Analysis of interatomic Contacts of Structural Units in PDB entry:
3JD1

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 3JD1 entry

There are 6 chains in PDB entry 3JD1 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 6	THR 501
B	ASP 6	THR 501
C	ASP 6	THR 501
D	ASP 6	THR 501
E	ASP 6	THR 501
F	ASP 6	THR 501

There are132 helices in PDB entry 3JD1. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	8	32	Right-handed alpha
Helix 2	2	A	37	53	Right-handed alpha
Helix 3	3	A	100	118	Right-handed alpha
Helix 4	4	A	132	136	Right-handed 310
Helix 5	5	A	140	154	Right-handed alpha
Helix 6	6	A	172	185	Right-handed alpha
Helix 7	7	A	187	191	Right-handed 310
Helix 8	8	A	193	198	Right-handed 310
Helix 9	9	A	202	206	Right-handed 310
Helix 10	10	A	212	228	Right-handed alpha
Helix 11	11	A	229	237	Right-handed alpha
Helix 12	12	A	241	244	Right-handed 310
Helix 13	13	A	253	265	Right-handed alpha
Helix 14	14	A	287	298	Right-handed alpha
Helix 15	15	A	313	317	Right-handed 310
Helix 16	16	A	335	339	Right-handed 310
Helix 17	17	A	353	363	Right-handed alpha
Helix 18	18	A	375	391	Right-handed alpha
Helix 19	19	A	398	421	Right-handed alpha
Helix 20	20	A	422	425	Right-handed 310
Helix 21	21	A	444	471	Right-handed alpha
Helix 22	22	A	476	496	Right-handed alpha
Helix 23	23	B	8	32	Right-handed alpha
Helix 24	24	B	37	53	Right-handed alpha
Helix 25	25	B	100	118	Right-handed alpha
Helix 26	26	B	132	136	Right-handed 310
Helix 27	27	B	140	154	Right-handed alpha
Helix 28	28	B	172	185	Right-handed alpha
Helix 29	29	B	187	191	Right-handed 310
Helix 30	30	B	193	198	Right-handed 310
Helix 31	31	B	202	206	Right-handed 310
Helix 32	32	B	212	228	Right-handed alpha
Helix 33	33	B	229	237	Right-handed alpha
Helix 34	34	B	241	244	Right-handed 310
Helix 35	35	B	253	265	Right-handed alpha
Helix 36	36	B	287	298	Right-handed alpha
Helix 37	37	B	313	317	Right-handed 310
Helix 38	38	B	335	339	Right-handed 310
Helix 39	39	B	353	363	Right-handed alpha
Helix 40	40	B	375	391	Right-handed alpha
Helix 41	41	B	398	421	Right-handed alpha
Helix 42	42	B	422	425	Right-handed 310
Helix 43	43	B	444	471	Right-handed alpha
Helix 44	44	B	476	496	Right-handed alpha
Helix 45	45	C	8	32	Right-handed alpha
Helix 46	46	C	37	53	Right-handed alpha
Helix 47	47	C	100	118	Right-handed alpha
Helix 48	48	C	132	136	Right-handed 310
Helix 49	49	C	140	154	Right-handed alpha
Helix 50	50	C	172	185	Right-handed alpha
Helix 51	51	C	187	191	Right-handed 310
Helix 52	52	C	193	198	Right-handed 310
Helix 53	53	C	202	206	Right-handed 310
Helix 54	54	C	212	228	Right-handed alpha
Helix 55	55	C	229	237	Right-handed alpha
Helix 56	56	C	241	244	Right-handed 310
Helix 57	57	C	253	265	Right-handed alpha
Helix 58	58	C	287	298	Right-handed alpha
Helix 59	59	C	313	317	Right-handed 310
Helix 60	60	C	335	339	Right-handed 310
Helix 61	61	C	353	363	Right-handed alpha
Helix 62	62	C	375	391	Right-handed alpha
Helix 63	63	C	398	421	Right-handed alpha
Helix 64	64	C	422	425	Right-handed 310
Helix 65	65	C	444	471	Right-handed alpha
Helix 66	66	C	476	496	Right-handed alpha
Helix 67	67	D	8	32	Right-handed alpha
Helix 68	68	D	37	53	Right-handed alpha
Helix 69	69	D	100	118	Right-handed alpha
Helix 70	70	D	132	136	Right-handed 310
Helix 71	71	D	140	154	Right-handed alpha
Helix 72	72	D	172	185	Right-handed alpha
Helix 73	73	D	187	191	Right-handed 310
Helix 74	74	D	193	198	Right-handed 310
Helix 75	75	D	202	206	Right-handed 310
Helix 76	76	D	212	228	Right-handed alpha
Helix 77	77	D	229	237	Right-handed alpha
Helix 78	78	D	241	244	Right-handed 310
Helix 79	79	D	253	265	Right-handed alpha
Helix 80	80	D	287	298	Right-handed alpha
Helix 81	81	D	313	317	Right-handed 310
Helix 82	82	D	335	339	Right-handed 310
Helix 83	83	D	353	363	Right-handed alpha
Helix 84	84	D	375	391	Right-handed alpha
Helix 85	85	D	398	421	Right-handed alpha
Helix 86	86	D	422	425	Right-handed 310
Helix 87	87	D	444	471	Right-handed alpha
Helix 88	88	D	476	496	Right-handed alpha
Helix 89	89	E	8	32	Right-handed alpha
Helix 90	90	E	37	53	Right-handed alpha
Helix 91	91	E	100	118	Right-handed alpha
Helix 92	92	E	132	136	Right-handed 310
Helix 93	93	E	140	154	Right-handed alpha
Helix 94	94	E	172	185	Right-handed alpha
Helix 95	95	E	187	191	Right-handed 310
Helix 96	96	E	193	198	Right-handed 310
Helix 97	97	E	202	206	Right-handed 310
Helix 98	98	E	212	228	Right-handed alpha
Helix 99	99	E	229	237	Right-handed alpha
Helix 100	100	E	241	244	Right-handed 310
Helix 101	101	E	253	265	Right-handed alpha
Helix 102	102	E	287	298	Right-handed alpha
Helix 103	103	E	313	317	Right-handed 310
Helix 104	104	E	335	339	Right-handed 310
Helix 105	105	E	353	363	Right-handed alpha
Helix 106	106	E	375	391	Right-handed alpha
Helix 107	107	E	398	421	Right-handed alpha
Helix 108	108	E	422	425	Right-handed 310
Helix 109	109	E	444	471	Right-handed alpha
Helix 110	110	E	476	496	Right-handed alpha
Helix 111	111	F	8	32	Right-handed alpha
Helix 112	112	F	37	53	Right-handed alpha
Helix 113	113	F	100	118	Right-handed alpha
Helix 114	114	F	132	136	Right-handed 310
Helix 115	115	F	140	154	Right-handed alpha
Helix 116	116	F	172	185	Right-handed alpha
Helix 117	117	F	187	191	Right-handed 310
Helix 118	118	F	193	198	Right-handed 310
Helix 119	119	F	202	206	Right-handed 310
Helix 120	120	F	212	228	Right-handed alpha
Helix 121	121	F	229	237	Right-handed alpha
Helix 122	122	F	241	244	Right-handed 310
Helix 123	123	F	253	265	Right-handed alpha
Helix 124	124	F	287	298	Right-handed alpha
Helix 125	125	F	313	317	Right-handed 310
Helix 126	126	F	335	339	Right-handed 310
Helix 127	127	F	353	363	Right-handed alpha
Helix 128	128	F	375	391	Right-handed alpha
Helix 129	129	F	398	421	Right-handed alpha
Helix 130	130	F	422	425	Right-handed 310
Helix 131	131	F	444	471	Right-handed alpha
Helix 132	132	F	476	496	Right-handed alpha

There are 12 sheets in PDB entry 3JD1. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L,

There are 8 strands in A sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	95	96	first strand
Strand 2	A	123	130	parallel
Strand 3	A	72	81	anti-parallel
Strand 4	A	57	66	anti-parallel
Strand 5	E	57	66	anti-parallel
Strand 6	E	72	81	anti-parallel
Strand 7	E	123	130	anti-parallel
Strand 8	E	95	96	parallel

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There are 10 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	163	166	first strand
Strand 2	A	89	92	parallel
Strand 3	A	123	130	parallel
Strand 4	A	72	81	anti-parallel
Strand 5	A	57	66	anti-parallel
Strand 6	E	57	66	anti-parallel
Strand 7	E	72	81	anti-parallel
Strand 8	E	123	130	anti-parallel
Strand 9	E	89	92	parallel
Strand 10	E	163	166	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	308	310	first strand
Strand 2	A	278	281	anti-parallel
Strand 3	A	269	275	anti-parallel
Strand 4	A	246	250	parallel
Strand 5	A	321	324	parallel
Strand 6	A	343	345	parallel
Strand 7	A	366	368	parallel

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There are 8 strands in D sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	95	96	first strand
Strand 2	B	123	130	parallel
Strand 3	B	72	81	anti-parallel
Strand 4	B	57	66	anti-parallel
Strand 5	D	57	66	anti-parallel
Strand 6	D	72	81	anti-parallel
Strand 7	D	123	130	anti-parallel
Strand 8	D	95	96	parallel

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There are 10 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	163	166	first strand
Strand 2	B	89	92	parallel
Strand 3	B	123	130	parallel
Strand 4	B	72	81	anti-parallel
Strand 5	B	57	66	anti-parallel
Strand 6	D	57	66	anti-parallel
Strand 7	D	72	81	anti-parallel
Strand 8	D	123	130	anti-parallel
Strand 9	D	89	92	parallel
Strand 10	D	163	166	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	308	310	first strand
Strand 2	B	278	281	anti-parallel
Strand 3	B	269	275	anti-parallel
Strand 4	B	246	250	parallel
Strand 5	B	321	324	parallel
Strand 6	B	343	345	parallel
Strand 7	B	366	368	parallel

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There are 8 strands in G sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	95	96	first strand
Strand 2	C	123	130	parallel
Strand 3	C	72	81	anti-parallel
Strand 4	C	57	66	anti-parallel
Strand 5	F	57	66	anti-parallel
Strand 6	F	72	81	anti-parallel
Strand 7	F	123	130	anti-parallel
Strand 8	F	95	96	parallel

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There are 10 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	163	166	first strand
Strand 2	C	89	92	parallel
Strand 3	C	123	130	parallel
Strand 4	C	72	81	anti-parallel
Strand 5	C	57	66	anti-parallel
Strand 6	F	57	66	anti-parallel
Strand 7	F	72	81	anti-parallel
Strand 8	F	123	130	anti-parallel
Strand 9	F	89	92	parallel
Strand 10	F	163	166	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	308	310	first strand
Strand 2	C	278	281	anti-parallel
Strand 3	C	269	275	anti-parallel
Strand 4	C	246	250	parallel
Strand 5	C	321	324	parallel
Strand 6	C	343	345	parallel
Strand 7	C	366	368	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	308	310	first strand
Strand 2	D	278	281	anti-parallel
Strand 3	D	269	275	anti-parallel
Strand 4	D	246	250	parallel
Strand 5	D	321	324	parallel
Strand 6	D	343	345	parallel
Strand 7	D	366	368	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	308	310	first strand
Strand 2	E	278	281	anti-parallel
Strand 3	E	269	275	anti-parallel
Strand 4	E	246	250	parallel
Strand 5	E	321	324	parallel
Strand 6	E	343	345	parallel
Strand 7	E	366	368	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	308	310	first strand
Strand 2	F	278	281	anti-parallel
Strand 3	F	269	275	anti-parallel
Strand 4	F	246	250	parallel
Strand 5	F	321	324	parallel
Strand 6	F	343	345	parallel
Strand 7	F	366	368	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: 3JD1

Analysis of interatomic Contacts of Structural Units in PDB entry:
3JD1