Analysis of interatomic Contacts of Structural Units in PDB entry:
3GPD

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 3GPD entry

There are 2 chains in PDB entry 3GPD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
R	GLY 1	GLU 334
G	GLY 1	GLU 334

There are 8 helices in PDB entry 3GPD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	RBA	R	13	25	Right-handed alpha
Helix 2	RBB	R	39	47	Right-handed alpha
Helix 3	RBD	R	104	113	Right-handed alpha
Helix 4	RBE	R	132	135	Right-handed alpha
Helix 5	RCA	R	151	166	Right-handed alpha
Helix 6	RCB	R	212	219	Right-handed alpha
Helix 7	RCC	R	254	269	Right-handed alpha
Helix 8	RCD	R	317	333	Right-handed alpha

There are 6 sheets in PDB entry 3GPD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	5	8	first strand
Strand 2	R	93	96	parallel
Strand 3	R	117	121	parallel
Strand 4	R	145	148	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	32	33	first strand
Strand 2	R	71	76	parallel
Strand 3	R	65	68	anti-parallel
Strand 4	R	59	60	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	48	49	first strand
Strand 2	R	53	54	anti-parallel

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There are 6 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	206	209	first strand
Strand 2	R	227	233	anti-parallel
Strand 3	R	170	178	parallel
Strand 4	R	241	247	anti-parallel
Strand 5	R	306	310	anti-parallel
Strand 6	R	301	303	anti-parallel

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There are 9 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	59	62	first strand
Strand 2	G	65	68	anti-parallel
Strand 3	G	71	76	anti-parallel
Strand 4	G	32	33	parallel
Strand 5	G	5	8	parallel
Strand 6	G	93	96	parallel
Strand 7	G	117	121	parallel
Strand 8	G	145	148	parallel
Strand 9	G	129	130	parallel

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There are 6 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	206	209	first strand
Strand 2	G	229	233	anti-parallel
Strand 3	G	170	177	parallel
Strand 4	G	241	247	anti-parallel
Strand 5	G	306	312	anti-parallel
Strand 6	G	301	303	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: 3GPD

Analysis of interatomic Contacts of Structural Units in PDB entry:
3GPD