Analysis of the impact of solvent on contacts prediction in proteins

Samsonov, Sergey A; Teyra, Joan; Anders, Gerd; Pisabarro, M Teresa

doi:10.1186/1472-6807-9-22

BMC Structural Biology

Table 2 Dataset used for intradomain contact predictions.

From: Analysis of the impact of solvent on contacts prediction in proteins

PFAM ID	PDB ID^a	R (Å)	N^b	% id^c	L^d	Ran acc^e	Acc^f	R^g	Opt α^h	X_{d dry}ⁱ	Opt_Xd α^j	X_{d wet}\|_{opt α}^k
PF00014	6PTI	1.70	151	33	52	0.096	0.346	3.61	1	9.37	1	11.16
PF03705	1AF7	2.00	85	20	57	0.081	0.241	2.65	0.5, 4, 10	6.14	2	7.63
PF00062	5LYZ	2.00	22	46	127	0.043	0.078	1.91	0, 0.5	2.68	0	2.68
PF00018	1BU1	2.60	61	28	56	0.088	0.357	4.06	0.5	12.99	0	12.99
PF03900	1PDA	1.76	21	25	74	0.062	0.237	3.82	2	9.18	0.2	9.99
PF00034	1CTJ	1.10	35	17	89	0.061	0.250	4.10	1	9.13	0.1	10.34
PF01568	1DMR	1.82	88	18	113	0.044	0.050	1.14	0.2, 0.5	10.62	2	12.53
PF00127	8PAZ	1.60	31	29	89	0.055	0.102	1.85	2	0.50	1	4.82
PF01814	2MHR	1.30	295	12	49	0.098	0.400	4.08	0.5, 2	8.39	2	13.14
PF00017	1BMB	1.80	59	28	93	0.058	0.212	3.66	0 – 0.5	5.98	1	8.37
PF01320	1AYI	2.00	45	47	86	0.056	0.233	4.15	0.2	16.04	0	16.04
PF08666	1AME	1.65	171	14	66	0.074	0.273	3.69	0	10.25	0	10.25
PF01337	1A19	2.76	30	25	89	0.065	0.178	2.87	0, 0.1	4.55	0.1	4.72
PF00595	2HB2	2.30	56	19	85	0.062	0.233	3.75	0.5 – 2	10.16	1	11.67
PF00531	1WMG	2.10	92	14	82	0.066	0.250	3.79	0 – 0.5	7.67	0.2	7.95
PF00397	1EG3	2.00	73	32	30	0.143	0.467	3.26	2 – 20	6.59	2	8.81
PF01335	2F1S	1.40	40	21	76	0.072	0.237	3.88	0.1, 0.2	5.66	0.2	5.96
PF00619	1CY5	1.30	61	16	85	0.066	0.209	3.43	0.2 – 2	5.09	2	9.42
PF02213	1SYX	2.35	112	28	58	0.083	0.241	2.91	0.5 – 2	7.37	0.5	7.77
PF05743	1UZX	1.85	28	27	118	0.035	0.068	1.98	0.1	7.22	0	7.22
PF00536	1B4F	1.95	69	28	74	0.076	0.395	5.19	0.2 – 2	15.53	2	16.36
PF03114	1ZWW	2.30	29	19	195	0.021	0.074	3.53	0.2	2.41	20	3.99
PF00169	1NTY	1.70	139	10	112	0.050	0.071	1.43	0, 0.2, 0.5	5.46	2	7.53
PF08416	1WVH	1.50	49	28	132	0.040	0.106	2.65	2, 4	0.53	0.1	1.24
PF01981	1WN2	1.20	69	43	116	0.049	0.172	3.52	0.1 – 0.5	7.63	20	12.38
PF03992	1XBW	1.90	116	15	65	0.068	0.125	1.84	0.5	3.34	0	3.34
PF00907	1H6F	1.70	23	49	183	0.032	0.033	1.03	0 – 20	3.30	2	6.03
PF02237	1WPY	1.60	47	21	48	0.094	0.167	1.77	0.5 – 2	-2.83	0.5	0.22
PF08031	2AXR	1.98	64	34	34	0.135	0.235	1.74	0.1, 0.2	-0.05	2	3.37
PF02861	1K6K	1.80	165	21	51	0.098	0.440	4.49	1, 4, 10, 20	9.55	20	13.21
PF02834	1VGJ	1.94	106	14	85	0.048	0.119	2.48	4 – 20	-0.51	4, 10	3.21
PF01423	1KQ1	1.55	128	23	60	0.079	0.167	2.11	0.2, 0.5	5.78	0.1, 0.2	7.14
PF01472	1AS0	1.80	106	24	78	0.058	0.128	2.21	1 – 20	3.57	2, 4	11.45
PF01909	1NO5	1.80	119	14	91	0.059	0.133	2.26	0.1 – 1	4.97	0.2	6.01
PF09261	1R34	1.95	79	31	78	0.069	0.205	2.97	0.1, 0.2	4.87	0.1	6.64
PF01315	1VLB	1.28	28	19	117	0.041	0.207	5.05	1, 2	7.70	2	10.28
PF04545	1KU3	1.80	128	31	54	0.096	0.370	3.86	0, 0.1, 1, 10, 20	12.37	10, 20	12.76
PF00984	1MV8	1.55	24	17	98	0.048	0.184	3.83	0.5 – 20	8.27	0.2	9.78
PF01658	1U1I	1.90	20	31	105	0.049	0.096	1.96	0.1 – 20	1.93	0.5	6.28
PF00745	1GPJ	1.95	34	23	99	0.048	0.100	2.08	0.1 – 0.5	3.17	0.1	4.17
PF03099	1WNL	1.60	65	14	117	0.043	0.121	2.81	0	13.7	0.2	14.20
PF01985	1JO0	1.37	50	23	84	0.064	0.167	2.60	0 – 0.2	6.96	0	6.96
PF08436	1Q0Q	1.90	77	57	94	0.049	0.213	4.34	0 – 0.1	6.91	10	10.15
PF02881	1JPN	1.90	52	19	85	0.063	0.119	1.89	0 – 20	3.94	2	5.78
PF01966	1YNB	1.76	158	12	91	0.057	0.333	5.85	0 – 0.2	-0.79	2	2.20
PF00191	1YII	1.42	178	28	66	0.076	0.273	3.59	0 – 0.2	-0.35	10	1.05
PF00317	1XJE	1.90	79	23	90	0.056	0.178	3.17	0.5 – 2	10.01	0.5	13.16
PF00046	1PUF	1.90	184	37	60	0.082	0.333	4.07	1, 2	6.07	2	8.60
PF00077	5FIV	1.90	48	27	108	0.049	0.093	1.89	2	-1.37	1	3.63
PF00042	1ECN	1.40	73	18	101	0.046	0.163	3.56	1, 2	6.89	2	7.19

^aPDB ID; ^bNumber of sequences; ^cAverage sequences pairwise similarity (%); ^dReference sequence length; ^eRandom accuracy; ^fAccuracy for optimal α; ^gImprovement ratio over random prediction for optimal α; ^hValues for α = 0; ⁱα corresponding to the highest accuracy; ^jα corresponding to the highest X_d; ^kX_d highest value.

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ISSN: 1472-6807

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