Analysis of interatomic Contacts of Structural Units in PDB entry:
8GDZ

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 8GDZ entry

There are 4 chains in PDB entry 8GDZ (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ARG 13	LEU 394
B	LEU 4	ASN 340
G	ALA 10	ARG 62
R	ASP 29	LEU 340

There are 27 helices in PDB entry 8GDZ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	13	40	Right-handed alpha
Helix 2	AA2	A	48	51	Right-handed 310
Helix 3	AA3	A	52	61	Right-handed alpha
Helix 4	AA4	A	233	239	Right-handed 310
Helix 5	AA5	A	264	278	Right-handed alpha
Helix 6	AA6	A	293	303	Right-handed alpha
Helix 7	AA7	A	307	312	Right-handed alpha
Helix 8	AA8	A	313	316	Right-handed 310
Helix 9	AA9	A	331	352	Right-handed alpha
Helix 10	AB1	A	370	391	Right-handed alpha
Helix 11	AB2	B	5	26	Right-handed alpha
Helix 12	AB3	B	29	34	Right-handed alpha
Helix 13	AB4	B	35	37	Right-handed 310
Helix 14	AB5	B	280	282	Right-handed 310
Helix 15	AB6	G	11	23	Right-handed alpha
Helix 16	AB7	G	29	45	Right-handed alpha
Helix 17	AB8	G	46	48	Right-handed 310
Helix 18	AB9	R	30	61	Right-handed alpha
Helix 19	AC1	R	66	97	Right-handed alpha
Helix 20	AC2	R	102	137	Right-handed alpha
Helix 21	AC3	R	140	145	Right-handed alpha
Helix 22	AC4	R	146	171	Right-handed alpha
Helix 23	AC5	R	178	187	Right-handed alpha
Helix 24	AC6	R	196	238	Right-handed alpha
Helix 25	AC7	R	269	299	Right-handed alpha
Helix 26	AC8	R	304	327	Right-handed alpha
Helix 27	AC9	R	329	340	Right-handed alpha

There are 8 sheets in PDB entry 8GDZ. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

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	208	214	first strand
Strand 2	A	217	223	anti-parallel
Strand 3	A	41	45	parallel
Strand 4	A	243	249	parallel
Strand 5	A	287	292	parallel
Strand 6	A	359	363	parallel

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There are 4 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	46	51	first strand
Strand 2	B	336	340	anti-parallel
Strand 3	B	327	331	anti-parallel
Strand 4	B	315	320	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	B	58	61	first strand
Strand 2	B	72	74	anti-parallel
Strand 3	B	78	82	anti-parallel
Strand 4	B	89	94	anti-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	B	103	105	first strand
Strand 2	B	111	114	anti-parallel
Strand 3	B	121	125	anti-parallel
Strand 4	B	135	139	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	B	146	151	first strand
Strand 2	B	157	161	anti-parallel
Strand 3	B	165	169	anti-parallel
Strand 4	B	176	181	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	187	192	first strand
Strand 2	B	198	203	anti-parallel
Strand 3	B	208	212	anti-parallel
Strand 4	B	218	222	anti-parallel

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There are 4 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	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	250	254	anti-parallel
Strand 4	B	259	264	anti-parallel

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There are 4 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	273	278	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	304	308	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: 8GDZ

Analysis of interatomic Contacts of Structural Units in PDB entry:
8GDZ