sbliven
commented
8 years ago We inspected all benchmark members of folds annotated as 4-helical bundles (a.24, a.26, and f.21), as well as some additional folds identified manually as potentially having 4-helix bundles (a.29, a.47, a.48, a.60, and f.36).
An initial assignment was made based on topology:
D2: H2:
1-2 1-2
| /
4-3 3-4Cases that significantly diverged from four parallel helices underwent further consideration. Reasons for diverging from the standard D2/H2 assignments are given as comments.
| Domain | SCOP | Call | Comments |
|---|---|---|---|
| d1ea8a_ | a.24.1.1 | D2 | |
| d1rmva_ | a.24.5.1 | C1 | not enough coverage by bundle |
| d1hy5a_ | a.24.11.1 | C1 | too kinked |
| d2ga0e_ | a.24.12.0 | D2 | |
| d1wola_ | a.24.16.0 | C1 | not parallel |
| d1v74b_ | a.24.20.1 | D2 | |
| d3g50b_ | a.24.22.1 | D2 | |
| d1ug7a_ | a.24.24.1 | D2 | |
| d2ap3a1 | a.24.27.1 | D2 | |
| d2j9wa_ | a.24.28.0 | D2 | |
| d2p61a1 | a.24.29.1 | D2 | but poor angles |
| d1x91a_ | a.29.6.1 | D2 | |
| d1v9va1 | a.29.10.1 | D2 | |
| d2fefc1 | a.29.11.1 | D2 | |
| d3dbyh2 | a.29.13.1 | D2 | |
| d2gscb_ | a.29.16.1 | D2 | |
| d1bg1a1 | a.47.1.1 | H2 | |
| d1s2xa_ | a.47.3.1 | C1 | fourth helix too kinked to align |
| d3pmra_ | a.47.4.0 | C1 | wildly different lengths |
| d1t98a2 | a.47.6.1 | C1 | N-term is too short, inconsistent orientation |
| d2okua1 | a.48.5.1 | H2 | |
| d1a0pa1 | a.60.9.1 | C2 | secondary axis is off-center, helix lengths match in C2 |
| d3ezea1 | a.60.10.1 | C2 | off-center |
| d1ryka_ | a.60.11.1 | C1 | not parallel |
| d3ci0k1 | a.60.16.1 | C1 | too short for a bundle |
| d1y5ic1 | f.21.3.1 | C1 | not 4-helix, despite description |
| d1oedd_ | f.36.1.1 | D2 |
4 helical bundles are not consistently annotated in the benchmark. The criteria is as follows:
Zig-zag (crossed) connectivity: 12 34 Parallel connectivity: 12 43