 3.70 17.42 -12.95 -176.24 27 5xus G-leu B.G-8 A.LEU779 7.47 -163.02 -3.75 0.25 6.46 -2.37 -15.94 -162.85 28 5xus U-tyr B.U-7 A.TYR781 -4.97 -67.51 3.33 1.48 -3.39 -1.37 60.90 -30.61 29 5xus U-lys B.U-5 A.LYS707 12.13 -143.10 -4.82 11.12 -0.43 44.68 -21.03 -139.23 30 5xus G-asn B.G-3 A.ASN718 8.16 -89.22 0.14 5.54 5.98 -26.06 20.52 -84.06 31 5xus G-ser B.G-3 A.SER905 8.71 151.95 0.26 8.31 2.61 1.99 -25.49 151.22 32 5xus A-asn B.A-2 A.ASN718 6.61 -123.66 0.20 6.08 2.56 -19.94 20.84 -121.66 33 5xus U-arg B.U-1 A.ARG18 7.17 -48.25 -2.28 -3.70 5.70 -4.33 -33.91 -34.57 34 5xus U-asn B.U-1 A.ASN718 -4.86 -167.09 0.95 4.70 -0.78 -11.03 18.01 -166.87 35 5xus U-leu B.U-1 A.LEU719 6.18 119.76 4.95 -2.93 -2.27 -43.38 -54.16 104.77 36 5xus U-his B.U-1 A.HIS720 4.58 -65.77 3.15 -1.06 3.14 -64.24 -12.38 -7.22 37 5xus G-ser B.G0 A.SER14 -4.41 -102.76 -1.48 1.91 -3.68 -23.86 -32.41 -96.68 38 5xus G-lys B.G0 A.LYS15 -5.60 -120.86 -4.06 2.23 -3.15 -67.59 1.29 -107.14 39 5xus G-thr B.G0 A.THR16 -7.13 -115.23 -6.85 -1.36 1.48 -45.55 -76.11 -82.99 40 5xus G-pro B.G0 A.PRO799 -7.00 122.21 -2.91 5.07 -3.86 -18.55 37.31 117.74 41 5xus G-thr B.G1 A.THR16 -8.86 -125.65 -8.31 3.06 -0.13 -61.81 -52.17 -106.25 42 5xus A-asn B.A3 A.ASN157 8.08 65.91 -5.86 2.65 4.89 -35.24 -36.44 43.60 43 5xus A-asn B.A4 A.ASN157 -9.58 59.98 -6.06 7.04 2.33 -51.89 -27.19 13.52 44 5xus A-thr B.A4 A.THR169 8.18 -156.70 -1.10 -7.63 -2.72 -63.02 30.62 -151.44 45 5xus U-thr B.U5 A.THR169 -8.90 -179.85 -2.93 -5.62 -6.24 -52.41 38.34 -179.82 46 5xus G-arg B.G9 A.ARG887 10.81 83.95 -8.37 -0.67 6.80 -22.71 -2.44 81.34 47 5xus U-arg B.U10 A.ARG887 8.63 60.02 -7.18 3.17 3.59 -27.52 0.93 53.87 48 5xus C-arg B.C12 A.ARG508 -11.09 165.03 1.66 10.64 2.65 -34.78 80.00 159.27 49 5xus G-asp B.G13 A.ASP505 -10.56 88.25 0.55 8.53 -6.20 27.51 57.92 64.23 50 5xus G-arg B.G13 A.ARG508 -13.23 130.73 8.26 10.32 -0.50 -25.81 77.76 112.98 51 5xus U-lys B.U15 A.LYS251 -9.41 -38.65 -8.53 3.58 -1.72 19.53 -22.57 -24.84 52 5xus U-leu B.U16 A.LEU261 9.01 126.86 -2.36 4.09 7.67 -66.29 -51.12 106.19 53 5xus G-gln B.G17 A.GLN264 9.89 75.52 -8.99 2.97 2.85 -71.29 21.22 14.17 54 5xus G-gln B.G18 A.GLN264 -11.13 -72.96 -6.50 8.94 1.29 -61.35 35.39 -18.83 55 5xus C-ser B.C19 A.SER345 6.33 -79.00 6.20 0.48 1.15 -37.07 -47.16 -54.01 56 5xus C-trp B.C19 A.TRP355 5.54 133.05 -2.72 -4.18 2.40 -59.32 38.46 121.53 57 5xus G-ser C.DG-19 A.SER345 -6.35 -138.33 0.79 6.17 -1.27 -51.92 -34.95 -130.81 58 5xus G-lys C.DG-19 A.LYS349 -9.10 -161.39 -6.26 6.55 -0.80 -75.69 -32.56 -155.18 59 5xus G-trp C.DG-19 A.TRP355 -5.52 88.68 4.26 2.51 -2.45 -35.65 64.13 53.78 60 5xus A-asn C.DA-16 A.ASN260 9.12 163.95 0.08 8.62 2.99 -22.46 63.03 160.74 61 5xus A-gln C.DA-16 A.GLN264 -10.28 147.26 3.35 8.95 -3.80 -1.48 73.01 138.94 62 5xus A-glu C.DA-15 A.GLU257 8.32 100.72 -2.12 7.12 -3.75 43.48 66.37 68.05 63 5xus A-asn C.DA-15 A.ASN260 -10.08 137.93 5.17 8.65 0.32 -5.99 75.91 125.74 64 5xus G-lys C.DG-14 A.LYS251 -9.07 173.99 0.03 8.86 -1.97 15.22 -20.91 173.83 65 5xus G-glu C.DG-14 A.GLU257 -10.91 72.50 1.87 7.17 -8.00 45.40 39.78 42.21 66 5xus G-arg C.DG-12 A.ARG508 11.01 86.50 -10.81 -1.73 -1.18 -67.91 44.77 32.40 67 5xus C-arg C.DC-11 A.ARG508 -10.79 -83.08 -9.28 3.76 -4.02 -59.52 57.40 -8.84 68 5xus C-asn C.DC-11 A.ASN509 9.69 101.98 -2.24 6.60 6.73 -73.87 -12.91 75.00 69 5xus T-ser C.DT-4 A.SER168 -8.96 56.41 -6.92 3.95 -4.09 53.66 13.46 11.47 70 5xus T-thr C.DT-4 A.THR169 7.94 -56.93 -7.01 -0.43 3.69 11.03 -52.07 -20.97 71 5xus T-asn C.DT-3 A.ASN160 10.94 158.78 3.08 10.50 0.13 18.34 27.36 157.86 72 5xus T-thr C.DT-3 A.THR169 -9.42 -78.92 -9.15 2.20 0.54 -1.93 -55.14 -58.83 73 5xus T-asn C.DT-2 A.ASN157 -9.22 106.00 -0.03 5.50 -7.40 52.06 33.04 91.01 74 5xus C-ser C.DC0 A.SER14 4.57 -95.82 1.50 -1.78 3.94 -30.33 -28.84 -88.29 75 5xus C-pro C.DC0 A.PRO799 7.29 71.27 -5.30 3.33 3.72 -41.61 15.23 57.31 76 5xus T-pro C.DT1 A.PRO587 -8.73 89.45 -4.53 3.08 -6.80 72.97 -12.08 54.40 77 5xus T-met C.DT1 A.MET592 -7.84 -90.93 -3.11 -4.06 -5.94 -52.56 34.05 -69.65 78 5xus A-lys C.DA2 A.LYS538 11.18 92.34 8.41 7.23 -1.34 8.67 -59.55 73.67 79 5xus A-tyr C.DA2 A.TYR542 12.60 125.62 8.04 -2.86 9.26 -36.51 72.97 105.74 80 5xus A-met C.DA2 A.MET592 -8.90 -133.65 -2.11 -4.03 -7.65 -52.79 55.79 -119.70 81 5xus A-lys C.DA2 A.LYS595 9.58 78.96 -9.55 0.30 0.76 -71.69 -1.80 35.53 82 5xus A-gln C.DA3 A.GLN529 -9.88 169.95 -1.30 -9.72 1.28 26.45 71.18 167.25 83 5xus A-lys C.DA3 A.LYS538 -10.32 75.45 7.82 5.29 -4.17 -14.06 -58.87 47.37 84 5xus A-lys C.DA3 A.LYS595 -10.75 78.45 -9.35 4.80 -2.23 -76.78 15.96 2.40 85 5xus A-lys C.DA4 A.LYS538 -10.46 56.19 7.08 2.47 -7.30 -34.30 -44.46 2.21 86 5xus A-lys C.DA4 A.LYS595 -12.18 -89.21 -6.08 9.29 -5.00 -65.02 48.75 -40.52 87 5xus C-asp D.DC-6 A.ASP541 10.52 -87.73 -3.07 7.32 6.91 -25.93 -13.02 -83.74 88 5xus C-gln D.DC-5 A.GLN529 11.55 98.79 9.84 4.17 4.39 -34.28 -52.54 80.68 89 5xus C-asp D.DC-5 A.ASP541 9.32 -120.37 -1.09 8.37 3.97 -21.83 -8.98 -118.95 90 5xus T-thr D.DT-4 A.THR149 10.45 -84.37 -3.99 6.93 6.73 -58.28 56.43 -25.49 91 5xus T-gln D.DT-4 A.GLN529 10.64 74.63 10.07 3.15 1.39 -43.14 -41.87 46.47 92 5xus T-thr D.DT-3 A.THR149 -10.06 100.55 7.43 4.75 -4.84 -47.93 -73.71 54.78 93 5xus T-lys D.DT-2 A.LYS595 9.32 157.74 -0.31 9.25 1.17 20.72 68.20 152.52 94 5xus A-lys D.DA-1 A.LYS591 7.56 156.16 1.09 6.43 3.81 18.16 68.10 150.70 95 5xus A-met D.DA-1 A.MET592 7.85 -116.97 -4.61 -2.94 5.63 29.91 -64.65 -99.96 96 5xus A-lys D.DA-1 A.LYS595 -8.89 123.58 2.61 7.73 -3.53 31.40 69.74 106.00 **************************************************************************** List of 66 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 5xus AU-leu B.A-19 B.U-11 A.LEU779 -8.54 -108.32 3.83 -5.62 -5.17 17.76 31.84 -103.88 2 5xus AU-tyr B.A-19 B.U-11 A.TYR781 -9.33 167.97 0.28 0.22 -9.33 64.59 11.79 165.68 3 5xus AU-val B.A-19 B.U-11 A.VAL783 -6.74 140.25 1.52 3.42 -5.61 -43.39 -33.60 134.95 4 5xus AU-lys B.A-13 B.U-5 A.LYS707 -12.02 -69.15 11.00 -4.86 0.06 -25.14 50.16 -42.18 5 5xus GC-asn B.G-3 B.C-15 A.ASN718 8.14 -89.73 0.17 5.24 6.22 -21.74 18.03 -86.08 6 5xus GC-ser B.G-3 B.C-15 A.SER905 8.68 151.08 0.23 8.35 2.36 -2.85 -27.62 150.19 7 5xus AU-arg B.A-2 B.U-16 A.ARG18 9.65 41.77 2.14 -4.72 8.13 13.92 -36.99 13.80 8 5xus AU-lys B.A-2 B.U-16 A.LYS707 -10.28 129.69 1.92 -9.69 -2.82 -39.78 67.53 113.48 9 5xus AU-asn B.A-2 B.U-16 A.ASN718 6.61 -117.79 -0.19 5.84 3.08 -12.04 13.49 -116.92 10 5xus UU-arg B.U-1 B.U-17 A.ARG18 6.72 -54.79 -1.30 -4.24 5.05 -3.26 -44.14 -33.14 11 5xus UU-asn B.U-1 B.U-17 A.ASN706 8.72 123.58 -6.23 -6.03 0.98 70.11 55.49 96.61 12 5xus UU-asn B.U-1 B.U-17 A.ASN718 -6.19 -163.92 1.89 5.89 -0.05 -1.90 14.13 -163.79 13 5xus UU-leu B.U-1 B.U-17 A.LEU719 7.09 127.44 5.00 -4.43 -2.38 -51.33 -59.21 110.34 14 5xus UU-his B.U-1 B.U-17 A.HIS720 5.34 -70.46 4.12 -1.69 2.94 -65.92 -22.46 -11.45 15 5xus GC-ser B.G0 C.DC0 A.SER14 -4.49 -100.76 -1.63 1.71 -3.81 -26.35 -31.35 -94.20 16 5xus GC-lys B.G0 C.DC0 A.LYS15 -5.70 -120.53 -4.16 2.06 -3.30 -70.67 1.52 -105.10 17 5xus GC-thr B.G0 C.DC0 A.THR16 -7.24 -112.68 -6.89 -1.52 1.60 -46.86 -75.19 -78.50 18 5xus GC-pro B.G0 C.DC0 A.PRO799 -7.14 124.72 -3.12 5.19 -3.79 -16.87 39.45 120.21 19 5xus GC-thr B.G1 C.DC-1 A.THR16 -8.77 -131.46 -8.17 3.09 -0.70 -58.83 -58.32 -113.53 20 5xus AT-asn B.A2 C.DT-2 A.ASN157 9.21 92.68 -5.06 -0.46 7.69 -25.01 -44.52 80.18 21 5xus AT-asn B.A3 C.DT-3 A.ASN157 8.13 77.35 -6.39 2.83 4.16 -43.44 -46.82 46.16 22 5xus AT-asn B.A3 C.DT-3 A.ASN160 10.85 30.59 -10.43 -2.88 0.80 -21.03 -6.49 21.38 23 5xus AT-thr B.A3 C.DT-3 A.THR169 9.34 -128.50 2.13 -9.10 -0.01 -63.76 8.45 -118.25 24 5xus AT-asn B.A4 C.DT-4 A.ASN157 -9.55 71.14 -6.15 7.21 1.19 -61.31 -33.74 13.71 25 5xus AT-ser B.A4 C.DT-4 A.SER168 9.05 164.84 -3.92 6.78 4.54 -6.19 -61.12 162.35 26 5xus AT-thr B.A4 C.DT-4 A.THR169 8.05 -158.92 -0.79 -7.34 -3.21 -57.75 20.74 -155.44 27 5xus GC-arg B.G9 C.DC-9 A.ARG887 11.02 86.53 -8.69 -0.55 6.75 -27.16 -5.81 82.80 28 5xus GC-arg B.G11 C.DC-11 A.ARG508 10.79 -172.52 3.67 -9.11 4.46 50.84 -59.23 -170.37 29 5xus GC-asn B.G11 C.DC-11 A.ASN509 -9.71 124.75 -6.71 2.61 -6.52 18.76 76.86 106.06 30 5xus GC-asp B.G13 C.DC-13 A.ASP505 -10.55 84.51 0.69 8.23 -6.58 23.34 53.78 63.82 31 5xus GC-arg B.G13 C.DC-13 A.ARG508 -13.21 127.64 8.34 10.19 -1.04 -30.66 75.66 108.67 32 5xus GC-gln B.G17 C.DC-17 A.GLN264 10.27 77.69 -9.53 2.91 2.48 -74.15 17.79 16.14 33 5xus GC-gln B.G18 C.DC-18 A.GLN264 -11.16 -73.43 -6.79 8.77 1.25 -62.85 34.28 -17.54 34 5xus GC-ser C.DG-19 B.C19 A.SER345 -6.34 -136.02 0.63 6.19 -1.21 -49.55 -36.06 -128.40 35 5xus GC-lys C.DG-19 B.C19 A.LYS349 -9.10 -159.15 -6.43 6.39 -0.73 -73.41 -33.98 -152.49 36 5xus GC-trp C.DG-19 B.C19 A.TRP355 -5.53 88.92 4.22 2.62 -2.43 -37.11 61.74 56.12 37 5xus AU-asn C.DA-16 B.U16 A.ASN260 9.17 162.99 0.10 8.77 2.67 -25.46 64.34 159.30 38 5xus AU-leu C.DA-16 B.U16 A.LEU261 -8.93 109.56 -4.10 2.62 -7.49 54.16 67.60 75.15 39 5xus AU-gln C.DA-16 B.U16 A.GLN264 -10.33 145.70 3.36 8.82 -4.20 -4.50 73.65 136.73 40 5xus AU-lys C.DA-15 B.U15 A.LYS251 9.39 -159.31 3.31 -8.43 2.47 -30.65 18.54 -158.25 41 5xus AU-glu C.DA-15 B.U15 A.GLU257 -8.30 97.45 -1.99 6.96 -4.07 40.23 58.84 71.48 42 5xus AU-asn C.DA-15 B.U15 A.ASN260 -10.07 133.58 5.21 8.62 -0.03 -11.63 69.60 122.27 43 5xus GC-lys C.DG-14 B.C14 A.LYS251 -9.19 176.71 -0.19 8.83 -2.55 8.36 -20.54 176.65 44 5xus GC-glu C.DG-14 B.C14 A.GLU257 -10.92 69.23 2.09 7.01 -8.11 41.64 34.04 45.32 45 5xus GC-arg C.DG-12 B.C12 A.ARG508 11.05 87.61 -10.76 -1.67 -1.87 -74.15 39.96 26.73 46 5xus AU-arg C.DA-10 B.U10 A.ARG887 -8.80 130.74 -3.39 7.43 -3.28 2.38 31.91 128.61 47 5xus AU-thr C.DA-5 B.U5 A.THR169 8.97 56.54 -5.45 -2.57 6.64 32.70 -46.12 0.15 48 5xus AT-lys C.DA2 D.DT-2 A.LYS538 11.17 100.46 8.35 7.37 -0.91 8.39 -68.32 78.32 49 5xus AT-tyr C.DA2 D.DT-2 A.TYR542 12.66 120.75 7.33 -2.46 10.02 -41.15 64.47 101.99 50 5xus AT-met C.DA2 D.DT-2 A.MET592 -8.79 -125.88 -1.87 -3.31 -7.92 -45.48 52.99 -112.60 51 5xus AT-lys C.DA2 D.DT-2 A.LYS595 -9.45 77.04 -9.45 0.30 -0.23 -70.34 -11.33 31.50 52 5xus AT-thr C.DA3 D.DT-3 A.THR149 9.97 -128.59 9.41 0.29 -3.26 72.29 -45.04 -107.81 53 5xus AT-gln C.DA3 D.DT-3 A.GLN529 9.99 169.03 -1.45 -9.71 1.82 20.52 62.66 166.92 54 5xus AT-lys C.DA3 D.DT-3 A.LYS538 10.38 80.25 8.30 5.38 -3.16 -9.15 -67.90 44.61 55 5xus AT-lys C.DA3 D.DT-3 A.LYS595 -10.60 -69.48 -9.10 4.89 -2.40 -68.85 9.37 -0.09 56 5xus AT-thr C.DA4 D.DT-4 A.THR149 -10.49 -157.09 7.03 -4.79 -6.13 46.25 -62.20 -150.49 57 5xus AT-gln C.DA4 D.DT-4 A.GLN529 -10.67 138.34 -3.53 -9.90 -1.82 48.90 49.93 128.58 58 5xus AT-lys C.DA4 D.DT-4 A.LYS538 -10.46 60.97 7.79 2.82 -6.38 -28.63 -53.82 1.01 59 5xus AT-lys C.DA4 D.DT-4 A.LYS595 -11.99 -79.47 -6.07 9.29 -4.53 -58.86 40.31 -37.61 60 5xus GC-gln C.DG5 D.DC-5 A.GLN529 -11.56 113.26 -4.40 -9.59 -4.74 58.93 35.43 96.41 61 5xus GC-asp C.DG5 D.DC-5 A.ASP541 -9.41 -66.12 8.20 -1.24 -4.44 -11.20 -15.75 -63.54 62 5xus GC-asp C.DG6 D.DC-6 A.ASP541 -10.40 -98.01 7.04 -2.96 -7.06 -16.77 -19.79 -95.37 63 5xus AT-pro D.DA-1 C.DT1 A.PRO587 8.75 138.26 -2.84 4.78 6.75 8.75 -66.82 129.30 64 5xus AT-lys D.DA-1 C.DT1 A.LYS591 7.56 157.25 0.84 6.28 4.11 21.51 61.35 152.96 65 5xus AT-met D.DA-1 C.DT1 A.MET592 7.85 -119.10 -4.34 -3.03 5.79 31.99 -58.63 -105.26 66 5xus AT-lys D.DA-1 C.DT1 A.LYS595 -8.89 125.96 2.71 7.96 -2.89 36.67 64.85 110.40 **************************************************************************** List of 78 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 5xus OP1@B.A-19 N@A.ASP786 3.31 po4:backbone 2 5xus OP2@B.U-18 N@A.ARG788 2.94 po4:backbone 3 5xus OP2@B.U-18 NH1@A.ARG788 3.10 po4:sidechain:salt-bridge 4 5xus OP1@B.U-17 N@A.LYS707 2.85 po4:backbone 5 5xus OP1@B.U-16 NH1@A.ARG747 2.73 po4:sidechain:salt-bridge 6 5xus OP1@B.U-16 NH2@A.ARG747 2.78 po4:sidechain:salt-bridge 7 5xus OP1@B.U-16 NE2@A.GLN793 3.12 po4:sidechain 8 5xus O3'@B.U-17 NE2@A.GLN793 3.23 po4:sidechain 9 5xus OP2@B.C-15 NE@A.ARG788 2.99 po4:sidechain:salt-bridge 10 5xus OP2@B.C-15 NH2@A.ARG788 2.67 po4:sidechain:salt-bridge 11 5xus OP2@B.C-12 NZ@A.LYS768 3.25 po4:sidechain:salt-bridge 12 5xus OP1@B.U-11 N@A.ASN769 3.15 po4:backbone 13 5xus OP1@B.U-11 ND2@A.ASN772 3.25 po4:sidechain 14 5xus OP2@B.U-11 N@A.LYS768 2.78 po4:backbone 15 5xus OP1@B.A-10 ND2@A.ASN772 3.00 po4:sidechain 16 5xus OP2@B.A-10 NZ@A.LYS774 3.07 po4:sidechain:salt-bridge 17 5xus OP2@B.A-10 OG1@A.THR777 3.54 po4:sidechain 18 5xus O3'@B.U-11 OG1@A.THR777 3.13 po4:sidechain 19 5xus OP2@B.A-9 NE2.A@A.HIS714 2.41 po4:sidechain:salt-bridge 20 5xus OP2@B.U-7 NZ@A.LYS712 3.34 po4:sidechain:salt-bridge 21 5xus OP1@B.G-6 OG@A.SER710 2.56 po4:sidechain 22 5xus OP1@B.U-5 OG@A.SER713 3.55 po4:sidechain 23 5xus OP1@B.U-5 N@A.HIS714 3.23 po4:backbone 24 5xus OP1@B.U-5 N@A.GLY715 2.87 po4:backbone 25 5xus OP1@B.A-4 N@A.THR716 2.94 po4:backbone 26 5xus OP2@B.A-4 O@A.THR716 3.01 po4:backbone 27 5xus OP2@B.G-3 NZ@A.LYS960 2.72 po4:sidechain:salt-bridge 28 5xus OP2@B.U-1 NZ@A.LYS953 2.67 po4:sidechain:salt-bridge 29 5xus OP1@B.G0 NZ@A.LYS15 3.09 po4:sidechain:salt-bridge 30 5xus OP2@B.G0 NE2@A.HIS720 2.99 po4:sidechain:salt-bridge 31 5xus OP1@B.A2 NZ@A.LYS520 3.06 po4:sidechain:salt-bridge 32 5xus OP1@B.A4 NZ@A.LYS51 3.01 po4:sidechain:salt-bridge 33 5xus O3'@B.A3 NZ@A.LYS51 3.46 po4:sidechain 34 5xus OP1@B.U5 NH2@A.ARG158 3.48 po4:sidechain:salt-bridge 35 5xus O3'@B.A4 NH2@A.ARG158 3.10 po4:sidechain 36 5xus OP1@B.U6 NZ@A.LYS278 2.55 po4:sidechain:salt-bridge 37 5xus OP1@B.U6 N@A.LEU281 2.90 po4:backbone 38 5xus OP1@B.A7 N@A.LYS278 2.92 po4:backbone 39 5xus O3'@B.U6 NH2@A.ARG174 3.09 po4:sidechain 40 5xus OP1@B.C12 NE2@A.GLN888 3.08 po4:sidechain 41 5xus OP1@B.C14 NZ@A.LYS464 2.34 po4:sidechain:salt-bridge 42 5xus O3'@B.G13 NZ@A.LYS464 2.99 po4:sidechain 43 5xus OP1@B.C19 NH1@A.ARG386 2.68 po4:sidechain:salt-bridge 44 5xus OP2@B.C19 NH1@A.ARG359 3.33 po4:sidechain:salt-bridge 45 5xus OP2@B.C19 NZ@A.LYS390 2.85 po4:sidechain:salt-bridge 46 5xus O3'@B.G18 NH1@A.ARG386 3.08 po4:sidechain 47 5xus OP1@C.DG-14 ND2@A.ASN256 2.71 po4:sidechain 48 5xus O3'@C.DG-14 O@A.GLY242 3.17 po4:backbone 49 5xus OP1@C.DG-12 OG@A.SER286 2.51 po4:sidechain 50 5xus OP1@C.DC-9 N@A.LYS514 2.89 po4:backbone 51 5xus OP1@C.DT-7 N@A.ILE896 2.65 po4:backbone 52 5xus OP1@C.DT-7 N@A.LYS897 2.86 po4:backbone 53 5xus OP2@C.DT-7 NZ@A.LYS897 2.52 po4:sidechain:salt-bridge 54 5xus O3'@C.DC-8 NH2@A.ARG883 3.03 po4:sidechain 55 5xus OP1@C.DA-6 NZ@A.LYS945 2.80 po4:sidechain:salt-bridge 56 5xus OP2@C.DA-6 NZ@A.LYS945 2.73 po4:sidechain:salt-bridge 57 5xus OP1@C.DT-4 N@A.LYS984 3.03 po4:backbone 58 5xus OP2@C.DT-4 N@A.PHE983 2.89 po4:backbone 59 5xus OP1@C.DT-3 N@A.SER168 3.02 po4:backbone 60 5xus OP1@C.DT-3 NZ@A.LYS984 2.70 po4:sidechain:salt-bridge 61 5xus OP1@C.DT-2 NZ@A.LYS167 2.81 po4:sidechain:salt-bridge 62 5xus OP2@C.DT1 N@A.GLY740 2.99 po4:backbone 63 5xus O3'@C.DC0 N@A.GLY740 3.37 po4:backbone 64 5xus OP1@C.DA2 N@A.ASP535 3.21 po4:backbone 65 5xus OP2@C.DA2 OH@A.TYR542 2.65 po4:sidechain 66 5xus OP1@C.DA3 NE1@A.TRP649 2.99 po4:sidechain 67 5xus OP2@C.DA3 OD2@A.ASP537 2.91 po4:sidechain 68 5xus OP1@C.DA4 OH@A.TYR646 2.82 po4:sidechain 69 5xus OP2@C.DA4 NZ@A.LYS601 2.91 po4:sidechain:salt-bridge 70 5xus OP1@C.DG5 N@A.LYS600 3.05 po4:backbone 71 5xus OP2@C.DG5 N@A.LYS601 2.95 po4:backbone 72 5xus OP1@D.DC-5 NZ@A.LYS560 3.12 po4:sidechain:salt-bridge 73 5xus OP1@D.DT-4 N@A.GLY146 3.73 po4:backbone 74 5xus OP1@D.DT-4 N@A.THR148 3.12 po4:backbone 75 5xus OP1@D.DT-4 OG1@A.THR148 2.73 po4:sidechain 76 5xus OP2@D.DT-4 N@A.THR149 2.73 po4:backbone 77 5xus OP2@D.DT-4 OG1@A.THR149 2.91 po4:sidechain 78 5xus OP2@D.DT-3 N@A.LYS121 2.83 po4:backbone **************************************************************************** List of 20 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 5xus O4'@B.A-20 ND1@A.HIS759 3.40 sugar:sidechain 2 5xus O2'@B.U-14 OH@A.TYR872 2.67 sugar:sidechain 3 5xus O2'@B.A-13 OG1@A.THR870 3.16 sugar:sidechain 4 5xus O2'@B.U-11 OD1@A.ASN767 3.29 sugar:sidechain 5 5xus O2'@B.U-11 OG1@A.THR777 2.65 sugar:sidechain 6 5xus O4'@B.G0 N@A.THR16 2.83 sugar:backbone 7 5xus O2'@B.G1 ND1@A.HIS797 2.92 sugar:sidechain 8 5xus O2'@B.A3 OD1@A.ASN157 2.67 sugar:sidechain 9 5xus O2'@B.A4 NH1@A.ARG158 2.94 sugar:sidechain 10 5xus O2'@B.U6 NH1@A.ARG174 3.03 sugar:sidechain 11 5xus O2'@B.C12 NH1@A.ARG508 3.28 sugar:sidechain 12 5xus O4'@B.G13 NH1@A.ARG508 3.11 sugar:sidechain 13 5xus O2'@B.G13 OD1@A.ASP505 2.77 sugar:sidechain 14 5xus O2'@B.G13 OD2@A.ASP505 2.73 sugar:sidechain 15 5xus O2'@B.U16 NZ@A.LYS253 3.02 sugar:sidechain 16 5xus O2'@B.G17 NE2@A.GLN264 2.81 sugar:sidechain 17 5xus O4'@C.DA-10 OG1@A.THR512 3.58 sugar:sidechain 18 5xus O4'@C.DT-3 OG@A.SER168 3.58 sugar:sidechain 19 5xus O4'@C.DT-2 ND2@A.ASN160 2.95 sugar:sidechain 20 5xus O4'@C.DA4 NZ@A.LYS595 2.98 sugar:sidechain **************************************************************************** List of 25 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 5xus N6@B.A-20 O@A.ALA766 2.85 base:backbone 2 5xus N6@B.A-20 OD1@A.ASN767 3.11 base:sidechain 3 5xus N1@B.A-19 OH@A.TYR781 2.85 base:sidechain 4 5xus O2@B.U-17 NE@A.ARG18 3.02 base:sidechain 5 5xus O2@B.U-17 NH1@A.ARG18 3.13 base:sidechain 6 5xus O4@B.U-17 ND2@A.ASN718 3.50 base:sidechain 7 5xus N1@B.A-9 ND2@A.ASN864 3.06 base:sidechain 8 5xus O6@B.G-8 NZ@A.LYS774 2.60 base:sidechain 9 5xus N2@B.G-3 OG@A.SER905 3.73 base:sidechain 10 5xus N6@B.A-2 OD1@A.ASN718 3.09 base:sidechain 11 5xus O2@B.U-1 NH1@A.ARG18 3.79 base:sidechain 12 5xus O4@B.U-1 N@A.LEU719 3.35 base:backbone 13 5xus O4@B.U-1 N@A.HIS720 3.02 base:backbone 14 5xus N2@B.G0 OG1@A.THR16 3.00 base:sidechain 15 5xus N3@B.G0 OG1@A.THR16 2.87 base:sidechain 16 5xus N3@B.A3 ND2@A.ASN157 3.00 base:sidechain 17 5xus N2@B.G17 OE1@A.GLN264 2.71 base:sidechain 18 5xus N3@B.G17 NE2@A.GLN264 3.03 base:sidechain 19 5xus N3@C.DA-16 ND2@A.ASN260 2.97 base:sidechain 20 5xus O2@C.DT-4 OG@A.SER168 3.19 base:sidechain 21 5xus N7@C.DA2 OH@A.TYR542 3.27 base:sidechain 22 5xus N7@C.DA3 NZ@A.LYS538 2.96 base:sidechain 23 5xus N3@C.DA3 NZ@A.LYS595 3.03 base:sidechain 24 5xus N4@D.DC-5 OD1@A.ASP541 3.95 base:sidechain 25 5xus O2@D.DT-2 NZ@A.LYS595 2.83 base:sidechain **************************************************************************** List of 9 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 5xus A-asn B.A-20 A.ASN767 1.40 17 2 5xus A-tyr B.A-19 A.TYR781 2.11 52 3 5xus U-arg B.U-17 A.ARG18 2.45 55 4 5xus U-arg B.U-1 A.ARG18 0.99 49 5 5xus A-asn B.A3 A.ASN157 0.74 44 6 5xus G-gln B.G17 A.GLN264 0.64 15 7 5xus A-asn C.DA-16 A.ASN260 0.69 36 8 5xus A-tyr C.DA2 A.TYR542 0.46 30 9 5xus C-asp D.DC-5 A.ASP541 1.24 59 **************************************************************************** List of 8 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 5xus A-his B.A-20 A.HIS759 5.16 51 2 5xus U-arg B.U-18 A.ARG788 4.75 53 3 5xus U-tyr B.U-7 A.TYR781 3.65 9 4 5xus U-his B.U-1 A.HIS720 3.58 8 5 5xus A-asn B.A4 A.ASN157 4.19 40 6 5xus C-trp B.C19 A.TRP355 3.40 3 7 5xus G-trp C.DG-19 A.TRP355 3.27 5 8 5xus A-asn C.DA-15 A.ASN260 3.83 38 **************************************************************************** List of 2 interface stacks with 3+ planar moieties Note: an interface stack is an ordered list of three and more nucleobases and planar moieties of amino acids, assembled together via stacking interactions (nucleobases within to a stem are excluded by default). 1 size=3 HUA A.HIS720,B.U-1,B.A-2 2 size=4 HAUC A.HIS759,B.A-20,B.U-11,B.C-12 **************************************************************************** List of 3 additional files 1 -- 5xus-baseAA-pairs.pdb 2 -- 5xus-baseAA-stacks.pdb 3 -- 5xus-pairs.pdb