Analysis of interatomic Contacts of Structural Units in PDB entry:
5VMM

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 5VMM entry

There are 8 chains in PDB entry 5VMM (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	VAL 1	ARG 141
B	VAL 1	HIS 143
C	VAL 1	ARG 141
D	VAL 1	ALA 142
E	SER 125	ALA 453
F	GLN 127	PHE 454
H	SER 125	ASP 265
J	GLU 131	ASP 265

There are 50 helices in PDB entry 5VMM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	3	18	Right-handed alpha
Helix 2	AA2	A	20	36	Right-handed alpha
Helix 3	AA3	A	37	43	Right-handed alpha
Helix 4	AA4	A	43	52	Right-handed alpha
Helix 5	AA5	A	53	72	Right-handed alpha
Helix 6	AA6	A	78	85	Right-handed alpha
Helix 7	AA7	A	94	113	Right-handed alpha
Helix 8	AA8	A	118	140	Right-handed alpha
Helix 9	AA9	B	4	15	Right-handed alpha
Helix 10	AB1	B	16	18	Right-handed 310
Helix 11	AB2	B	19	35	Right-handed alpha
Helix 12	AB3	B	36	42	Right-handed 310
Helix 13	AB4	B	50	56	Right-handed alpha
Helix 14	AB5	B	57	78	Right-handed alpha
Helix 15	AB6	B	100	119	Right-handed alpha
Helix 16	AB7	B	120	122	Right-handed 310
Helix 17	AB8	B	123	138	Right-handed alpha
Helix 18	AB9	C	3	17	Right-handed alpha
Helix 19	AC1	C	20	36	Right-handed alpha
Helix 20	AC2	C	38	43	Right-handed alpha
Helix 21	AC3	C	52	73	Right-handed alpha
Helix 22	AC4	C	81	85	Right-handed 310
Helix 23	AC5	C	95	112	Right-handed alpha
Helix 24	AC6	C	118	139	Right-handed alpha
Helix 25	AC7	D	6	17	Right-handed alpha
Helix 26	AC8	D	19	35	Right-handed alpha
Helix 27	AC9	D	36	41	Right-handed 310
Helix 28	AD1	D	50	57	Right-handed alpha
Helix 29	AD2	D	57	77	Right-handed alpha
Helix 30	AD3	D	100	119	Right-handed alpha
Helix 31	AD4	D	120	122	Right-handed 310
Helix 32	AD5	D	123	141	Right-handed alpha
Helix 33	AD6	E	128	133	Right-handed alpha
Helix 34	AD7	E	163	169	Right-handed alpha
Helix 35	AD8	E	271	285	Right-handed alpha
Helix 36	AD9	E	287	299	Right-handed alpha
Helix 37	AE1	E	306	329	Right-handed alpha
Helix 38	AE2	E	362	367	Right-handed 310
Helix 39	AE3	F	129	134	Right-handed alpha
Helix 40	AE4	F	135	139	Right-handed 310
Helix 41	AE5	F	163	169	Right-handed alpha
Helix 42	AE6	F	271	279	Right-handed alpha
Helix 43	AE7	F	279	285	Right-handed alpha
Helix 44	AE8	F	287	300	Right-handed alpha
Helix 45	AE9	F	303	332	Right-handed alpha
Helix 46	AF1	F	451	454	Right-handed 310
Helix 47	AF2	H	163	169	Right-handed alpha
Helix 48	AF3	J	135	139	Right-handed 310
Helix 49	AF4	J	163	169	Right-handed alpha
Helix 50	AF5	J	192	195	Right-handed 310

There are 12 sheets in PDB entry 5VMM. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 5 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	148	151	first strand
Strand 2	E	174	177	anti-parallel
Strand 3	E	184	190	anti-parallel
Strand 4	E	220	225	anti-parallel
Strand 5	E	209	214	anti-parallel

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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	153	156	first strand
Strand 2	E	245	256	anti-parallel
Strand 3	E	233	242	anti-parallel
Strand 4	E	195	201	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	E	346	347	first strand
Strand 2	E	372	376	anti-parallel
Strand 3	E	379	386	anti-parallel
Strand 4	E	413	419	anti-parallel
Strand 5	E	403	408	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	351	353	first strand
Strand 2	E	444	449	anti-parallel
Strand 3	E	426	433	anti-parallel
Strand 4	E	392	397	anti-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	F	148	151	first strand
Strand 2	F	174	177	anti-parallel
Strand 3	F	184	190	anti-parallel
Strand 4	F	220	226	anti-parallel
Strand 5	F	210	215	anti-parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	153	157	first strand
Strand 2	F	247	260	anti-parallel
Strand 3	F	231	240	anti-parallel
Strand 4	F	195	202	anti-parallel
Strand 5	F	205	207	anti-parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	351	353	first strand
Strand 2	F	444	449	anti-parallel
Strand 3	F	426	433	anti-parallel
Strand 4	F	392	397	anti-parallel
Strand 5	F	400	401	anti-parallel

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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	367	376	first strand
Strand 2	F	379	386	anti-parallel
Strand 3	F	413	419	anti-parallel
Strand 4	F	403	408	anti-parallel

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There are 5 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	149	151	first strand
Strand 2	H	174	177	anti-parallel
Strand 3	H	184	190	anti-parallel
Strand 4	H	220	226	anti-parallel
Strand 5	H	213	214	anti-parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	153	156	first strand
Strand 2	H	245	256	anti-parallel
Strand 3	H	233	242	anti-parallel
Strand 4	H	195	202	anti-parallel
Strand 5	H	205	207	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	149	151	first strand
Strand 2	J	174	177	anti-parallel
Strand 3	J	184	190	anti-parallel
Strand 4	J	220	226	anti-parallel
Strand 5	J	210	215	anti-parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	153	156	first strand
Strand 2	J	248	260	anti-parallel
Strand 3	J	231	239	anti-parallel
Strand 4	J	199	201	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: 5VMM

Analysis of interatomic Contacts of Structural Units in PDB entry:
5VMM