Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD3

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 8JD3 entry

There are 5 chains in PDB entry 8JD3 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
2	LYS 23	PHE 819
3	ARG 30	GLN 829
A	GLU 8	PHE 354
B	LEU 4	TRP 339
C	ILE 9	ARG 62

There are 59 helices in PDB entry 8JD3. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	2	59	75	Right-handed alpha
Helix 2	AA2	2	94	108	Right-handed alpha
Helix 3	AA3	2	144	158	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	260	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	342	354	Right-handed alpha
Helix 11	AB2	2	356	360	Right-handed 310
Helix 12	AB3	2	375	377	Right-handed 310
Helix 13	AB4	2	378	400	Right-handed alpha
Helix 14	AB5	2	407	411	Right-handed 310
Helix 15	AB6	2	414	422	Right-handed alpha
Helix 16	AB7	2	568	592	Right-handed alpha
Helix 17	AB8	2	595	600	Right-handed alpha
Helix 18	AB9	2	604	624	Right-handed alpha
Helix 19	AC1	2	628	663	Right-handed alpha
Helix 20	AC2	2	677	701	Right-handed alpha
Helix 21	AC3	2	724	727	Right-handed 310
Helix 22	AC4	2	728	747	Right-handed alpha
Helix 23	AC5	2	762	784	Right-handed alpha
Helix 24	AC6	2	788	810	Right-handed alpha
Helix 25	AC7	2	810	819	Right-handed alpha
Helix 26	AC8	3	66	82	Right-handed alpha
Helix 27	AC9	3	101	110	Right-handed alpha
Helix 28	AD1	3	150	162	Right-handed alpha
Helix 29	AD2	3	193	208	Right-handed alpha
Helix 30	AD3	3	222	237	Right-handed alpha
Helix 31	AD4	3	257	266	Right-handed alpha
Helix 32	AD5	3	277	292	Right-handed alpha
Helix 33	AD6	3	330	339	Right-handed alpha
Helix 34	AD7	3	348	359	Right-handed alpha
Helix 35	AD8	3	389	412	Right-handed alpha
Helix 36	AD9	3	419	423	Right-handed 310
Helix 37	AE1	3	426	433	Right-handed alpha
Helix 38	AE2	3	449	451	Right-handed 310
Helix 39	AE3	3	493	497	Right-handed 310
Helix 40	AE4	3	574	602	Right-handed alpha
Helix 41	AE5	3	611	634	Right-handed alpha
Helix 42	AE6	3	637	666	Right-handed alpha
Helix 43	AE7	3	685	710	Right-handed alpha
Helix 44	AE8	3	733	759	Right-handed alpha
Helix 45	AE9	3	767	793	Right-handed alpha
Helix 46	AF1	3	795	829	Right-handed alpha
Helix 47	AF2	A	9	33	Right-handed alpha
Helix 48	AF3	A	190	194	Right-handed 310
Helix 49	AF4	A	207	213	Right-handed alpha
Helix 50	AF5	A	214	216	Right-handed 310
Helix 51	AF6	A	241	256	Right-handed alpha
Helix 52	AF7	A	272	279	Right-handed alpha
Helix 53	AF8	A	296	308	Right-handed alpha
Helix 54	AF9	A	311	317	Right-handed alpha
Helix 55	AG1	A	331	350	Right-handed alpha
Helix 56	AG2	B	5	36	Right-handed alpha
Helix 57	AG3	C	10	28	Right-handed alpha
Helix 58	AG4	C	32	41	Right-handed alpha
Helix 59	AG5	C	47	52	Right-handed alpha

There are 24 sheets in PDB entry 8JD3. 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,

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	84	90	first strand
Strand 2	2	32	38	parallel
Strand 3	2	136	141	parallel
Strand 4	2	162	164	parallel
Strand 5	2	182	183	parallel

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There are 4 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	234	241	first strand
Strand 2	2	206	212	parallel
Strand 3	2	265	269	parallel
Strand 4	2	290	292	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	315	319	first strand
Strand 2	2	453	459	anti-parallel
Strand 3	2	467	474	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	427	428	first strand
Strand 2	2	441	442	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	509	510	first strand
Strand 2	2	523	524	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	545	548	first strand
Strand 2	2	552	554	anti-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	2	706	710	first strand
Strand 2	2	713	720	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	3	91	97	first strand
Strand 2	3	39	45	parallel
Strand 3	3	142	146	parallel
Strand 4	3	168	169	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	3	48	50	first strand
Strand 2	3	57	60	anti-parallel

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There are 7 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	3	240	247	first strand
Strand 2	3	212	218	parallel
Strand 3	3	271	275	parallel
Strand 4	3	296	299	parallel
Strand 5	3	320	325	parallel
Strand 6	3	466	474	anti-parallel
Strand 7	3	477	486	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	3	439	441	first strand
Strand 2	3	453	455	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	3	518	521	first strand
Strand 2	3	530	533	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	3	538	542	first strand
Strand 2	3	545	548	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	3	553	554	first strand
Strand 2	3	563	564	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	3	714	717	first strand
Strand 2	3	727	730	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	A	38	40	first strand
Strand 2	A	220	224	parallel
Strand 3	A	263	267	parallel
Strand 4	A	319	321	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	A	186	189	first strand
Strand 2	A	196	199	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	50	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 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	B	70	73	first strand
Strand 2	B	79	82	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	100	103	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	121	125	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	149	151	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 3 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	198	201	first strand
Strand 2	B	209	212	anti-parallel
Strand 3	B	218	220	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	240	241	first strand
Strand 2	B	253	254	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	B	273	278	first strand
Strand 2	B	285	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	303	308	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: 8JD3

Analysis of interatomic Contacts of Structural Units in PDB entry:
8JD3