Table 3 The initial set of 24 residue properties
# | ATTRIBUTE | PROGRAM/DATABASE USED |
|---|---|---|
Residue Identity | ||
1. | AA_identity | PDB database [41, 1L] |
2. | AA_type | [23] |
Sequence Conservation | ||
3. | entropy | 9-Component Dirichlet |
4. | relative_entropy | Mixture algorithm [30] |
5. | conservation_score | Scorecons server [32, 7L] |
Flexibility | ||
6. | B_factor | PDB database [41, 1L] |
Solvent Accessibility | ||
7. | SAS_all_atoms_ABS | Naccess program [34] |
8. | SAS_all_atoms_REL | Â |
9. | SAS_total_side_ABS | Â |
10. | SAS_total_side_REL | Â |
11. | SAS_main_chain_ABS | Â |
12. | SAS_main_chain_REL | Â |
13. | SAS_non_polar_ABS | Â |
14. | SAS_non_polar_REL | Â |
15. | SAS_all_polar_ABS | Â |
16. | SAS_all_polar_REL | Â |
| Â | Relative Position on protein Surface | |
17. | nearest_cleft_rank | CASTp server [36, 8L], |
18. | nearest_cleft_SA_volume | PDB database [41, 1L] |
19. | nearest_cleft_SA_area | Â |
20. | nearest_cleft_distance | Â |
21. | distance_to_3_largest_clefts | Â |
| Â | Hydrogen Bonds | |
22. | HB_main_chain_protein | MolMol Program [37] |
23. | HB_side_chain_protein | Â |
| Â | Secondary Structure | |
24. | 2D_structure | DSSP program [38] |