Table 3.
Salt bridges between Apaf-1 and cytochrome c in the PatchDock’ model
| Amino acid pair | Distance, Å | Contact time during simulation | ||||
|---|---|---|---|---|---|---|
| after energy minimization | during MD simulation | <3 Å | <4 Å | <5 Å | <6 Å | |
| Lys7-Asp902 | 2.65 | 7.55 ± 2.44 | 12 % | 13 % | 17 % | 24 % |
| Lys7-Asp903 | 2.77 | 6.34 ± 1.48 | 0 % | 1 % | 32 % | 47 % |
| Lys8-Asp1147 | 2.65 | 3.51 ± 0.75 | 29 % | 78 % | 97 % | 98 % |
| Lys25-Asp877 | 2.63 | 6.80 ± 1.48 | 3 % | 4 % | 11 % | 25 % |
| Lys25-Asp941 | 11.37 | 6.87 ± 1.85 | 0 % | 0 % | 14 % | 34 % |
| Lys27-Glu925 | 3.8 | 3.98 ± 0.89 | 28 % | 34 % | 99 % | 100 % |
| Lys39-Glu791 | 2.67 | 21.52 ± 5.12 | 1 % | 1 % | 2 % | 2 % |
| Lys39-Asp792 | 12.44 | 21.25 ± 5.99 | 0 % | 0 % | 2 % | 3 % |
| Lys72-Asp1024 | 4.57 | 7.37 ± 1.02 | 0 % | 0 % | 1 % | 8 % |
| Lys72-Asp1023 | 2.64 | 3.32 ± 0.77 | 57 % | 69 % | 100 % | 100 % |
| Lys79-Glu981 | 2.63 | 4.06 ± 1.57 | 40 % | 53 % | 78 % | 88 % |
| Lys86-Glu1045 | 7.01 | 4.37 ± 2.26 | 38 % | 60 % | 77 % | 81 % |
| Lys86-Asp1064 | 8.95 | 5.67 ± 1.73 | 9 % | 23 % | 37 % | 47 % |
| Lys87-Asp1106 | 9.56 | 5.11 ± 2.29 | 27 % | 41 % | 56 % | 69 % |
Distances between amino group nitrogens and the nearest of two carboxyl group oxygens are given for the structure after energy minimization (static parameter) and in the course of the MD simulation (dynamic parameter)