Table 4. Parameters of protein-protein interfaces for the 5′ complex (with pol-β in open conformation).
| 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 | 818 | 5.9 | 3.1 | 30 & 23 | 51 | 49 | 8963 | 5.4 | 5 | 0 | −10.0 |
| 0.2 | 801 | 5.7 | 3.1 | 27 & 24 | 51 | 49 | 9757 | 5.9 | 6 | 1 | −13.5 |
| 0.3 | 789 | 5.6 | 3.9 | 32 & 25 | 57 | 43 | 7156 | 4.4 | 8 | 1 | −6.7 |
| 0.4 | 775 | 5.4 | 3.0 | 29 & 22 | 49 | 51 | 8847 | 5.5 | 6 | 1 | −6.6 |
| 0.5 | 757 | 5.2 | 3.1 | 29 & 24 | 47 | 53 | 7978 | 5.2 | 8 | 0 | −10.9 |
| 0.6 | 693 | 4.8 | 3.0 | 29 & 23 | 46 | 52 | 7762 | 5.4 | 8 | 0 | −6.1 |
| 0.7 | 783 | 5.4 | 3.8 | 33 & 24 | 54 | 46 | 7337 | 4.5 | 8 | 0 | −7.4 |
| 0.8 | 667 | 4.5 | 3.9 | 33 & 23 | 45 | 55 | 7622 | 5.4 | 5 | 0 | −5.8 |
| 0.9 | 729 | 4.8 | 2.9 | 27 & 23 | 52 | 48 | 8707 | 5.9 | 6 | 0 | −6.1 |
| 1.0 | 654 | 4.4 | 2.7 | 26 & 22 | 51 | 49 | 8235 | 6.1 | 6 | 0 | −5.2 |
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.