Analysis of interatomic Contacts of Structural Units in PDB entry:
6VMD

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 6VMD entry

There are 9 chains in PDB entry 6VMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 6	GLN 506
B	MET 1	LEU 503
C	ARG 5	GLN 504
D	LYS 17	SER 494
E	GLU 16	LEU 496
F	LYS 17	LEU 496
d	ASP 72	MET 250
e	MET 1	THR 131
g	CYS 41	CYS 363

There are123 helices in PDB entry 6VMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	6	25	Right-handed alpha
Helix 2	AA2	A	151	156	Right-handed alpha
Helix 3	AA3	A	177	186	Right-handed alpha
Helix 4	AA4	A	187	191	Right-handed 310
Helix 5	AA5	A	202	217	Right-handed alpha
Helix 6	AA6	A	232	253	Right-handed alpha
Helix 7	AA7	A	263	277	Right-handed alpha
Helix 8	AA8	A	283	287	Right-handed 310
Helix 9	AA9	A	288	289	Right-handed 310
Helix 10	AB1	A	290	300	Right-handed alpha
Helix 11	AB2	A	323	326	Right-handed 310
Helix 12	AB3	A	329	339	Right-handed alpha
Helix 13	AB4	A	346	353	Right-handed alpha
Helix 14	AB5	A	367	372	Right-handed 310
Helix 15	AB6	A	373	381	Right-handed alpha
Helix 16	AB7	A	382	399	Right-handed alpha
Helix 17	AB8	A	404	421	Right-handed alpha
Helix 18	AB9	A	430	443	Right-handed alpha
Helix 19	AC1	A	453	468	Right-handed alpha
Helix 20	AC2	A	469	480	Right-handed alpha
Helix 21	AC3	A	483	505	Right-handed alpha
Helix 22	AC4	B	9	18	Right-handed alpha
Helix 23	AC5	B	101	105	Right-handed 310
Helix 24	AC6	B	151	156	Right-handed alpha
Helix 25	AC7	B	177	187	Right-handed alpha
Helix 26	AC8	B	202	216	Right-handed alpha
Helix 27	AC9	B	232	252	Right-handed alpha
Helix 28	AD1	B	263	278	Right-handed alpha
Helix 29	AD2	B	283	287	Right-handed 310
Helix 30	AD3	B	290	300	Right-handed alpha
Helix 31	AD4	B	329	339	Right-handed alpha
Helix 32	AD5	B	346	353	Right-handed alpha
Helix 33	AD6	B	367	371	Right-handed 310
Helix 34	AD7	B	373	396	Right-handed alpha
Helix 35	AD8	B	409	421	Right-handed alpha
Helix 36	AD9	B	430	444	Right-handed alpha
Helix 37	AE1	B	453	469	Right-handed alpha
Helix 38	AE2	B	469	479	Right-handed alpha
Helix 39	AE3	B	483	503	Right-handed alpha
Helix 40	AE4	C	6	20	Right-handed alpha
Helix 41	AE5	C	101	105	Right-handed 310
Helix 42	AE6	C	151	157	Right-handed alpha
Helix 43	AE7	C	175	187	Right-handed alpha
Helix 44	AE8	C	202	217	Right-handed alpha
Helix 45	AE9	C	218	221	Right-handed 310
Helix 46	AF1	C	232	253	Right-handed alpha
Helix 47	AF2	C	263	278	Right-handed alpha
Helix 48	AF3	C	283	287	Right-handed 310
Helix 49	AF4	C	288	289	Right-handed 310
Helix 50	AF5	C	290	300	Right-handed alpha
Helix 51	AF6	C	329	339	Right-handed alpha
Helix 52	AF7	C	346	352	Right-handed alpha
Helix 53	AF8	C	373	393	Right-handed alpha
Helix 54	AF9	C	394	399	Right-handed 310
Helix 55	AG1	C	404	421	Right-handed alpha
Helix 56	AG2	C	430	444	Right-handed alpha
Helix 57	AG3	C	453	469	Right-handed alpha
Helix 58	AG4	C	469	480	Right-handed alpha
Helix 59	AG5	C	483	504	Right-handed alpha
Helix 60	AG6	D	103	107	Right-handed 310
Helix 61	AG7	D	153	159	Right-handed alpha
Helix 62	AG8	D	177	190	Right-handed alpha
Helix 63	AG9	D	205	220	Right-handed alpha
Helix 64	AH1	D	245	263	Right-handed alpha
Helix 65	AH2	D	274	289	Right-handed alpha
Helix 66	AH3	D	301	311	Right-handed alpha
Helix 67	AH4	D	336	344	Right-handed alpha
Helix 68	AH5	D	353	358	Right-handed alpha
Helix 69	AH6	D	376	381	Right-handed alpha
Helix 70	AH7	D	381	408	Right-handed alpha
Helix 71	AH8	D	409	413	Right-handed 310
Helix 72	AH9	D	414	431	Right-handed alpha
Helix 73	AI1	D	436	440	Right-handed 310
Helix 74	AI2	D	451	463	Right-handed alpha
Helix 75	AI3	D	470	475	Right-handed 310
Helix 76	AI4	D	479	492	Right-handed alpha
Helix 77	AI5	E	153	159	Right-handed alpha
Helix 78	AI6	E	177	192	Right-handed alpha
Helix 79	AI7	E	205	220	Right-handed alpha
Helix 80	AI8	E	242	265	Right-handed alpha
Helix 81	AI9	E	274	290	Right-handed alpha
Helix 82	AJ1	E	301	311	Right-handed alpha
Helix 83	AJ2	E	329	333	Right-handed 310
Helix 84	AJ3	E	336	344	Right-handed alpha
Helix 85	AJ4	E	353	360	Right-handed alpha
Helix 86	AJ5	E	376	381	Right-handed alpha
Helix 87	AJ6	E	381	409	Right-handed alpha
Helix 88	AJ7	E	414	431	Right-handed alpha
Helix 89	AJ8	E	451	463	Right-handed alpha
Helix 90	AJ9	E	470	474	Right-handed 310
Helix 91	AK1	E	479	496	Right-handed alpha
Helix 92	AK2	F	153	158	Right-handed alpha
Helix 93	AK3	F	179	193	Right-handed alpha
Helix 94	AK4	F	205	220	Right-handed alpha
Helix 95	AK5	F	242	247	Right-handed alpha
Helix 96	AK6	F	248	263	Right-handed alpha
Helix 97	AK7	F	274	287	Right-handed alpha
Helix 98	AK8	F	301	312	Right-handed alpha
Helix 99	AK9	F	329	333	Right-handed 310
Helix 100	AL1	F	336	346	Right-handed alpha
Helix 101	AL2	F	353	359	Right-handed alpha
Helix 102	AL3	F	376	381	Right-handed alpha
Helix 103	AL4	F	382	406	Right-handed alpha
Helix 104	AL5	F	414	431	Right-handed alpha
Helix 105	AL6	F	437	441	Right-handed 310
Helix 106	AL7	F	451	463	Right-handed alpha
Helix 107	AL8	F	479	496	Right-handed alpha
Helix 108	AL9	d	73	89	Right-handed alpha
Helix 109	AM1	d	91	106	Right-handed alpha
Helix 110	AM2	d	109	117	Right-handed alpha
Helix 111	AM3	d	121	137	Right-handed alpha
Helix 112	AM4	d	139	152	Right-handed alpha
Helix 113	AM5	d	154	156	Right-handed 310
Helix 114	AM6	d	157	174	Right-handed alpha
Helix 115	AM7	d	187	202	Right-handed alpha
Helix 116	AM8	d	237	249	Right-handed alpha
Helix 117	AM9	e	88	103	Right-handed alpha
Helix 118	AN1	e	109	131	Right-handed alpha
Helix 119	AN2	g	42	100	Right-handed alpha
Helix 120	AN3	g	133	152	Right-handed alpha
Helix 121	AN4	g	163	171	Right-handed alpha
Helix 122	AN5	g	187	204	Right-handed alpha
Helix 123	AN6	g	287	361	Right-handed alpha

There are 28 sheets in PDB entry 6VMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1,

There are 6 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	54	55	first strand
Strand 2	A	88	91	anti-parallel
Strand 3	A	29	36	anti-parallel
Strand 4	A	39	44	anti-parallel
Strand 5	A	71	76	anti-parallel
Strand 6	A	62	63	anti-parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	97	98	first strand
Strand 2	A	128	129	anti-parallel

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There are 5 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	108	109	first strand
Strand 2	A	222	227	parallel
Strand 3	A	193	199	parallel
Strand 4	A	257	260	parallel
Strand 5	A	314	316	parallel

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There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	319	321	first strand
Strand 2	A	166	170	parallel
Strand 3	A	341	344	parallel

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There are 5 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	39	43	first strand
Strand 2	B	71	76	anti-parallel
Strand 3	B	61	67	anti-parallel
Strand 4	B	52	56	anti-parallel
Strand 5	B	89	95	anti-parallel

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There are 9 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	39	43	first strand
Strand 2	B	71	76	anti-parallel
Strand 3	B	61	67	anti-parallel
Strand 4	D	23	27	anti-parallel
Strand 5	D	30	33	anti-parallel
Strand 6	D	73	78	anti-parallel
Strand 7	D	63	70	anti-parallel
Strand 8	D	46	49	anti-parallel
Strand 9	D	91	93	anti-parallel

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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	146	147	first strand
Strand 2	B	160	161	anti-parallel

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There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	168	170	first strand
Strand 2	B	319	321	parallel

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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	222	223	first strand
Strand 2	B	192	196	parallel
Strand 3	B	256	260	parallel
Strand 4	B	316	317	parallel

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There are 14 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	91	93	first strand
Strand 2	E	45	49	anti-parallel
Strand 3	E	61	68	anti-parallel
Strand 4	E	73	78	anti-parallel
Strand 5	E	30	34	anti-parallel
Strand 6	E	23	27	anti-parallel
Strand 7	C	61	67	anti-parallel
Strand 8	C	53	55	anti-parallel
Strand 9	C	88	91	anti-parallel
Strand 10	C	27	35	anti-parallel
Strand 11	d	231	234	anti-parallel
Strand 12	d	222	225	anti-parallel
Strand 13	d	177	182	anti-parallel
Strand 14	d	208	213	parallel

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There are 14 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	91	93	first strand
Strand 2	E	45	49	anti-parallel
Strand 3	E	61	68	anti-parallel
Strand 4	E	73	78	anti-parallel
Strand 5	E	30	34	anti-parallel
Strand 6	E	23	27	anti-parallel
Strand 7	C	61	67	anti-parallel
Strand 8	C	71	76	anti-parallel
Strand 9	C	39	43	anti-parallel
Strand 10	C	27	35	anti-parallel
Strand 11	d	231	234	anti-parallel
Strand 12	d	222	225	anti-parallel
Strand 13	d	177	182	anti-parallel
Strand 14	d	208	213	parallel

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There are 2 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	98	100	first strand
Strand 2	C	126	128	anti-parallel

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There are 5 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	108	109	first strand
Strand 2	C	224	227	parallel
Strand 3	C	193	199	parallel
Strand 4	C	256	260	parallel
Strand 5	C	313	316	parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	146	147	first strand
Strand 2	C	160	161	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	99	101	first strand
Strand 2	D	129	131	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	110	111	first strand
Strand 2	D	234	235	parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	148	149	first strand
Strand 2	D	162	163	anti-parallel

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There are 5 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	197	199	first strand
Strand 2	D	269	273	parallel
Strand 3	D	323	328	parallel
Strand 4	D	171	172	parallel
Strand 5	D	351	352	parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	99	100	first strand
Strand 2	E	130	131	anti-parallel

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There are 7 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	110	111	first strand
Strand 2	E	232	235	parallel
Strand 3	E	197	199	parallel
Strand 4	E	268	272	parallel
Strand 5	E	321	325	parallel
Strand 6	E	167	170	parallel
Strand 7	E	349	350	parallel

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There are 7 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	30	31	first strand
Strand 2	F	74	78	anti-parallel
Strand 3	F	62	68	anti-parallel
Strand 4	F	46	49	anti-parallel
Strand 5	F	90	93	anti-parallel
Strand 6	F	21	23	anti-parallel
Strand 7	F	33	34	anti-parallel

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There are 2 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	99	101	first strand
Strand 2	F	129	131	anti-parallel

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There are 8 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	110	111	first strand
Strand 2	F	232	235	parallel
Strand 3	F	197	200	parallel
Strand 4	F	268	272	parallel
Strand 5	F	321	325	parallel
Strand 6	F	167	172	parallel
Strand 7	F	348	352	parallel
Strand 8	F	371	372	anti-parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	148	149	first strand
Strand 2	F	162	163	anti-parallel

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There are 5 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	e	13	14	first strand
Strand 2	e	7	8	anti-parallel
Strand 3	e	76	78	parallel
Strand 4	e	65	68	anti-parallel
Strand 5	e	41	42	anti-parallel

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There are 3 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	e	48	52	first strand
Strand 2	e	57	62	anti-parallel
Strand 3	e	81	83	anti-parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	156	159	first strand
Strand 2	g	119	122	parallel
Strand 3	g	211	216	parallel
Strand 4	g	224	229	anti-parallel

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There are 2 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	g	251	257	first strand
Strand 2	g	266	272	anti-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: 6VMD

Analysis of interatomic Contacts of Structural Units in PDB entry:
6VMD