Table 3. Parameters of protein-protein interfaces for the 3′ 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	453	3.4	2.2	25 & 23	48	52	9600	10.3	2	0	−5.4
0.2	530	3.8	2.1	26 & 18	41	59	11612	10.7	1	0	−5.2
0.3	569	4.1	2.1	26 & 19	47	53	10579	9.2	2	0	−3.4
0.4	603	4.3	2.2	29 & 21	52	48	8305	6.7	3	0	−10.0
0.5	573	4.1	2.3	29 & 17	51	49	12766	10.7	6	0	−7.1
0.6	644	4.5	2.4	31 & 23	48	52	11227	8.4	5	0	−5.2
0.7	639	4.3	2.8	29 & 19	44	56	13134	10.0	5	0	−9.6
0.8	645	4.3	2.5	34 & 19	49	51	11145	8.5	3	0	−6.5
0.9	687	4.5	3.4	31 & 34	46	54	13799	10.0	4	0	−7.7
1.0	732	4.8	3.6	42 & 30	49	51	13752	9.4	3	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.