Analysis of interatomic Contacts of Structural Units in PDB entry:
1GPD

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 1GPD entry

There are 2 chains in PDB entry 1GPD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
G	SER 1	ALA 334
R	SER 1	ALA 334

There are 14 helices in PDB entry 1GPD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	B	G	9	22	Right-handed alpha
Helix 2	C	G	36	46	Right-handed alpha
Helix 3	E	G	101	112	Right-handed alpha
Helix 4	H4	G	148	166	Right-handed alpha
Helix 5	H5	G	209	218	Right-handed alpha
Helix 6	H6	G	251	265	Right-handed alpha
Helix 7	H7	G	313	334	Right-handed alpha
Helix 8	B	R	9	22	Right-handed alpha
Helix 9	C	R	36	46	Right-handed alpha
Helix 10	E	R	101	112	Right-handed alpha
Helix 11	H4	R	148	166	Right-handed alpha
Helix 12	H5	R	209	218	Right-handed alpha
Helix 13	H6	R	251	265	Right-handed alpha
Helix 14	H7	R	313	334	Right-handed alpha

There are 6 sheets in PDB entry 1GPD. Click on sheet of interest to get list of strands forming it: GBD, GC1, GC2, RBD, RC1, RC2,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	56	60	first strand
Strand 2	G	63	67	anti-parallel
Strand 3	G	72	74	anti-parallel
Strand 4	G	27	32	parallel
Strand 5	G	2	7	parallel
Strand 6	G	90	95	parallel
Strand 7	G	115	120	parallel
Strand 8	G	142	147	parallel
Strand 9	G	126	128	parallel

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There are 8 strands in GC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	185	191	first strand
Strand 2	G	192	194	anti-parallel
Strand 3	G	204	208	anti-parallel
Strand 4	G	224	233	anti-parallel
Strand 5	G	168	179	parallel
Strand 6	G	236	246	anti-parallel
Strand 7	G	303	312	anti-parallel
Strand 8	G	299	301	anti-parallel

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There are 9 strands in GC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	185	191	first strand
Strand 2	G	192	194	anti-parallel
Strand 3	G	204	208	anti-parallel
Strand 4	G	224	233	anti-parallel
Strand 5	G	168	179	parallel
Strand 6	G	236	246	anti-parallel
Strand 7	G	303	312	anti-parallel
Strand 8	G	290	293	anti-parallel
Strand 9	G	271	273	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	56	60	first strand
Strand 2	R	63	67	anti-parallel
Strand 3	R	72	74	anti-parallel
Strand 4	R	27	32	parallel
Strand 5	R	2	7	parallel
Strand 6	R	90	95	parallel
Strand 7	R	115	120	parallel
Strand 8	R	142	147	parallel
Strand 9	R	126	128	parallel

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There are 8 strands in RC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	185	191	first strand
Strand 2	R	192	194	anti-parallel
Strand 3	R	204	208	anti-parallel
Strand 4	R	224	233	anti-parallel
Strand 5	R	168	179	parallel
Strand 6	R	236	246	anti-parallel
Strand 7	R	303	312	anti-parallel
Strand 8	R	299	301	anti-parallel

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There are 9 strands in RC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	185	191	first strand
Strand 2	R	192	194	anti-parallel
Strand 3	R	204	208	anti-parallel
Strand 4	R	224	233	anti-parallel
Strand 5	R	168	179	parallel
Strand 6	R	236	246	anti-parallel
Strand 7	R	303	312	anti-parallel
Strand 8	R	290	293	anti-parallel
Strand 9	R	271	273	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: 1GPD

Analysis of interatomic Contacts of Structural Units in PDB entry:
1GPD