Protein Docking Potentials - Tobi Dror and Bahar Ivet


	ALA	ARG	ASN	ASP	CYS	GLN	GLU	GLY	HIS	ILE	LEU	LYS	MET	PHE	PRO	SER	THR	TRP	TYR	VAL	NH	OC
ALA	-3.56	4.17	1.69	-1.45	-3.00	-2.52	3.56	0.54	-0.07	-0.65	-0.58	4.26	5.39	-0.17	4.50	1.23	-0.21	-3.36	-0.60	-2.05	0.60	-0.44
ARG	4.17	-1.66	-0.12	-2.00	-1.02	4.20	-1.80	-0.04	0.29	2.80	-1.80	0.90	-1.10	-3.04	1.33	-0.02	-0.55	-4.65	-3.18	-2.69	1.60	-1.37
ASN	1.69	-0.12	-0.33	-1.09	6.52	-2.25	-2.20	1.13	0.95	-0.86	2.20	1.22	-1.33	-1.83	-0.42	-0.09	-0.99	-2.81	-1.58	0.66	0.17	-0.71
ASP	-1.45	-2.00	-1.09	0.97	2.57	0.63	1.45	0.67	-0.71	0.01	-0.62	-2.45	1.21	6.05	1.11	-2.42	-0.92	-0.90	-1.03	-1.61	0.85	0.07
CYS	-3.00	-1.02	6.52	2.57	10.00	-0.63	-3.34	0.94	-4.93	-1.13	-2.02	-2.95	0.00	6.01	4.87	-1.74	5.30	2.60	-0.36	1.37	0.44	-0.72
GLN	-2.52	4.20	-2.25	0.63	-0.63	9.72	1.25	-0.76	1.65	-1.83	-2.63	1.23	1.94	8.05	0.80	-0.75	1.01	-3.60	-2.36	-0.68	1.35	-1.28
GLU	3.56	-1.80	-2.20	1.45	-3.34	1.25	1.49	0.89	-0.81	3.26	0.05	-3.01	-0.91	0.36	2.76	-1.26	-0.63	-0.53	-1.74	1.04	-0.38	0.05
GLY	0.54	-0.04	1.13	0.67	0.94	-0.76	0.89	-0.34	0.44	-1.86	0.35	-0.26	-0.90	-0.16	2.87	1.20	0.43	0.10	-1.63	-1.06	-1.28	0.49
HIS	-0.07	0.29	0.95	-0.71	-4.93	1.65	-0.81	0.44	1.04	-1.82	2.20	0.42	-4.03	-2.13	1.65	1.24	0.35	1.68	-4.25	-0.20	-0.65	-1.15
ILE	-0.65	2.80	-0.86	0.01	-1.13	-1.83	3.26	-1.86	-1.82	-3.27	-4.09	1.34	0.50	-6.05	0.25	-1.24	1.66	-5.01	-2.88	-3.78	2.55	-0.09
LEU	-0.58	-1.80	2.20	-0.62	-2.02	-2.63	0.05	0.35	2.20	-4.09	-3.43	0.80	-1.90	-2.21	-1.40	0.29	0.72	-0.39	-1.43	-1.80	-0.70	-0.09
LYS	4.26	0.90	1.22	-2.45	-2.95	1.23	-3.01	-0.26	0.42	1.34	0.80	3.24	3.64	-2.39	3.85	1.71	0.65	-3.37	-2.34	-2.01	1.02	-0.57
MET	5.39	-1.10	-1.33	1.21	0.00	1.94	-0.91	-0.90	-4.03	0.50	-1.90	3.64	10.00	-4.17	-4.02	-0.55	-2.81	-5.89	-2.28	-1.32	0.74	-1.22
PHE	-0.17	-3.04	-1.83	6.05	6.01	8.05	0.36	-0.16	-2.13	-6.05	-2.21	-2.39	-4.17	-6.42	-3.96	0.17	-1.08	-2.65	-3.51	-2.17	0.49	-0.79
PRO	4.50	1.33	-0.42	1.11	4.87	0.80	2.76	2.87	1.65	0.25	-1.40	3.85	-4.02	-3.96	-2.50	-0.29	-1.18	-4.56	-2.23	0.22	0.01	-0.69
SER	1.23	-0.02	-0.09	-2.42	-1.74	-0.75	-1.26	1.20	1.24	-1.24	0.29	1.71	-0.55	0.17	-0.29	0.45	-1.01	-0.86	-1.38	1.27	0.65	-0.94
THR	-0.21	-0.55	-0.99	-0.92	5.30	1.01	-0.63	0.43	0.35	1.66	0.72	0.65	-2.81	-1.08	-1.18	-1.01	0.22	2.43	-1.76	0.83	0.76	-1.22
TRP	-3.36	-4.65	-2.81	-0.90	2.60	-3.60	-0.53	0.10	1.68	-5.01	-0.39	-3.37	-5.89	-2.65	-4.56	-0.86	2.43	8.64	-2.83	-1.87	-0.28	-0.70
TYR	-0.60	-3.18	-1.58	-1.03	-0.36	-2.36	-1.74	-1.63	-4.25	-2.88	-1.43	-2.34	-2.28	-3.51	-2.23	-1.38	-1.76	-2.83	-2.15	-1.37	1.38	-1.50
VAL	-2.05	-2.69	0.66	-1.61	1.37	-0.68	1.04	-1.06	-0.20	-3.78	-1.80	-2.01	-1.32	-2.17	0.22	1.27	0.83	-1.87	-1.37	-0.37	-0.22	-0.27
NH	0.60	1.60	0.17	0.85	0.44	1.35	-0.38	-1.28	-0.65	2.55	-0.70	1.02	0.74	0.49	0.01	0.65	0.76	-0.28	1.38	-0.22	6.84	-2.14
OC	-0.44	-1.37	-0.71	0.07	-0.72	-1.28	0.05	0.49	-1.15	-0.09	-0.09	-0.57	-1.22	-0.79	-0.69	-0.94	-1.22	-0.70	-1.50	-0.27	-2.14	1.82


Remarks:

Each side chain is represented by three interaction sites:
1) side-chain (S) centroid        (ALA - VAL).
2) backbone   (B) amid nitrogen   (NH).
3) backbone   (B) carbonyl oxygen (OC).


Cutoff Distances:
B-B = 4.0 angstrom.
B-S = 5.6 angstrom.
S-S = 6.8 angstrom.

Reference
Tobi D. and Bahar I. “Optimal Design of Protein Docking Potentials: Efficiency and Limitations” Proteins: Structure, Function, and Bioinformatics, 62 970-981.