Supplement Materials: A combinatorial score to distinguish biological and non-biological protein-protein interfaces
Shiyong Liu, Qingliang Li and Luhua Lai*
State Key Laboratory of Structural Chemistry for Stable and Unstable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
Center for Theoretical Biology, Peking University, Beijing 100871, China
Correspondence to: Prof. Luhua Lai, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China. Telephone: (86)-010-62757486; Fax: (86)-010-62751725; E-mail:
Table S1: All interfaces of 74 homodimers.
PDBcodea / Chainsb / Statec / Contact
sized / SCScored / PMFScored / Packing
densityd / ΔASA(Å2)d
1a3c / A:B / 0 / 18 / 84 / -16946 / 0.695 / 1301.1
1a3c / A:C / 1 / 26 / 141 / -138061 / 0.715 / 1975.4
1a3c / A:G / 0 / 14 / 49 / -38526 / 0.758 / 787.9
1a3c / A:I / 0 / 10 / 49 / -41959 / 0.752 / 787.8
1ad3 / A:B / 1 / 108 / 483 / -435065 / 0.725 / 7882.2
1ad3 / A:D / 0 / 12 / 54 / 3021 / 0.734 / 650.6
1ad3 / A:H / 0 / 12 / 72 / -38362 / 0.732 / 717.7
1af5 / A:B / 0 / 13 / 70 / -50551 / 0.779 / 710.4
1af5 / A:C / 0 / 10 / 58 / -49552 / 0.785 / 710.4
1af5 / A:E / 1 / 24 / 110 / -61411 / 0.746 / 1712.2
1afw / A:B / 1 / 69 / 318 / -279624 / 0.723 / 4800.7
1afw / A:C / 0 / 13 / 78 / -25084 / 0.699 / 849.8
1afw / A:K / 0 / 11 / 25 / 3767 / 0.669 / 491.1
1afw / A:L / 0 / 15 / 49 / 392 / 0.778 / 473.1
1ajs / A:B / 1 / 96 / 531 / -373393 / 0.690 / 6852.7
1ajs / A:N / 0 / 15 / 95 / -32973 / 0.650 / 986.0
1ajs / B:P / 0 / 16 / 78 / -34692 / 0.643 / 986.1
1alk / A:B / 1 / 103 / 463 / -519767 / 0.711 / 7665.9
1alk / A:E / 0 / 21 / 41 / -38692 / 0.728 / 1167.3
1alk / A:F / 0 / 14 / 27 / -27428 / 0.699 / 737.9
1alk / A:H / 0 / 13 / 28 / -32013 / 0.685 / 737.9
1alk / B:D / 0 / 12 / 29 / -22528 / 0.694 / 789.3
1alk / B:H / 0 / 11 / 43 / -9936 / 0.704 / 629.1
1amk / A:B / 1 / 39 / 265 / -259872 / 0.723 / 2953.9
1amk / A:D / 0 / 13 / 66 / -29236 / 0.696 / 904.8
1amk / A:F / 0 / 12 / 76 / -29883 / 0.695 / 904.8
1aom / A:B / 1 / 34 / 165 / -239468 / 0.709 / 2482.6
1aom / A:D / 0 / 13 / 37 / -22930 / 0.725 / 815.6
1aom / A:J / 0 / 20 / 46 / 17618 / 0.653 / 846.1
1aom / B:C / 0 / 12 / 38 / -20921 / 0.696 / 815.3
1aom / B:G / 0 / 15 / 46 / 12073 / 0.644 / 846.0
1aor / A:B / 1 / 33 / 122 / -141904 / 0.714 / 2464.5
1aor / A:E / 0 / 14 / 11 / -11433 / 0.688 / 752.6
1aor / B:D / 0 / 17 / 20 / -27352 / 0.726 / 672.3
1aor / B:G / 0 / 17 / 11 / -11144 / 0.664 / 752.4
1aq6 / A:B / 1 / 53 / 246 / -303181 / 0.737 / 4444.6
1aq6 / A:D / 0 / 12 / 28 / -13587 / 0.628 / 694.0
1aq6 / A:K / 0 / 21 / 61 / -38249 / 0.690 / 1371.6
1aq6 / B:C / 0 / 11 / 28 / -9279 / 0.663 / 693.8
1aq6 / B:L / 0 / 24 / 61 / -42038 / 0.666 / 1371.6
1auo / A:B / 1 / 19 / 147 / -50230 / 0.773 / 1332.6
1auo / A:D / 0 / 12 / 45 / -30780 / 0.724 / 970.5
1auo / A:F / 0 / 11 / 43 / -42483 / 0.712 / 970.5
1auo / B:J / 0 / 20 / 33 / -49909 / 0.701 / 1333.9
1bam / A:D / 1 / 18 / 113 / -62079 / 0.782 / 1489.9
1bif / A:D / 1 / 27 / 291 / -115156 / 0.710 / 1797.0
1bif / A:E / 0 / 11 / 61 / -39737 / 0.701 / 577.1
1bif / A:G / 0 / 11 / 27 / -11540 / 0.728 / 711.6
1bif / A:H / 0 / 14 / 16 / -29054 / 0.712 / 887.5
1bif / A:I / 0 / 14 / 16 / -34761 / 0.700 / 887.6
1bsr / A:B / 1 / 48 / 326 / -208063 / 0.734 / 3843.7
1buo / A:B / 1 / 48 / 271 / -230946 / 0.750 / 3944.0
1buo / A:G / 0 / 13 / 90 / -38591 / 0.740 / 1012.8
1cg2 / A:B / 0 / 11 / 13 / -8745 / 0.571 / 550.7
1cg2 / A:C / 0 / 16 / 44 / -30627 / 0.742 / 1006.1
1cg2 / A:D / 1 / 39 / 291 / -135257 / 0.724 / 2610.3
1chm / A:B / 1 / 91 / 641 / -299882 / 0.698 / 6642.1
1chm / A:L / 0 / 11 / 86 / -4692 / 0.671 / 818.6
1chm / B:J / 0 / 12 / 54 / -3256 / 0.696 / 818.7
1cmb / A:B / 1 / 39 / 154 / -283317 / 0.747 / 3626.7
1cmb / A:H / 0 / 10 / 5 / 2262 / 0.702 / 652.3
1cmb / A:I / 0 / 12 / 67 / -331 / 0.683 / 971.1
1cmb / B:J / 0 / 13 / 5 / 4154 / 0.708 / 652.2
1cmb / B:L / 0 / 14 / 52 / -7719 / 0.678 / 970.9
1cmb / B:R / 0 / 10 / 41 / 6878 / 0.661 / 556.3
1cp2 / A:B / 1 / 29 / 124 / -83496 / 0.675 / 1903.7
1cp2 / A:I / 0 / 10 / 64 / -25872 / 0.763 / 632.6
1cp2 / A:O / 0 / 14 / 33 / 16703 / 0.693 / 608.0
1cp2 / A:P / 0 / 12 / 43 / 12908 / 0.701 / 670.0
1cp2 / B:G / 0 / 11 / 64 / -23894 / 0.763 / 632.6
1cp2 / B:J / 0 / 11 / 34 / 16144 / 0.745 / 608.0
1cp2 / B:L / 0 / 13 / 43 / 8827 / 0.697 / 670.0
1cp2 / B:N / 0 / 11 / 53 / -6352 / 0.727 / 665.5
1csh / A:B / 0 / 13 / 32 / -18756 / 0.686 / 838.4
1csh / A:C / 0 / 11 / 35 / -25764 / 0.686 / 838.4
1csh / A:D / 1 / 115 / 503 / -720829 / 0.726 / 10114.7
1csh / A:E / 0 / 12 / 77 / -29677 / 0.715 / 674.6
1csh / A:F / 0 / 17 / 47 / -3269 / 0.683 / 1083.0
1csh / A:G / 0 / 18 / 47 / -2426 / 0.655 / 1083.0
1csh / B:D / 0 / 12 / 77 / -29677 / 0.715 / 674.6
1ctt / A:B / 0 / 13 / 36 / -9114 / 0.707 / 868.7
1ctt / A:C / 0 / 20 / 54 / -10078 / 0.715 / 868.6
1ctt / A:D / 1 / 53 / 429 / -253478 / 0.698 / 3980.3
1czj / A:B / 0 / 12 / 17 / -12914 / 0.747 / 712.6
1czj / A:C / 0 / 13 / 14 / -9150 / 0.708 / 712.7
1czj / A:D / 1 / 20 / 111 / -93993 / 0.783 / 1657.8
1daa / A:B / 1 / 62 / 151 / -223061 / 0.706 / 4604.2
1daa / A:C / 0 / 18 / 48 / -19143 / 0.669 / 1034.0
1daa / A:J / 0 / 10 / 32 / -4501 / 0.732 / 622.6
1daa / B:D / 0 / 13 / 48 / -18017 / 0.642 / 1034.0
1daa / B:E / 0 / 10 / 36 / -1745 / 0.716 / 385.6
1fip / A:B / 1 / 38 / 184 / -223770 / 0.760 / 3223.8
1fip / A:F / 0 / 12 / 66 / -24452 / 0.744 / 723.9
1fro / A:B / 1 / 99 / 302 / -365649 / 0.719 / 7259.0
1gvp / A:B / 0 / 18 / 44 / -28199 / 0.701 / 931.6
1gvp / A:C / 0 / 14 / 76 / -24704 / 0.691 / 931.6
1gvp / A:D / 1 / 24 / 54 / -78623 / 0.745 / 1815.6
1hjr / A:B / 0 / 14 / 74 / 29879 / 0.729 / 947.0
1hjr / A:C / 1 / 25 / 167 / -62081 / 0.762 / 1905.7
1hjr / A:E / 0 / 22 / 78 / 40407 / 0.699 / 1084.4
1hjr / A:I / 0 / 13 / 53 / 37350 / 0.682 / 1084.4
1hjr / A:J / 0 / 15 / 74 / 25112 / 0.714 / 1109.3
1hjr / A:S / 0 / 12 / 51 / 6327 / 0.698 / 648.5
1hjr / B:D / 1 / 26 / 177 / -88064 / 0.760 / 1931.1
1hjr / B:E / 0 / 16 / 64 / 24651 / 0.697 / 1109.3
1hjr / B:F / 0 / 17 / 55 / 33591 / 0.724 / 899.2
1hss / A:B / 1 / 31 / 95 / -118817 / 0.718 / 2194.9
1hss / A:L / 0 / 12 / 88 / -17248 / 0.695 / 971.2
1hss / A:T / 0 / 16 / 58 / -18703 / 0.717 / 971.2
1hss / B:C / 0 / 21 / 49 / -5255 / 0.639 / 1229.2
1hss / B:R / 0 / 11 / 76 / 17709 / 0.721 / 804.4
1icw / A:B / 1 / 28 / 160 / -125545 / 0.704 / 1971.1
1icw / B:D / 0 / 10 / 46 / -13470 / 0.718 / 744.0
1imb / A:B / 1 / 44 / 183 / -134264 / 0.678 / 3299.6
1imb / A:I / 0 / 17 / 22 / -20534 / 0.658 / 926.7
1imb / B:J / 0 / 18 / 22 / -15872 / 0.658 / 926.7
1isa / A:B / 1 / 23 / 131 / -39842 / 0.704 / 1842.7
1isa / A:K / 0 / 12 / 57 / -23852 / 0.661 / 710.2
1isa / B:J / 0 / 12 / 23 / -21327 / 0.717 / 607.2
1isa / B:L / 0 / 11 / 38 / -25773 / 0.681 / 710.2
1iso / A:B / 0 / 18 / 117 / -58822 / 0.722 / 1231.5
1iso / A:C / 0 / 19 / 119 / -57853 / 0.729 / 1231.5
1iso / A:D / 0 / 11 / 20 / -15108 / 0.735 / 532.6
1iso / A:F / 1 / 80 / 469 / -394948 / 0.726 / 6613.8
1jhg / A:D / 1 / 51 / 138 / -184227 / 0.718 / 4414.8
1jhg / A:H / 0 / 10 / 58 / -12298 / 0.734 / 739.1
1jhg / A:J / 0 / 13 / 57 / -11320 / 0.756 / 739.1
1jsg / A:D / 1 / 21 / 72 / -114046 / 0.739 / 1588.9
1jsg / A:E / 0 / 12 / 45 / 3735 / 0.802 / 713.0
1jsg / A:F / 0 / 16 / 82 / -18712 / 0.742 / 1181.0
1jsg / A:G / 0 / 18 / 81 / -15461 / 0.760 / 1181.1
1jsg / B:F / 0 / 18 / 82 / -15461 / 0.760 / 1181.1
1kpf / A:F / 0 / 17 / 41 / -20086 / 0.688 / 948.4
1kpf / A:G / 0 / 12 / 40 / -16274 / 0.672 / 948.4
1kpf / A:H / 1 / 46 / 426 / -282547 / 0.758 / 3734.9
1lyn / A:B / 1 / 24 / 88 / 1992 / 0.692 / 1898.6
1lyn / A:L / 0 / 21 / 187 / -41314 / 0.704 / 1766.6
1lyn / B:G / 0 / 10 / 42 / -4986 / 0.777 / 627.4
1mjl / A:B / 1 / 38 / 160 / -250724 / 0.742 / 3549.8
1mjl / A:G / 0 / 11 / 19 / -11172 / 0.712 / 623.3
1mjl / A:H / 0 / 13 / 29 / -19437 / 0.669 / 997.9
1mjl / B:I / 0 / 12 / 19 / -12378 / 0.687 / 623.2
1mjl / B:K / 0 / 15 / 30 / -22523 / 0.683 / 997.9
1mjl / B:Q / 0 / 12 / 20 / -1528 / 0.632 / 596.5
1mka / A:B / 1 / 46 / 272 / -252824 / 0.723 / 3237.4
1mka / A:I / 0 / 18 / 58 / -30421 / 0.682 / 865.3
1mka / B:J / 0 / 15 / 58 / -34844 / 0.676 / 865.3
1moq / A:D / 1 / 66 / 402 / -222756 / 0.726 / 5064.8
1moq / A:E / 0 / 16 / 136 / -73310 / 0.723 / 998.3
1nox / A:B / 1 / 75 / 314 / -463680 / 0.713 / 6066.4
1nox / A:D / 0 / 10 / 32 / -7991 / 0.752 / 566.7
1nox / A:E / 0 / 11 / 62 / -41215 / 0.698 / 842.6
1nox / A:G / 0 / 14 / 62 / -39105 / 0.702 / 842.6
1nox / B:H / 0 / 10 / 33 / -7991 / 0.752 / 566.7
1nsy / A:B / 1 / 63 / 193 / -171886 / 0.719 / 5232.6
1nsy / A:H / 0 / 10 / 60 / -20732 / 0.690 / 528.8
1nsy / A:N / 0 / 13 / 34 / -29210 / 0.662 / 1065.0
1nsy / B:J / 0 / 12 / 43 / -19096 / 0.689 / 528.8
1nsy / B:O / 0 / 18 / 34 / -28550 / 0.671 / 1065.0
1oac / A:B / 1 / 191 / 1099 / -1149015 / 0.714 / 14334.3
1oac / A:C / 0 / 11 / 24 / -12576 / 0.763 / 755.2
1oac / A:D / 0 / 21 / 52 / -26287 / 0.675 / 1583.0
1oac / A:E / 0 / 10 / 24 / -12611 / 0.777 / 755.2
1oac / B:E / 0 / 26 / 52 / -26508 / 0.682 / 1583.1
1oac / B:I / 0 / 10 / 22 / -10350 / 0.679 / 422.8
1opy / A:D / 0 / 19 / 73 / -2767 / 0.724 / 1298.5
1opy / A:F / 1 / 30 / 142 / -68746 / 0.740 / 2095.2
1opy / A:G / 0 / 10 / 49 / -36464 / 0.704 / 700.2
1opy / A:H / 0 / 13 / 49 / -37129 / 0.717 / 700.2
1opy / B:G / 0 / 13 / 48 / -37152 / 0.717 / 700.4
1otp / A:C / 0 / 21 / 64 / 19855 / 0.635 / 1028.2
1otp / A:D / 1 / 23 / 149 / -102479 / 0.770 / 1645.3
1otp / A:E / 0 / 20 / 67 / -40903 / 0.690 / 1023.6
1otp / A:F / 0 / 17 / 67 / -35127 / 0.684 / 1023.6
1otp / B:G / 0 / 20 / 67 / -40392 / 0.690 / 1023.9
1pgt / A:B / 1 / 30 / 195 / -117451 / 0.732 / 2464.7
1pgt / A:C / 0 / 13 / 27 / -24505 / 0.694 / 808.3
1pgt / B:J / 0 / 10 / 14 / -12726 / 0.679 / 498.8
1pre / A:B / 1 / 76 / 181 / -116065 / 0.715 / 4591.8
1pre / A:K / 0 / 10 / 32 / -12775 / 0.712 / 549.1
1pre / B:E / 0 / 14 / 48 / -15297 / 0.706 / 924.9
1pre / B:G / 0 / 18 / 39 / -23659 / 0.715 / 924.8
1puc / A:D / 1 / 46 / 248 / -361383 / 0.757 / 4350.1
1puc / A:E / 0 / 17 / 19 / -24112 / 0.730 / 998.8
1rfb / A:B / 1 / 71 / 281 / 47539 / 0.659 / 5298.5
1rfb / A:I / 0 / 10 / 46 / 18113 / 0.779 / 642.8
1rfb / A:N / 0 / 10 / 50 / -24442 / 0.807 / 697.7
1rfb / A:P / 0 / 13 / 79 / -30105 / 0.809 / 697.7
1rfb / B:C / 0 / 10 / 47 / 3072 / 0.776 / 489.2
1rpo / A:C / 1 / 35 / 240 / -113462 / 0.763 / 2809.6
1ses / A:B / 1 / 60 / 267 / -344838 / 0.729 / 4466.6
1ses / A:G / 0 / 14 / 51 / -21158 / 0.728 / 821.9
1ses / A:I / 0 / 10 / 59 / -27121 / 0.756 / 588.4
1ses / A:K / 0 / 14 / 107 / -8786 / 0.768 / 992.5
1ses / B:L / 0 / 14 / 91 / -14598 / 0.782 / 992.6
1slt / A:B / 1 / 16 / 162 / -121767 / 0.719 / 1093.5
1slt / A:I / 0 / 14 / 36 / -6353 / 0.742 / 671.3
1slt / A:L / 0 / 13 / 25 / 1861 / 0.656 / 713.3
1slt / B:J / 0 / 15 / 25 / 1964 / 0.659 / 713.2
1smn / A:B / 1 / 27 / 117 / -111473 / 0.700 / 1734.6
1smn / A:K / 0 / 10 / 31 / -12584 / 0.732 / 742.4
1smn / A:L / 0 / 14 / 45 / 236 / 0.702 / 763.8
1smn / B:M / 0 / 13 / 43 / -16194 / 0.731 / 742.4
1smn / B:N / 0 / 11 / 45 / 3195 / 0.685 / 763.7
1smt / A:B / 1 / 49 / 95 / -156176 / 0.744 / 3934.3
1smt / A:D / 0 / 14 / 46 / -17631 / 0.708 / 821.8
1smt / A:E / 0 / 12 / 67 / -32545 / 0.753 / 696.2
1smt / B:G / 0 / 13 / 46 / -17601 / 0.701 / 821.8
1smt / B:H / 0 / 13 / 67 / -19150 / 0.778 / 595.8
1smt / B:L / 0 / 12 / 19 / -33212 / 0.721 / 650.3
1sox / A:B / 1 / 46 / 204 / -124612 / 0.692 / 2827.5
1sox / A:E / 0 / 12 / 19 / -12164 / 0.704 / 550.2
1sox / A:G / 0 / 13 / 101 / -7745 / 0.736 / 782.2
1sox / B:H / 0 / 11 / 101 / -9127 / 0.726 / 782.1
1sox / B:J / 0 / 12 / 79 / -36037 / 0.723 / 639.1
1tox / A:G / 1 / 116 / 408 / -196447 / 0.677 / 7441.2
1tox / A:J / 0 / 18 / 22 / -6691 / 0.634 / 1167.8
1tox / A:L / 0 / 20 / 21 / -8033 / 0.646 / 1167.8
1trk / A:B / 1 / 118 / 654 / -553559 / 0.708 / 8973.5
1trk / A:E / 0 / 18 / 63 / -37834 / 0.684 / 1206.2
1trk / A:G / 0 / 19 / 69 / -31412 / 0.682 / 1206.3
1trk / A:H / 0 / 16 / 5 / 2910 / 0.597 / 662.4
1trk / B:E / 0 / 12 / 6 / -1439 / 0.616 / 662.3
1trk / B:F / 0 / 22 / 89 / -63173 / 0.688 / 1204.2
1trk / B:H / 0 / 17 / 72 / -63414 / 0.673 / 1204.5
1trk / B:I / 0 / 17 / 40 / -48925 / 0.689 / 1085.0
1trk / B:J / 0 / 19 / 56 / -45097 / 0.676 / 1085.0
1tys / A:C / 0 / 11 / 26 / -8531 / 0.681 / 434.4
1tys / A:D / 0 / 19 / 86 / -49261 / 0.697 / 966.3
1tys / A:E / 0 / 13 / 97 / -49755 / 0.689 / 966.3
1tys / A:F / 1 / 61 / 333 / -168358 / 0.699 / 4656.6
1uby / A:B / 1 / 49 / 194 / 60394 / 0.728 / 3533.5
1uby / A:C / 0 / 51 / 168 / -134509 / 0.695 / 4335.6
1uby / A:D / 0 / 20 / 52 / -6969 / 0.670 / 1032.9
1utg / A:B / 1 / 39 / 99 / -80500 / 0.729 / 2970.7
1utg / A:E / 0 / 10 / 8 / -17293 / 0.761 / 491.6
1wgj / A:B / 1 / 23 / 109 / -83206 / 0.710 / 1917.8
1wgj / A:C / 0 / 15 / 107 / -64298 / 0.715 / 1139.5
1wgj / A:F / 0 / 12 / 69 / -41721 / 0.687 / 660.0
1wgj / B:D / 0 / 20 / 106 / -61841 / 0.707 / 1139.5
1xso / A:B / 1 / 21 / 112 / -62592 / 0.769 / 1370.1
1xso / A:J / 0 / 13 / 52 / -55045 / 0.754 / 800.8
1xso / A:O / 0 / 10 / 24 / -14308 / 0.687 / 445.3
1xso / B:G / 0 / 10 / 18 / -719 / 0.685 / 424.4
1xso / B:K / 0 / 13 / 53 / -61578 / 0.734 / 800.8
2ccy / A:B / 1 / 19 / 52 / -58667 / 0.734 / 1613.6
2ccy / A:G / 0 / 10 / 13 / -12890 / 0.744 / 516.5
2ilk / A:B / 0 / 13 / 62 / -28529 / 0.740 / 987.9
2ilk / A:E / 0 / 17 / 59 / -16704 / 0.741 / 987.9