Analysis of interatomic Contacts of Structural Units in PDB entry:
4JD2

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 4JD2 entry

There are 4 chains in PDB entry 4JD2 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLY 3	VAL 416
B	GLN 4	LYS 388
C	MET 1	VAL 372
D	MET 1	TYR 153

There are 82 helices in PDB entry 4JD2. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	55	59	Right-handed 310
Helix 2	2	A	64	67	Right-handed 310
Helix 3	3	A	85	99	Right-handed alpha
Helix 4	4	A	104	108	Right-handed 310
Helix 5	5	A	119	133	Right-handed alpha
Helix 6	6	A	144	152	Right-handed alpha
Helix 7	7	A	153	156	Right-handed 310
Helix 8	8	A	187	190	Right-handed 310
Helix 9	9	A	196	212	Right-handed alpha
Helix 10	10	A	216	218	Right-handed 310
Helix 11	11	A	219	232	Right-handed alpha
Helix 12	12	A	237	248	Right-handed alpha
Helix 13	13	A	273	281	Right-handed alpha
Helix 14	14	A	282	283	Right-handed 310
Helix 15	15	A	284	288	Right-handed 310
Helix 16	16	A	295	307	Right-handed alpha
Helix 17	17	A	308	310	Right-handed 310
Helix 18	18	A	311	317	Right-handed alpha
Helix 19	19	A	323	327	Right-handed 310
Helix 20	20	A	330	353	Right-handed alpha
Helix 21	21	A	370	374	Right-handed 310
Helix 22	22	A	375	387	Right-handed alpha
Helix 23	23	A	388	394	Right-handed alpha
Helix 24	24	A	397	403	Right-handed alpha
Helix 25	25	A	404	410	Right-handed 310
Helix 26	26	B	58	64	Right-handed alpha
Helix 27	27	B	81	94	Right-handed alpha
Helix 28	28	B	101	104	Right-handed 310
Helix 29	29	B	116	130	Right-handed alpha
Helix 30	30	B	141	148	Right-handed alpha
Helix 31	31	B	176	179	Right-handed 310
Helix 32	32	B	185	200	Right-handed alpha
Helix 33	33	B	209	221	Right-handed alpha
Helix 34	34	B	226	237	Right-handed alpha
Helix 35	35	B	256	261	Right-handed alpha
Helix 36	36	B	262	266	Right-handed 310
Helix 37	37	B	267	272	Right-handed 310
Helix 38	38	B	277	288	Right-handed alpha
Helix 39	39	B	290	299	Right-handed alpha
Helix 40	40	B	305	309	Right-handed 310
Helix 41	41	B	312	329	Right-handed alpha
Helix 42	42	B	336	340	Right-handed 310
Helix 43	43	B	349	351	Right-handed 310
Helix 44	44	B	352	365	Right-handed alpha
Helix 45	45	B	375	380	Right-handed alpha
Helix 46	46	C	232	234	Right-handed 310
Helix 47	47	C	359	366	Right-handed alpha
Helix 48	48	D	8	23	Right-handed alpha
Helix 49	49	D	48	51	Right-handed 310
Helix 50	50	D	63	69	Right-handed alpha
Helix 51	51	D	71	81	Right-handed alpha
Helix 52	52	D	106	115	Right-handed alpha
Helix 53	53	D	115	135	Right-handed alpha
Helix 54	54	D	171	187	Right-handed alpha
Helix 55	55	D	228	233	Right-handed alpha
Helix 56	56	D	236	245	Right-handed alpha
Helix 57	57	D	246	279	Right-handed alpha
Helix 58	58	E	40	53	Right-handed alpha
Helix 59	59	E	62	83	Right-handed alpha
Helix 60	60	E	87	101	Right-handed alpha
Helix 61	61	E	123	148	Right-handed alpha
Helix 62	62	E	157	162	Right-handed alpha
Helix 63	63	E	167	171	Right-handed 310
Helix 64	64	F	4	20	Right-handed alpha
Helix 65	65	F	36	41	Right-handed alpha
Helix 66	66	F	43	47	Right-handed 310
Helix 67	67	F	80	97	Right-handed alpha
Helix 68	68	F	120	126	Right-handed alpha
Helix 69	69	F	127	166	Right-handed alpha
Helix 70	70	G	15	20	Right-handed 310
Helix 71	71	G	38	49	Right-handed alpha
Helix 72	72	G	50	59	Right-handed alpha
Helix 73	73	G	68	86	Right-handed alpha
Helix 74	74	G	87	89	Right-handed 310
Helix 75	75	G	90	98	Right-handed alpha
Helix 76	76	G	99	114	Right-handed alpha
Helix 77	77	G	120	147	Right-handed alpha
Helix 78	78	H	11	23	Right-handed alpha
Helix 79	79	H	53	61	Right-handed alpha
Helix 80	80	H	97	116	Right-handed alpha
Helix 81	81	H	125	129	Right-handed 310
Helix 82	82	H	130	139	Right-handed alpha

There are 26 sheets in PDB entry 4JD2. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z,

There are 6 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	29	32	first strand
Strand 2	A	16	21	anti-parallel
Strand 3	A	8	12	anti-parallel
Strand 4	A	110	114	parallel
Strand 5	A	138	143	parallel
Strand 6	A	395	396	anti-parallel

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There are 3 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	61	62	first strand
Strand 2	A	35	37	anti-parallel
Strand 3	A	73	75	anti-parallel

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There are 2 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	78	79	first strand
Strand 2	A	82	83	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	184	185	first strand
Strand 2	A	175	181	anti-parallel
Strand 3	A	191	193	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	184	185	first strand
Strand 2	A	175	181	anti-parallel
Strand 3	A	165	170	anti-parallel
Strand 4	A	319	322	parallel
Strand 5	A	367	368	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	254	259	first strand
Strand 2	A	266	271	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	30	33	first strand
Strand 2	B	17	21	anti-parallel
Strand 3	B	10	13	anti-parallel
Strand 4	B	106	111	parallel
Strand 5	B	135	140	parallel
Strand 6	B	373	374	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	56	57	first strand
Strand 2	B	36	39	anti-parallel
Strand 3	B	68	71	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	74	75	first strand
Strand 2	B	78	79	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	173	174	first strand
Strand 2	B	164	170	anti-parallel
Strand 3	B	180	182	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	173	174	first strand
Strand 2	B	164	170	anti-parallel
Strand 3	B	154	159	anti-parallel
Strand 4	B	301	304	parallel
Strand 5	B	344	345	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	242	245	first strand
Strand 2	B	251	254	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	2	5	first strand
Strand 2	C	353	358	anti-parallel
Strand 3	C	344	349	anti-parallel
Strand 4	C	329	336	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	14	16	first strand
Strand 2	C	22	25	anti-parallel
Strand 3	C	31	38	anti-parallel
Strand 4	C	41	49	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	55	61	first strand
Strand 2	C	66	71	anti-parallel
Strand 3	C	76	82	anti-parallel
Strand 4	C	85	91	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	99	104	first strand
Strand 2	C	110	115	anti-parallel
Strand 3	C	120	126	anti-parallel
Strand 4	C	131	137	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	145	150	first strand
Strand 2	C	156	161	anti-parallel
Strand 3	C	166	170	anti-parallel
Strand 4	C	194	197	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	205	210	first strand
Strand 2	C	216	221	anti-parallel
Strand 3	C	225	230	anti-parallel
Strand 4	C	237	241	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	247	254	first strand
Strand 2	C	257	262	anti-parallel
Strand 3	C	268	273	anti-parallel
Strand 4	C	278	284	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	32	37	first strand
Strand 2	D	41	46	anti-parallel
Strand 3	D	54	60	anti-parallel
Strand 4	D	93	98	anti-parallel
Strand 5	D	84	85	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	142	147	first strand
Strand 2	D	150	156	anti-parallel
Strand 3	D	161	168	anti-parallel
Strand 4	D	220	227	anti-parallel
Strand 5	D	197	201	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	15	16	first strand
Strand 2	E	19	20	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	149	150	first strand
Strand 2	E	155	156	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	51	54	first strand
Strand 2	F	60	66	anti-parallel
Strand 3	F	69	75	anti-parallel
Strand 4	F	114	119	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	9	10	first strand
Strand 2	H	42	50	parallel
Strand 3	H	30	37	anti-parallel
Strand 4	H	67	72	anti-parallel
Strand 5	H	86	91	anti-parallel
Strand 6	H	119	123	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	75	76	first strand
Strand 2	H	82	83	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: 4JD2

Analysis of interatomic Contacts of Structural Units in PDB entry:
4JD2