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

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 6VGD entry

There are 5 chains in PDB entry 6VGD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 275	HIS 372
B	C 1	C 16
C	G 2	G 17
D	ALA 111	PRO 227
G	PRO 2	ALA 139

There are 8 helices in PDB entry 6VGD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	283	288	Right-handed alpha
Helix 2	AA2	A	293	297	Right-handed 310
Helix 3	AA3	A	313	326	Right-handed alpha
Helix 4	AA4	A	331	346	Right-handed alpha
Helix 5	AA5	G	7	13	Right-handed alpha
Helix 6	AA6	G	15	20	Right-handed alpha
Helix 7	AA7	G	36	51	Right-handed alpha
Helix 8	AA8	G	128	138	Right-handed alpha

There are 7 sheets in PDB entry 6VGD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7,

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	300	302	first strand
Strand 2	A	309	311	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	348	350	first strand
Strand 2	A	358	360	anti-parallel

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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	113	114	first strand
Strand 2	D	121	124	anti-parallel
Strand 3	D	140	144	anti-parallel
Strand 4	D	179	182	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	D	129	131	first strand
Strand 2	D	218	220	parallel

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There are 10 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	172	174	first strand
Strand 2	D	153	157	anti-parallel
Strand 3	D	200	204	anti-parallel
Strand 4	D	209	210	anti-parallel
Strand 5	G	102	103	parallel
Strand 6	G	106	109	anti-parallel
Strand 7	G	120	127	anti-parallel
Strand 8	G	25	29	anti-parallel
Strand 9	G	52	57	anti-parallel
Strand 10	G	62	67	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	D	172	174	first strand
Strand 2	D	153	157	anti-parallel
Strand 3	D	200	204	anti-parallel
Strand 4	D	209	210	anti-parallel
Strand 5	G	102	103	parallel
Strand 6	G	106	109	anti-parallel
Strand 7	G	120	127	anti-parallel
Strand 8	G	114	115	anti-parallel
Strand 9	G	94	95	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	D	168	169	first strand
Strand 2	D	186	187	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: 6VGD

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