Table V.
Comparison of Relative Accessible Surface Area in Amyloidogenic and Non-amyloidogenic β-Strand Residues
| Number of β-strand residuesa |
Average relative ASA per β-strand residueb % |
|||||
|---|---|---|---|---|---|---|
| PDB ID | Amyloidogenic sequence(s) | Amyloidogenic | Non-amyloidogenic | Amyloidogenic | Non-amyloidogenic | |
| β-Lactoglobulin | 1BEB (dimer) | 11–20 | 52 | 98 | 11.3 | 22.0 |
| 101–110 | ||||||
| 116–126 | ||||||
| 146–152 | ||||||
| β2-Microglobulin | 1BOG | 58–71 | 16 | 38 | 27.5 | 20.2 |
| 83–89 | ||||||
| 91–96 | ||||||
| B. subtilis cspB protein | 2ES2 | 1–22 | 15 | 23 | 23.9 | 26.8 |
| Gelsolin | 1KCQ | 182–192 | 8 | 27 | 3.44 | 28.9 |
| Human complement receptor 1 | 1GKG | 1038–1054 | 5 | 41 | 23.5 | 34.2 |
| Lactoferrin | 1LFH | 538–545 | 4 | 138 | 0 | 12.6 |
| Laminin | 2JD4 (biol. mol.1) | 2919–2930 | 9 | 187 | 6.3 | 18.3 |
| Medin | 3BN6 | 299–308 | 15 | 69 | 14.1 | 18.3 |
| 309–316 (70–87 in 3BN6) | ||||||
| Transthyretin | 1TTA (tetramer) | 105–115 | 40 | 232 | 10.6 | 16.4 |
| B. subtilis ‘YjcG’ protein | 2D4G (dimer) | 151–156 | 8 | 110 | 11.7 | 19.6 |
| DNA polymerase III subunit alpha, E. coli | 2HNH | 513–518 | 6 | 81 | 1.52 | 10.6 |
| 20S proteasome Bos taurus | 1IRU | 18–23 (chains N and 2) | 10 | 144 | 0.41 | 11.3 |
| Na+/Ca2+-exchange protein 1, C. familiaris | 2DPK | 455–459 | 5 | 73 | 17.5 | 26.7 |
| Thymidine kinase, cystolic, human | 1W4R | 133–137 (chains A,B,C & D) | 4 | 232 | 8.03 | 15.3 |
| Glycyl-tRNA synthetase, Thermus thermophilus | 1ATI (dimer) | 399–403 | 6 | 294 | 0.50 | 16.4 |
| Leucine-binding protein, E. coli | 1USG | 3–7 | 5 | 74 | 14.3 | 18.1 |
| Mean ± SD | 11 ± 9 | 20 ± 7 | ||||
| t-test, t | −3.20 | |||||
| t-test, df | 27.7 | |||||
| t-test, P-value | 0.0035 | |||||
| Mann-Whitney test, P-value | 0.0045 | |||||
1
Secondary structure according to DeepView: Swiss-PdbViewer (Guex and Peitsch, 1997).
2
Accessible surface area (ASA), average relative surface area per residue (%) computed by the NACCESS program (Hubbard and Thornton, 1993).