Analysis of interatomic Contacts of Structural Units in PDB entry:
4MD8

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 4MD8 entry

There are 6 chains in PDB entry 4MD8 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 6	PHE 207
B	VAL 7	PHE 207
C	GLU 6	PHE 207
D	VAL 7	PHE 207
E	SER 2	ARG 333
F	SER 2	THR 96

There are131 helices in PDB entry 4MD8. 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	16	Right-handed alpha
Helix 2	2	A	18	22	Right-handed 310
Helix 3	3	A	26	32	Right-handed alpha
Helix 4	4	A	33	37	Right-handed 310
Helix 5	5	A	38	42	Right-handed 310
Helix 6	6	A	45	54	Right-handed alpha
Helix 7	7	A	67	88	Right-handed alpha
Helix 8	8	A	90	104	Right-handed alpha
Helix 9	9	A	111	115	Right-handed 310
Helix 10	10	A	148	152	Right-handed 310
Helix 11	11	A	155	159	Right-handed 310
Helix 12	12	A	162	171	Right-handed alpha
Helix 13	13	A	172	175	Right-handed 310
Helix 14	14	A	194	207	Right-handed alpha
Helix 15	15	B	8	14	Right-handed alpha
Helix 16	16	B	18	22	Right-handed 310
Helix 17	17	B	26	32	Right-handed alpha
Helix 18	18	B	33	37	Right-handed 310
Helix 19	19	B	38	42	Right-handed 310
Helix 20	20	B	45	54	Right-handed alpha
Helix 21	21	B	67	88	Right-handed alpha
Helix 22	22	B	90	102	Right-handed alpha
Helix 23	23	B	111	115	Right-handed 310
Helix 24	24	B	148	152	Right-handed 310
Helix 25	25	B	155	159	Right-handed 310
Helix 26	26	B	162	171	Right-handed alpha
Helix 27	27	B	172	175	Right-handed 310
Helix 28	28	B	194	207	Right-handed alpha
Helix 29	29	C	8	14	Right-handed alpha
Helix 30	30	C	18	22	Right-handed 310
Helix 31	31	C	26	32	Right-handed alpha
Helix 32	32	C	33	37	Right-handed 310
Helix 33	33	C	38	42	Right-handed 310
Helix 34	34	C	45	54	Right-handed alpha
Helix 35	35	C	67	88	Right-handed alpha
Helix 36	36	C	90	103	Right-handed alpha
Helix 37	37	C	111	115	Right-handed 310
Helix 38	38	C	148	152	Right-handed 310
Helix 39	39	C	155	159	Right-handed 310
Helix 40	40	C	162	171	Right-handed alpha
Helix 41	41	C	172	175	Right-handed 310
Helix 42	42	C	193	207	Right-handed alpha
Helix 43	43	D	8	14	Right-handed alpha
Helix 44	44	D	18	22	Right-handed 310
Helix 45	45	D	26	32	Right-handed alpha
Helix 46	46	D	33	37	Right-handed 310
Helix 47	47	D	38	42	Right-handed 310
Helix 48	48	D	45	54	Right-handed alpha
Helix 49	49	D	67	88	Right-handed alpha
Helix 50	50	D	90	104	Right-handed alpha
Helix 51	51	D	111	115	Right-handed 310
Helix 52	52	D	148	152	Right-handed 310
Helix 53	53	D	155	159	Right-handed 310
Helix 54	54	D	162	171	Right-handed alpha
Helix 55	55	D	172	175	Right-handed 310
Helix 56	56	D	193	207	Right-handed alpha
Helix 57	57	E	20	25	Right-handed alpha
Helix 58	58	E	26	29	Right-handed 310
Helix 59	59	E	35	37	Right-handed 310
Helix 60	60	E	74	88	Right-handed alpha
Helix 61	61	E	120	125	Right-handed alpha
Helix 62	62	E	129	150	Right-handed alpha
Helix 63	63	E	158	160	Right-handed 310
Helix 64	64	E	194	198	Right-handed 310
Helix 65	65	E	199	204	Right-handed alpha
Helix 66	66	E	211	228	Right-handed alpha
Helix 67	67	E	237	250	Right-handed alpha
Helix 68	68	E	250	261	Right-handed alpha
Helix 69	69	E	266	270	Right-handed 310
Helix 70	70	E	280	285	Right-handed 310
Helix 71	71	E	294	305	Right-handed alpha
Helix 72	72	E	308	312	Right-handed 310
Helix 73	73	E	314	320	Right-handed alpha
Helix 74	74	E	321	323	Right-handed 310
Helix 75	75	E	324	332	Right-handed alpha
Helix 76	76	F	20	25	Right-handed alpha
Helix 77	77	F	26	29	Right-handed 310
Helix 78	78	F	35	37	Right-handed 310
Helix 79	79	F	74	88	Right-handed alpha
Helix 80	80	F	121	126	Right-handed alpha
Helix 81	81	F	129	150	Right-handed alpha
Helix 82	82	F	158	160	Right-handed 310
Helix 83	83	F	166	169	Right-handed 310
Helix 84	84	F	199	204	Right-handed alpha
Helix 85	85	F	211	228	Right-handed alpha
Helix 86	86	F	237	250	Right-handed alpha
Helix 87	87	F	250	261	Right-handed alpha
Helix 88	88	F	269	274	Right-handed alpha
Helix 89	89	F	280	285	Right-handed 310
Helix 90	90	F	294	305	Right-handed alpha
Helix 91	91	F	308	312	Right-handed 310
Helix 92	92	F	314	320	Right-handed alpha
Helix 93	93	F	321	323	Right-handed 310
Helix 94	94	F	324	331	Right-handed alpha
Helix 95	95	G	20	24	Right-handed 310
Helix 96	96	G	25	29	Right-handed 310
Helix 97	97	G	35	37	Right-handed 310
Helix 98	98	G	74	89	Right-handed alpha
Helix 99	99	G	120	126	Right-handed alpha
Helix 100	100	G	129	150	Right-handed alpha
Helix 101	101	G	158	160	Right-handed 310
Helix 102	102	G	194	198	Right-handed 310
Helix 103	103	G	199	204	Right-handed alpha
Helix 104	104	G	211	228	Right-handed alpha
Helix 105	105	G	237	250	Right-handed alpha
Helix 106	106	G	250	261	Right-handed alpha
Helix 107	107	G	280	285	Right-handed 310
Helix 108	108	G	294	303	Right-handed alpha
Helix 109	109	G	308	312	Right-handed 310
Helix 110	110	G	314	320	Right-handed alpha
Helix 111	111	G	321	323	Right-handed 310
Helix 112	112	G	324	332	Right-handed alpha
Helix 113	113	H	20	24	Right-handed 310
Helix 114	114	H	25	29	Right-handed 310
Helix 115	115	H	35	37	Right-handed 310
Helix 116	116	H	74	88	Right-handed alpha
Helix 117	117	H	121	126	Right-handed alpha
Helix 118	118	H	129	150	Right-handed alpha
Helix 119	119	H	158	160	Right-handed 310
Helix 120	120	H	166	169	Right-handed 310
Helix 121	121	H	194	198	Right-handed 310
Helix 122	122	H	199	204	Right-handed alpha
Helix 123	123	H	211	228	Right-handed alpha
Helix 124	124	H	237	250	Right-handed alpha
Helix 125	125	H	250	261	Right-handed alpha
Helix 126	126	H	280	285	Right-handed 310
Helix 127	127	H	294	305	Right-handed alpha
Helix 128	128	H	308	312	Right-handed 310
Helix 129	129	H	314	320	Right-handed alpha
Helix 130	130	H	321	323	Right-handed 310
Helix 131	131	H	324	332	Right-handed alpha

There are 17 sheets in PDB entry 4MD8. 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,

There are 3 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	120	122	first strand
Strand 2	A	134	136	anti-parallel
Strand 3	A	143	144	anti-parallel

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There are 2 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	186	187	first strand
Strand 2	A	190	191	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	120	122	first strand
Strand 2	B	134	136	anti-parallel
Strand 3	B	143	144	anti-parallel

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There are 7 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	186	187	first strand
Strand 2	B	190	192	anti-parallel
Strand 3	E	39	47	parallel
Strand 4	E	51	58	anti-parallel
Strand 5	E	64	70	anti-parallel
Strand 6	E	109	114	anti-parallel
Strand 7	E	97	102	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	120	122	first strand
Strand 2	C	134	136	anti-parallel
Strand 3	C	143	144	anti-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	C	186	187	first strand
Strand 2	C	190	192	anti-parallel
Strand 3	G	39	47	parallel
Strand 4	G	51	58	anti-parallel
Strand 5	G	63	70	anti-parallel
Strand 6	G	109	114	anti-parallel
Strand 7	G	97	102	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	120	122	first strand
Strand 2	D	134	136	anti-parallel
Strand 3	D	143	144	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	186	187	first strand
Strand 2	D	190	192	anti-parallel
Strand 3	H	39	47	parallel
Strand 4	H	51	58	anti-parallel
Strand 5	H	64	70	anti-parallel
Strand 6	H	109	114	anti-parallel
Strand 7	H	97	102	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	E	152	153	first strand
Strand 2	E	180	181	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	162	165	first strand
Strand 2	E	170	173	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	F	39	47	first strand
Strand 2	F	51	58	anti-parallel
Strand 3	F	64	70	anti-parallel
Strand 4	F	109	114	anti-parallel
Strand 5	F	97	102	anti-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	F	152	153	first strand
Strand 2	F	180	181	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	162	165	first strand
Strand 2	F	170	173	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	152	153	first strand
Strand 2	G	180	181	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	162	165	first strand
Strand 2	G	170	173	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	152	153	first strand
Strand 2	H	180	181	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	162	165	first strand
Strand 2	H	170	173	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: 4MD8

Analysis of interatomic Contacts of Structural Units in PDB entry:
4MD8