Analysis of interatomic Contacts of Structural Units in PDB entry:
1VKM

Contacts of Structural Units (CSU) are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332).
This page provides analyses of contacts formed by:

chains
helices
sheets
residues

For analysis of ligand-protein contacts, use:

LPC software

3D structure can be seen in additional window with STING software for 1VKM entry

There are 6 chains in PDB entry 1VKM (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS -7	ARG 284
B	LYS -7	ARG 284
C	LYS -7	ARG 284
D	LYS -7	ARG 284
E	LYS -7	ARG 284
F	LYS -7	ARG 284

There are 84 helices in PDB entry 1VKM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	18	23	Right-handed alpha
Helix 2	2	A	26	45	Right-handed alpha
Helix 3	3	A	63	74	Right-handed alpha
Helix 4	4	A	79	81	Right-handed 310
Helix 5	5	A	82	90	Right-handed alpha
Helix 6	6	A	96	107	Right-handed alpha
Helix 7	7	A	128	135	Right-handed alpha
Helix 8	8	A	151	162	Right-handed alpha
Helix 9	9	A	191	205	Right-handed alpha
Helix 10	10	A	218	222	Right-handed 310
Helix 11	11	A	224	234	Right-handed alpha
Helix 12	12	A	240	242	Right-handed 310
Helix 13	13	A	243	256	Right-handed alpha
Helix 14	14	A	258	283	Right-handed alpha
Helix 15	15	B	18	23	Right-handed alpha
Helix 16	16	B	26	45	Right-handed alpha
Helix 17	17	B	63	74	Right-handed alpha
Helix 18	18	B	79	81	Right-handed 310
Helix 19	19	B	82	90	Right-handed alpha
Helix 20	20	B	96	107	Right-handed alpha
Helix 21	21	B	128	135	Right-handed alpha
Helix 22	22	B	151	162	Right-handed alpha
Helix 23	23	B	191	205	Right-handed alpha
Helix 24	24	B	218	222	Right-handed 310
Helix 25	25	B	224	233	Right-handed alpha
Helix 26	26	B	240	242	Right-handed 310
Helix 27	27	B	243	257	Right-handed alpha
Helix 28	28	B	258	284	Right-handed alpha
Helix 29	29	C	18	23	Right-handed alpha
Helix 30	30	C	26	45	Right-handed alpha
Helix 31	31	C	63	74	Right-handed alpha
Helix 32	32	C	79	81	Right-handed 310
Helix 33	33	C	82	90	Right-handed alpha
Helix 34	34	C	96	107	Right-handed alpha
Helix 35	35	C	128	135	Right-handed alpha
Helix 36	36	C	151	162	Right-handed alpha
Helix 37	37	C	191	205	Right-handed alpha
Helix 38	38	C	218	222	Right-handed 310
Helix 39	39	C	224	233	Right-handed alpha
Helix 40	40	C	240	242	Right-handed 310
Helix 41	41	C	243	256	Right-handed alpha
Helix 42	42	C	258	283	Right-handed alpha
Helix 43	43	D	18	23	Right-handed alpha
Helix 44	44	D	26	45	Right-handed alpha
Helix 45	45	D	63	74	Right-handed alpha
Helix 46	46	D	79	81	Right-handed 310
Helix 47	47	D	82	90	Right-handed alpha
Helix 48	48	D	96	107	Right-handed alpha
Helix 49	49	D	128	135	Right-handed alpha
Helix 50	50	D	151	162	Right-handed alpha
Helix 51	51	D	191	205	Right-handed alpha
Helix 52	52	D	218	222	Right-handed 310
Helix 53	53	D	224	234	Right-handed alpha
Helix 54	54	D	240	242	Right-handed 310
Helix 55	55	D	243	256	Right-handed alpha
Helix 56	56	D	258	284	Right-handed alpha
Helix 57	57	E	18	23	Right-handed alpha
Helix 58	58	E	26	45	Right-handed alpha
Helix 59	59	E	63	74	Right-handed alpha
Helix 60	60	E	79	81	Right-handed 310
Helix 61	61	E	82	90	Right-handed alpha
Helix 62	62	E	96	107	Right-handed alpha
Helix 63	63	E	128	135	Right-handed alpha
Helix 64	64	E	151	162	Right-handed alpha
Helix 65	65	E	191	205	Right-handed alpha
Helix 66	66	E	218	222	Right-handed 310
Helix 67	67	E	224	235	Right-handed alpha
Helix 68	68	E	240	242	Right-handed 310
Helix 69	69	E	243	256	Right-handed alpha
Helix 70	70	E	258	284	Right-handed alpha
Helix 71	71	F	18	23	Right-handed alpha
Helix 72	72	F	26	45	Right-handed alpha
Helix 73	73	F	63	74	Right-handed alpha
Helix 74	74	F	79	81	Right-handed 310
Helix 75	75	F	82	90	Right-handed alpha
Helix 76	76	F	96	107	Right-handed alpha
Helix 77	77	F	128	135	Right-handed alpha
Helix 78	78	F	151	162	Right-handed alpha
Helix 79	79	F	191	205	Right-handed alpha
Helix 80	80	F	218	222	Right-handed 310
Helix 81	81	F	224	234	Right-handed alpha
Helix 82	82	F	240	242	Right-handed 310
Helix 83	83	F	243	256	Right-handed alpha
Helix 84	84	F	258	284	Right-handed alpha

There are 12 sheets in PDB entry 1VKM. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L,

There are 5 strands in A sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	3	5	first strand
Strand 2	A	57	60	parallel
Strand 3	A	47	54	anti-parallel
Strand 4	A	93	95	anti-parallel
Strand 5	A	76	78	parallel

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There are 9 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	3	5	first strand
Strand 2	A	57	60	parallel
Strand 3	A	47	54	anti-parallel
Strand 4	A	13	16	parallel
Strand 5	A	111	113	parallel
Strand 6	A	139	143	parallel
Strand 7	A	210	214	parallel
Strand 8	A	166	169	parallel
Strand 9	A	188	189	parallel

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There are 5 strands in C sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	3	5	first strand
Strand 2	B	57	60	parallel
Strand 3	B	47	54	anti-parallel
Strand 4	B	93	95	anti-parallel
Strand 5	B	76	78	parallel

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There are 9 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	3	5	first strand
Strand 2	B	57	60	parallel
Strand 3	B	47	54	anti-parallel
Strand 4	B	13	16	parallel
Strand 5	B	111	113	parallel
Strand 6	B	139	143	parallel
Strand 7	B	210	214	parallel
Strand 8	B	166	169	parallel
Strand 9	B	188	189	parallel

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There are 5 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	3	5	first strand
Strand 2	C	57	60	parallel
Strand 3	C	47	54	anti-parallel
Strand 4	C	93	95	anti-parallel
Strand 5	C	76	78	parallel

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There are 9 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	3	5	first strand
Strand 2	C	57	60	parallel
Strand 3	C	47	54	anti-parallel
Strand 4	C	13	16	parallel
Strand 5	C	111	113	parallel
Strand 6	C	139	143	parallel
Strand 7	C	210	214	parallel
Strand 8	C	166	169	parallel
Strand 9	C	188	189	parallel

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There are 5 strands in G sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	5	first strand
Strand 2	D	57	60	parallel
Strand 3	D	47	54	anti-parallel
Strand 4	D	93	95	anti-parallel
Strand 5	D	76	78	parallel

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There are 9 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	5	first strand
Strand 2	D	57	60	parallel
Strand 3	D	47	54	anti-parallel
Strand 4	D	13	16	parallel
Strand 5	D	111	113	parallel
Strand 6	D	139	143	parallel
Strand 7	D	210	214	parallel
Strand 8	D	166	169	parallel
Strand 9	D	188	189	parallel

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There are 5 strands in I sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	3	5	first strand
Strand 2	E	57	60	parallel
Strand 3	E	47	54	anti-parallel
Strand 4	E	93	95	anti-parallel
Strand 5	E	76	78	parallel

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There are 9 strands in J sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	3	5	first strand
Strand 2	E	57	60	parallel
Strand 3	E	47	54	anti-parallel
Strand 4	E	13	16	parallel
Strand 5	E	111	113	parallel
Strand 6	E	139	143	parallel
Strand 7	E	210	214	parallel
Strand 8	E	166	169	parallel
Strand 9	E	188	189	parallel

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There are 5 strands in K sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	3	5	first strand
Strand 2	F	57	60	parallel
Strand 3	F	47	54	anti-parallel
Strand 4	F	93	95	anti-parallel
Strand 5	F	76	78	parallel

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There are 9 strands in L sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	3	5	first strand
Strand 2	F	57	60	parallel
Strand 3	F	47	54	anti-parallel
Strand 4	F	13	16	parallel
Strand 5	F	111	113	parallel
Strand 6	F	139	143	parallel
Strand 7	F	210	214	parallel
Strand 8	F	166	169	parallel
Strand 9	F	188	189	parallel

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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 1VKM

Analysis of interatomic Contacts of Structural Units in PDB entry:
1VKM