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

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 3GMD entry

There are 8 chains in PDB entry 3GMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 26	PHE 289
B	GLU 26	PHE 289
C	GLU 26	PHE 289
D	GLU 26	PHE 289
E	GLU 26	PHE 289
F	GLU 26	PHE 289
G	GLU 26	PHE 289
H	GLU 26	PHE 289

There are107 helices in PDB entry 3GMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	28	33	Right-handed 310
Helix 2	2	A	44	58	Right-handed alpha
Helix 3	3	A	67	82	Right-handed alpha
Helix 4	4	A	95	111	Right-handed alpha
Helix 5	5	A	132	144	Right-handed alpha
Helix 6	6	A	144	162	Right-handed alpha
Helix 7	7	A	172	174	Right-handed 310
Helix 8	8	A	180	204	Right-handed alpha
Helix 9	9	A	220	228	Right-handed alpha
Helix 10	10	A	237	252	Right-handed alpha
Helix 11	11	A	263	268	Right-handed alpha
Helix 12	12	A	270	280	Right-handed alpha
Helix 13	13	A	281	284	Right-handed 310
Helix 14	14	A	285	289	Right-handed 310
Helix 15	15	B	28	33	Right-handed 310
Helix 16	16	B	44	57	Right-handed alpha
Helix 17	17	B	67	81	Right-handed alpha
Helix 18	18	B	95	111	Right-handed alpha
Helix 19	19	B	132	144	Right-handed alpha
Helix 20	20	B	144	162	Right-handed alpha
Helix 21	21	B	170	174	Right-handed 310
Helix 22	22	B	180	204	Right-handed alpha
Helix 23	23	B	220	228	Right-handed alpha
Helix 24	24	B	237	251	Right-handed alpha
Helix 25	25	B	270	280	Right-handed alpha
Helix 26	26	B	281	284	Right-handed 310
Helix 27	27	B	285	289	Right-handed 310
Helix 28	28	C	28	33	Right-handed 310
Helix 29	29	C	44	58	Right-handed alpha
Helix 30	30	C	67	82	Right-handed alpha
Helix 31	31	C	95	111	Right-handed alpha
Helix 32	32	C	132	144	Right-handed alpha
Helix 33	33	C	144	162	Right-handed alpha
Helix 34	34	C	172	174	Right-handed 310
Helix 35	35	C	180	204	Right-handed alpha
Helix 36	36	C	220	227	Right-handed alpha
Helix 37	37	C	237	251	Right-handed alpha
Helix 38	38	C	262	268	Right-handed alpha
Helix 39	39	C	270	280	Right-handed alpha
Helix 40	40	C	281	284	Right-handed 310
Helix 41	41	C	285	289	Right-handed 310
Helix 42	42	D	28	32	Right-handed 310
Helix 43	43	D	44	57	Right-handed alpha
Helix 44	44	D	67	82	Right-handed alpha
Helix 45	45	D	95	111	Right-handed alpha
Helix 46	46	D	132	144	Right-handed alpha
Helix 47	47	D	144	162	Right-handed alpha
Helix 48	48	D	172	174	Right-handed 310
Helix 49	49	D	180	204	Right-handed alpha
Helix 50	50	D	220	228	Right-handed alpha
Helix 51	51	D	237	251	Right-handed alpha
Helix 52	52	D	263	268	Right-handed alpha
Helix 53	53	D	270	281	Right-handed alpha
Helix 54	54	D	285	289	Right-handed 310
Helix 55	55	E	28	33	Right-handed 310
Helix 56	56	E	44	57	Right-handed alpha
Helix 57	57	E	67	81	Right-handed alpha
Helix 58	58	E	95	111	Right-handed alpha
Helix 59	59	E	132	144	Right-handed alpha
Helix 60	60	E	144	162	Right-handed alpha
Helix 61	61	E	170	174	Right-handed 310
Helix 62	62	E	180	204	Right-handed alpha
Helix 63	63	E	220	228	Right-handed alpha
Helix 64	64	E	237	251	Right-handed alpha
Helix 65	65	E	270	281	Right-handed alpha
Helix 66	66	E	282	284	Right-handed 310
Helix 67	67	E	285	289	Right-handed 310
Helix 68	68	F	28	33	Right-handed 310
Helix 69	69	F	44	57	Right-handed alpha
Helix 70	70	F	67	82	Right-handed alpha
Helix 71	71	F	95	111	Right-handed alpha
Helix 72	72	F	132	144	Right-handed alpha
Helix 73	73	F	144	162	Right-handed alpha
Helix 74	74	F	172	174	Right-handed 310
Helix 75	75	F	180	204	Right-handed alpha
Helix 76	76	F	220	228	Right-handed alpha
Helix 77	77	F	237	251	Right-handed alpha
Helix 78	78	F	270	280	Right-handed alpha
Helix 79	79	F	281	284	Right-handed 310
Helix 80	80	F	285	289	Right-handed 310
Helix 81	81	G	28	33	Right-handed 310
Helix 82	82	G	44	58	Right-handed alpha
Helix 83	83	G	67	81	Right-handed alpha
Helix 84	84	G	95	111	Right-handed alpha
Helix 85	85	G	132	144	Right-handed alpha
Helix 86	86	G	144	162	Right-handed alpha
Helix 87	87	G	172	174	Right-handed 310
Helix 88	88	G	180	204	Right-handed alpha
Helix 89	89	G	220	227	Right-handed alpha
Helix 90	90	G	237	251	Right-handed alpha
Helix 91	91	G	263	268	Right-handed alpha
Helix 92	92	G	270	281	Right-handed alpha
Helix 93	93	G	285	289	Right-handed 310
Helix 94	94	H	28	32	Right-handed 310
Helix 95	95	H	44	57	Right-handed alpha
Helix 96	96	H	67	82	Right-handed alpha
Helix 97	97	H	95	111	Right-handed alpha
Helix 98	98	H	132	144	Right-handed alpha
Helix 99	99	H	144	162	Right-handed alpha
Helix 100	100	H	172	174	Right-handed 310
Helix 101	101	H	180	204	Right-handed alpha
Helix 102	102	H	220	228	Right-handed alpha
Helix 103	103	H	237	251	Right-handed alpha
Helix 104	104	H	263	268	Right-handed alpha
Helix 105	105	H	270	281	Right-handed alpha
Helix 106	106	H	282	284	Right-handed 310
Helix 107	107	H	285	289	Right-handed 310

There are 8 sheets in PDB entry 3GMD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

There are 7 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	85	90	first strand
Strand 2	A	60	65	parallel
Strand 3	A	36	40	parallel
Strand 4	A	115	118	parallel
Strand 5	A	164	170	parallel
Strand 6	A	209	215	parallel
Strand 7	A	255	258	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	85	90	first strand
Strand 2	B	60	65	parallel
Strand 3	B	36	40	parallel
Strand 4	B	115	118	parallel
Strand 5	B	164	168	parallel
Strand 6	B	209	215	parallel
Strand 7	B	255	258	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	C	85	90	first strand
Strand 2	C	60	65	parallel
Strand 3	C	36	39	parallel
Strand 4	C	115	118	parallel
Strand 5	C	164	170	parallel
Strand 6	C	209	215	parallel
Strand 7	C	255	258	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	D	85	90	first strand
Strand 2	D	60	65	parallel
Strand 3	D	36	40	parallel
Strand 4	D	115	118	parallel
Strand 5	D	164	170	parallel
Strand 6	D	209	215	parallel
Strand 7	D	255	258	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	85	90	first strand
Strand 2	E	60	65	parallel
Strand 3	E	36	40	parallel
Strand 4	E	115	118	parallel
Strand 5	E	164	168	parallel
Strand 6	E	209	215	parallel
Strand 7	E	255	258	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	F	85	90	first strand
Strand 2	F	60	65	parallel
Strand 3	F	36	40	parallel
Strand 4	F	115	118	parallel
Strand 5	F	164	170	parallel
Strand 6	F	209	215	parallel
Strand 7	F	255	258	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	85	90	first strand
Strand 2	G	60	65	parallel
Strand 3	G	36	40	parallel
Strand 4	G	115	118	parallel
Strand 5	G	164	170	parallel
Strand 6	G	209	215	parallel
Strand 7	G	255	258	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	H	85	88	first strand
Strand 2	H	60	64	parallel
Strand 3	H	36	40	parallel
Strand 4	H	115	118	parallel
Strand 5	H	164	170	parallel
Strand 6	H	209	215	parallel
Strand 7	H	255	258	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: 3GMD

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