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

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 5VDN entry

There are 2 chains in PDB entry 5VDN (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 12	ARG 460
B	THR 12	ARG 460

There are 34 helices in PDB entry 5VDN. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	23	36	Right-handed alpha
Helix 2	AA2	A	49	56	Right-handed alpha
Helix 3	AA3	A	56	75	Right-handed alpha
Helix 4	AA4	A	76	80	Right-handed 310
Helix 5	AA5	A	90	116	Right-handed alpha
Helix 6	AA6	A	160	164	Right-handed 310
Helix 7	AA7	A	166	173	Right-handed alpha
Helix 8	AA8	A	186	200	Right-handed alpha
Helix 9	AA9	A	217	232	Right-handed alpha
Helix 10	AB1	A	281	286	Right-handed 310
Helix 11	AB2	A	312	316	Right-handed 310
Helix 12	AB3	A	320	337	Right-handed alpha
Helix 13	AB4	A	365	374	Right-handed alpha
Helix 14	AB5	A	387	392	Right-handed alpha
Helix 15	AB6	A	421	435	Right-handed alpha
Helix 16	AB7	A	438	444	Right-handed alpha
Helix 17	AB8	A	452	458	Right-handed 310
Helix 18	AB9	B	23	36	Right-handed alpha
Helix 19	AC1	B	49	56	Right-handed alpha
Helix 20	AC2	B	56	75	Right-handed alpha
Helix 21	AC3	B	76	80	Right-handed 310
Helix 22	AC4	B	90	116	Right-handed alpha
Helix 23	AC5	B	160	164	Right-handed 310
Helix 24	AC6	B	166	173	Right-handed alpha
Helix 25	AC7	B	186	200	Right-handed alpha
Helix 26	AC8	B	217	232	Right-handed alpha
Helix 27	AC9	B	281	286	Right-handed 310
Helix 28	AD1	B	312	316	Right-handed 310
Helix 29	AD2	B	320	337	Right-handed alpha
Helix 30	AD3	B	365	374	Right-handed alpha
Helix 31	AD4	B	387	392	Right-handed alpha
Helix 32	AD5	B	421	435	Right-handed alpha
Helix 33	AD6	B	438	444	Right-handed alpha
Helix 34	AD7	B	452	458	Right-handed 310

There are 13 sheets in PDB entry 5VDN. 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 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	119	122	first strand
Strand 2	A	40	44	parallel
Strand 3	A	13	20	parallel
Strand 4	A	138	147	parallel
Strand 5	A	132	135	anti-parallel
Strand 6	A	126	129	anti-parallel

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There are 5 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	119	122	first strand
Strand 2	A	40	44	parallel
Strand 3	A	13	20	parallel
Strand 4	A	138	147	parallel
Strand 5	A	308	310	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	82	89	first strand
Strand 2	B	82	89	anti-parallel

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There are 2 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	151	153	first strand
Strand 2	A	273	275	anti-parallel

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There are 4 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	234	236	first strand
Strand 2	A	202	206	parallel
Strand 3	A	179	183	parallel
Strand 4	A	266	269	parallel

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There are 3 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	241	246	first strand
Strand 2	A	252	256	anti-parallel
Strand 3	A	261	264	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	A	351	353	first strand
Strand 2	A	359	363	anti-parallel
Strand 3	A	411	418	anti-parallel
Strand 4	A	398	406	anti-parallel
Strand 5	A	378	386	anti-parallel

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There are 6 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	119	122	first strand
Strand 2	B	40	44	parallel
Strand 3	B	13	20	parallel
Strand 4	B	138	147	parallel
Strand 5	B	132	135	anti-parallel
Strand 6	B	126	129	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	B	119	122	first strand
Strand 2	B	40	44	parallel
Strand 3	B	13	20	parallel
Strand 4	B	138	147	parallel
Strand 5	B	308	310	parallel

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There are 2 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	151	153	first strand
Strand 2	B	273	275	anti-parallel

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There are 4 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	234	236	first strand
Strand 2	B	202	206	parallel
Strand 3	B	179	183	parallel
Strand 4	B	266	269	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	241	246	first strand
Strand 2	B	252	256	anti-parallel
Strand 3	B	261	264	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	351	353	first strand
Strand 2	B	359	363	anti-parallel
Strand 3	B	411	418	anti-parallel
Strand 4	B	398	406	anti-parallel
Strand 5	B	378	386	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: 5VDN

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