RIPC

The RIPC set contains protein pairs with very difficult structural relations including repetitions, large InDels, circular permutations and conformational variability. The complete set used in Mayr et al. [1] contains 40 cases. At the moment there are 23 cases for which we also know a reference alignment. The RIPC set is domain based. For each pair of domains we added a letter R,I,P or C indicating the class of problem the pair belongs to. The table can be sorted alphabetically or numerically by a mouse click in the column header.

Domain1 Domain2 Length1 Length2 SeqId SCOP1 SCOP2 Caveats Eqr Class
-> d1hcyb2 -> d1lnlb1 263 307 11.03 -> a.86.1.1 -> a.86.1.1 4 I
-> d1ay9b_ -> d1b12a_ 108 239 14.81 -> b.87.1.1 -> b.87.1.2 10 I
-> d1gbga_ -> d1ovwa_ 214 398 16.82 -> b.29.1.2 -> b.29.1.10 aL 3 I
-> d1crla_ -> d1edea_ 534 310 17.10 -> c.69.1.17 -> c.69.1.8 3 I
-> d1jj7a_ -> d1lvga_ 251 190 22.63 -> c.37.1.12 -> c.37.1.1 aL 8 I C
-> d2adma1 -> d2hmyb_ 215 327 16.74 -> c.66.1.27 -> c.66.1.26 12 I
-> d1an9a1 -> d1npxa1 247 198 19.19 -> c.4.1.2 -> c.3.1.5 11 I
-> d1nkla_ -> d1qdma1 1560 78 17.95 -> a.64.1.1 -> a.64.1.2 iC 72 P
-> d1nlsa_ -> d2bqpa_ 237 228 21.05 -> b.29.1.1 -> b.29.1.1 aL 6 P
-> d1qasa2 -> d1rsya_ 126 135 21.43 -> b.7.1.1 -> b.7.1.2 iC 75 P
-> d1b5ta_ -> d1k87a2 275 351 15.64 -> c.1.23.1 -> c.1.23.2 8 R P
-> d1jwyb_ -> d1puja_ 281 261 18.77 -> c.37.1.8 -> c.37.1.8 12 I P
-> d1jwyb_ -> d1u0la2 281 212 15.09 -> c.37.1.8 -> c.37.1.8 11 I P
-> d1nw5a_ -> d2adma1 270 215 24.19 -> c.66.1.11 -> c.66.1.27 13 I P
-> d1gsaa1 -> d2hgsa1 122 102 15.69 -> c.30.1.3 -> c.30.1.4 5 P C
-> d1qq5a_ -> d3chya_ 245 128 17.97 -> c.108.1.1 -> c.23.1.1 aL 3 I P
-> d1kiaa_ -> d1nw5a_ 275 270 19.26 -> c.66.1.5 -> c.66.1.11 12 I P
-> d2bbma_ -> d4clna_ 148 148 100.00 -> a.39.1.5 -> a.39.1.5 148 C
-> d1dlia1 -> d1mv8a1 98 98 25.51 -> a.100.1.4 -> a.100.1.4 aL 4 C
-> d1hava_ -> d1kxfa_ 216 159 21.38 -> b.47.1.4 -> b.47.1.3 4 I C
-> d1l5ba_ -> d1l5ea_ 101 101 100.00 -> b.89.1.1 -> b.89.1.1 101 C
-> d1ggga_ -> d1wdna_ 220 223 99.55 -> c.94.1.1 -> c.94.1.1 220 C
-> d1d5fa_ -> d1nd7a_ 350 374 34.57 -> d.148.1.1 -> d.148.1.1 6 I C

Table Description

Domain1 SCOP domain name of first domain
Domain2 SCOP domain name of second domain
Length1 Number of residues in the first domain
Length2 Number of residues in the second domain
SeqID Sequence similarity using local alignment
SCOP1 SCOP Classification of first domain
SCOP2 SCOP Classification of second domain
Caveats Structure may cause a problem because of:
iC … insertion codes in the PDB
mC … multi chain domains
aL … alternate locations in the PDB
Eqr Number of reference residues
Class Difficulty class, combination or R,I,P and C