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

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 8GAP entry

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

Chain ID	Initial residue	Terminal residue
A	LYS 11	LYS 1110
D	GLN 511	ASN 697
E	PRO 28	GLU 175
F	GLN 5	GLN 121
G	MET 1	ILE 184
C	G 47	G 60
B	A 1	U 159
H	GLN 82	LYS 532

There are 83 helices in PDB entry 8GAP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	19	25	Right-handed alpha
Helix 2	AA2	A	36	43	Right-handed alpha
Helix 3	AA3	A	53	63	Right-handed alpha
Helix 4	AA4	A	88	101	Right-handed alpha
Helix 5	AA5	A	127	133	Right-handed alpha
Helix 6	AA6	A	133	144	Right-handed alpha
Helix 7	AA7	A	144	155	Right-handed alpha
Helix 8	AA8	A	173	178	Right-handed 310
Helix 9	AA9	A	225	230	Right-handed 310
Helix 10	AB1	A	245	250	Right-handed alpha
Helix 11	AB2	A	282	289	Right-handed alpha
Helix 12	AB3	A	289	294	Right-handed alpha
Helix 13	AB4	A	300	319	Right-handed alpha
Helix 14	AB5	A	322	331	Right-handed alpha
Helix 15	AB6	A	336	350	Right-handed alpha
Helix 16	AB7	A	355	368	Right-handed alpha
Helix 17	AB8	A	372	386	Right-handed alpha
Helix 18	AB9	A	394	410	Right-handed alpha
Helix 19	AC1	A	419	424	Right-handed alpha
Helix 20	AC2	A	427	431	Right-handed 310
Helix 21	AC3	A	444	475	Right-handed alpha
Helix 22	AC4	A	493	511	Right-handed alpha
Helix 23	AC5	A	521	528	Right-handed alpha
Helix 24	AC6	A	560	580	Right-handed alpha
Helix 25	AC7	A	589	608	Right-handed alpha
Helix 26	AC8	A	622	626	Right-handed 310
Helix 27	AC9	A	627	638	Right-handed alpha
Helix 28	AD1	A	691	694	Right-handed 310
Helix 29	AD2	A	713	718	Right-handed alpha
Helix 30	AD3	A	742	755	Right-handed alpha
Helix 31	AD4	A	777	794	Right-handed alpha
Helix 32	AD5	A	794	804	Right-handed alpha
Helix 33	AD6	A	823	842	Right-handed alpha
Helix 34	AD7	A	845	847	Right-handed 310
Helix 35	AD8	A	895	901	Right-handed alpha
Helix 36	AD9	A	908	910	Right-handed 310
Helix 37	AE1	A	911	926	Right-handed alpha
Helix 38	AE2	A	927	932	Right-handed 310
Helix 39	AE3	A	938	965	Right-handed alpha
Helix 40	AE4	A	966	967	Right-handed 310
Helix 41	AE5	A	968	971	Right-handed 310
Helix 42	AE6	A	972	980	Right-handed alpha
Helix 43	AE7	A	983	1009	Right-handed alpha
Helix 44	AE8	A	1014	1038	Right-handed alpha
Helix 45	AE9	A	1045	1075	Right-handed alpha
Helix 46	AF1	A	1081	1095	Right-handed alpha
Helix 47	AF2	A	1102	1109	Right-handed alpha
Helix 48	AF3	D	516	527	Right-handed alpha
Helix 49	AF4	D	603	615	Right-handed alpha
Helix 50	AF5	D	621	634	Right-handed alpha
Helix 51	AF6	D	636	645	Right-handed alpha
Helix 52	AF7	D	679	697	Right-handed alpha
Helix 53	AF8	E	35	49	Right-handed alpha
Helix 54	AF9	E	110	123	Right-handed alpha
Helix 55	AG1	E	153	175	Right-handed alpha
Helix 56	AG2	F	17	22	Right-handed alpha
Helix 57	AG3	F	62	64	Right-handed 310
Helix 58	AG4	F	99	111	Right-handed alpha
Helix 59	AG5	F	111	119	Right-handed alpha
Helix 60	AG6	G	2	7	Right-handed alpha
Helix 61	AG7	G	9	29	Right-handed alpha
Helix 62	AG8	G	33	41	Right-handed alpha
Helix 63	AG9	G	87	94	Right-handed alpha
Helix 64	AH1	G	151	157	Right-handed alpha
Helix 65	AH2	G	158	161	Right-handed 310
Helix 66	AH3	G	162	184	Right-handed alpha
Helix 67	AH4	H	83	107	Right-handed alpha
Helix 68	AH5	H	117	130	Right-handed alpha
Helix 69	AH6	H	131	139	Right-handed alpha
Helix 70	AH7	H	140	148	Right-handed alpha
Helix 71	AH8	H	155	160	Right-handed alpha
Helix 72	AH9	H	164	168	Right-handed 310
Helix 73	AI1	H	203	215	Right-handed alpha
Helix 74	AI2	H	236	247	Right-handed alpha
Helix 75	AI3	H	259	267	Right-handed alpha
Helix 76	AI4	H	296	306	Right-handed alpha
Helix 77	AI5	H	333	350	Right-handed alpha
Helix 78	AI6	H	357	368	Right-handed alpha
Helix 79	AI7	H	369	374	Right-handed alpha
Helix 80	AI8	H	376	378	Right-handed 310
Helix 81	AI9	H	391	401	Right-handed alpha
Helix 82	AJ1	H	468	480	Right-handed alpha
Helix 83	AJ2	H	503	531	Right-handed alpha

There are 18 sheets in PDB entry 8GAP. 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,

There are 7 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	32	35	first strand
Strand 2	A	64	67	anti-parallel
Strand 3	A	156	160	anti-parallel
Strand 4	A	165	170	anti-parallel
Strand 5	A	729	733	parallel
Strand 6	A	644	655	anti-parallel
Strand 7	A	696	706	anti-parallel

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There are 7 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	32	35	first strand
Strand 2	A	64	67	anti-parallel
Strand 3	A	156	160	anti-parallel
Strand 4	A	165	170	anti-parallel
Strand 5	A	729	733	parallel
Strand 6	A	644	655	anti-parallel
Strand 7	A	738	741	anti-parallel

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There are 2 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	112	115	first strand
Strand 2	A	118	121	anti-parallel

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There are 2 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	476	479	first strand
Strand 2	A	489	492	anti-parallel

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There are 5 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	512	514	first strand
Strand 2	A	763	767	anti-parallel
Strand 3	A	757	760	anti-parallel
Strand 4	A	531	538	parallel
Strand 5	A	541	547	anti-parallel

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There are 5 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	808	813	first strand
Strand 2	A	816	821	anti-parallel
Strand 3	A	613	618	anti-parallel
Strand 4	A	849	852	anti-parallel
Strand 5	A	867	870	parallel

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There are 3 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	874	876	first strand
Strand 2	A	879	881	anti-parallel
Strand 3	A	888	890	anti-parallel

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There are 6 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	532	545	first strand
Strand 2	D	587	592	anti-parallel
Strand 3	D	597	602	anti-parallel
Strand 4	D	665	676	parallel
Strand 5	D	649	662	anti-parallel
Strand 6	D	532	545	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	D	551	554	first strand
Strand 2	D	582	585	anti-parallel

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There are 2 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	562	564	first strand
Strand 2	D	570	572	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	E	31	33	first strand
Strand 2	E	66	76	parallel
Strand 3	E	84	90	anti-parallel
Strand 4	E	95	96	anti-parallel

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There are 7 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	31	33	first strand
Strand 2	E	66	76	parallel
Strand 3	E	129	135	anti-parallel
Strand 4	E	143	149	anti-parallel
Strand 5	E	99	101	parallel
Strand 6	E	84	90	anti-parallel
Strand 7	E	95	96	anti-parallel

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There are 7 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	87	91	first strand
Strand 2	F	70	79	anti-parallel
Strand 3	F	82	83	anti-parallel
Strand 4	F	53	60	parallel
Strand 5	F	40	44	anti-parallel
Strand 6	F	25	32	anti-parallel
Strand 7	F	70	79	anti-parallel

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There are 6 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	46	51	first strand
Strand 2	G	103	117	anti-parallel
Strand 3	G	59	66	anti-parallel
Strand 4	G	71	76	anti-parallel
Strand 5	G	79	85	anti-parallel
Strand 6	G	144	147	parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	46	51	first strand
Strand 2	G	103	117	anti-parallel
Strand 3	G	120	135	anti-parallel
Strand 4	G	79	85	parallel
Strand 5	G	144	147	parallel

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There are 3 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	153	154	first strand
Strand 2	H	228	231	anti-parallel
Strand 3	H	220	221	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	H	272	276	first strand
Strand 2	H	291	294	anti-parallel
Strand 3	H	248	250	anti-parallel
Strand 4	H	331	332	anti-parallel

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There are 5 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	406	409	first strand
Strand 2	H	462	466	anti-parallel
Strand 3	H	380	384	anti-parallel
Strand 4	H	494	499	anti-parallel
Strand 5	H	488	491	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: 8GAP

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