Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD5

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 8JD5 entry

There are 6 chains in PDB entry 8JD5 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
2	LYS 23	THR 832
4	ASN 41	GLU 850
A	SER 6	PHE 354
B	LEU 7	ASN 340
C	ILE 9	PRO 60
H	ASP 1	LEU 245

There are 66 helices in PDB entry 8JD5. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	2	58	74	Right-handed alpha
Helix 2	AA2	2	94	102	Right-handed alpha
Helix 3	AA3	2	103	107	Right-handed 310
Helix 4	AA4	2	144	158	Right-handed alpha
Helix 5	AA5	2	191	202	Right-handed alpha
Helix 6	AA6	2	216	231	Right-handed alpha
Helix 7	AA7	2	246	258	Right-handed alpha
Helix 8	AA8	2	271	284	Right-handed alpha
Helix 9	AA9	2	324	333	Right-handed alpha
Helix 10	AB1	2	344	352	Right-handed alpha
Helix 11	AB2	2	377	400	Right-handed alpha
Helix 12	AB3	2	414	423	Right-handed alpha
Helix 13	AB4	2	485	493	Right-handed 310
Helix 14	AB5	2	565	568	Right-handed 310
Helix 15	AB6	2	569	592	Right-handed alpha
Helix 16	AB7	2	597	601	Right-handed 310
Helix 17	AB8	2	602	621	Right-handed alpha
Helix 18	AB9	2	622	624	Right-handed 310
Helix 19	AC1	2	628	662	Right-handed alpha
Helix 20	AC2	2	675	701	Right-handed alpha
Helix 21	AC3	2	728	747	Right-handed alpha
Helix 22	AC4	2	753	757	Right-handed 310
Helix 23	AC5	2	758	783	Right-handed alpha
Helix 24	AC6	2	786	818	Right-handed alpha
Helix 25	AC7	4	75	90	Right-handed alpha
Helix 26	AC8	4	111	120	Right-handed alpha
Helix 27	AC9	4	158	170	Right-handed alpha
Helix 28	AD1	4	184	188	Right-handed 310
Helix 29	AD2	4	201	216	Right-handed alpha
Helix 30	AD3	4	230	246	Right-handed alpha
Helix 31	AD4	4	261	275	Right-handed alpha
Helix 32	AD5	4	286	300	Right-handed alpha
Helix 33	AD6	4	312	315	Right-handed 310
Helix 34	AD7	4	318	322	Right-handed 310
Helix 35	AD8	4	341	349	Right-handed alpha
Helix 36	AD9	4	360	372	Right-handed alpha
Helix 37	AE1	4	394	398	Right-handed 310
Helix 38	AE2	4	405	428	Right-handed alpha
Helix 39	AE3	4	435	439	Right-handed 310
Helix 40	AE4	4	442	452	Right-handed alpha
Helix 41	AE5	4	585	588	Right-handed 310
Helix 42	AE6	4	589	612	Right-handed alpha
Helix 43	AE7	4	617	621	Right-handed 310
Helix 44	AE8	4	626	644	Right-handed alpha
Helix 45	AE9	4	648	687	Right-handed alpha
Helix 46	AF1	4	695	721	Right-handed alpha
Helix 47	AF2	4	749	774	Right-handed alpha
Helix 48	AF3	4	780	783	Right-handed 310
Helix 49	AF4	4	784	800	Right-handed alpha
Helix 50	AF5	4	801	806	Right-handed alpha
Helix 51	AF6	4	819	847	Right-handed alpha
Helix 52	AF7	A	7	32	Right-handed alpha
Helix 53	AF8	A	46	50	Right-handed 310
Helix 54	AF9	A	208	213	Right-handed alpha
Helix 55	AG1	A	214	216	Right-handed 310
Helix 56	AG2	A	241	256	Right-handed alpha
Helix 57	AG3	A	270	281	Right-handed alpha
Helix 58	AG4	A	282	286	Right-handed 310
Helix 59	AG5	A	295	309	Right-handed alpha
Helix 60	AG6	A	330	352	Right-handed alpha
Helix 61	AG7	B	8	29	Right-handed alpha
Helix 62	AG8	C	10	25	Right-handed alpha
Helix 63	AG9	C	31	44	Right-handed alpha
Helix 64	AH1	H	53	56	Right-handed 310
Helix 65	AH2	H	62	65	Right-handed 310
Helix 66	AH3	H	87	91	Right-handed 310

There are 25 sheets in PDB entry 8JD5. 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,

There are 5 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	2	87	90	first strand
Strand 2	2	33	38	parallel
Strand 3	2	136	141	parallel
Strand 4	2	162	164	parallel
Strand 5	2	181	183	parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	2	41	43	first strand
Strand 2	2	50	53	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	2	234	235	first strand
Strand 2	2	206	212	parallel
Strand 3	2	239	241	parallel

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There are 7 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	2	234	235	first strand
Strand 2	2	206	212	parallel
Strand 3	2	265	269	parallel
Strand 4	2	290	293	parallel
Strand 5	2	314	319	parallel
Strand 6	2	453	459	anti-parallel
Strand 7	2	467	474	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	2	428	429	first strand
Strand 2	2	440	441	anti-parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	2	509	511	first strand
Strand 2	2	522	524	anti-parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	4	101	107	first strand
Strand 2	4	49	55	parallel
Strand 3	4	150	154	parallel
Strand 4	4	176	178	parallel
Strand 5	4	195	197	parallel

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There are 7 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	4	249	256	first strand
Strand 2	4	220	226	parallel
Strand 3	4	280	284	parallel
Strand 4	4	307	310	parallel
Strand 5	4	332	336	parallel
Strand 6	4	475	481	anti-parallel
Strand 7	4	488	494	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	4	455	456	first strand
Strand 2	4	462	463	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	4	531	533	first strand
Strand 2	4	540	542	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	4	564	566	first strand
Strand 2	4	573	575	anti-parallel

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There are 3 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	33	34	first strand
Strand 2	A	194	200	parallel
Strand 3	A	185	191	anti-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	36	39	first strand
Strand 2	A	220	226	parallel
Strand 3	A	263	269	parallel
Strand 4	A	319	322	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	B	58	62	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	91	94	anti-parallel

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There are 4 strands in AB6 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	122	125	anti-parallel
Strand 4	B	134	135	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	149	150	first strand
Strand 2	B	156	159	anti-parallel
Strand 3	B	167	170	anti-parallel
Strand 4	B	176	179	anti-parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	207	209	first strand
Strand 2	B	221	223	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	229	232	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	250	254	anti-parallel
Strand 4	B	260	264	anti-parallel

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There are 3 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	284	286	first strand
Strand 2	B	293	298	anti-parallel
Strand 3	B	303	309	anti-parallel

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There are 3 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	315	320	first strand
Strand 2	B	327	331	anti-parallel
Strand 3	B	336	339	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	6	7	first strand
Strand 2	H	20	23	anti-parallel
Strand 3	H	78	82	anti-parallel
Strand 4	H	69	73	anti-parallel

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There are 5 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	58	60	first strand
Strand 2	H	45	51	anti-parallel
Strand 3	H	33	39	anti-parallel
Strand 4	H	93	99	anti-parallel
Strand 5	H	110	111	anti-parallel

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There are 5 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	58	60	first strand
Strand 2	H	45	51	anti-parallel
Strand 3	H	33	39	anti-parallel
Strand 4	H	93	99	anti-parallel
Strand 5	H	115	116	anti-parallel

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There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	140	141	first strand
Strand 2	H	155	161	anti-parallel
Strand 3	H	211	216	anti-parallel
Strand 4	H	204	208	anti-parallel

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There are 5 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	194	195	first strand
Strand 2	H	186	190	anti-parallel
Strand 3	H	174	179	anti-parallel
Strand 4	H	226	231	anti-parallel
Strand 5	H	243	244	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: 8JD5

Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD5