Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

Pahlke, Doreen; Freund, Christian; Leitner, Dietmar; Labudde, Dirk

doi:10.1186/1472-6807-5-8

Table 3 Occurrence matrix. Occurrence matrix for the amino acid combinations of trans and cis proline in the fixed position (i). The total number N_totalis the occurrence of an amino acid in all investigated sequence fragments. The number of the proline at the position (i) in the trans conformation is 14388 and in the cis conformation it is 1390. The absolute and relative occurrence of one amino acid is shown at all positions (rel and abs). The relative occurrence is the relation of the number of the amino acid at the position to the total number of all amino acid at this position.

From: Statistically significant dependence of the Xaa-Pro peptide bond conformation on secondary structure and amino acid sequence

			trans Pro								cis Pro
			Position								position
AA	Total		i-2		i-1		i+1		i+2		i-2		i-1		i+1		i+2
	abs	rel	abs	rel	abs	rel	abs	rel	abs	rel	abs	rel	abs	rel	abs	rel	abs	rel
A:	4343	0.075	1024	0.071	1030	0.072	1169	0.081	1120	0.078	90	0.065	111	0.080	134	0.096	79	0.057
C:	810	0.014	204	0.014	256	0.018	166	0.012	184	0.013	38	0.027	25	0.018	24	0.017	33	0.024
D:	3565	0.062	818	0.057	972	0.068	956	0.066	819	0.057	57	0.041	59	0.042	52	0.037	83	0.060
E:	3604	0.063	799	0.056	685	0.048	1208	0.084	912	0.063	70	0.050	84	0.060	47	0.034	61	0.044
F:	2426	0.042	656	0.046	562	0.039	596	0.041	612	0.043	59	0.042	82	0.059	96	0.069	58	0.042
G:	4275	0.074	1202	0.084	824	0.057	1113	0.077	1136	0.079	112	0.081	154	0.111	112	0.081	106	0.076
H:	1418	0.025	323	0.022	418	0.029	313	0.022	364	0.025	32	0.023	29	0.021	40	0.029	32	0.023
I:	3178	0.055	780	0.054	915	0.064	711	0.049	772	0.054	68	0.049	38	0.027	54	0.039	62	0.045
K:	2804	0.049	654	0.045	745	0.052	703	0.049	702	0.049	76	0.055	66	0.047	57	0.041	70	0.050
L:	5279	0.092	1336	0.093	1423	0.099	1179	0.082	1341	0.093	96	0.069	90	0.065	134	0.096	96	0.069
M:	1131	0.020	292	0.020	272	0.019	263	0.018	304	0.021	35	0.025	21	0.015	22	0.016	28	0.020
N:	2683	0.047	684	0.048	816	0.057	608	0.042	575	0.040	65	0.047	79	0.057	56	0.040	70	0.050
P:	3121	0.054	896	0.062	687	0.048	691	0.048	847	0.059	98	0.071	82	0.059	78	0.056	149	0.107
Q:	2105	0.037	480	0.033	556	0.039	574	0.040	495	0.034	72	0.052	56	0.040	53	0.038	45	0.032
R:	2591	0.045	644	0.045	675	0.047	655	0.046	617	0.043	61	0.044	49	0.035	54	0.039	64	0.046
S:	3596	0.062	886	0.062	887	0.062	877	0.061	946	0.066	108	0.078	84	0.060	91	0.065	79	0.057
T:	3479	0.060	876	0.061	948	0.066	818	0.057	837	0.058	84	0.060	61	0.044	77	0.055	102	0.073
V:	4165	0.072	1021	0.071	1036	0.072	1073	0.075	1035	0.072	101	0.073	65	0.047	97	0.070	101	0.073
W:	815	0.014	221	0.015	169	0.012	206	0.014	219	0.015	18	0.013	44	0.032	23	0.017	19	0.014
Y:	2164	0.038	592	0.041	512	0.036	509	0.035	551	0.038	50	0.036	111	0.080	89	0.064	53	0.038

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ISSN: 1472-6807

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