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

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 8GDA entry

There are 5 chains in PDB entry 8GDA (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 9	LEU 394
B	GLY 1	ASN 340
G	ASN 5	ARG 62
N	GLN 1	SER 128
R	SER 19	ILE 344

There are 29 helices in PDB entry 8GDA. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	10	32	Right-handed alpha
Helix 2	AA2	A	33	38	Right-handed alpha
Helix 3	AA3	A	52	57	Right-handed alpha
Helix 4	AA4	A	264	278	Right-handed alpha
Helix 5	AA5	A	293	304	Right-handed alpha
Helix 6	AA6	A	307	311	Right-handed 310
Helix 7	AA7	A	337	350	Right-handed alpha
Helix 8	AA8	A	372	388	Right-handed alpha
Helix 9	AA9	A	389	391	Right-handed 310
Helix 10	AB1	B	2	25	Right-handed alpha
Helix 11	AB2	B	29	34	Right-handed alpha
Helix 12	AB3	G	6	23	Right-handed alpha
Helix 13	AB4	G	29	44	Right-handed alpha
Helix 14	AB5	N	28	32	Right-handed 310
Helix 15	AB6	N	87	91	Right-handed 310
Helix 16	AB7	R	22	44	Right-handed alpha
Helix 17	AB8	R	46	50	Right-handed 310
Helix 18	AB9	R	52	83	Right-handed alpha
Helix 19	AC1	R	88	123	Right-handed alpha
Helix 20	AC2	R	123	131	Right-handed alpha
Helix 21	AC3	R	132	152	Right-handed alpha
Helix 22	AC4	R	153	157	Right-handed 310
Helix 23	AC5	R	178	206	Right-handed alpha
Helix 24	AC6	R	211	221	Right-handed alpha
Helix 25	AC7	R	267	298	Right-handed alpha
Helix 26	AC8	R	305	309	Right-handed 310
Helix 27	AC9	R	311	319	Right-handed alpha
Helix 28	AD1	R	320	330	Right-handed alpha
Helix 29	AD2	R	333	344	Right-handed alpha

There are 10 sheets in PDB entry 8GDA. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1,

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	207	214	first strand
Strand 2	A	217	224	anti-parallel
Strand 3	A	40	46	parallel
Strand 4	A	243	249	parallel
Strand 5	A	286	292	parallel
Strand 6	A	360	361	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	47	51	first strand
Strand 2	B	336	339	anti-parallel
Strand 3	B	327	330	anti-parallel
Strand 4	B	317	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	63	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	88	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	100	105	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	120	125	anti-parallel
Strand 4	B	134	140	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	156	161	anti-parallel
Strand 3	B	165	170	anti-parallel
Strand 4	B	175	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	249	254	anti-parallel
Strand 4	B	259	265	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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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	N	4	7	first strand
Strand 2	N	16	24	anti-parallel
Strand 3	N	78	86	anti-parallel
Strand 4	N	68	73	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	N	11	12	first strand
Strand 2	N	122	126	parallel
Strand 3	N	92	95	anti-parallel
Strand 4	N	34	39	anti-parallel
Strand 5	N	45	51	anti-parallel
Strand 6	N	58	60	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: 8GDA

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