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

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 4GDP entry

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

Chain ID	Initial residue	Terminal residue
A	ALA 7	GLU 510
B	ALA 7	GLU 510
C	LYS 8	LEU 509
D	LYS 9	GLU 510

There are 91 helices in PDB entry 4GDP. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	17	30	Right-handed alpha
Helix 2	2	A	54	56	Right-handed 310
Helix 3	3	A	72	86	Right-handed alpha
Helix 4	4	A	114	131	Right-handed alpha
Helix 5	5	A	140	153	Right-handed alpha
Helix 6	6	A	154	156	Right-handed 310
Helix 7	7	A	157	168	Right-handed alpha
Helix 8	8	A	171	176	Right-handed alpha
Helix 9	9	A	200	210	Right-handed alpha
Helix 10	10	A	211	212	Right-handed 310
Helix 11	11	A	213	215	Right-handed 310
Helix 12	12	A	254	259	Right-handed alpha
Helix 13	13	A	260	263	Right-handed 310
Helix 14	14	A	279	286	Right-handed alpha
Helix 15	15	A	287	289	Right-handed 310
Helix 16	16	A	320	330	Right-handed alpha
Helix 17	17	A	332	345	Right-handed alpha
Helix 18	18	A	363	368	Right-handed alpha
Helix 19	19	A	379	386	Right-handed alpha
Helix 20	20	A	390	409	Right-handed alpha
Helix 21	21	A	458	468	Right-handed alpha
Helix 22	22	A	488	509	Right-handed alpha
Helix 23	23	B	17	30	Right-handed alpha
Helix 24	24	B	54	56	Right-handed 310
Helix 25	25	B	72	86	Right-handed alpha
Helix 26	26	B	114	130	Right-handed alpha
Helix 27	27	B	140	153	Right-handed alpha
Helix 28	28	B	154	156	Right-handed 310
Helix 29	29	B	157	168	Right-handed alpha
Helix 30	30	B	171	176	Right-handed alpha
Helix 31	31	B	183	188	Right-handed alpha
Helix 32	32	B	200	210	Right-handed alpha
Helix 33	33	B	211	212	Right-handed 310
Helix 34	34	B	213	215	Right-handed 310
Helix 35	35	B	254	259	Right-handed alpha
Helix 36	36	B	260	263	Right-handed 310
Helix 37	37	B	279	286	Right-handed alpha
Helix 38	38	B	320	330	Right-handed alpha
Helix 39	39	B	332	346	Right-handed alpha
Helix 40	40	B	363	368	Right-handed alpha
Helix 41	41	B	379	387	Right-handed alpha
Helix 42	42	B	390	409	Right-handed alpha
Helix 43	43	B	419	423	Right-handed 310
Helix 44	44	B	459	469	Right-handed alpha
Helix 45	45	B	488	510	Right-handed alpha
Helix 46	46	C	17	30	Right-handed alpha
Helix 47	47	C	54	56	Right-handed 310
Helix 48	48	C	72	86	Right-handed alpha
Helix 49	49	C	114	131	Right-handed alpha
Helix 50	50	C	140	153	Right-handed alpha
Helix 51	51	C	154	156	Right-handed 310
Helix 52	52	C	157	169	Right-handed alpha
Helix 53	53	C	171	176	Right-handed alpha
Helix 54	54	C	183	188	Right-handed alpha
Helix 55	55	C	200	210	Right-handed alpha
Helix 56	56	C	211	212	Right-handed 310
Helix 57	57	C	213	215	Right-handed 310
Helix 58	58	C	254	259	Right-handed alpha
Helix 59	59	C	260	263	Right-handed 310
Helix 60	60	C	279	286	Right-handed alpha
Helix 61	61	C	287	289	Right-handed 310
Helix 62	62	C	320	330	Right-handed alpha
Helix 63	63	C	332	345	Right-handed alpha
Helix 64	64	C	363	368	Right-handed alpha
Helix 65	65	C	379	386	Right-handed alpha
Helix 66	66	C	390	409	Right-handed alpha
Helix 67	67	C	458	469	Right-handed alpha
Helix 68	68	C	488	508	Right-handed alpha
Helix 69	69	D	17	30	Right-handed alpha
Helix 70	70	D	54	56	Right-handed 310
Helix 71	71	D	72	83	Right-handed alpha
Helix 72	72	D	114	131	Right-handed alpha
Helix 73	73	D	140	153	Right-handed alpha
Helix 74	74	D	154	156	Right-handed 310
Helix 75	75	D	157	168	Right-handed alpha
Helix 76	76	D	171	176	Right-handed alpha
Helix 77	77	D	183	188	Right-handed alpha
Helix 78	78	D	200	210	Right-handed alpha
Helix 79	79	D	211	212	Right-handed 310
Helix 80	80	D	213	215	Right-handed 310
Helix 81	81	D	254	259	Right-handed alpha
Helix 82	82	D	260	263	Right-handed 310
Helix 83	83	D	279	286	Right-handed alpha
Helix 84	84	D	320	330	Right-handed alpha
Helix 85	85	D	332	345	Right-handed alpha
Helix 86	86	D	363	367	Right-handed alpha
Helix 87	87	D	379	386	Right-handed alpha
Helix 88	88	D	390	409	Right-handed alpha
Helix 89	89	D	419	423	Right-handed 310
Helix 90	90	D	459	469	Right-handed alpha
Helix 91	91	D	488	509	Right-handed alpha

There are 24 sheets in PDB entry 4GDP. 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,

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	217	218	first strand
Strand 2	A	35	38	parallel
Strand 3	A	8	14	parallel
Strand 4	A	243	251	parallel
Strand 5	A	234	238	anti-parallel
Strand 6	A	223	228	anti-parallel
Strand 7	A	273	275	parallel

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There are 5 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	217	218	first strand
Strand 2	A	35	38	parallel
Strand 3	A	8	14	parallel
Strand 4	A	243	251	parallel
Strand 5	A	474	476	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	50	52	first strand
Strand 2	A	58	60	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	65	66	first strand
Strand 2	A	196	198	anti-parallel
Strand 3	A	90	91	anti-parallel

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There are 8 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	105	106	first strand
Strand 2	A	98	101	anti-parallel
Strand 3	A	312	315	parallel
Strand 4	A	358	362	anti-parallel
Strand 5	A	371	376	anti-parallel
Strand 6	A	295	301	anti-parallel
Strand 7	A	431	437	anti-parallel
Strand 8	A	415	416	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	290	291	first strand
Strand 2	A	451	452	anti-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	B	217	218	first strand
Strand 2	B	36	38	parallel
Strand 3	B	8	14	parallel
Strand 4	B	243	251	parallel
Strand 5	B	234	238	anti-parallel
Strand 6	B	223	228	anti-parallel
Strand 7	B	273	275	parallel

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There are 5 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	217	218	first strand
Strand 2	B	36	38	parallel
Strand 3	B	8	14	parallel
Strand 4	B	243	251	parallel
Strand 5	B	474	476	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	50	52	first strand
Strand 2	B	58	60	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	65	66	first strand
Strand 2	B	196	198	anti-parallel
Strand 3	B	90	92	anti-parallel

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There are 8 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	105	106	first strand
Strand 2	B	98	101	anti-parallel
Strand 3	B	312	315	parallel
Strand 4	B	358	362	anti-parallel
Strand 5	B	371	376	anti-parallel
Strand 6	B	295	301	anti-parallel
Strand 7	B	431	437	anti-parallel
Strand 8	B	415	416	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	290	292	first strand
Strand 2	B	450	452	anti-parallel

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There are 7 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	217	218	first strand
Strand 2	C	35	38	parallel
Strand 3	C	9	14	parallel
Strand 4	C	243	251	parallel
Strand 5	C	234	238	anti-parallel
Strand 6	C	223	227	anti-parallel
Strand 7	C	273	275	parallel

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There are 5 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	217	218	first strand
Strand 2	C	35	38	parallel
Strand 3	C	9	14	parallel
Strand 4	C	243	251	parallel
Strand 5	C	474	476	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	C	50	52	first strand
Strand 2	C	58	60	anti-parallel

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There are 3 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	65	66	first strand
Strand 2	C	196	198	anti-parallel
Strand 3	C	90	91	anti-parallel

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There are 8 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	105	106	first strand
Strand 2	C	98	101	anti-parallel
Strand 3	C	312	315	parallel
Strand 4	C	358	362	anti-parallel
Strand 5	C	371	376	anti-parallel
Strand 6	C	295	301	anti-parallel
Strand 7	C	431	437	anti-parallel
Strand 8	C	415	416	parallel

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There are 2 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	290	292	first strand
Strand 2	C	450	452	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	217	218	first strand
Strand 2	D	36	38	parallel
Strand 3	D	11	14	parallel
Strand 4	D	248	251	parallel
Strand 5	D	474	476	parallel

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There are 2 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	50	52	first strand
Strand 2	D	58	60	anti-parallel

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There are 3 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	65	66	first strand
Strand 2	D	196	198	anti-parallel
Strand 3	D	90	91	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	105	106	first strand
Strand 2	D	98	101	anti-parallel
Strand 3	D	312	315	parallel
Strand 4	D	358	362	anti-parallel
Strand 5	D	371	376	anti-parallel
Strand 6	D	295	301	anti-parallel
Strand 7	D	431	437	anti-parallel
Strand 8	D	415	416	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	243	246	first strand
Strand 2	D	234	238	anti-parallel
Strand 3	D	223	228	anti-parallel
Strand 4	D	273	275	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	290	291	first strand
Strand 2	D	451	452	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: 4GDP

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