. Author manuscript; available in PMC: 2013 Oct 13.

Published in final edited form as: J Mol Graph Model. 2012 Oct 13;38:430–445. doi: 10.1016/j.jmgm.2012.10.001

Table 3.

Decomposition of ΔG on a per-residue basis (GB) ^a

Residue	S_vdw	B_vdw	T_vdw	S_ele	B_ele	T_ele	S_GB	B_GB	T_GB	T_SUR	T_GBTOT
WT-SWCNT
Arg08	−2.82	−0.14	−2.96	−1.41	0.03	−1.38	2.74	0.06	2.80	−0.22	−1.77
Leu23^[b]	−0.80	−0.11	−0.91	0.01	−0.01	0.00	0.07	0.04	0.11	−0.05	−0.85
Gly27	0.00	−2.29	−2.29	0.00	−0.17	−0.17	0.00	1.04	1.04	−0.10	−1.51
Ala28	−0.83	−1.79	−2.62	−0.01	−0.03	−0.04	−0.04	0.06	0.02	−0.17	−2.81
Gly49	0.00	−2.35	−2.35	0.00	−0.23	−0.23	0.00	1.52	1.52	−0.12	−1.19
Ile50	−2.45	−1.83	−4.28	0.00	−0.23	−0.23	0.11	0.24	0.35	−0.19	−4.07
Pro81^[b]	−0.82	−0. 23	−1.05	0.15	−0.05	0.10	0.04	0.03	0.07	−0.07	−0.95
Val82	−0.93	−0. 19	−1.12	0.03	−0.08	−0.05	0.04	0.12	0.16	−0.06	−1.07
Ile84	−1.67	−0.13	−1.80	0.06	−0.03	0.03	−0.05	0.04	−0.01	−0.12	−1.91
Arg08’	−2.73	−0.07	−2.80	0.54	0.01	0.55	1.09	0.06	1.15	−0.25	−1.36
Leu23’	−1.48	−0.11	−1.59	0.07	−0.04	0.03	0.01	0.03	0.04	−0.04	−1.56
Gly27’	0.00	−1.72	−1.72	0.00	0.23	0.23	0.00	0.09	0.09	−0.09	−1.48
Ala28’	−0.69	−1.54	−2.23	0.00	0.09	0.09	−0.05	0.32	0.27	−0.13	−1.99
Asp29’^[b]	−0.38	−0.51	−0.89	−0.02	−0.01	−0.03	0.19	0.04	0.23	−0.06	−0.75
Gly49’^[b]	0.00	−1.29	−1.29	0.00	0.12	0.12	0.00	0.50	0.50	−0.10	−0.88
Ile50’	−2.32	−1.30	−3.62	0.08	−0.08	0.00	0.03	0.30	0.33	−0.18	−3.47
Pro81’	−1.49	−1.03	−2.52	0.27	−0. 16	0.11	−0.05	0.44	0.39	−0.21	−2.02
Val82’	−1.88	−0.64	−2.52	0.14	−0.13	0.01	0.10	0.22	0.32	−0.17	−2.35
Ile84’	−1.94	−0.14	−2.08	0.07	−0.06	0.01	−0.03	0.05	0.02	−0.11	−2.15
I50V-SWCNT
Leu23	−1.41	−0.10	−1.51	0.05	−0.05	0.00	0.02	0.05	0.07	−0.10	−1.53
Gly27	0.00	−1.66	−1.66	0.00	−0. 03	−0. 03	0.00	0.39	0.39	−0.06	−1.36
Ala28	−0.77	−1.65	−2.42	−0.01	0.11	0.10	−0.05	0.52	0.47	−0.11	−1.96
Asp29	−1.29	−0.90	−2.19	−0.99	−0.07	−1.06	1.24	0.18	1.42	−0.16	−1.99
Val50	−2.10	−1.87	−3.97	0.05	−0.11	−0.06	0.30	0.48	0.78	−0.16	−3.41
Pro81	−1.45	−0. 50	−1.95	0.19	−0.03	0.16	0.04	0.12	0.16	−0.16	−1.79
Val82	−1.40	−0.43	−1.83	0.06	−0. 10	−0.04	0.07	0.19	0.26	−0.15	−1.75
Ile84	−1.89	−0.15	−2.03	0.08	−0.05	0.03	−0.02	0.07	0.05	−0.17	−2.13
Arg08’^[b]	−2.02	−0.06	−2.08	0.21	0.03	0.24	1.04	0.05	1.09	−0.18	−0.93
Leu23’	−1.43	−0.11	−1.54	0.08	−0.04	0.03	−0.01	0.05	0.04	−0.08	−1.53
Ala28’	−0.08	−0.95	−1.03	−0.01	0.07	0.06	−0.01	−0.03	−0.4	−0.08	−1.08
Asp29’^[b]	−0.69	−0.35	−1.04	−0.04	−0.07	−0.11	0.47	−0.01	0.46	−0.10	−0.85
Gly49’	0.0	−2.28	−2.28	0.0	−0.09	−0.09	0.0	1.1	1.1	−0.09	−1.36
Val50’	−1.91	−1.53	−3.44	−0.09	0.06	−0.03	0.18	0.13	0.31	−0.17	−3.33
Pro81’	−1.49	−0.49	−1.98	0.20	−0.06	0.14	0.12	0.08	0.20	−0.13	−1.77
Val82’	−1.56	−0.40	−1.96	0.08	−0.09	−0.01	0.06	0.17	0.22	−0.13	−1.87
Ile84’	−1.85	−0.14	−1.99	0.08	−0.05	0.03	−0.06	0.05	−0.01	−0.15	−2.11
V82A-SWCNT
Arg08	−2.14	−0.07	−2.21	0.25	0.03	0.28	0.95	0.05	1.00	−0.22	−1.15
Leu23	−1.64	−0.11	−1.75	0.07	−0.02	0.05	0.07	0.05	0.12	−0.16	−1.76
Gly27^[b]	0.0	−1.08	−1.08	0.0	0.12	0.12	0.00	0.02	0.02	−0.04	−0.98
Ala28	−0.68	−0.96	−1.65	−0.01	0.11	0.10	−0.04	0.13	0.08	−0.18	−1.64
Ile50	−2.32	−1.58	−3.90	0.09	−0.11	−0.02	0.13	0.37	0.50	−0.16	−3.57
Pro81	−1.71	−0. 98	−2.69	0.22	−0.14	0.08	−0.01	0.51	0.50	−0.21	−2.32
Ala82	−0.77	−0. 70	−1.47	0.01	−0.04	−0.03	−0.02	0.23	0.21	−0.10	−1.39
Ile84	−1.83	−0.12	−1.95	0.09	−0.07	0.02	−0.06	0.07	0.01	−0.17	−2.12
Gly27’	0.00	−2.03	−2.03	0.00	−0.08	−0.08	0.00	0.34	0.34	−0.08	−1.86
Ala28’	−0.80	−1.82	−2.62	0.01	−0.04	−0.03	−0.05	0.57	0.51	−0.09	−2.23
Asp29’	−1.70	−1.09	−2.79	−0.83	−0.08	−0.91	0.99	0.31	1.29	−0.17	−2.59
Gly48’^[b]	0.00	−2.23	−2.23	0.00	0.23	0.23	0.00	1.27	1.27	−0.10	−0.92
Gly49’	0.00	−2.80	−2.80	0.00	−0.19	−0.19	0.00	1.25	1.25	−0.10	−1.85
Ile50’	−2.31	−1.72	−4.03	0.08	0.00	0.08	0.09	0.13	0.22	−0.18	−3.92
Phe53’^[b]	−0.97	−0.11	−1.08	0.02	0.01	0.03	0.15	0.08	0.23	−0.14	−0.96
Pro81’	−0.94	−0.53	−1.47	−0.04	−0. 05	−0.09	0.19	0.02	0.21	−0.09	−1.44
Ala82’^[b]	−0.29	−0.86	−1.15	−0.02	−0.08	−0.10	0.01	0.36	0.37	−0.07	−0.94
Ile84’	−2.04	−0.21	−2.25	0.08	−0.03	0.05	−0.04	0.04	0.00	−0.15	−2.35
I84V-SWCNT
Gly27	0.00	−1.76	−1.76	0.00	0. 00	0. 00	0.00	0.25	0.25	−0.15	−1.66
Ala28	−0.32	−0.96	−1.28	−0.01	0.11	0.10	−0.01	0.14	0.13	−0.16	−1.21
Gly49	−0.00	−1.65	−1.65	0.00	0.06	0.06	0.00	0.58	0.55	−0.11	−1.15
Ile50	−2.39	−1.13	−3.52	0.04	−0.06	−0.02	0.03	0.27	0.30	−0.17	−3.41
Pro81	−1.57	−0. 46	−2.03	0.20	−0.11	0.09	−0.04	0.23	0.19	−0.18	−1.93
Val82^[b]	−0.60	−0.14	−0.74	0.07	−0.04	0.03	−0.07	0.08	0.01	−0.15	−0.85
Arg08’	−2.46	−0.09	−2.55	0.09	−0.17	−0.08	0.25	1.43	1.68	−0.18	−1.13
Leu23’	−1.55	−0.13	−1.68	0.07	−0.02	0.05	0.03	0.02	0.05	−0.13	−1.71
Gly27’	0.00	−1.75	−1.75	0.00	0.09	0.09	0.00	0.26	0.26	−0.12	−1.52
Ala28’	−0.68	−1.65	−2.33	−0.03	0.12	0.09	−0.06	0.35	0.29	−0.13	−2.08
Asp29’	−1.04	−0.76	−1.80	0.02	−0.05	0.03	0.37	0.11	0.48	−0.15	−1.44
Ile47’	−1.58	−0.41	−1.99	0.05	0.01	0.06	−0.01	0.15	0.14	−0.17	−1.96
Gly48’^[b]	0.00	−2.16	−2.16	0.00	−0.09	−0.09	0.00	1.41	1.41	−0.14	−0.98
Gly49’	0.00	−2.23	−2.23	0.00	−0.21	−0.21	0.00	1.14	1.14	−0.10	−1.40
Ile50’	−2.37	−1.55	−3.92	0.04	−0.07	−0.03	0.11	0.18	0.29	−0.19	−3.85
Pro81’	−1.23	−0.44	−1.67	0.15	−0. 05	0.10	0.02	0.11	0.13	−0.14	−1.58
Val82’	−1.36	−0.47	−1.83	0.06	−0.07	−0.01	0.08	0.16	0.24	−0.11	−1.71
Val84’	−1.05	−0.13	−1.18	0.17	−0.05	0.12	0.07	0.08	0.15	−0.12	−1.03

^[a]

Energies shown as contributions from van der Waals energy (vdw), electrostatic energy (ele), polar solvation energy (GB), the non-polar solvation energy (SUR) of side chain atoms (S), backbone atoms (B), and the sum of them, total (T) of protein-inhibitor complex. Only residues of |ΔG| ≥ 1.0 kcal /mol were listed (except few ^[b]). All values are given in kcal/mol.