Table 5 Correlation between physical properties and the first discriminant function Brief descriptions of 49 selected physico-chemical, energetic and conformational properties, their correlation coefficient with the first discriminate function, and q-value. Asterisks in the last column shows q-value is less than 5%
From: Application of amino acid occurrence for discriminating different folding types of globular proteins
No. | Description | Corr. Coef. | q-value [%] | q ≤ 5% |
|---|---|---|---|---|
1. | Compressibility | 0.04 | 38.6 | Â |
2. | Thermodynamic transfer hydrophobicity | 0.54 | 1.9 | * |
3. | Surrounding hydrophobicity | 0.74 | 0.4 | * |
4. | Polarity | 0.36 | 9.2 | Â |
5. | Isoelectric point | 0.02 | 41.2 | Â |
6. | Equilibrium constant with reference to the ionization property | 0.01 | 41.7 | Â |
7. | Molecular weight | 0.06 | 38.4 | Â |
8. | Bulkiness | 0.49 | 3.0 | * |
9. | Chromatographic index | 0.51 | 2.7 | * |
10. | Refractive index | 0.36 | 9.2 | Â |
11. | Normalized consensus hydrophobicity | 0.48 | 3.4 | * |
12. | Short and medium range non-bonded energy | 0.11 | 32.7 | Â |
13. | Long-range non-bonded energy | 0.65 | 0.7 | * |
14. | Total non-bonded energy | 0.57 | 1.5 | * |
15. | Alpha-helical tendency | 0.29 | 14.1 | Â |
16. | Beta-helical tendency | 0.63 | 0.8 | * |
17. | Turn tendency | 0.61 | 0.9 | * |
18. | Coil tendency | 0.60 | 1.1 | * |
19. | Helical contact area | 0.20 | 23.0 | Â |
20. | Mean rms fluctuational displacement | 0.57 | 1.5 | * |
21. | Buriedness | 0.63 | 0.8 | * |
22. | Solvent accessible reduction ratio | 0.70 | 0.4 | * |
23. | Average number of surrounding residues | 0.72 | 0.4 | * |
24. | Power to be at the N-terminal of alpha helix | 0.57 | 1.5 | * |
25. | Power to be at the C-terminal of alpha helix | 0.18 | 26.4 | Â |
26. | Power to be at the middle of alpha helix | 0.05 | 38.6 | Â |
27. | Partial-specific volume | 0.25 | 18.8 | Â |
28. | Average medium-range contacts | 0.11 | 32.7 | Â |
29. | Average long-range contacts | 0.65 | 0.7 | * |
30. | Combined surrounding hydrophobicity (globular and membrane) | 0.69 | 0.4 | * |
31. | Solvent accessible surface area for denatured protein | 0.12 | 32.7 | Â |
32. | Solvent accessible surface area for native protein | 0.52 | 2.5 | * |
33. | Solvent accessible surface area for protein unfolding | 0.47 | 3.7 | * |
34. | Gibbs free energy change of hydration for unfolding | 0.30 | 14.1 | Â |
35. | Gibbs free energy change of hydration for denatured protein | 0.40 | 7.3 | Â |
36. | Gibbs free energy change of hydration for native protein | 0.46 | 4.1 | * |
37. | Unfolding enthalpy change of hydration | 0.05 | 38.6 | Â |
38. | Unfolding entropy change of hydration | 0.37 | 8.9 | Â |
39. | Unfolding hydration heat capacity change | 0.54 | 1.9 | * |
40. | Unfolding Gibbs free energy change of chain | 0.16 | 27.6 | Â |
41. | Unfolding enthalpy change of chain | 0.22 | 21.7 | Â |
42. | Unfolding entropy change of chain | 0.44 | 4.7 | * |
43. | Unfolding Gibbs free energy change | 0.33 | 11.0 | Â |
44. | Unfolding enthalpy change | 0.35 | 10.2 | Â |
45. | Unfolding entropy change | 0.34 | 10.3 | Â |
46. | Volume (number of non-hydrogen side chain atoms) | 0.11 | 32.7 | Â |
47. | Shape (position of branch point in a side-chain) | 0.10 | 32.8 | Â |
48. | Flexibility (number of side-chain dihedral angles) | 0.24 | 19.5 | Â |
49. | Backbone dihedral probability | 0.51 | 2.5 | * |