Analysis of interatomic Contacts of Structural Units in PDB entry:
8VBD

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 8VBD entry

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

Chain ID	Initial residue	Terminal residue
A	PRO 1	ALA 538
B	VAL 8	PRO 421
F	A -2	C 1
F	C 3	C 3
F	C 5	G 33

There are 25 helices in PDB entry 8VBD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	27	44	Right-handed alpha
Helix 2	AA2	A	77	84	Right-handed alpha
Helix 3	AA3	A	96	100	Right-handed 310
Helix 4	AA4	A	114	118	Right-handed 310
Helix 5	AA5	A	121	125	Right-handed 310
Helix 6	AA6	A	155	175	Right-handed alpha
Helix 7	AA7	A	194	212	Right-handed alpha
Helix 8	AA8	A	253	268	Right-handed alpha
Helix 9	AA9	A	276	281	Right-handed alpha
Helix 10	AB1	A	282	284	Right-handed 310
Helix 11	AB2	A	296	310	Right-handed alpha
Helix 12	AB3	A	363	383	Right-handed alpha
Helix 13	AB4	A	394	404	Right-handed alpha
Helix 14	AB5	A	473	488	Right-handed alpha
Helix 15	AB6	A	499	508	Right-handed alpha
Helix 16	AB7	A	515	528	Right-handed alpha
Helix 17	AB8	B	27	43	Right-handed alpha
Helix 18	AB9	B	77	82	Right-handed alpha
Helix 19	AC1	B	112	118	Right-handed 310
Helix 20	AC2	B	134	138	Right-handed 310
Helix 21	AC3	B	154	160	Right-handed alpha
Helix 22	AC4	B	255	266	Right-handed alpha
Helix 23	AC5	B	302	310	Right-handed alpha
Helix 24	AC6	B	363	383	Right-handed alpha
Helix 25	AC7	B	394	406	Right-handed alpha

There are 13 sheets in PDB entry 8VBD. 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,

There are 2 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	60	64	first strand
Strand 2	A	71	75	anti-parallel

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There are 3 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	105	110	first strand
Strand 2	A	186	191	anti-parallel
Strand 3	A	179	183	anti-parallel

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There are 2 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	130	132	first strand
Strand 2	A	142	144	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	A	227	229	first strand
Strand 2	A	232	234	anti-parallel
Strand 3	A	238	241	anti-parallel
Strand 4	A	316	317	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	A	347	354	first strand
Strand 2	A	336	344	anti-parallel
Strand 3	A	326	333	anti-parallel
Strand 4	A	388	391	parallel
Strand 5	A	414	416	parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	361	362	first strand
Strand 2	A	512	513	anti-parallel

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There are 3 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	429	430	first strand
Strand 2	A	531	535	parallel
Strand 3	A	493	497	parallel

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There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	441	443	first strand
Strand 2	A	452	459	anti-parallel
Strand 3	A	463	470	anti-parallel

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There are 2 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	11	12	first strand
Strand 2	B	84	85	anti-parallel

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There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	47	49	first strand
Strand 2	B	142	146	anti-parallel
Strand 3	B	129	132	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	60	64	first strand
Strand 2	B	71	75	anti-parallel

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There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	109	110	first strand
Strand 2	B	186	188	anti-parallel
Strand 3	B	181	182	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	B	348	354	first strand
Strand 2	B	337	342	anti-parallel
Strand 3	B	326	331	anti-parallel
Strand 4	B	388	391	parallel
Strand 5	B	414	416	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: 8VBD

Analysis of interatomic Contacts of Structural Units in PDB entry:
8VBD