Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD6

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 8JD6 entry

Note, this PDB entry contains modified residue(s) PHOSPHOSERINE (SEP) . This residue is treated as heterogroup (ligand) both in the PDB entry and in LPC/CSU analysis.

There are 6 chains in PDB entry 8JD6 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
S	ASN 41	HIS 848
R	ASN 41	VAL 853
D	VAL 2	LEU 247
C	LYS 29	GLU 47
B	VAL 40	ASN 340
A	SER 6	TYR 354

There are 58 helices in PDB entry 8JD6. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	S	74	92	Right-handed alpha
Helix 2	AA2	S	111	124	Right-handed alpha
Helix 3	AA3	S	158	172	Right-handed alpha
Helix 4	AA4	S	183	187	Right-handed 310
Helix 5	AA5	S	201	216	Right-handed alpha
Helix 6	AA6	S	228	245	Right-handed alpha
Helix 7	AA7	S	264	274	Right-handed alpha
Helix 8	AA8	S	286	300	Right-handed alpha
Helix 9	AA9	S	311	315	Right-handed 310
Helix 10	AB1	S	341	349	Right-handed alpha
Helix 11	AB2	S	361	370	Right-handed alpha
Helix 12	AB3	S	405	427	Right-handed alpha
Helix 13	AB4	S	435	439	Right-handed 310
Helix 14	AB5	S	442	452	Right-handed alpha
Helix 15	AB6	S	502	506	Right-handed 310
Helix 16	AB7	S	588	612	Right-handed alpha
Helix 17	AB8	S	623	644	Right-handed alpha
Helix 18	AB9	S	648	683	Right-handed alpha
Helix 19	AC1	S	695	719	Right-handed alpha
Helix 20	AC2	S	749	775	Right-handed alpha
Helix 21	AC3	S	784	808	Right-handed alpha
Helix 22	AC4	S	817	838	Right-handed alpha
Helix 23	AC5	S	838	848	Right-handed alpha
Helix 24	AC6	R	74	92	Right-handed alpha
Helix 25	AC7	R	111	127	Right-handed alpha
Helix 26	AC8	R	158	170	Right-handed alpha
Helix 27	AC9	R	183	188	Right-handed 310
Helix 28	AD1	R	201	216	Right-handed alpha
Helix 29	AD2	R	230	244	Right-handed alpha
Helix 30	AD3	R	263	275	Right-handed alpha
Helix 31	AD4	R	286	301	Right-handed alpha
Helix 32	AD5	R	341	350	Right-handed alpha
Helix 33	AD6	R	359	367	Right-handed alpha
Helix 34	AD7	R	405	428	Right-handed alpha
Helix 35	AD8	R	435	439	Right-handed 310
Helix 36	AD9	R	442	452	Right-handed alpha
Helix 37	AE1	R	502	506	Right-handed 310
Helix 38	AE2	R	588	612	Right-handed alpha
Helix 39	AE3	R	615	621	Right-handed alpha
Helix 40	AE4	R	623	645	Right-handed alpha
Helix 41	AE5	R	648	685	Right-handed alpha
Helix 42	AE6	R	695	721	Right-handed alpha
Helix 43	AE7	R	749	774	Right-handed alpha
Helix 44	AE8	R	784	808	Right-handed alpha
Helix 45	AE9	R	813	848	Right-handed alpha
Helix 46	AF1	D	52	56	Right-handed 310
Helix 47	AF2	D	87	91	Right-handed 310
Helix 48	AF3	C	30	36	Right-handed alpha
Helix 49	AF4	A	7	33	Right-handed alpha
Helix 50	AF5	A	45	50	Right-handed alpha
Helix 51	AF6	A	207	212	Right-handed alpha
Helix 52	AF7	A	213	216	Right-handed 310
Helix 53	AF8	A	241	254	Right-handed alpha
Helix 54	AF9	A	270	279	Right-handed alpha
Helix 55	AG1	A	282	286	Right-handed 310
Helix 56	AG2	A	295	308	Right-handed alpha
Helix 57	AG3	A	329	350	Right-handed alpha
Helix 58	AG4	A	351	353	Right-handed 310

There are 28 sheets in PDB entry 8JD6. 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,

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	S	105	107	first strand
Strand 2	S	50	55	parallel
Strand 3	S	150	154	parallel
Strand 4	S	176	177	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	S	249	256	first strand
Strand 2	S	220	226	parallel
Strand 3	S	280	283	parallel
Strand 4	S	307	310	parallel
Strand 5	S	331	336	parallel
Strand 6	S	475	480	anti-parallel
Strand 7	S	493	495	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	S	455	456	first strand
Strand 2	S	462	463	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	S	530	532	first strand
Strand 2	S	541	543	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	S	550	551	first strand
Strand 2	S	557	558	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	S	578	579	first strand
Strand 2	S	742	743	parallel

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There are 6 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	43	45	first strand
Strand 2	R	101	107	anti-parallel
Strand 3	R	49	55	parallel
Strand 4	R	152	154	parallel
Strand 5	R	176	178	parallel
Strand 6	R	195	197	parallel

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There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	58	60	first strand
Strand 2	R	67	70	anti-parallel

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There are 7 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	249	256	first strand
Strand 2	R	220	226	parallel
Strand 3	R	280	283	parallel
Strand 4	R	307	310	parallel
Strand 5	R	331	336	parallel
Strand 6	R	475	481	anti-parallel
Strand 7	R	488	495	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	R	454	455	first strand
Strand 2	R	463	464	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	R	530	532	first strand
Strand 2	R	541	543	anti-parallel

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There are 2 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	549	550	first strand
Strand 2	R	558	559	anti-parallel

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There are 2 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	R	565	566	first strand
Strand 2	R	573	574	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	7	first strand
Strand 2	D	21	25	anti-parallel

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There are 3 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	50	51	first strand
Strand 2	D	33	35	anti-parallel
Strand 3	D	97	99	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	D	45	46	first strand
Strand 2	D	38	39	anti-parallel
Strand 3	D	92	94	anti-parallel
Strand 4	D	115	117	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	D	159	160	first strand
Strand 2	D	211	212	anti-parallel

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There are 3 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	185	187	first strand
Strand 2	D	174	179	anti-parallel
Strand 3	D	229	231	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	D	189	190	first strand
Strand 2	D	194	195	anti-parallel

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There are 4 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	47	51	first strand
Strand 2	B	336	339	anti-parallel
Strand 3	B	327	331	anti-parallel
Strand 4	B	315	320	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	B	60	63	first strand
Strand 2	B	70	73	anti-parallel
Strand 3	B	78	82	anti-parallel
Strand 4	B	91	94	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	103	105	first strand
Strand 2	B	111	114	anti-parallel
Strand 3	B	121	125	anti-parallel
Strand 4	B	134	139	anti-parallel

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There are 2 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	146	148	first strand
Strand 2	B	160	161	anti-parallel

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There are 3 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	156	157	first strand
Strand 2	B	168	170	anti-parallel
Strand 3	B	176	178	anti-parallel

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There are 4 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	187	191	first strand
Strand 2	B	199	203	anti-parallel
Strand 3	B	209	211	anti-parallel
Strand 4	B	220	221	anti-parallel

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There are 3 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	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	251	254	anti-parallel

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There are 3 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	273	278	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel

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There are 6 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	186	190	first strand
Strand 2	A	195	199	anti-parallel
Strand 3	A	34	39	parallel
Strand 4	A	220	226	parallel
Strand 5	A	264	269	parallel
Strand 6	A	319	323	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: 8JD6

Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD6