SISY pairwise

The SISY pairwise set contains protein pairs selected from all three SISYPHUS categories Homologous, Fold, Fragment [3]. In general, the difficulty for a comparison method increases from homology to fragment [1]. Note that the SISYPHUS database contains multi-chain domains, which means that a molecule in the alignment may consist of more than one peptide chain.

To extract the most difficult case from a family (not more than one per family) we applied the following strategy for each family:

  • Check all possible pairs for a permutation and take the one with the lowest sequence similarity. Assign class P. Done with this family and proceed to the next one.
  • Superimpose all pairs according to the SISYPHUS alignment. If there are one or more pairs with rmsd > 4A, take the one with the largest rmsd. Assign class C. Done with this family and proceed to the next one.
  • A so called SISYPHUS construct contains for each structure all the residues between the first aligned residue pair and the last aligned residue pair. If the larger construct is more then twice a long as the smaller one take it. If there are multiple pairs above the cutoff, take the one with the largest size difference. Assign class I. Done with this family and proceed to the next one.
  • Run a Smith-Waterman sequence alignment for all pairs. If there is a pair with less than 40% sequence identity, take it. If there are multiple pairs below the cutoff, take the one with the lowest sequence identity. Done with this family and proceed to the next one.
  • If none of these rules applies no pair is selected for this family.
    •

    The corresponding PDB files contain only the chain(s) used in the alignment. The table can be sorted alphabetically or numerically by a mouse click in the column header.

    Chain(s)1 Chain(s)2 Length1 Length2 SeqID SisyAlId Category Caveats Eqr Class
    -> 1s0uA -> 1vloA 391 364 14.29 -> AL00050464 fold aL 48
    -> 1r5bA -> 1s0uA 409 391 21.48 -> AL00050465 homologous 61
    -> 1g60A -> 1pjzA 238 201 5.97 -> AL10053335 fragment aL 22
    -> 2f6uA -> 2tpsA 231 226 5.75 -> AL10051350 fragment aL 28
    -> 1iapA -> 1zv4X 190 138 10.87 -> AL00048098 homologous 88
    -> 1orjA -> 1vh6AB 126 210 23.81 -> AL00101117 homologous aL, mC 94
    -> 1hx1B -> 1ugoA 112 99 15.15 -> AL00063492 homologous 71
    -> 1yadA -> 2tpsA 190 226 26.32 -> AL00051392 homologous aL 168
    -> 1ej0A -> 1qamA 180 235 11.67 -> AL00053335 homologous 71
    -> 1b9mA -> 1fr3KL 258 134 24.63 -> AL00050331 homologous aL, mC 55 P
    -> 1tv5A -> 1vizA 371 225 18.67 -> AL00051395 homologous aL 118 C
    -> 1fohA -> 2gb0B 649 389 11.83 -> AL00051913 homologous aL 100
    -> 1ezvA -> 1ie0A 430 155 13.55 -> AL00063410 homologous 59 P, C
    -> 1ezvA -> 1ezvB 430 352 20.45 -> AL00063412 homologous 72
    -> 1gl0I -> 1pmcA 32 36 37.50 -> AL00057282 homologous 30
    -> 1egaB -> 1j5eC 293 206 10.19 -> AL00054814 homologous 59
    -> 1dnlA -> 1rfeA 199 159 11.32 -> AL00050475 homologous aL 76
    -> 1bx4A -> 1lioA 342 329 33.74 -> AL00053617 homologous 309
    -> 1ec6A -> 2fmrA 87 65 9.23 -> AL00054790 homologous 57
    -> 1l0bA -> 1l7bA 190 92 9.78 -> AL00052113 homologous 45
    -> 2nacA -> 3gpdG 374 334 13.47 -> AL00051735 homologous 78 P
    -> 1jclA -> 1n7kA 252 234 24.79 -> AL00069394 homologous aL 197
    -> 1r5pA -> 1t4yA 90 105 31.11 -> AL00102449 homologous 42
    -> 1ie0A -> 1j6wA 155 161 33.55 -> AL00064294 homologous 137
    -> 2ch9A -> 4monAB 126 94 3.19 -> AL00054403 homologous aL, mC 55
    -> 1cewI -> 1n9jAB 108 196 12.96 -> AL00054407 homologous mC 70
    -> 1jhdA -> 1sgvA 396 262 19.85 -> AL00088696 fold 40 I
    -> 1b10A -> 1i17A 104 107 19.23 -> AL00054097 homologous 68
    -> 1wv3A -> 2g1lA 186 103 10.68 -> AL00049879 homologous 47 P
    -> 1ugmA -> 1wz3AB 113 168 15.93 -> AL00054253 homologous mC 80
    -> 1t3tA -> 1t4aAB 1283 160 17.50 -> AL00109622 homologous mC 115
    -> 1i6vE -> 1qklA 98 127 16.33 -> AL10063562 fragment 33
    -> 1auaA -> 1vc1A 296 110 16.36 -> AL00052086 fold 83 C
    -> 1mbyAB -> 1umwA 150 222 22.67 -> AL00082614 fragment mC 60 P
    -> 1cr5A -> 3engA 178 213 19.66 -> AL00050684 fold 39 I
    -> 1n10A -> 3engA 228 213 13.62 -> AL00050685 homologous 69
    -> 1mpyA -> 1ss4AB 307 294 12.24 -> AL10054593 homologous mC 152 P
    -> 1fc9A -> 1ky9B 386 396 15.28 -> AL10074933 homologous 69
    -> 1r9cA -> 1xy7B 125 122 4.92 -> AL10054592 fragment aL 30
    -> 1mvfDE -> 1n0gA 88 141 14.77 -> AL20089447 homologous mC 73
    -> 1orbA -> 1qxnA 293 137 16.79 -> AL00052821 homologous 66
    -> 1d4dA -> 1jnrA 560 642 18.39 -> AL00051934 homologous aL 205
    -> 1ukvG -> 1vg9A 442 501 27.38 -> AL00051931 homologous aL 285
    -> 1j5pA -> 1ps9A 235 671 21.28 -> AL10051735 fragment 27 I
    -> 1j5xA -> 1nriA 319 248 12.50 -> AL00053697 homologous aL 64
    -> 1r18A -> 1vbfA 223 224 24.66 -> AL00053354 homologous 168
    -> 1mhmAB -> 1tluAB 307 234 15.38 -> AL00056276 homologous aL, mC 162
    -> 1olzA -> 1shyB 621 499 19.64 -> AL00103575 homologous 38
    -> 1rieA -> 1zinA 127 217 10.24 -> AL10050021 fold 22 P
    -> 1pohA -> 1sphA 85 87 30.59 -> AL00055594 homologous 80
    -> 1y8qA -> 1zfnA 313 244 16.39 -> AL00069572 homologous 176
    -> 1j5yA -> 1pchA 172 88 11.36 -> AL00055593 fold aL 66
    -> 1f33A -> 1j30B 156 137 8.76 -> AL00047241 homologous 106 C
    -> 1d00A -> 1k2fA 168 190 13.10 -> AL00049599 homologous 86
    -> 1eu1A -> 1qcsA 766 195 9.74 -> AL00050692 homologous aL 51
    -> 1iw4A -> 1lr7A 55 73 27.27 -> AL00057468 homologous 36 C
    -> 1it8A -> 2ashA 577 361 24.93 -> AL00051713 homologous aL 298
    -> 1jr1A -> 2bleA 436 337 21.96 -> AL00051412 homologous aL 242
    -> 1h0zA -> 1hdlA 68 55 27.27 -> AL00069960 homologous 39
    -> 1awwA -> 1gxiE 67 73 2.99 -> AL10063763 fold 29
    -> 1qf6A -> 1v7oA 641 155 20.65 -> AL00055186 homologous 125
    -> 1omhA -> 1r9wA 282 138 3.62 -> AL00055464 homologous aL 51 P
    -> 1h9mA -> 1q12A 141 367 14.89 -> AL10050335 homologous aL 81
    -> 1qftA -> 1u0xA 175 184 16.57 -> AL00050815 homologous aL 79 C
    -> 1szwA -> 2apoA 334 304 15.46 -> AL00100877 homologous aL 69 P
    -> 1lw3A -> 1r6hA 513 172 22.09 -> AL00052799 homologous 67 C
    -> 1oa8A -> 1v06A 128 138 29.69 -> AL00102031 homologous 71
    -> 1nn4A -> 1uslA 159 157 31.21 -> AL00089623 homologous 143
    -> 1nw6A -> 1xvaA 271 292 18.82 -> AL10053377 homologous 129 P
    -> 1jvnA -> 1uwcA 536 261 17.24 -> AL10053473 fragment aL 26 C
    -> 1l3aA -> 1pcfA 166 66 19.70 -> AL10054446 fragment 40
    -> 1v7oA -> 1vjeA 155 148 11.49 -> AL10063410 homologous 77 P
    -> 1c7qA -> 1gzdA 442 554 23.08 -> AL00053701 homologous 372
    -> 1mk5A -> 1wbiA 121 123 28.93 -> AL00050876 homologous aL 105
    -> 1kncA -> 2gmyA 174 147 10.20 -> AL00069117 fragment 53
    -> 1fybA -> 1pjuA 111 115 50.45 -> AL00100897 homologous 32 P
    -> 1hkyA -> 1i8nA 86 89 6.98 -> AL10057491 fragment 17
    -> 1ecmA -> 2csmA 91 246 21.98 -> AL10048599 fragment 62 C
    -> 1i8nA -> 2hgfA 89 97 11.24 -> AL00057413 homologous 61
    -> 1fyeA -> 1q7rA 220 202 13.37 -> AL00052317 homologous aL 63 P
    -> 1dqxA -> 1v5xA 267 200 19.00 -> AL00051366 homologous 113 C
    -> 1s3sE -> 1wlfA 436 164 15.85 -> AL10050712 fragment 32
    -> 1ecmAB -> 2csmA 186 246 22.04 -> AL00048599 homologous mC 156 C
    -> 1vk1A -> 1vz0AC 223 377 20.63 -> AL00110848 homologous aL, mC 69
    -> 1booA -> 1nw6A 282 271 21.77 -> AL00053377 homologous 186
    -> 1n1cAB -> 1s9uA 397 201 21.89 -> AL00089155 homologous aL, mC 143
    -> 1pe31 -> 2pspA 59 105 38.98 -> AL00057492 homologous 42
    -> 1eq6A -> 1tu1AB 189 288 14.81 -> AL00055723 homologous aL, mC 109
    -> 1efcA -> 1vloA 386 364 16.48 -> AL10050412 fragment aL 23 C
    -> 1b12A -> 2mysA 239 755 14.23 -> AL10051306 fold 36 I
    -> 1d9cAB -> 1itfA 240 165 20.61 -> AL00047305 homologous mC 81 C
    -> 1b56A -> 2ft9A 133 125 18.40 -> AL00050847 homologous 114
    -> 1h9cA -> 1phrA 105 154 9.52 -> AL00052787 homologous 83
    -> 1hmsA -> 1smpI 131 100 9.00 -> AL10050875 homologous aL 42 C
    -> 1omhA -> 1p4dA 282 275 35.27 -> AL00103120 homologous aL 214
    -> 1l9lA -> 1qdmA 74 433 14.86 -> AL00047861 homologous aL, iC 56 P
    -> 1otrA -> 2di0A 49 71 16.33 -> AL00088995 homologous 38
    -> 1qftA -> 1yupA 175 162 8.02 -> AL10050815 homologous aL 44
    -> 1l3aA -> 1pcfAB 166 132 18.94 -> AL00054446 homologous mC 94
    -> 1cjyA -> 1mlaA 633 305 15.08 -> AL00052150 homologous 134 C
    -> 1k32A -> 1vaeA 1023 111 9.01 -> AL10050155 homologous 60 P
    -> 1ihrAB -> 1tolA 147 156 10.20 -> AL00074653 homologous aL, mC 48
    -> 1mvfD -> 1n0gA 44 141 15.91 -> AL00089447 fragment 34
    -> 1e0dA -> 1p3dA 429 463 22.84 -> AL00051984 homologous aL 79
    -> 1m7oA -> 1w0mA 246 226 15.04 -> AL00051352 homologous 193
    -> 1si7A -> 1z2zA 340 437 26.76 -> AL00103021 homologous 264
    -> 1a62A -> 1pqhA 125 118 2.54 -> AL10089447 fragment aL 20
    -> 1d1nA -> 1exmA 99 403 13.13 -> AL10050464 homologous aL 46 P
    -> 1l9gA -> 1oe4A 191 245 9.95 -> AL00052141 homologous aL 88
    -> 1j4wA -> 2fmrA 145 65 27.69 -> AL10054814 fragment 22 C
    -> 1bx4A -> 2ajrA 342 320 17.50 -> AL00053614 homologous aL 213
    -> 1l9lA -> 1o82A 74 70 11.43 -> AL10047861 fold aL 54 C
    -> 1gsoA -> 1w93A 419 549 11.22 -> AL00052441 homologous aL 52
    -> 1a49A -> 1o65A 519 218 10.55 -> AL00050799 homologous 63
    -> 1msvA -> 1tluA 319 117 17.09 -> AL10056276 homologous aL 68
    -> 1ay9A -> 1b12A 108 239 14.81 -> AL00051306 homologous 71 I
    -> 2ackA -> 2cutA 527 198 19.70 -> AL00053473 homologous 90 I
    -> 1qo2A -> 1thfD 241 253 23.65 -> AL10051367 fragment aL 79
    -> 1t3tA -> 1t4aA 1283 80 20.00 -> AL10109622 fragment 53
    -> 1mr1C -> 1oqjA 97 90 17.78 -> AL00063763 homologous 56 C
    -> 1feuD -> 1qtqA 189 529 17.99 -> AL00050715 homologous 52 P
    -> 1sjgA -> 1vf5D 112 168 18.75 -> AL00050021 homologous 82 C
    -> 1p8cADE -> 2gmyA 348 147 13.61 -> AL10069117 homologous mC 123
    -> 1kwaA -> 1ujvA 88 96 6.82 -> AL00050155 homologous 63
    -> 1p6oA -> 1wkqAB 156 313 24.36 -> AL00089800 homologous aL, mC 116
    -> 1gt8A -> 1o94A 1017 729 16.32 -> AL00051906 homologous 95
    -> 1d5tA -> 1gt8A 433 1017 17.55 -> AL00051904 homologous aL 81 I, P
    -> 1gn0A -> 1jl3A 108 137 3.70 -> AL10052799 fragment aL 25
    -> 3ssiA -> 4sgbI 108 51 5.88 -> AL10057468 fragment 25 P
    -> 1ps9A -> 1v0jA 671 388 12.89 -> AL00051971 homologous 80 I

    Table Description

    Chain(s)1 Pdb code and chain id(s) of the first molecule
    Chain(s)2 Pdb code and chain id(s) of the second molecule
    Length1 Number of residues in the first molecule
    Length2 Number of residues in the second molecule
    SeqId Sequence similarity using local alignment
    SisyAlId Alignment ID in the Sisyphus database
    Category Category in the Sisyphus database
    Caveats Structure may cause a problem because of:iC … insertion codes in the PDBmC … multi chain domainsaL … alternate locations in the PDB
    Eqr Number of reference residues
    Class Difficulty class, combination or R,I,P and C