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 5 Secondary structure matrix. The occurrence of the secondary structure types of proline in the cis and trans conformation is shown. For the five defined secondary structure elements (bend, coil, helix, strand and turn) we analyzed the surrounding of the fixed proline in the mid-position. Rows indicate the secondary structure type with fixed secondary structure of the proline. Columns show the relative occurrences of the secondary structure at the 4 positions around proline. Bold face highlights the most probable secondary structure. For the cis peptide bond conformation of the central proline in helix and strand not enough entries could be collected from the PDB to reach significance.

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

secondary structure	structure of trans Pro									structure of cis Pro
	position									position
	i-2		i-1		bend	i+1		i+2		i-2		i-1		bend	i+1		i+2
bend:	257	0.21	317	0.26	1211	684	0.56	229	0.19	176	0.24	467	0.63	742	143	0.19	105	0.14
coil:	462	0.38	813	0.67	1211	334	0.28	545	0.45	329	0.44	180	0.24	742	433	0.58	321	0.43
helix:	77	0.06	2	0.00	1211	22	0.02	107	0.09	31	0.04	0	0.00	742	28	0.04	70	0.09
strand:	254	0.21	74	0.06	1211	135	0.11	228	0.19	164	0.22	95	0.13	742	104	0.14	174	0.23
turn:	161	0.13	5	0.00	1211	36	0.03	102	0.08	42	0.06	0	0.00	742	34	0.05	72	0.10
	i-2		i-1		coil	i+1		i+2		i-2		i-1		coil	i+1		i+2
bend:	1401	0.22	1614	0.25	6505	952	0.15	901	0.14	41	0.18	80	0.35	231	29	0.13	37	0.16
coil:	2966	0.46	4430	0.68	6505	3749	0.58	2656	0.41	112	0.48	137	0.59	231	127	0.55	81	0.35
helix:	377	0.06	8	0.00	6505	532	0.08	862	0.13	9	0.04	0	0.00	231	9	0.04	14	0.06
strand:	934	0.14	360	0.06	6505	788	0.12	1312	0.20	41	0.18	13	0.06	231	62	0.27	91	0.39
turn:	827	0.13	93	0.01	6505	484	0.07	774	0.12	28	0.12	1	0.00	231	4	0.02	8	0.03
	i-2		i-1		helix	i+1		i+2		i-2		i-1		helix	i+1		i+2
bend:	361	0.14	193	0.07	2603	1	0.00	12	0.00	0	0.00	0	0.00	8	0	0.00	1	0.13
coil:	752	0.29	913	0.35	2603	1	0.00	38	0.01	0	0.00	0	0.00	8	0	0.00	2	0.25
helix:	722	0.28	935	0.36	2603	2597	1.00	2489	0.96	8	1.00	8	1.00	8	8	1.00	0	0.00
strand:	165	0.06	43	0.02	2603	0	0.00	6	0.00	0	0.00	0	0.00	8	0	0.00	0	0.00
turn:	603	0.23	519	0.20	2603	4	0.00	58	0.02	0	0.00	0	0.00	8	0	0.00	5	0.63
	i-2		i-1		strand	i+1		i+2		i-2		i-1		strand	i+1		i+2
bend:	124	0.09	98	0.07	1352	123	0.09	202	0.15	0	0.00	2	0.22	9	1	0.11	1	0.11
coil:	268	0.20	157	0.12	1352	391	0.29	322	0.24	4	0.44	2	0.22	9	2	0.22	2	0.22
helix:	10	0.01	0	0.00	1352	80	0.06	115	0.09	0	0.00	0	0.00	9	0	0.00	0	0.00
strand:	788	0.58	1096	0.81	1352	703	0.52	603	0.45	3	0.33	4	0.44	9	6	0.67	4	0.44
turn:	162	0.12	1	0.00	1352	55	0.04	110	0.08	2	0.22	1	0.11	9	0	0.00	2	0.22
	i-2		i-1		turn	i+1		i+2		i-2		i-1		turn	i+1		i+2
bend:	334	0.12	247	0.09	2717	12	0.00	450	0.17	57	0.14	0	0.00	400	54	0.14	39	0.10
coil:	777	0.29	1266	0.47	2717	26	0.01	835	0.31	142	0.36	9	0.02	400	88	0.22	138	0.35
helix:	534	0.20	127	0.05	2717	239	0.09	414	0.15	34	0.09	0	0.00	400	57	0.14	74	0.19
strand:	447	0.16	155	0.06	2717	20	0.01	192	0.07	38	0.10	13	0.03	400	20	0.05	69	0.17
turn:	625	0.23	922	0.34	2717	2420	0.89	826	0.30	129	0.32	378	0.95	400	181	0.45	80	0.20

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ISSN: 1472-6807

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