Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD4

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 8JD4 entry

There are 2 chains in PDB entry 8JD4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
2	LYS 23	GLN 820
4	ASN 41	HIS 848

There are 51 helices in PDB entry 8JD4. 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	75	Right-handed alpha
Helix 2	AA2	2	94	106	Right-handed alpha
Helix 3	AA3	2	144	159	Right-handed alpha
Helix 4	AA4	2	169	174	Right-handed 310
Helix 5	AA5	2	187	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	285	Right-handed alpha
Helix 9	AA9	2	324	333	Right-handed alpha
Helix 10	AB1	2	344	353	Right-handed alpha
Helix 11	AB2	2	377	400	Right-handed alpha
Helix 12	AB3	2	407	411	Right-handed 310
Helix 13	AB4	2	414	425	Right-handed alpha
Helix 14	AB5	2	481	485	Right-handed 310
Helix 15	AB6	2	489	493	Right-handed 310
Helix 16	AB7	2	568	592	Right-handed alpha
Helix 17	AB8	2	603	626	Right-handed alpha
Helix 18	AB9	2	628	655	Right-handed alpha
Helix 19	AC1	2	679	700	Right-handed alpha
Helix 20	AC2	2	726	750	Right-handed alpha
Helix 21	AC3	2	759	783	Right-handed alpha
Helix 22	AC4	2	786	809	Right-handed alpha
Helix 23	AC5	2	810	818	Right-handed alpha
Helix 24	AC6	4	75	90	Right-handed alpha
Helix 25	AC7	4	111	120	Right-handed alpha
Helix 26	AC8	4	120	125	Right-handed alpha
Helix 27	AC9	4	158	170	Right-handed alpha
Helix 28	AD1	4	171	173	Right-handed 310
Helix 29	AD2	4	183	188	Right-handed 310
Helix 30	AD3	4	201	216	Right-handed alpha
Helix 31	AD4	4	230	246	Right-handed alpha
Helix 32	AD5	4	263	275	Right-handed alpha
Helix 33	AD6	4	286	300	Right-handed alpha
Helix 34	AD7	4	312	315	Right-handed 310
Helix 35	AD8	4	341	350	Right-handed alpha
Helix 36	AD9	4	361	371	Right-handed alpha
Helix 37	AE1	4	393	398	Right-handed alpha
Helix 38	AE2	4	405	428	Right-handed alpha
Helix 39	AE3	4	442	451	Right-handed alpha
Helix 40	AE4	4	457	461	Right-handed 310
Helix 41	AE5	4	502	506	Right-handed 310
Helix 42	AE6	4	588	612	Right-handed alpha
Helix 43	AE7	4	614	622	Right-handed alpha
Helix 44	AE8	4	624	644	Right-handed alpha
Helix 45	AE9	4	648	654	Right-handed alpha
Helix 46	AF1	4	654	682	Right-handed alpha
Helix 47	AF2	4	695	721	Right-handed alpha
Helix 48	AF3	4	749	775	Right-handed alpha
Helix 49	AF4	4	781	800	Right-handed alpha
Helix 50	AF5	4	800	808	Right-handed alpha
Helix 51	AF6	4	814	848	Right-handed alpha

There are 11 sheets in PDB entry 8JD4. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2,

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	2	25	28	first strand
Strand 2	2	84	89	anti-parallel
Strand 3	2	32	37	parallel
Strand 4	2	136	141	parallel
Strand 5	2	162	164	parallel
Strand 6	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 7 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	235	241	first strand
Strand 2	2	207	212	parallel
Strand 3	2	265	269	parallel
Strand 4	2	290	293	parallel
Strand 5	2	315	319	parallel
Strand 6	2	452	458	anti-parallel
Strand 7	2	468	475	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	2	428	429	first strand
Strand 2	2	440	441	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	510	511	first strand
Strand 2	2	522	523	anti-parallel

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There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	4	43	45	first strand
Strand 2	4	101	107	anti-parallel
Strand 3	4	49	55	parallel
Strand 4	4	150	155	parallel
Strand 5	4	176	178	parallel
Strand 6	4	195	197	parallel

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There are 2 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	58	60	first strand
Strand 2	4	67	70	anti-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	283	parallel
Strand 4	4	307	310	parallel
Strand 5	4	332	336	parallel
Strand 6	4	475	481	anti-parallel
Strand 7	4	488	495	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	529	533	first strand
Strand 2	4	540	544	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	549	550	first strand
Strand 2	4	558	559	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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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il

Analysis of interatomic Contacts of Structural Units in PDB entry: 8JD4

Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD4