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

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 8GCD entry

There are 2 chains in PDB entry 8GCD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LEU 1	LEU 985
B	GLY 1	LEU 712

There are 31 helices in PDB entry 8GCD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	151	158	Right-handed alpha
Helix 2	AA2	A	187	192	Right-handed alpha
Helix 3	AA3	A	200	207	Right-handed alpha
Helix 4	AA4	A	227	231	Right-handed 310
Helix 5	AA5	A	259	264	Right-handed alpha
Helix 6	AA6	A	515	519	Right-handed 310
Helix 7	AA7	A	554	558	Right-handed 310
Helix 8	AA8	A	602	606	Right-handed 310
Helix 9	AA9	A	666	670	Right-handed 310
Helix 10	AB1	A	710	714	Right-handed 310
Helix 11	AB2	A	910	915	Right-handed alpha
Helix 12	AB3	A	970	985	Right-handed alpha
Helix 13	AB4	B	12	20	Right-handed alpha
Helix 14	AB5	B	41	47	Right-handed alpha
Helix 15	AB6	B	121	125	Right-handed 310
Helix 16	AB7	B	126	134	Right-handed 310
Helix 17	AB8	B	135	143	Right-handed alpha
Helix 18	AB9	B	169	173	Right-handed 310
Helix 19	AC1	B	200	207	Right-handed alpha
Helix 20	AC2	B	227	232	Right-handed alpha
Helix 21	AC3	B	232	237	Right-handed alpha
Helix 22	AC4	B	258	263	Right-handed 310
Helix 23	AC5	B	291	303	Right-handed alpha
Helix 24	AC6	B	314	323	Right-handed alpha
Helix 25	AC7	B	339	352	Right-handed alpha
Helix 26	AC8	B	435	440	Right-handed alpha
Helix 27	AC9	B	493	497	Right-handed 310
Helix 28	AD1	B	534	538	Right-handed 310
Helix 29	AD2	B	606	611	Right-handed alpha
Helix 30	AD3	B	612	616	Right-handed 310
Helix 31	AD4	B	694	712	Right-handed alpha

There are 30 sheets in PDB entry 8GCD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1, AD2, AD3,

There are 4 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	9	12	first strand
Strand 2	A	444	448	anti-parallel
Strand 3	A	435	439	anti-parallel
Strand 4	A	421	423	anti-parallel

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There are 3 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	23	28	first strand
Strand 2	A	31	39	anti-parallel
Strand 3	A	52	56	anti-parallel

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There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	86	87	first strand
Strand 2	A	112	113	anti-parallel
Strand 3	A	125	126	anti-parallel

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There are 3 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	107	108	first strand
Strand 2	A	129	132	anti-parallel
Strand 3	A	141	142	anti-parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	116	117	first strand
Strand 2	A	120	121	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	A	173	175	first strand
Strand 2	A	180	185	anti-parallel
Strand 3	A	194	199	anti-parallel
Strand 4	A	220	221	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	A	239	242	first strand
Strand 2	A	252	257	anti-parallel
Strand 3	A	266	269	anti-parallel
Strand 4	A	278	281	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	A	293	296	first strand
Strand 2	A	305	310	anti-parallel
Strand 3	A	327	331	anti-parallel
Strand 4	A	345	348	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	314	315	first strand
Strand 2	A	323	324	anti-parallel

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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	360	362	first strand
Strand 2	A	374	378	anti-parallel
Strand 3	A	388	392	anti-parallel
Strand 4	A	405	408	anti-parallel

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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	473	474	first strand
Strand 2	A	481	494	anti-parallel
Strand 3	A	544	552	anti-parallel
Strand 4	A	521	523	anti-parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	473	474	first strand
Strand 2	A	481	494	anti-parallel
Strand 3	A	453	462	anti-parallel
Strand 4	A	585	588	parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	530	536	first strand
Strand 2	A	503	510	anti-parallel
Strand 3	A	565	572	anti-parallel
Strand 4	A	591	596	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	612	619	first strand
Strand 2	A	630	639	anti-parallel
Strand 3	A	697	706	anti-parallel
Strand 4	A	658	663	anti-parallel

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There are 6 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	623	624	first strand
Strand 2	A	736	743	parallel
Strand 3	A	716	724	anti-parallel
Strand 4	A	647	653	anti-parallel
Strand 5	A	683	690	anti-parallel
Strand 6	A	674	677	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	748	749	first strand
Strand 2	A	787	788	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	758	761	first strand
Strand 2	A	953	957	parallel
Strand 3	A	923	924	anti-parallel
Strand 4	A	877	878	parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	797	798	first strand
Strand 2	A	891	892	anti-parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	801	804	first strand
Strand 2	A	885	888	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	815	818	first strand
Strand 2	A	905	907	anti-parallel

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There are 3 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	38	40	first strand
Strand 2	B	23	26	anti-parallel
Strand 3	B	54	55	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	61	65	first strand
Strand 2	B	87	90	anti-parallel
Strand 3	B	425	429	parallel
Strand 4	B	412	416	anti-parallel

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There are 3 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	97	100	first strand
Strand 2	B	399	403	anti-parallel
Strand 3	B	366	369	anti-parallel

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There are 2 strands in AC6 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	394	396	anti-parallel

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There are 6 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	194	197	first strand
Strand 2	B	149	156	anti-parallel
Strand 3	B	112	119	parallel
Strand 4	B	243	249	parallel
Strand 5	B	305	308	parallel
Strand 6	B	328	329	parallel

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There are 2 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	354	356	first strand
Strand 2	B	385	387	anti-parallel

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There are 2 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	499	502	first strand
Strand 2	B	505	508	anti-parallel

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There are 2 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	540	543	first strand
Strand 2	B	546	549	anti-parallel

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There are 2 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	579	582	first strand
Strand 2	B	585	588	anti-parallel

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There are 2 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	654	658	first strand
Strand 2	B	664	668	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: 8GCD

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