Table 1. Parameters of protein-protein interfaces for the 3′ complex (with pol-β in closed 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) | Area of segment #1 (Å2) | Area of segment #2 (Å2) | Area of segment #3 (Å2) |
| 0.1 | 565 | 4.2 | 2.7 | 37 & 24 | 47 | 53 | 8655 | 7.5 | 6 | 0 | −6.6 | 142 | 238 | 185 |
| 0.2 | 644 | 4.7 | 3.7 | 40 & 25 | 50 | 50 | 8731 | 6.7 | 3 | 0 | −6.6 | 159 | 281 | 204 |
| 0.3 | 530 | 3.8 | 3.1 | 37 & 24 | 49 | 51 | 8480 | 7.9 | 2 | 0 | −2.8 | 140 | 227 | 163 |
| 0.4 | 521 | 4.0 | 2.9 | 27 & 24 | 43 | 57 | 8894 | 8.3 | 5 | 0 | −8.3 | 166 | 191 | 164 |
| 0.5 | 544 | 4.1 | 3.0 | 35 & 21 | 43 | 57 | 9681 | 8.5 | 6 | 0 | −5.0 | 132 | 226 | 186 |
| 0.6 | 585 | 4.4 | 2.8 | 36 & 25 | 40 | 60 | 10060 | 8.4 | 5 | 0 | −6.1 | 148 | 230 | 207 |
| 0.7 | 540 | 4.1 | 3.0 | 35 & 26 | 49 | 51 | 9465 | 8.6 | 5 | 0 | −10.0 | 89 | 239 | 212 |
| 0.8 | 450 | 3.4 | 2.6 | 34 & 22 | 54 | 46 | 11862 | 12.8 | 3 | 0 | −5.8 | 108 | 215 | 127 |
| 0.9 | 478 | 3.6 | 2.7 | 40 & 24 | 51 | 49 | 10089 | 10.3 | 4 | 0 | −9.5 | 137 | 194 | 147 |
| 1.0 | 632 | 4.8 | 3.4 | 39 & 24 | 49 | 51 | 9879 | 7.7 | 5 | 0 | −7.3 | 247 | 200 | 185 |
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.