Table 6. Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation and straight DNA).
| Time (ns) | Interface Area (Å2) | Interface Area (% of Surface area) | Planarity RMSD (Å) | Length & Breadth (Å) | Polar Atoms (% of interface) | Non-polar Atoms (% of Interface) | Gap Volume (Å3) | Gap Volume/Interface Area | Hydrogen Bonds at Interface | Salt Bridges in Interface | Binding Energy (kcal/mol) |
| 0.1 | 592 | 4.3 | 3.3 | 40 & 22 | 48 | 52 | 11652 | 10.0 | 5 | 0 | −0.9 |
| 0.2 | 520 | 3.8 | 3.4 | 42 & 22 | 46 | 54 | 9425 | 8.9 | 7 | 0 | −5.6 |
| 0.3 | 504 | 3.5 | 3.4 | 43 & 23 | 42 | 58 | 9418 | 9.2 | 3 | 1 | −3.2 |
| 0.4 | 620 | 4.3 | 3.4 | 42 & 24 | 47 | 53 | 8806 | 7.0 | 5 | 1 | −4.4 |
| 0.5 | 671 | 3.9 | 3.8 | 41 & 59 | 41 | 59 | 8276 | 7.0 | 6 | 1 | −2.8 |
| 0.6 | 591 | 4.0 | 3.2 | 43 & 24 | 41 | 59 | 9664 | 8.1 | 4 | 1 | −3.8 |
| 0.7 | 582 | 4.0 | 3.1 | 42 & 23 | 46 | 54 | 9092 | 7.6 | 5 | 1 | −2.1 |
| 0.8 | 639 | 4.3 | 3.5 | 46 & 23 | 49 | 51 | 7459 | 5.7 | 5 | 1 | −8.4 |
| 0.9 | 701 | 4.7 | 3.6 | 39 & 25 | 47 | 53 | 6829 | 4.8 | 6 | 1 | −6.4 |
| 1.0 | 651 | 4.4 | 3.5 | 41 & 23 | 52 | 48 | 7150 | 5.5 | 5 | 1 | −5.1 |
Values are calculated for interface in APEX1 after 0.1 ns intervals of MD simulation. To calculate the ratio of “gap volume/interface area” the sum of interface areas in APEX1 and pol-β is used in denominator. The free energy of binding was calculated with FOLD-X server.