Sequence Based Features Extraction

ARGP820101

Hydrophobicity index (Argos et al. 1982)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.84	1.27	0.59	0.57	1.15	0.94	0.81	1.29	0.86	1.1	0.88	0.66	0.8	1.02	1.04	1.05	1.2	1.56	1.15	1.39
Normalized value	0.23	0.4	0.17	0.18	0.76	0.03	0.23	0.84	0.43	0.58	0.45	0.02	0.74	0	0.23	0.02	0.02	0.5	1	1

BIGC670101

Residue volume (Bigelow 1967)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.91	0.93	1.4	0.97	0.72	1.51	0.9	0.65	0.82	0.59	0.58	1.64	1.66	0.94	1	1.23	1.04	0.6	0.67	0.92
Normalized value	0.16	0.5	0.5	0.63	0.84	0.27	0.68	0.75	0.78	0.75	0.72	0.56	0.54	0.66	0.81	0.4	0.53	0.63	1	1

BIOV880102

Information value for accessibility; average fraction 23% (Biou et al. 1988)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	44	90	-91	-139	148	-8	47	100	-188	108	121	-72	-36	-117	-68	-60	-54	117	163	22
Normalized value	0.66	0.79	0.28	0.14	0.96	0.51	0.67	0.82	0	0.8	0.85	0.16	0.29	0	0	0	0	0.72	1	1

BURA740102

Normalized frequency of extended structure (Burgess et al. 1974)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	8.1	5.5	13	12.3	5.2	9	10.4	5.2	11.3	4.9	5.7	11.6	8	10.5	10.5	9.2	8.6	5.9	5.4	6.2
Normalized value	0.26	1	0.09	0.19	0.25	0.24	0.12	0.35	0.19	0.34	0.31	0.15	0.28	0.26	0.3	0.29	0.33	0.45	0.16	0.37

CHAM820101

Polarizability parameter (Charton-Charton 1982)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	31	55	54	83	132	3	96	111	119	111	105	56	32.5	85	124	32	61	84	170	136
Normalized value	0.11	0.31	0.26	0.37	0.71	0	0.32	0.26	0.31	0.26	0.31	0.19	0.18	0.25	0.41	0.09	0.15	0.2	0.58	0.42

CHOC760101

Residue accessible surface area in tripeptide (Chothia 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1	0.1	6.5	6.2	1.4	1.1	2.8	0.8	5.3	0.8	0.7	2.2	0.9	2.1	2.3	1.7	1.5	0.9	1.9	2.1
Normalized value	0.22	0.53	0.59	0.74	0.82	0.29	0.76	0.69	0.78	0.67	0.73	0.63	0.57	0.71	0.88	0.45	0.55	0.61	1	1

CHOP780202

Normalized frequency of beta-sheet (Chou-Fasman 1978b)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.86	1.39	0.69	0.66	1.16	0.7	1.06	1.31	0.77	1.01	1.06	0.74	1.16	0.89	0.98	1.09	1.24	1.4	1.17	1.28
Normalized value	0.35	0.62	0.14	0.15	0.79	0.39	0.47	0.94	0.38	0.74	0.58	0.48	0.26	0.61	0.51	0.39	0.67	1	0.92	1

CHOP780204

Normalized frequency of N-terminal helix (Chou-Fasman 1978b)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.78	0.6	1.5	0.97	0.67	1.73	0.83	0.4	1.01	0.57	0.3	1.56	1.55	0.78	1.06	1.19	1.09	0.44	0.74	1.14
Normalized value	0.43	0.12	0.82	1	0.26	0.34	0.32	0.29	0.29	0.24	0.31	0.37	1	0.82	0.24	0.46	0.71	0.36	1	0.64

DAYM780201

Relative mutability (Dayhoff et al. 1978b)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.09	0.5	0.77	0.92	0.5	1.25	0.67	0.66	1.25	0.44	0.45	1.14	2.96	0.83	0.97	1.21	1.33	0.56	0.62	0.94
Normalized value	0.71	0.14	0.79	0.76	0.31	0.36	0.49	0.72	0.42	0.3	0.7	1	0.47	0.77	0.54	1	1	1	0.44	1

EISD860101

Solvation free energy (Eisenberg-McLachlan 1986)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.87	1.52	0.66	0.67	2.87	0.1	0.87	3.15	1.64	2.17	1.67	0.09	2.77	0	0.85	0.07	0.07	1.87	3.77	2.67
Normalized value	0.59	0.53	0.19	0.29	0.94	0.45	0.58	0.85	0.33	0.85	0.96	0.32	0.7	0.4	0	0	0.2	0.58	1	1

FASG760101

Molecular weight (Fasman 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	5.3	1.3	3.6	3.3	2.3	4.8	1.4	3.1	4.1	4.7	1.1	3	2.5	2.4	2.6	4.5	3.7	4.2	0.8	2.3
Normalized value	0.11	0.59	0.65	0.72	0.81	0.37	0.76	0.64	0.72	0.64	0.73	0.65	0.56	0.72	0.85	0.51	0.58	0.57	1	1

FASG760102

Melting point (Fasman 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.81	1.17	0.71	0.53	1.2	0.88	0.92	1.48	0.77	1.24	1.05	0.62	0.61	0.98	0.85	0.92	1.18	1.66	1.18	1.23
Normalized value	0.72	0.52	0.78	0.72	0.83	0.84	0.8	0.83	0.65	0.98	0.82	0.69	0.64	0.54	0.69	0.66	0.74	0.85	0.82	1

FAUJ830101

Hydrophobic parameter pi (Fauchere-Pliska 1983)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.45	0.7	0.91	1.29	1.2	0.53	1.13	1.23	1.27	1.56	1.83	0.64	0.21	1.14	1.15	0.48	0.77	1.1	1.17	0.74
Normalized value	0.4	0.78	0.07	0.11	0.86	0.31	0.35	0.86	0.01	0.83	0.69	0.13	0.53	0.24	0	0	0.12	0.54	1	0.96

FAUJ880101

Graph shape index (Fauchere et al. 1988)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.041	0.96	1.033	1.094	0.93	1.142	0.982	1.002	1.093	0.967	0.947	1.117	1.055	1.165	1.038	1.169	1.073	0.982	0.925	0.961
Normalized value	0.31	0.42	0.38	0.37	0.7	0	0.71	1	0.51	0.71	0.64	0.44	0.73	0.43	0.64	0.36	0.83	1	1	1

FAUJ880106

STERIMOL maximum width of the side chain (Fauchere et al. 1988)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	4.6	-1	5.7	5.6	3.2	7.6	4.5	2.6	7.9	3.25	1.4	5.9	7	6.1	6.5	5.25	4.8	3.4	4	4.35
Normalized value	0.18	0.49	0.55	0.48	0.89	0.13	0.84	0.51	0.72	0.66	0.71	0.64	0.63	0.52	0.93	0.39	0.46	0.46	0.88	1

GEIM800105

Beta-strand indices (Geisow-Roberts 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	4.32	1.73	6.04	6.17	2.59	6.09	5.66	2.31	7.92	3.93	2.44	6.24	7.19	6.13	6.55	5.37	5.16	3.31	2.78	3.58
Normalized value	0.27	0.77	0.25	0.25	0.69	0.53	0.43	0.79	0.47	0.65	0.48	0.31	0.42	0.59	0.6	0.61	0.73	1	0.79	1

GEIM800108

Aperiodic indices (Geisow-Roberts 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.48	-0.32	-0.75	-0.71	1.03	0	-0.51	0.81	-0.09	1.02	0.81	-0.87	2.03	-0.32	-0.06	0.05	-0.35	0.56	0.66	1.24
Normalized value	0.31	0.46	0.81	0.49	0.31	0.89	0.44	0.25	0.4	0.24	0.24	0.99	1	0.71	0.77	1	1	0.47	0.57	0.89

GRAR740102

Polarity (Grantham 1974)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.5	-1	2.5	2.5	-2.5	0	-0.5	-1.8	3	-1.8	-1.3	0.2	-1.4	0.2	3	0.3	-0.4	-1.5	-3.4	-2.3
Normalized value	0.4	0.4	1	1	0.43	0.77	0.89	0.43	0.97	0.4	0.47	1	0.75	1	1	1	1	0.95	0.86	1

GRAR740103

Volume (Grantham 1974)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.92	1.16	0.48	0.61	1.25	0.61	0.93	1.81	0.7	1.3	1.19	0.6	0.4	0.95	0.93	0.82	1.12	1.81	1.54	1.53
Normalized value	0.17	0.32	0.32	0.49	0.78	0.02	0.56	0.65	0.7	0.65	0.62	0.33	0.19	0.5	0.73	0.19	0.36	0.49	1	1

HOPA770101

Hydration number (Hopfinger 1971) Cited by Charton-Charton (1982)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.9	1.24	0.47	0.62	1.23	0.56	1.12	1.54	0.74	1.26	1.09	0.62	0.42	1.18	1.02	0.87	1.3	1.53	1.75	1.68
Normalized value	0.14	0	1	1	0.26	0.21	0.53	0.15	1	0.35	0.3	0.96	0.39	0.91	1	0.81	0.71	0.43	0.9	1

ISOY800102

Normalized relative frequency of extended structure (Isogai et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	12.97	14.63	10.85	11.89	14	12.43	12.16	15.67	11.36	14.9	14.39	11.42	11.37	11.76	11.72	11.23	11.69	15.71	13.93	13.42
Normalized value	0.27	0.99	0.37	0.34	0.79	0.38	0.7	0.92	0.44	0.65	0.7	0.42	0.79	0.55	0.63	0.73	0.86	1	0.89	1

ISOY800103

Normalized relative frequency of bend (Isogai et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.86	1.17	0.72	0.62	1.16	0.97	1.06	1.24	0.79	0.98	1.08	0.74	1.22	0.89	0.94	1.04	1.18	1.33	1.07	1.25
Normalized value	0.34	0.21	0.85	0.5	0.3	1	0.46	0.14	0.61	0.3	0.11	1	1	0.62	0.88	1	0.95	0.32	0.61	1

ISOY800104

Normalized relative frequency of bend R (Isogai et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1	1.09	1.39	1.04	0.65	0.46	0.71	0.68	1.05	1.01	0.36	0.87	1.95	1.13	1.18	1.56	1.23	0.58	1.1	0.87
Normalized value	0.26	0.09	0.24	0.29	0.14	0.4	0.2	0.2	0.4	0.12	0.13	0.37	1	0.6	0.71	0.9	1	0.52	0.58	0.93

JOND750101

Hydrophobicity (Jones 1975)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	2.36	3.36	1.67	1.74	4.37	2.06	2.41	4.17	1.23	3.93	4.22	1.7	1.89	1.75	1.92	1.81	2.04	3.49	3.82	2.91
Normalized value	0.23	0.4	0.18	0.18	0.76	0.03	0.23	0.84	0.44	0.58	0.44	0.02	0.73	0	0.23	0.02	0.02	0.5	1	1

JUKT750101

Amino acid distribution (Jukes et al. 1975)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.96	1.13	0.9	0.33	1.37	0.9	0.87	1.54	0.81	1.26	1.29	0.72	0.75	1.18	0.67	0.77	1.23	1.41	1.13	1.07
Normalized value	1	0.13	0.74	0.68	0.47	1	0.28	0.65	0.87	1	0.22	0.66	0.54	0.52	0.57	1	0.88	1	0.31	1

KANM800102

Average relative probability of beta-sheet (Kanehisa-Tsong 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.72	1.01	1.04	0.75	0.58	1.35	0.76	0.8	0.84	0.63	0.62	1.38	1.43	0.81	1.33	1.34	1.03	0.83	0.87	1.35
Normalized value	0.25	0.65	0.33	0.2	0.68	0.47	0.49	0.88	0.39	0.71	0.58	0.29	0.28	0.53	0.45	0.49	0.67	1	0.95	1

KANM800103

Average relative probability of inner helix (Kanehisa-Tsong 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.288	0.533	0.271	0.262	0.318	0.312	0.2	0.411	0.265	0.4	0.375	0.229	0.34	0.327	0.362	0.354	0.388	0.495	0.231	0.429
Normalized value	0.77	0.3	0.43	0.67	0.61	0.2	0.57	0.63	0.66	0.83	1	0.45	0.01	0.97	0.98	0.4	0.65	0.94	1	0.74

KARP850101

Flexibility parameter for no rigid neighbors (Karplus-Schulz 1985)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.61	1.07	0.46	0.47	2.02	0.07	0.61	2.22	1.15	1.53	1.18	0.06	1.95	0	0.6	0.05	0.05	1.32	2.65	1.88
Normalized value	0.48	0.7	0.8	0.89	0.66	0.96	0.73	0.76	0.89	0.71	0.68	0.93	0.84	0.99	0.81	1	1	0.97	0.86	0.93

KRIW710101

Side chain interaction parameter (Krigbaum-Rubin 1971)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.22	4.66	-4.12	-3.64	5.27	-1.62	1.28	5.58	-4.18	5.01	3.51	-2.65	-3.03	-2.76	-0.93	-2.84	-1.2	4.45	5.2	2.15
Normalized value	0.63	0	0.72	0.71	0.41	0.96	0.57	0.33	1	0.46	0.2	0.84	1	0.94	1	1	1	0.78	0.92	1

KRIW790101

Side chain interaction parameter (Krigbaum-Komoriya 1979)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.491	-0.67	-0.356	-0.371	-0.729	-0.534	-0.54	-0.762	-0.3	-0.65	-0.659	-0.382	-0.463	-0.405	-0.554	-0.455	-0.515	-0.728	-0.839	-0.656
Normalized value	0.42	0.17	0.76	0.77	0.31	0.76	0.71	0.28	1	0.54	0.32	0.86	1	0.93	1	1	1	0.92	0.77	1

LAWE840101

Transfer free energy CHP/water (Lawson et al. 1984)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.46	0.2	-0.33	0.48	0.52	0.64	-1.31	3.28	-1.71	0.43	0.15	1.31	-0.58	-1.12	-1.54	-0.83	-1.52	0.54	1.25	-2.21
Normalized value	0.13	0.19	0.04	0.06	0.66	0.3	0.12	0.58	0.27	0.65	0.58	0	1	0.02	0.18	0.25	0	0.45	0.53	1

LEVM760101

Hydrophobic parameter (Levitt 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.046	0.128	0.105	0.151	0.29	0	0.23	0.186	0.219	0.186	0.221	0.134	0.131	0.18	0.291	0.062	0.108	0.14	0.409	0.298
Normalized value	0.45	0.38	0.92	0.92	0.14	0.53	0.45	0.25	1	0.25	0.33	0.56	0.31	0.56	1	0.84	0.68	0.43	0	0

LIFS790101

Conformational preference for all beta-strands (Lifson-Sander 1979)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	4.55	-0.78	2.85	5.16	4.37	9.14	4.48	2.1	10.68	3.24	2.18	5.56	5.14	4.15	5.97	6.78	8.6	3.81	1.97	2.4
Normalized value	0.37	0.55	0.08	0.31	0.68	0.31	0.49	1	0.36	0.71	0.64	0.3	0.19	0.5	0.49	0.43	0.6	1	1	1

LIFS790103

Conformational preference for antiparallel beta-strands (Lifson-Sander 1979)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	7.62	10.93	6.18	6.38	8.99	7.31	7.85	9.99	5.72	9.37	9.83	6.17	6.64	6.67	6.81	6.93	7.08	10.38	8.41	8.53
Normalized value	0.36	0.63	0.08	0.32	0.69	0.29	0.62	0.87	0.4	0.71	0.61	0.32	0.2	0.66	0.56	0.47	0.73	0.87	1	1

MANP780101

Average surrounding hydrophobicity (Manavalan-Ponnuswamy 1978)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	2.63	3.36	2.29	2.31	3.02	2.55	2.57	3.08	2.12	2.98	3.18	2.27	2.46	2.45	2.45	2.6	2.55	3.21	2.85	2.79
Normalized value	0.44	0.93	0.68	0.75	0.89	0.79	0.77	1	0.72	0.95	0.91	0.72	0.72	0.74	0.74	0.71	0.74	1	1	1

MAXF760102

Normalized frequency of extended structure (Maxfield-Scheraga 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	3.7	3.03	2.6	3.3	6.6	3.13	3.57	7.69	1.79	5.88	5.21	2.12	2.12	2.7	2.53	2.43	2.6	7.14	6.25	3.03
Normalized value	0.34	0.84	0.39	0.28	0.84	0.66	0.74	0.91	0.48	0.67	0.76	0.44	0.89	0.58	0.63	0.72	0.86	1	0.81	1

MAXF760106

Normalized frequency of alpha region (Maxfield-Scheraga 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.78	0.8	1.41	1	0.58	1.64	0.69	0.51	0.96	0.59	0.39	1.28	1.91	0.97	0.88	1.33	1.03	0.47	0.75	1.05
Normalized value	0.4	0.46	0.65	0.43	0.18	0.16	0.31	0.29	0.5	0.48	0.11	0.41	1	0.7	0.74	1	1	0.47	1	0.85

MIYS850101

Effective partition energy (Miyazawa-Jernigan 1985)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.934	0.9	0.994	0.986	0.773	1.015	0.882	0.766	1.04	0.825	0.804	0.986	1.047	1.047	0.962	1.056	1.008	0.825	0.848	0.931
Normalized value	0.36	0.75	0.33	0.35	1	0.45	0.54	0.99	0.23	0.93	1	0.41	0.46	0.42	0.47	0.44	0.5	0.91	1	1

NAGK730102

Normalized frequency of bata-structure (Nagano 1973)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.941	0.866	1.071	1.1	0.723	1.055	0.911	0.742	1.232	0.798	0.781	1.038	1.093	1.15	1.112	1.082	1.043	0.817	0.867	1.05
Normalized value	0.52	0.66	0.47	0	0.89	0.58	0.56	1	0.57	0.89	0.91	0.51	0.53	0.84	0.48	0.55	0.87	1	1	1

NAGK730103

Normalized frequency of coil (Nagano 1973)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	17.05	28.84	19.27	20.12	16.26	38.14	23.07	16.66	16.46	10.89	20.61	34.81	23.94	15.42	21.25	19.95	18.92	17.06	23.36	26.49
Normalized value	0.16	0.67	0.69	0.46	0.33	0.94	0.47	0.5	0.53	0.37	0.36	0.96	1	0.54	0.98	0.99	0.73	0.56	0.6	1

NISK860101

14 A contact number (Nishikawa-Ooi 1986)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	115	135	150	190	210	75	195	175	200	170	185	160	145	180	225	115	140	155	255	230
Normalized value	0.41	0.91	0.01	0.06	0.97	0.26	0.56	1	0	0.98	0.79	0.05	0	0.01	0.24	0	0	0.86	1	1

OOBM770103

Long range non-bonded energy per atom (Oobatake-Ooi 1977)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-2.3	4.4	-4.4	-5	2.6	-4.2	-2.5	6.7	-3.3	2.3	2.3	-4.1	-1.8	1.2	0.4	-1.7	1.3	6.8	-1	4
Normalized value	0.65	0.11	0.33	0.32	0.07	0.21	0.2	0.05	0.36	0.13	0.12	0.31	0.25	0.29	0.19	0.26	0.22	0.07	0	0

OOBM850103

Optimized transfer energy parameter (Oobatake et al. 1985)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.67	-2	1.57	1.78	-3.24	0	1.09	-3.02	2.46	-3.02	-1.67	2.27	-1.75	2.12	3.89	0.1	-0.42	-2.18	-2.86	0.98
Normalized value	0.49	0.44	0.34	0.49	0.5	0.52	0.16	1	0.14	0.75	0.67	1	0.47	0.32	0.19	0.4	0.2	0.79	1	0

OOBM850105

Optimized side chain interaction parameter (Oobatake et al. 1985)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.73	0.7	0.54	0.55	2.65	0	1.1	2.97	1.5	2.49	1.3	-0.01	2.6	-0.1	0.73	0.04	0.44	1.69	3	2.97
Normalized value	0.47	0	0.27	0.48	0.41	0.86	0.42	0.2	1	0.38	0.25	0.65	0.6	0.48	0.69	0.79	1	1	0.82	1

PONP800102

Average gain in surrounding hydrophobicity (Ponnuswamy et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	7	5.5	13	12.5	5	7.9	8.4	4.9	10.1	4.9	5.3	10	6.6	8.6	9.1	7.5	6.6	5.6	5.3	5.7
Normalized value	0.36	1	0.58	0.6	0.86	0.69	0.75	0.96	0.53	0.9	0.95	0.58	0.63	0.63	0.64	0.66	0.67	1	0.99	1

PONP800103

Average gain ratio in surrounding hydrophobicity (Ponnuswamy et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.83	1.19	0.54	0.37	1.38	0.75	0.87	1.6	0.74	1.3	1.05	0.89	0.55	1.1	0.93	0.75	1.19	1.7	1.37	1.47
Normalized value	0.41	1	0.67	0.68	0.93	0.76	0.77	0.95	0.61	0.92	0.99	0.66	0.73	0.73	0.73	0.78	0.76	1	1	1

PONP800107

Accessibility reduction ratio (Ponnuswamy et al. 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	6.8	8.3	7	4.9	8.3	6.4	9.2	10	7.5	12.2	8.4	6.2	6.9	8.5	0	8	7	9.4	5.7	6.8
Normalized value	0.32	0.37	0.31	0.41	0.85	0.38	0.44	1	0.22	0.82	0.72	0.27	0.27	0.36	0.33	0.32	0.34	1	1	1

PRAM900104

Relative frequency in reverse-turn (Prabhakaran 1990)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.83	1.48	0.64	0.65	2.75	0.1	1.1	3.07	1.6	2.52	1.4	0.09	2.7	0	0.83	0.14	0.54	1.79	0.31	2.97
Normalized value	0.26	0.33	0.7	0.45	0.2	0.84	0.29	0.18	0.45	0.24	0.12	0.65	1	0.7	0.63	1	0.98	0.38	0.68	1

RACS770101

Average reduced distance for C-alpha (Rackovsky-Scheraga 1977)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	11.5	13.46	11.68	13.57	19.8	3.4	13.69	21.4	15.71	21.4	16.25	12.82	17.43	14.45	14.28	9.47	15.77	21.57	21.67	18.03
Normalized value	0.58	0.67	0.87	0.85	0.41	0.94	0.73	0.55	0.98	0.64	0.61	0.89	0.99	0.99	0.86	1	1	0.71	0.74	0.88

RACS770102

Average reduced distance for side chain (Rackovsky-Scheraga 1977)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	9.9	2.8	2.8	3.2	18.8	5.6	8.2	17.1	3.5	17.6	14.9	5.4	14.8	9	4.6	6.9	9.5	14.3	17.1	15
Normalized value	0.43	0.54	0.8	0.84	0.37	0.8	0.63	0.43	1	0.55	0.53	0.86	0.93	1	1	1	0.99	0.66	0.73	1

RACS820113

Value of theta(i) (Rackovsky-Scheraga 1982)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.29	0.66	2.02	2.44	0.61	0.76	0.73	0.67	0.66	0.58	0.71	0.81	2.01	1.22	0.44	0.74	1.08	0.61	1.47	0.68
Normalized value	0.23	0.75	0.5	0.52	0.42	1	0.66	0.48	0.47	0.31	0.59	1	0.9	0.58	0.8	0.75	0.71	0.64	0.88	1

ROBB760105

Information measure for extended (Robson-Suzuki 1976)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.77	-0.23	-0.15	-0.27	-0.41	0	-0.06	-0.23	-0.65	-0.62	-0.5	-0.07	3	-0.33	-0.68	-0.35	-0.11	-0.14	-0.45	-0.17
Normalized value	0.23	0.8	0.05	0	0.62	0	0.15	0.99	0.07	0.59	0.59	0	0	0.34	0.25	0	0.29	1	0	1

ROSM880102

Side chain hydropathy corrected for solvation (Roseman 1988)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.984	0.906	1.068	1.094	0.915	1.031	0.95	0.927	1.102	0.935	0.952	1.048	1.049	1.037	1.008	1.046	0.997	0.931	0.904	0.929
Normalized value	0.36	0.17	0.67	0.7	0	0.44	0.59	0	0.79	0	0.18	0.76	0.16	0.74	1	0.77	0.63	0.18	0	0.98

SIMZ760101

Transfer free energy (Simon 1976) Cited by Charton-Charton (1982)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	58	116	-97	-131	92	-11	-73	107	-24	95	78	-93	-79	-139	-184	-34	-7	100	59	-11
Normalized value	0.27	0.26	0.21	0.21	0.89	0.03	0.39	0.99	0.52	0.84	0.45	0.03	0.87	0	0.24	0.01	0.15	0.56	1	1

WOEC730101

Polar requirement (Woese 1973)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	51	137	-78	-115	108	-13	-55	106	-205	103	73	-84	-79	-128	-144	-26	-3	108	69	11
Normalized value	0.26	0.41	1	1	0.48	0.78	0.83	0.47	1	0.48	0.52	1	0.72	0.94	1	1	1	0.98	0.93	1

YUTK870102

Unfolding Gibbs energy in water pH9.0 (Yutani et al. 1987)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	32	182	-29	-74	132	-22	-25	106	-124	104	82	-73	-82	-95	-95	-34	20	113	118	44
Normalized value	0.56	0.68	0.57	0.4	0.68	0.52	0.75	0.82	0.61	1	0.89	0.66	0.73	0.9	0	0.85	0.74	1	0.84	1

ZIMJ680101

Hydrophobicity (Zimmerman et al. 1968)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	24	194	0	-57	131	-28	-31	102	-9	103	90	-76	-85	-87	-79	-36	34	111	116	43
Normalized value	0.27	0.48	0.21	0.21	0.9	0.03	0.36	1	0.54	0.85	0.47	0.03	0.91	0	0.28	0.05	0.18	0.6	0.1	1

ZIMJ680102

Bulkiness (Zimmerman et al. 1968)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	6.77	0.31	8.57	12.93	1.92	7.95	2.8	2.72	10.2	4.43	1.87	5.5	4.79	5.24	6.87	5.41	5.36	3.57	0.54	2.26
Normalized value	0.44	0.61	0.53	0.62	0.91	0.14	0.63	0.99	0.72	0.99	0.75	0.59	0.8	0.66	0.66	0.43	0.73	1	1	1

ZIMJ680105

RF rank (Zimmerman et al. 1968)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	7.43	0.42	8.71	5.86	1.18	9.4	1.49	1.76	9.67	2.74	0.6	9.12	5.6	5.42	4.51	9.6	8.95	3.1	1.18	3.26
Normalized value	0.44	0.13	0.14	0.16	1	0.31	0.46	0.97	0.19	1	0.87	0.31	0.86	0.52	0.26	0.4	0.55	0.84	1	1

ONEK900102

Helix formation parameters (delta delta G) (O'Neil-DeGrado 1990)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.78	0.55	1.35	1.45	0.47	0.68	0.99	0.47	1.1	0.56	0.66	1.2	0.69	1.19	1.58	1	1.05	0.51	0.7	1
Normalized value	0	0.12	0.14	0.11	0.07	0.18	0.17	0.12	0.01	0.02	0.05	0.17	1	0.21	0	0.07	0.23	0.21	0	0

VINM940101

Normalized flexibility parameters (B-values) average (Vihinen et al. 1994)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	2.18	3.89	1.75	1.89	5.88	1.17	2.51	4.5	2.12	4.71	3.63	1.85	2.09	2.16	2.71	1.66	2.18	3.77	6.46	5.01
Normalized value	0.4	0.72	0.95	0.99	0.73	0.9	0.78	0.75	1	0.82	0.85	1	1	0.99	0.94	1	0.99	0.88	0.84	0.88

NADH010101

Hydropathy scale based on self-information values in the two-state model (5% accessibility) (Naderi-Manesh et al. 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.79	2.22	2.33	2.52	4.84	0.7	3.06	4.59	2.5	4.72	3.91	2.83	2.45	2.37	3.2	1.82	2.45	3.67	5.64	4.46
Normalized value	0.81	1	0.3	0.18	0.95	0.59	0.38	1	0.56	0.98	0.92	0.32	0.37	0.16	0	0	0.04	1	1	0

NADH010102

Hydropathy scale based on self-information values in the two-state model (9% accessibility) (Naderi-Manesh et al. 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	13.4	22.6	8.2	7.3	23.9	7	11.3	20.3	6.1	20.8	15.7	7.6	9.9	8.5	8.5	8.2	10.3	19.5	24.5	19.5
Normalized value	0.75	1	0.41	0.29	1	0.61	0.48	0.99	0	0.98	0.86	0.24	0.26	0.06	0	0	0	1	1	1

NADH010104

Hydropathy scale based on self-information values in the two-state model (20% accessibility) (Naderi-Manesh et al. 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	91.5	114.4	135.2	154.6	198.8	67.5	163.2	162.6	162.5	163.4	165.9	138.3	123.4	156.4	196.1	102	126	138.4	209.8	237.2
Normalized value	0.51	1	0.37	0.2	1	0.42	0.41	0.95	0	0.93	0.83	0.1	0.06	0	0	0	0.17	0.96	1	1

NADH010105

Hydropathy scale based on self-information values in the two-state model (25% accessibility) (Naderi-Manesh et al. 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.12	0.59	-0.83	-0.92	0.67	1.2	-0.93	1.16	-0.8	1.18	0.55	-0.83	0.54	-0.78	-2.55	-0.05	-0.02	1.13	-0.19	-0.23
Normalized value	0.4	1	0.4	0.14	1	0.29	0.28	0.93	0.38	0.94	0.87	0.05	0.01	0	0	0	0.29	0.96	1	1

FUKS010102

Surface composition of amino acids in intracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.38	1.43	0.52	0.71	1.72	1.34	0.66	2.32	0.15	1.47	1.78	0.37	0.85	0.22	0	0.86	0.89	1.99	0.82	0.47
Normalized value	0.51	0	0.66	1	0.19	0.78	0.27	0.27	1	0.64	0.27	0.8	0.7	0.76	1	1	1	1	0.24	1

FUKS010103

Surface composition of amino acids in extracellular proteins of mesophiles (percent) (Fukuchi-Nishikawa 2001)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.27	-1.05	0.81	1.17	-1.43	-0.16	0.28	-0.77	1.7	-1.1	-0.73	0.81	-0.75	1.1	1.87	0.42	0.63	-0.4	-1.57	-0.56
Normalized value	0.76	0	0.9	0.61	0.12	0.97	0.15	0.18	1	0.29	0.06	0.95	0.58	0.56	0.47	1	1	0.95	0.36	1

KUHL950101

Hydrophilicity scale (Kuhn et al. 1995)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.414	0.162	-1.31	-1.218	1.938	-0.684	-0.63	1.237	-0.67	1.215	1.02	-0.916	-0.503	-0.905	-0.584	-0.563	-0.289	0.899	0.514	1.699
Normalized value	0.28	0.21	0.83	0.91	0.19	0.35	0.58	0.2	0.65	0.27	0.34	0.73	0.36	0.72	1	0.94	1	0.39	0.63	1

ZHOH040101

The stability scale from the knowledge-based atom-atom potential (Zhou-Zhou 2004)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.26	0.83	-1.3	-0.73	1.09	-0.4	-0.18	1.1	-1.01	1.52	1.09	-0.46	-0.62	-0.83	0.08	-0.55	-0.71	1.15	-0.13	0.69
Normalized value	0.19	0.59	0.25	0.27	0.91	0.16	0.37	0.69	0.31	0.72	0.55	0.27	0.31	0.32	0.41	0.24	0.32	0.57	1	1

ZHOH040102

The relative stability scale extracted from mutation experiments (Zhou-Zhou 2004)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-1.35	4.37	-11.88	-4.56	11.35	-5.82	6.54	10.93	-11.92	9.88	7.47	-10.96	-10.86	-1.34	-3.89	-6.21	-4.83	8.2	1.8	7.61
Normalized value	0.22	0.37	0.39	0.42	0.85	0.09	0.54	0.81	0.43	0.83	0.69	0.49	0.43	0.41	0.56	0.31	0.43	0.65	1	1

ZHOH040103

Buriability (Zhou-Zhou 2004)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.37	-4.47	8.93	4.04	-7.96	3.39	-1.65	-7.92	7.7	-8.68	-7.13	6.29	6.25	3.88	1.33	4.08	4.02	-6.94	0.79	-4.73
Normalized value	0.4	0.92	0.32	0.29	0.98	0.28	0.46	0.83	0.24	0.85	0.64	0.3	0.4	0.34	0.34	0.33	0.41	0.79	1	1

PONJ960101

Average volumes of residues (Pontius et al. 1996)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.02	-0.96	0.72	0.74	-2.22	0.38	0	-1.89	1.01	-2.29	-1.36	0.63	0.47	0.56	0.44	0.55	0.25	-1.34	-1.28	-0.88
Normalized value	0.14	0.48	0.57	0.65	0.84	0.28	0.69	0.69	0.68	0.69	0.7	0.58	0.52	0.66	0.83	0.43	0.53	0.58	0.88	1

WOLR790101

Hydrophobicity index (Wolfenden et al. 1979)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	-0.21	-6.04	1.36	2.3	-4.65	0	-1.23	-4.81	3.88	-4.68	-3.66	0.96	0.75	1.52	2.11	1.74	0.78	-3.5	-3.32	-1.01
Normalized value	0.98	0.84	0.46	0.43	0.86	1	0.43	0.99	0.47	1	0.84	0.47	0.84	0.48	0	0.13	0.15	1	0.03	0

OLSK800101

Average internal preferences (Olsen 1980)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	100	20	106	102	41	49	66	96	56	40	94	134	56	93	65	120	97	74	18	41
Normalized value	0.59	0.62	0.22	0.31	0.74	0.58	0.28	1	0.08	0.74	0.89	0.19	0.43	0.11	0	0.43	0.45	1	0.82	0.47

KIDA850101

Hydrophobicity-related index (Kidera et al. 1985)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.67	0.38	-1.2	-0.76	2.3	0	0.64	1.9	-0.57	1.9	2.4	-0.6	1.2	-0.22	-2.1	0.01	0.52	1.5	2.6	1.6
Normalized value	0.38	0.15	0.69	0.8	0.04	0.41	0.54	0.23	0.95	0.14	0.24	0.69	0.24	0.78	1	0.77	0.86	0.46	0	0

CORJ870102

SWEIG index (Cornette et al. 1987)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	89.09	121.15	133.1	147.13	165.19	75.07	155.16	131.17	146.19	131.17	149.21	132.12	115.13	146.15	174.2	105.09	119.12	117.15	204.24	181.19
Normalized value	0.28	0.45	0	0	1	0.09	0.11	0.82	0.09	0.81	0.74	0	0.15	0	0	0	0	0.53	0.3	1

CORJ870104

PRILS index (Cornette et al. 1987)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	297	178	270	249	284	290	277	284	224	337	283	236	222	185	238	228	253	293	282	344
Normalized value	0.37	0.76	0	0.11	0.83	0.24	0.33	0.83	0	1	0.97	0.19	0.11	0	0.42	0.09	0	1	0	0.69

CORJ870106

ALTLS index (Cornette et al. 1987)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	0.31	1.54	-0.77	-0.64	1.79	0	0.13	1.8	-0.99	1.7	1.23	-0.6	0.72	-0.22	-1.01	-0.04	0.26	1.22	2.25	0.96
Normalized value	0.45	0.7	0	0.32	1	0.27	0.81	1	0	1	0.96	0	0	0.34	0.16	0	0	1	0.24	1

CORJ870108

TOTLS index (Cornette et al. 1987)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	1.28	1.77	1.6	1.56	2.94	0	2.99	4.19	1.89	2.59	2.35	1.6	2.67	1.56	2.34	1.31	3.03	3.67	3.21	2.94
Normalized value	0.57	0.24	1	0.78	0.04	0.74	0.43	0.05	1	0	0	1	1	0.98	0.75	1	1	0	0.96	0

MIYS990101

Relative partition energies derived by the Bethe approximation (Miyazawa-Jernigan 1999)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	2.04	3.41	3.78	3.31	6.02	1	5.66	3.49	4.87	4.45	4.8	4.37	4.31	3.53	6.24	2.7	3.17	3.17	5.9	6.72
Normalized value	0.36	0.75	0.33	0.35	1	0.45	0.54	0.99	0.23	0.93	1	0.41	0.46	0.42	0.47	0.44	0.5	0.91	1	1

FASG890101

Hydrophobicity index (Fasman 1989)

Amino acid	A	D	C	E	F	G	H	I	K	L	M	N	P	Q	R	S	T	V	W	Y
Actual value	52.6	68.3	68.4	84.7	113.9	36.3	91.9	102	105.1	102	97.7	75.7	73.6	89.7	109.1	54.9	71.2	85.1	135.4	116.2
Normalized value	0.59	0	0.71	0.82	0.02	0.55	0.41	0	1	0	0	0.8	0.76	0.89	1	1	0.95	0	0	0

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Kawashima, S., Pokarowski, P., Pokarowska, M., Kolinski, A., Katayama, T., and Kanehisa, M."AAindex: amino acid index database, progress report 2008."Nucleic Acids Res. 36, D202-D205 (2008)."

AMINO ACID PROPERTIES