**************************************************************************** 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/4aqx.pdb -o=4aqx.out --type=base File name: 4aqx.pdb no. of peptide chains: 2 [A=152,B=152] no. of DNA/RNA chains: 4 [C=14,D=10,E=14,F=10] no. of amino acids: 304 no. of nucleotides: 48 no. of atoms: 3619 no. of waters: 133 no. of metals: 3 [Mg=3] **************************************************************************** List of 1 type of 1 modified nucleotide nt count list 1 5CM-c 1 E.5CM614 **************************************************************************** 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=24 strand-1 5'-TCAAAACGTCGTGAGACAGTTTGG-3' bp-type |||||||||||||||||||||||| strand-2 3'-AGTTTTGCAGcACTCTGTCAAACC-5' helix-form BBBBBB.B.x..BxBB.BBBBBB 1 C.DT501 F.DA624 T-A WC 20-XX cWW cW-W 2 C.DC502 F.DG623 C-G WC 19-XIX cWW cW-W 3 C.DA503 F.DT622 A-T WC 20-XX cWW cW-W 4 C.DA504 F.DT621 A-T WC 20-XX cWW cW-W 5 C.DA505 F.DT620 A-T WC 20-XX cWW cW-W 6 C.DA506 F.DT619 A-T WC 20-XX cWW cW-W 7 C.DC507 F.DG618 C-G WC 19-XIX cWW cW-W 8 C.DG508 F.DC617 G-C WC 19-XIX cWW cW-W 9 C.DT509 F.DA616 T-A WC 20-XX cWW cW-W 10 C.DC510 F.DG615 C-G WC 19-XIX cWW cW-W 11 C.DG511 E.5CM614 G-c WC 19-XIX cWW cW-W 12 C.DT512 E.DA613 T-A WC 20-XX cWW cW-W 13 C.DG513 E.DC612 G-C WC 19-XIX cWW cW-W 14 C.DA514 E.DT611 A-T WC 20-XX cWW cW-W 15 D.DG515 E.DC610 G-C WC 19-XIX cWW cW-W 16 D.DA516 E.DT609 A-T WC 20-XX cWW cW-W 17 D.DC517 E.DG608 C-G WC 19-XIX cWW cW-W 18 D.DA518 E.DT607 A-T WC 20-XX cWW cW-W 19 D.DG519 E.DC606 G-C WC 19-XIX cWW cW-W 20 D.DT520 E.DA605 T-A WC 20-XX cWW cW-W 21 D.DT521 E.DA604 T-A WC 20-XX cWW cW-W 22 D.DT522 E.DA603 T-A WC 20-XX cWW cW-W 23 D.DG523 E.DC602 G-C WC 19-XIX cWW cW-W 24 D.DG524 E.DC601 G-C WC 19-XIX cWW cW-W **************************************************************************** List of 82 nucleotide/amino-acid interactions id nt-aa nt aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4aqx T-ser C.DT501 B.SER32 8.24 -108.41 -2.34 7.66 1.92 54.62 -42.44 -89.45 2 4aqx C-ser C.DC502 B.SER32 -8.44 -118.44 -2.29 7.81 -2.24 20.89 -45.32 -111.27 3 4aqx C-tyr C.DC502 B.TYR33 -9.67 -157.20 -6.30 4.04 6.12 -78.44 -41.32 -147.91 4 4aqx A-tyr C.DA503 B.TYR33 -10.05 165.67 5.55 -7.67 3.36 80.32 29.69 160.42 5 4aqx A-gln C.DA503 B.GLN38 9.53 -130.71 -3.20 8.45 3.03 -9.36 -8.55 -130.39 6 4aqx A-tyr C.DA504 B.TYR33 -10.88 136.91 3.29 -10.37 0.25 84.39 10.47 120.23 7 4aqx A-gln C.DA504 B.GLN38 -8.79 -164.94 -1.55 8.64 -0.38 -14.46 -11.63 -164.74 8 4aqx A-lys C.DA505 B.LYS28 -8.86 138.11 -0.96 -8.80 -0.44 6.99 14.52 137.68 9 4aqx A-tyr C.DA505 B.TYR66 14.85 -131.92 -13.18 6.15 -3.00 3.25 64.30 -122.45 10 4aqx A-lys C.DA506 B.LYS28 -8.80 102.11 -3.00 -7.37 -3.75 8.51 10.10 101.49 11 4aqx A-tyr C.DA506 B.TYR66 14.57 -160.24 -9.84 8.82 -6.12 25.55 59.20 -156.59 12 4aqx C-arg C.DC507 B.ARG68 11.02 -125.93 -4.46 10.08 -0.07 7.65 26.11 -124.24 13 4aqx G-arg C.DG508 B.ARG68 11.02 -153.30 -2.23 10.55 -2.29 32.67 21.04 -151.65 14 4aqx T-arg C.DT509 B.ARG68 -11.70 -178.10 0.05 10.45 -5.25 39.15 4.96 -177.98 15 4aqx T-arg C.DT509 B.ARG70 9.14 -149.16 -2.54 8.78 0.20 16.32 11.88 -148.67 16 4aqx C-thr C.DC510 B.THR140 -9.05 41.87 -7.33 5.02 -1.75 -41.68 1.43 3.87 17 4aqx G-lys C.DG511 B.LYS139 -10.38 -53.92 -9.07 4.96 -0.97 -6.31 -51.29 -15.97 18 4aqx G-val C.DG513 A.VAL73 10.31 -103.69 -6.99 6.33 4.18 -18.55 21.09 -100.89 19 4aqx A-thr C.DA514 A.THR46 10.53 -99.85 -8.41 5.94 2.25 -19.31 42.10 -91.11 20 4aqx A-arg C.DA514 A.ARG70 11.77 -137.79 -3.39 10.07 5.06 -35.72 25.63 -134.30 21 4aqx A-val C.DA514 A.VAL73 -10.11 -129.67 -5.32 8.59 0.11 -24.92 29.70 -126.41 22 4aqx G-gln D.DG515 A.GLN44 12.60 -93.57 -7.08 8.36 6.23 -32.25 31.32 -84.36 23 4aqx G-thr D.DG515 A.THR46 -10.23 -127.49 -6.05 8.09 -1.66 -7.74 29.55 -125.41 24 4aqx G-arg D.DG515 A.ARG70 10.97 -169.72 -0.65 10.66 2.50 -21.97 19.21 -169.37 25 4aqx A-ser D.DA516 A.SER22 -10.69 -120.22 -7.05 7.94 -1.27 -20.45 24.52 -117.56 26 4aqx A-ile D.DA516 A.ILE24 11.23 -80.54 -6.92 7.63 4.49 -19.44 23.88 -75.37 27 4aqx A-gln D.DA516 A.GLN44 10.86 -130.32 -4.39 9.77 1.79 -23.81 30.71 -127.10 28 4aqx A-arg D.DA516 A.ARG68 11.68 171.95 -0.11 -10.21 5.67 39.92 -3.74 171.43 29 4aqx A-arg D.DA516 A.ARG70 -9.26 151.13 -3.35 -8.62 -0.29 10.85 -15.28 150.73 30 4aqx C-ile D.DC517 A.ILE24 -11.12 -107.84 -5.20 9.82 0.42 -22.44 31.82 -102.69 31 4aqx C-gln D.DC517 A.GLN26 11.42 -89.35 -6.90 7.72 4.81 -12.53 31.32 -84.02 32 4aqx C-arg D.DC517 A.ARG68 -10.77 146.19 -1.90 -10.49 1.50 46.37 -7.62 143.03 33 4aqx C-thr D.DC517 A.THR140 -10.53 -70.63 -9.23 4.09 -2.98 -41.66 33.71 -47.84 34 4aqx A-gln D.DA518 A.GLN26 10.80 -123.29 -4.20 9.84 1.47 4.89 29.07 -121.17 35 4aqx A-lys D.DA518 A.LYS28 10.13 -84.72 -3.71 6.71 6.62 1.18 13.71 -83.81 36 4aqx G-lys D.DG519 A.LYS28 9.19 -108.96 -2.70 8.21 3.11 0.80 4.25 -108.90 37 4aqx T-lys D.DT520 A.LYS28 -9.07 -143.93 -1.55 8.91 -0.67 0.02 4.89 -143.89 38 4aqx T-pro D.DT520 A.PRO29 10.80 109.08 7.96 2.93 6.69 51.18 69.35 74.80 39 4aqx T-gln D.DT520 A.GLN38 9.54 -164.75 -0.06 9.24 2.35 8.22 2.89 -164.71 40 4aqx T-asn D.DT521 A.ASN30 9.40 -147.96 -1.15 9.17 1.71 -17.09 41.00 -145.32 41 4aqx C-ser E.DC601 A.SER32 8.61 -97.32 -2.03 8.27 1.23 38.89 -45.03 -80.94 42 4aqx C-ser E.DC602 A.SER32 -8.20 -120.59 -1.74 7.79 -1.89 18.22 -52.08 -112.02 43 4aqx C-tyr E.DC602 A.TYR33 -9.45 102.22 5.19 4.78 -6.28 20.68 -86.27 57.18 44 4aqx A-tyr E.DA603 A.TYR33 -9.88 92.15 3.64 1.34 -9.08 -14.45 -83.64 39.90 45 4aqx A-gln E.DA603 A.GLN38 9.60 -132.84 -3.06 8.61 2.93 -16.43 -10.19 -132.11 46 4aqx A-tyr E.DA604 A.TYR33 -10.67 89.40 1.06 0.78 -10.58 -44.35 -76.51 14.77 47 4aqx A-gln E.DA604 A.GLN38 -8.73 -166.19 -1.42 8.61 -0.35 -19.42 -13.59 -165.88 48 4aqx A-lys E.DA605 A.LYS28 -8.96 141.57 -1.44 -8.84 -0.29 12.68 10.23 141.16 49 4aqx A-gln E.DA605 A.GLN38 -9.59 161.65 -0.35 -8.84 -3.70 23.42 9.52 161.19 50 4aqx C-lys E.DC606 A.LYS28 -8.86 106.25 -3.38 -7.46 -3.37 10.80 6.14 105.74 51 4aqx C-tyr E.DC606 A.TYR66 14.82 -160.28 -10.30 8.96 -5.78 23.59 59.82 -156.67 52 4aqx T-arg E.DT607 A.ARG68 11.43 -118.45 -4.62 10.44 0.49 23.60 25.76 -115.12 53 4aqx G-arg E.DG608 A.ARG68 11.25 -148.06 -2.17 10.78 -2.37 37.11 15.47 -145.92 54 4aqx T-arg E.DT609 A.ARG68 -11.97 -173.37 -0.12 10.59 -5.57 41.32 2.51 -172.91 55 4aqx T-arg E.DT609 A.ARG70 9.63 -152.63 -3.38 9.01 0.40 12.27 14.24 -152.25 56 4aqx C-arg E.DC610 A.ARG70 -10.58 167.28 -0.86 -9.90 -3.63 -9.34 -13.46 167.15 57 4aqx C-thr E.DC610 A.THR140 -8.86 -44.02 -7.78 3.44 -2.47 -41.21 3.73 -15.36 58 4aqx T-lys E.DT611 A.LYS139 -10.21 -63.93 -8.56 5.56 0.07 -9.47 -63.14 -3.45 59 4aqx A-val E.DA613 B.VAL73 10.91 -106.28 -7.79 6.71 3.65 -11.55 21.83 -104.23 60 4aqx C-thr E.5CM614 B.THR46 11.00 -96.68 -8.71 6.19 2.62 -14.98 37.73 -89.75 61 4aqx C-arg E.5CM614 B.ARG70 12.02 -141.32 -4.12 9.58 5.98 -30.58 21.68 -139.06 62 4aqx C-val E.5CM614 B.VAL73 10.85 -132.78 -6.20 8.91 -0.04 -10.57 29.29 -130.87 63 4aqx G-gln F.DG615 B.GLN44 12.58 -93.39 -7.20 8.31 6.10 -29.62 30.94 -85.08 64 4aqx G-thr F.DG615 B.THR46 -10.26 -128.15 -6.14 8.10 -1.40 -8.95 28.20 -126.23 65 4aqx G-arg F.DG615 B.ARG70 10.67 -176.02 -1.18 10.20 2.89 -22.93 16.21 -175.90 66 4aqx A-ser F.DA616 B.SER22 -10.67 -117.80 -6.78 8.20 -0.77 -24.68 23.20 -114.64 67 4aqx A-ile F.DA616 B.ILE24 11.27 -80.39 -6.88 7.77 4.39 -19.80 23.42 -75.25 68 4aqx A-gln F.DA616 B.GLN44 10.79 -130.90 -4.37 9.72 1.71 -22.37 29.25 -128.06 69 4aqx A-arg F.DA616 B.ARG68 11.63 172.89 -0.28 -10.18 5.61 36.04 -5.58 172.52 70 4aqx A-arg F.DA616 B.ARG70 -9.00 144.17 -2.84 -8.54 0.15 12.73 -12.17 143.73 71 4aqx C-ile F.DC617 B.ILE24 11.16 -104.47 -4.97 9.97 0.67 -19.34 33.92 -98.95 72 4aqx C-gln F.DC617 B.GLN26 11.14 -89.68 -6.87 7.15 5.08 -10.72 32.21 -84.30 73 4aqx C-arg F.DC617 B.ARG68 -11.01 150.47 -2.00 -10.76 1.19 42.52 -12.82 148.04 74 4aqx C-thr F.DC617 B.THR140 -10.28 -82.09 -9.33 2.45 -3.55 -42.53 39.28 -60.95 75 4aqx G-gln F.DG618 B.GLN26 10.81 -122.56 -4.71 9.56 1.80 5.63 30.87 -120.12 76 4aqx G-lys F.DG618 B.LYS28 10.00 -76.83 -2.97 6.49 7.01 3.23 10.94 -76.10 77 4aqx T-gln F.DT619 B.GLN26 10.97 -151.96 -2.26 10.64 -1.44 15.48 15.89 -151.41 78 4aqx T-lys F.DT619 B.LYS28 8.99 -108.95 -2.14 7.96 3.59 3.02 -2.26 -108.90 79 4aqx T-lys F.DT620 B.LYS28 -8.82 -139.38 -0.88 8.77 -0.36 -3.50 0.58 -139.36 80 4aqx T-pro F.DT620 B.PRO29 10.64 106.43 7.95 3.09 6.35 50.26 70.72 69.05 81 4aqx T-asn F.DT620 B.ASN30 9.48 -109.88 -2.89 7.23 5.42 -24.54 32.12 -104.51 82 4aqx T-asn F.DT621 B.ASN30 -9.29 -143.58 -0.33 9.13 1.71 -22.32 37.62 -140.64 **************************************************************************** List of 70 base-pair/amino-acid interactions id bp-aa nt1 nt2 aa Tdst Rdst Tx Ty Tz Rx Ry Rz 1 4aqx AT-arg F.DA616 C.DT509 B.ARG68 11.66 175.51 -0.11 -10.32 5.43 37.59 -5.31 175.25 2 4aqx AT-arg F.DA616 C.DT509 B.ARG70 -9.07 146.67 -2.69 -8.66 -0.03 14.52 -12.06 146.20 3 4aqx AT-arg C.DA514 E.DT611 A.ARG70 11.91 -139.83 -3.47 9.88 5.68 -27.38 17.21 -138.10 4 4aqx AT-arg D.DA516 E.DT609 A.ARG68 11.82 172.66 -0.12 -10.40 5.62 40.62 -3.13 172.17 5 4aqx AT-arg D.DA516 E.DT609 A.ARG70 -9.44 151.88 -3.37 -8.82 -0.34 11.56 -14.77 151.49 6 4aqx AT-arg D.DA518 E.DT607 A.ARG68 -11.30 115.49 -4.83 -10.14 -1.18 29.06 -25.95 111.05 7 4aqx AT-asn C.DA504 F.DT621 B.ASN30 -9.09 140.85 -0.64 -8.82 -2.08 -18.04 -31.75 138.69 8 4aqx AT-asn C.DA505 F.DT620 B.ASN30 -9.52 108.03 -3.32 -7.10 -5.40 -22.03 -23.21 104.64 9 4aqx AT-asn E.DA604 D.DT521 A.ASN30 -9.22 145.78 -1.48 -8.88 -2.00 -13.52 -31.65 144.12 10 4aqx AT-gln C.DA503 F.DT622 B.GLN38 9.51 -130.02 -3.22 8.23 3.53 -1.79 -10.82 -129.77 11 4aqx AT-gln C.DA504 F.DT621 B.GLN38 -9.00 -163.75 -1.60 8.85 0.24 -7.43 -9.26 -163.66 12 4aqx AT-gln C.DA506 F.DT619 B.GLN26 -10.84 147.52 -2.61 -10.46 1.13 18.78 -13.50 146.83 13 4aqx AT-gln F.DA616 C.DT509 B.GLN44 10.78 -128.72 -4.49 9.66 1.63 -24.00 29.93 -125.46 14 4aqx AT-gln D.DA516 E.DT609 A.GLN44 10.87 -129.76 -4.29 9.84 1.74 -24.77 30.61 -126.40 15 4aqx AT-gln D.DA518 E.DT607 A.GLN26 10.72 -119.29 -4.37 9.65 1.65 7.17 23.79 -117.67 16 4aqx AT-gln E.DA605 D.DT520 A.GLN38 -9.56 163.12 -0.18 -9.06 -3.03 15.77 3.38 162.95 17 4aqx AT-gln E.DA604 D.DT521 A.GLN38 -8.93 -164.63 -1.48 8.80 0.45 -11.72 -7.26 -164.52 18 4aqx AT-gln E.DA603 D.DT522 A.GLN38 9.44 -132.38 -3.08 8.29 3.30 -9.56 -11.68 -131.94 19 4aqx AT-ile F.DA616 C.DT509 B.ILE24 11.20 -78.30 -6.93 7.62 4.41 -20.68 24.45 -72.43 20 4aqx AT-ile D.DA516 E.DT609 A.ILE24 11.12 -80.03 -6.77 7.61 4.46 -20.26 24.12 -74.55 21 4aqx AT-lys C.DA505 F.DT620 B.LYS28 -8.84 138.60 -0.90 -8.79 -0.04 1.67 7.02 138.52 22 4aqx AT-lys C.DA506 F.DT619 B.LYS28 -8.89 105.43 -2.58 -7.68 -3.68 5.64 6.27 105.20 23 4aqx AT-lys C.DA514 E.DT611 A.LYS139 10.15 73.78 -8.29 -5.86 0.01 -5.17 72.83 11.46 24 4aqx AT-lys D.DA518 E.DT607 A.LYS28 10.08 -81.43 -4.06 6.46 6.58 2.00 7.68 -81.11 25 4aqx AT-lys E.DA605 D.DT520 A.LYS28 -9.01 142.60 -1.48 -8.89 0.20 6.28 2.72 142.53 26 4aqx AT-pro C.DA505 F.DT620 B.PRO29 -10.66 -99.21 7.83 -3.57 -6.29 41.87 -67.31 -65.41 27 4aqx AT-pro E.DA605 D.DT520 A.PRO29 -10.74 -101.54 7.72 -3.40 -6.64 42.13 -65.64 -71.07 28 4aqx AT-ser F.DA624 C.DT501 B.SER32 -8.31 106.27 -2.43 -7.73 -1.87 53.66 48.89 83.79 29 4aqx AT-ser F.DA616 C.DT509 B.SER22 -10.64 -115.52 -6.91 8.05 -0.80 -26.03 23.93 -111.90 30 4aqx AT-ser D.DA516 E.DT609 A.SER22 -10.63 -119.61 -6.93 7.95 -1.32 -21.36 24.51 -116.82 31 4aqx AT-thr C.DA514 E.DT611 A.THR46 10.53 -98.92 -8.36 6.13 1.83 -14.63 31.04 -94.28 32 4aqx AT-tyr C.DA503 F.DT622 B.TYR33 -10.06 165.60 5.46 -7.44 4.00 72.59 28.13 161.46 33 4aqx AT-tyr C.DA504 F.DT621 B.TYR33 -11.04 139.89 3.67 -10.36 1.03 80.07 6.44 126.67 34 4aqx AT-tyr C.DA505 F.DT620 B.TYR66 14.87 -126.93 -13.43 5.95 -2.32 10.82 65.08 -115.63 35 4aqx AT-tyr C.DA506 F.DT619 B.TYR66 14.59 -155.25 -10.15 8.79 -5.69 28.02 60.72 -150.24 36 4aqx AT-tyr E.DA604 D.DT521 A.TYR33 -10.76 144.89 3.00 -10.26 1.27 88.02 5.02 130.35 37 4aqx AT-tyr E.DA603 D.DT522 A.TYR33 -9.78 166.81 4.81 -7.64 3.78 82.68 30.66 161.59 38 4aqx AT-val E.DA613 C.DT512 B.VAL73 10.90 -104.23 -7.92 6.40 3.89 -2.59 13.76 -103.56 39 4aqx AT-val C.DA514 E.DT611 A.VAL73 -10.14 -130.79 -5.04 8.78 0.43 -17.25 20.41 -129.33 40 4aqx GC-arg F.DG618 C.DC507 B.ARG68 -11.08 121.55 -4.59 -10.03 -1.07 19.40 -27.49 118.66 41 4aqx GC-arg C.DG508 F.DC617 B.ARG68 11.02 -151.84 -2.10 10.67 -1.74 37.64 16.98 -149.87 42 4aqx GC-arg F.DG615 C.DC510 B.ARG70 10.74 -175.70 -1.11 10.00 3.76 -15.34 15.94 -175.62 43 4aqx GC-arg C.DG511 E.5CM614 B.ARG70 -12.08 142.17 -4.50 -9.11 -6.53 -24.03 -13.73 140.99 44 4aqx GC-arg D.DG515 E.DC610 A.ARG70 10.78 -168.48 -0.75 10.30 3.09 -15.66 16.32 -168.25 45 4aqx GC-arg E.DG608 D.DC517 A.ARG68 11.01 -147.08 -2.03 10.65 -1.92 41.78 11.59 -144.50 46 4aqx GC-gln F.DG618 C.DC507 B.GLN26 10.59 -116.85 -5.24 9.05 1.68 9.77 19.44 -115.56 47 4aqx GC-gln C.DG508 F.DC617 B.GLN26 -11.13 87.54 -6.97 -6.74 -5.46 -4.73 -29.69 83.22 48 4aqx GC-gln F.DG615 C.DC510 B.GLN44 12.60 -91.54 -7.41 8.02 6.30 -24.36 25.54 -85.89 49 4aqx GC-gln D.DG515 E.DC610 A.GLN44 12.53 -91.64 -7.53 8.03 5.98 -29.40 24.90 -84.84 50 4aqx GC-gln E.DG608 D.DC517 A.GLN26 -11.28 87.50 -6.77 -7.46 -5.08 -6.97 -28.74 83.32 51 4aqx GC-ile C.DG508 F.DC617 B.ILE24 -11.06 102.22 -4.98 -9.79 -1.31 -13.09 -32.17 97.74 52 4aqx GC-ile E.DG608 D.DC517 A.ILE24 -11.05 106.01 -4.97 -9.82 -0.92 -16.55 -30.18 101.90 53 4aqx GC-lys F.DG618 C.DC507 B.LYS28 9.89 -73.14 -4.03 6.15 6.61 3.34 -1.60 -73.06 54 4aqx GC-lys C.DG511 E.5CM614 B.LYS139 -10.11 -62.16 -8.60 5.23 -0.95 -0.31 -58.91 -20.80 55 4aqx GC-lys D.DG519 E.DC606 A.LYS28 9.02 -107.43 -3.04 7.84 3.26 5.74 -1.00 -107.32 56 4aqx GC-ser F.DG623 C.DC502 B.SER32 8.42 120.59 -2.02 -7.92 2.01 25.41 53.03 110.67 57 4aqx GC-ser D.DG523 E.DC602 A.SER32 8.18 120.85 -1.41 -7.77 2.15 16.90 58.46 110.16 58 4aqx GC-ser D.DG524 E.DC601 A.SER32 -8.63 94.96 -2.17 -8.33 -0.57 34.50 51.74 75.77 59 4aqx GC-thr C.DG508 F.DC617 B.THR140 10.20 78.05 -9.21 -2.48 3.61 -37.06 -35.71 60.83 60 4aqx GC-thr F.DG615 C.DC510 B.THR46 10.21 -126.95 -6.05 8.17 -0.89 -2.20 24.73 -125.57 61 4aqx GC-thr F.DG615 C.DC510 B.THR140 8.96 -42.04 -7.12 -5.01 2.11 -41.68 5.51 -0.25 62 4aqx GC-thr C.DG511 E.5CM614 B.THR46 -11.09 95.07 -8.98 -6.10 -2.29 -12.34 -27.71 91.23 63 4aqx GC-thr D.DG515 E.DC610 A.THR46 -10.09 -125.31 -6.09 7.90 -1.55 -3.05 24.52 -123.90 64 4aqx GC-thr D.DG515 E.DC610 A.THR140 8.66 41.80 -7.41 -3.50 2.82 -38.22 2.53 17.06 65 4aqx GC-thr E.DG608 D.DC517 A.THR140 10.29 66.94 -8.86 -4.19 3.13 -37.02 -29.78 48.60 66 4aqx GC-tyr F.DG623 C.DC502 B.TYR33 9.62 161.88 -6.51 -3.71 -6.03 -72.32 46.32 155.15 67 4aqx GC-tyr D.DG519 E.DC606 A.TYR66 -14.86 155.81 -10.38 -9.23 5.27 29.42 -59.99 150.93 68 4aqx GC-tyr D.DG523 E.DC602 A.TYR33 9.34 -103.10 5.17 -4.16 6.57 15.29 84.95 -63.06 69 4aqx GC-val C.DG511 E.5CM614 B.VAL73 -10.80 132.00 -6.23 -8.82 -0.30 -4.73 -20.62 131.11 70 4aqx GC-val C.DG513 E.DC612 A.VAL73 10.51 -99.01 -7.62 5.79 4.35 -9.92 11.00 -98.18 **************************************************************************** List of 37 phosphate/amino-acid H-bonds id nt-atom aa-atom dist type 1 4aqx OP2@C.DC502 N@B.LYS34 2.43 po4:backbone 2 4aqx OP1@C.DA503 NZ@B.LYS116 3.03 po4:sidechain:salt-bridge 3 4aqx OP2@C.DA504 N@B.ILE81 3.21 po4:backbone 4 4aqx OP1@C.DG513 NZ@A.LYS48 3.37 po4:sidechain:salt-bridge 5 4aqx OP1@C.DG513 NZ@B.LYS139 3.53 po4:sidechain:salt-bridge 6 4aqx OP1@C.DA514 NE2@A.GLN47 3.08 po4:sidechain 7 4aqx OP2@C.DA514 N@A.LYS48 2.81 po4:backbone 8 4aqx OP2@C.DA514 NH2@A.ARG51 2.62 po4:sidechain:salt-bridge 9 4aqx OP2@D.DG515 OD1@A.ASP20 3.08 po4:sidechain 10 4aqx OP2@D.DG515 OD1@B.ASP20 2.86 po4:sidechain 11 4aqx OP1@D.DA516 N@A.ASP137 2.86 po4:backbone 12 4aqx OP2@D.DA516 OG@A.SER22 2.68 po4:sidechain 13 4aqx OP2@D.DA516 NZ@A.LYS98 3.25 po4:sidechain:salt-bridge 14 4aqx OP1@D.DC517 OG@A.SER138 2.68 po4:sidechain 15 4aqx OP2@D.DC517 ND2@A.ASN136 2.95 po4:sidechain 16 4aqx OP1@D.DA518 N@A.LYS142 2.71 po4:backbone 17 4aqx OP1@D.DA518 N@A.THR143 2.94 po4:backbone 18 4aqx OP2@D.DA518 OE1@A.GLN26 3.06 po4:sidechain 19 4aqx OP2@E.DC602 N@A.LYS34 2.72 po4:backbone 20 4aqx OP1@E.DA603 NZ@A.LYS116 2.84 po4:sidechain:salt-bridge 21 4aqx OP2@E.DA604 N@A.ILE81 3.12 po4:backbone 22 4aqx OP1@E.DA613 NZ@A.LYS139 3.04 po4:sidechain:salt-bridge 23 4aqx OP1@E.5CM614 N@B.LYS48 2.92 po4:backbone 24 4aqx OP1@E.5CM614 NH2@B.ARG51 2.76 po4:sidechain:salt-bridge 25 4aqx OP2@E.5CM614 NE2@B.GLN47 3.27 po4:sidechain 26 4aqx OP1@F.DG615 OD1@A.ASP20 2.80 po4:sidechain 27 4aqx OP1@F.DG615 O@B.GLY19 2.98 po4:backbone 28 4aqx OP1@F.DG615 OD1@B.ASP20 3.20 po4:sidechain 29 4aqx OP1@F.DA616 N@B.ASP137 2.81 po4:backbone 30 4aqx OP2@F.DA616 OG@B.SER22 2.67 po4:sidechain 31 4aqx OP2@F.DA616 NZ@B.LYS98 3.31 po4:sidechain:salt-bridge 32 4aqx OP1@F.DC617 OG@B.SER138 2.61 po4:sidechain 33 4aqx OP2@F.DC617 ND2@B.ASN136 3.05 po4:sidechain 34 4aqx OP1@F.DG618 N@B.LYS142 2.81 po4:backbone 35 4aqx OP1@F.DG618 N@B.THR143 2.94 po4:backbone 36 4aqx OP2@F.DG618 NE2@B.GLN26 3.19 po4:sidechain 37 4aqx OP1@F.DT619 NZ@B.LYS142 3.11 po4:sidechain:salt-bridge **************************************************************************** List of 1 sugar/amino-acid H-bonds id nt-atom aa-atom dist type 1 4aqx O4'@E.DC610 OG1@A.THR140 3.60 sugar:sidechain **************************************************************************** List of 26 base/amino-acid H-bonds id nt-atom aa-atom dist type 1 4aqx N4@C.DC502 OG@B.SER32 3.59 base:sidechain 2 4aqx N7@C.DA503 OH@B.TYR33 2.40 base:sidechain 3 4aqx N6@C.DA503 OH@B.TYR33 3.08 base:sidechain 4 4aqx N7@C.DA504 NE2@B.GLN38 2.91 base:sidechain 5 4aqx N6@C.DA504 OE1@B.GLN38 3.06 base:sidechain 6 4aqx N6@C.DA506 NZ@B.LYS28 3.31 base:sidechain 7 4aqx N7@C.DG508 NH1@B.ARG68 3.11 base:sidechain 8 4aqx O6@C.DG508 NH2@B.ARG68 2.42 base:sidechain 9 4aqx N7@D.DG515 NH2@A.ARG70 3.30 base:sidechain 10 4aqx O6@D.DG515 NH1@A.ARG70 2.84 base:sidechain 11 4aqx N7@D.DA516 OE1@A.GLN44 3.04 base:sidechain 12 4aqx O6@D.DG519 NZ@A.LYS28 2.79 base:sidechain 13 4aqx O4@D.DT521 ND2@A.ASN30 3.34 base:sidechain 14 4aqx N4@E.DC602 OG@A.SER32 3.36 base:sidechain 15 4aqx N7@E.DA603 OH@A.TYR33 2.43 base:sidechain 16 4aqx N6@E.DA603 OH@A.TYR33 3.10 base:sidechain 17 4aqx N7@E.DA604 NE2@A.GLN38 2.85 base:sidechain 18 4aqx N6@E.DA604 OE1@A.GLN38 2.97 base:sidechain 19 4aqx N7@E.DG608 NH1@A.ARG68 3.04 base:sidechain 20 4aqx O6@E.DG608 NH2@A.ARG68 2.92 base:sidechain 21 4aqx N7@F.DG615 NH2@B.ARG70 3.09 base:sidechain 22 4aqx O6@F.DG615 NH1@B.ARG70 2.73 base:sidechain 23 4aqx N7@F.DA616 NE2@B.GLN44 2.95 base:sidechain 24 4aqx N7@F.DG618 NE2@B.GLN26 2.99 base:sidechain 25 4aqx O4@F.DT619 NZ@B.LYS28 2.86 base:sidechain 26 4aqx O4@F.DT621 ND2@B.ASN30 3.28 base:sidechain **************************************************************************** List of 11 base/amino-acid pairs id nt-aa nt aa vertical-distance plane-angle 1 4aqx A-tyr C.DA503 B.TYR33 0.35 32 2 4aqx A-gln C.DA504 B.GLN38 0.73 36 3 4aqx G-arg C.DG508 B.ARG68 0.05 33 4 4aqx G-arg D.DG515 A.ARG70 0.10 20 5 4aqx T-asn D.DT521 A.ASN30 1.36 55 6 4aqx A-tyr E.DA603 A.TYR33 0.16 40 7 4aqx A-gln E.DA604 A.GLN38 0.34 38 8 4aqx G-arg E.DG608 A.ARG68 0.42 36 9 4aqx G-arg F.DG615 B.ARG70 0.06 22 10 4aqx A-gln F.DA616 B.GLN44 1.16 64 11 4aqx G-gln F.DG618 B.GLN26 0.73 15 **************************************************************************** List of 4 base/amino-acid stacks id nt-aa nt aa vertical-distance plane-angle 1 4aqx C-tyr C.DC502 B.TYR33 3.49 27 2 4aqx A-gln C.DA503 B.GLN38 3.83 30 3 4aqx C-tyr E.DC602 A.TYR33 3.50 29 4 4aqx T-arg E.DT607 A.ARG68 3.28 32 **************************************************************************** List of 3 additional files 1 -- 4aqx-baseAA-pairs.pdb 2 -- 4aqx-baseAA-stacks.pdb 3 -- 4aqx-pairs.pdb