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

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 5VPM entry

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

Chain ID	Initial residue	Terminal residue
A	GLY 1	ARG 337
B	GLY 1	ARG 337

There are 20 helices in PDB entry 5VPM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	52	57	Right-handed alpha
Helix 2	AA2	A	62	66	Right-handed 310
Helix 3	AA3	A	112	117	Right-handed alpha
Helix 4	AA4	A	133	137	Right-handed 310
Helix 5	AA5	A	139	147	Right-handed alpha
Helix 6	AA6	A	179	183	Right-handed 310
Helix 7	AA7	A	232	244	Right-handed alpha
Helix 8	AA8	A	258	262	Right-handed 310
Helix 9	AA9	A	277	282	Right-handed alpha
Helix 10	AB1	A	313	318	Right-handed alpha
Helix 11	AB2	B	52	57	Right-handed alpha
Helix 12	AB3	B	62	66	Right-handed 310
Helix 13	AB4	B	112	117	Right-handed alpha
Helix 14	AB5	B	129	137	Right-handed 310
Helix 15	AB6	B	139	146	Right-handed alpha
Helix 16	AB7	B	179	181	Right-handed 310
Helix 17	AB8	B	232	244	Right-handed alpha
Helix 18	AB9	B	257	259	Right-handed 310
Helix 19	AC1	B	277	282	Right-handed alpha
Helix 20	AC2	B	313	318	Right-handed alpha

There are 12 sheets in PDB entry 5VPM. 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 9 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	70	80	first strand
Strand 2	A	83	96	anti-parallel
Strand 3	A	16	23	anti-parallel
Strand 4	A	5	12	anti-parallel
Strand 5	A	171	175	anti-parallel
Strand 6	A	154	157	anti-parallel
Strand 7	A	320	325	anti-parallel
Strand 8	A	330	335	anti-parallel
Strand 9	A	188	191	anti-parallel

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There are 13 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	70	80	first strand
Strand 2	A	83	96	anti-parallel
Strand 3	A	99	110	anti-parallel
Strand 4	A	41	44	parallel
Strand 5	A	123	126	anti-parallel
Strand 6	A	28	35	parallel
Strand 7	A	16	23	anti-parallel
Strand 8	A	5	12	anti-parallel
Strand 9	A	171	175	anti-parallel
Strand 10	A	154	157	anti-parallel
Strand 11	A	320	325	anti-parallel
Strand 12	A	330	335	anti-parallel
Strand 13	A	188	191	anti-parallel

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There are 3 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	199	202	first strand
Strand 2	A	218	222	anti-parallel
Strand 3	A	310	312	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	210	213	first strand
Strand 2	A	204	207	anti-parallel
Strand 3	A	265	269	anti-parallel
Strand 4	A	272	276	anti-parallel

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There are 2 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	229	231	first strand
Strand 2	A	297	299	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	246	247	first strand
Strand 2	A	252	255	anti-parallel
Strand 3	A	292	295	anti-parallel

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There are 9 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	75	78	first strand
Strand 2	B	85	96	anti-parallel
Strand 3	B	16	23	anti-parallel
Strand 4	B	5	12	anti-parallel
Strand 5	B	171	175	anti-parallel
Strand 6	B	154	159	anti-parallel
Strand 7	B	320	325	anti-parallel
Strand 8	B	330	336	anti-parallel
Strand 9	B	183	191	anti-parallel

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There are 13 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	75	78	first strand
Strand 2	B	85	96	anti-parallel
Strand 3	B	99	110	anti-parallel
Strand 4	B	41	44	parallel
Strand 5	B	123	126	anti-parallel
Strand 6	B	28	35	parallel
Strand 7	B	16	23	anti-parallel
Strand 8	B	5	12	anti-parallel
Strand 9	B	171	175	anti-parallel
Strand 10	B	154	159	anti-parallel
Strand 11	B	320	325	anti-parallel
Strand 12	B	330	336	anti-parallel
Strand 13	B	183	191	anti-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	210	213	first strand
Strand 2	B	199	207	anti-parallel
Strand 3	B	265	269	anti-parallel
Strand 4	B	272	276	anti-parallel

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There are 4 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	210	213	first strand
Strand 2	B	199	207	anti-parallel
Strand 3	B	218	222	anti-parallel
Strand 4	B	310	312	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	229	231	first strand
Strand 2	B	297	299	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	246	247	first strand
Strand 2	B	252	255	anti-parallel
Strand 3	B	292	294	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: 5VPM

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