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

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 4GDF entry

There are 8 chains in PDB entry 4GDF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 131	ASP 627
B	LYS 131	ASP 627
C	A 1	G 32
D	C 1	T 32
E	LYS 131	ASP 627
F	LYS 131	ASP 627
G	A 1	G 32
H	C 1	T 32

There are104 helices in PDB entry 4GDF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	142	146	Right-handed 310
Helix 2	2	A	164	179	Right-handed alpha
Helix 3	3	A	204	215	Right-handed alpha
Helix 4	4	A	228	238	Right-handed alpha
Helix 5	5	A	269	280	Right-handed alpha
Helix 6	6	A	284	295	Right-handed alpha
Helix 7	7	A	302	307	Right-handed alpha
Helix 8	8	A	310	315	Right-handed alpha
Helix 9	9	A	316	328	Right-handed alpha
Helix 10	10	A	332	354	Right-handed alpha
Helix 11	11	A	357	376	Right-handed alpha
Helix 12	12	A	383	395	Right-handed alpha
Helix 13	13	A	400	415	Right-handed alpha
Helix 14	14	A	431	443	Right-handed alpha
Helix 15	15	A	456	462	Right-handed alpha
Helix 16	16	A	463	465	Right-handed 310
Helix 17	17	A	489	495	Right-handed alpha
Helix 18	18	A	497	503	Right-handed alpha
Helix 19	19	A	534	540	Right-handed alpha
Helix 20	20	A	550	558	Right-handed alpha
Helix 21	21	A	561	566	Right-handed alpha
Helix 22	22	A	571	583	Right-handed alpha
Helix 23	23	A	589	591	Right-handed 310
Helix 24	24	A	592	607	Right-handed alpha
Helix 25	25	A	610	622	Right-handed alpha
Helix 26	26	B	142	144	Right-handed 310
Helix 27	27	B	164	180	Right-handed alpha
Helix 28	28	B	204	216	Right-handed alpha
Helix 29	29	B	228	238	Right-handed alpha
Helix 30	30	B	253	257	Right-handed 310
Helix 31	31	B	269	280	Right-handed alpha
Helix 32	32	B	284	294	Right-handed alpha
Helix 33	33	B	295	297	Right-handed 310
Helix 34	34	B	302	308	Right-handed alpha
Helix 35	35	B	310	315	Right-handed alpha
Helix 36	36	B	316	328	Right-handed alpha
Helix 37	37	B	332	355	Right-handed alpha
Helix 38	38	B	356	376	Right-handed alpha
Helix 39	39	B	383	395	Right-handed alpha
Helix 40	40	B	400	415	Right-handed alpha
Helix 41	41	B	431	444	Right-handed alpha
Helix 42	42	B	455	459	Right-handed 310
Helix 43	43	B	460	465	Right-handed 310
Helix 44	44	B	479	484	Right-handed 310
Helix 45	45	B	489	496	Right-handed alpha
Helix 46	46	B	497	503	Right-handed alpha
Helix 47	47	B	537	541	Right-handed 310
Helix 48	48	B	550	560	Right-handed alpha
Helix 49	49	B	561	566	Right-handed alpha
Helix 50	50	B	571	581	Right-handed alpha
Helix 51	51	B	592	607	Right-handed alpha
Helix 52	52	B	610	622	Right-handed alpha
Helix 53	53	E	142	146	Right-handed 310
Helix 54	54	E	164	179	Right-handed alpha
Helix 55	55	E	204	215	Right-handed alpha
Helix 56	56	E	228	238	Right-handed alpha
Helix 57	57	E	269	280	Right-handed alpha
Helix 58	58	E	284	295	Right-handed alpha
Helix 59	59	E	302	307	Right-handed alpha
Helix 60	60	E	310	315	Right-handed alpha
Helix 61	61	E	316	328	Right-handed alpha
Helix 62	62	E	332	354	Right-handed alpha
Helix 63	63	E	357	376	Right-handed alpha
Helix 64	64	E	383	395	Right-handed alpha
Helix 65	65	E	400	415	Right-handed alpha
Helix 66	66	E	431	443	Right-handed alpha
Helix 67	67	E	456	462	Right-handed alpha
Helix 68	68	E	463	465	Right-handed 310
Helix 69	69	E	489	495	Right-handed alpha
Helix 70	70	E	497	503	Right-handed alpha
Helix 71	71	E	534	540	Right-handed alpha
Helix 72	72	E	550	559	Right-handed alpha
Helix 73	73	E	561	566	Right-handed alpha
Helix 74	74	E	571	583	Right-handed alpha
Helix 75	75	E	589	591	Right-handed 310
Helix 76	76	E	592	607	Right-handed alpha
Helix 77	77	E	610	622	Right-handed alpha
Helix 78	78	F	142	144	Right-handed 310
Helix 79	79	F	164	180	Right-handed alpha
Helix 80	80	F	204	216	Right-handed alpha
Helix 81	81	F	228	238	Right-handed alpha
Helix 82	82	F	253	257	Right-handed 310
Helix 83	83	F	269	280	Right-handed alpha
Helix 84	84	F	284	294	Right-handed alpha
Helix 85	85	F	295	297	Right-handed 310
Helix 86	86	F	302	308	Right-handed alpha
Helix 87	87	F	310	315	Right-handed alpha
Helix 88	88	F	316	328	Right-handed alpha
Helix 89	89	F	332	355	Right-handed alpha
Helix 90	90	F	356	376	Right-handed alpha
Helix 91	91	F	383	395	Right-handed alpha
Helix 92	92	F	400	415	Right-handed alpha
Helix 93	93	F	431	444	Right-handed alpha
Helix 94	94	F	455	459	Right-handed 310
Helix 95	95	F	460	465	Right-handed 310
Helix 96	96	F	479	484	Right-handed 310
Helix 97	97	F	489	496	Right-handed alpha
Helix 98	98	F	497	503	Right-handed alpha
Helix 99	99	F	537	541	Right-handed 310
Helix 100	100	F	550	560	Right-handed alpha
Helix 101	101	F	561	566	Right-handed alpha
Helix 102	102	F	571	581	Right-handed alpha
Helix 103	103	F	592	607	Right-handed alpha
Helix 104	104	F	610	622	Right-handed alpha

There are 12 sheets in PDB entry 4GDF. 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 5 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	222	225	first strand
Strand 2	A	156	163	anti-parallel
Strand 3	A	192	203	anti-parallel
Strand 4	A	183	189	anti-parallel
Strand 5	A	242	243	anti-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	445	448	first strand
Strand 2	A	469	475	parallel
Strand 3	A	524	528	parallel
Strand 4	A	421	425	parallel
Strand 5	A	543	546	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	507	509	first strand
Strand 2	A	517	519	anti-parallel

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There are 6 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	146	147	first strand
Strand 2	B	222	226	anti-parallel
Strand 3	B	156	163	anti-parallel
Strand 4	B	192	203	anti-parallel
Strand 5	B	183	189	anti-parallel
Strand 6	B	242	246	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	B	445	448	first strand
Strand 2	B	469	475	parallel
Strand 3	B	524	528	parallel
Strand 4	B	421	425	parallel
Strand 5	B	543	546	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	B	507	511	first strand
Strand 2	B	514	519	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	222	225	first strand
Strand 2	E	156	163	anti-parallel
Strand 3	E	192	203	anti-parallel
Strand 4	E	183	189	anti-parallel
Strand 5	E	242	243	anti-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	E	445	448	first strand
Strand 2	E	469	475	parallel
Strand 3	E	524	528	parallel
Strand 4	E	421	425	parallel
Strand 5	E	543	546	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	507	509	first strand
Strand 2	E	517	519	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	146	147	first strand
Strand 2	F	222	226	anti-parallel
Strand 3	F	156	163	anti-parallel
Strand 4	F	192	203	anti-parallel
Strand 5	F	183	189	anti-parallel
Strand 6	F	242	246	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	445	448	first strand
Strand 2	F	469	475	parallel
Strand 3	F	524	528	parallel
Strand 4	F	421	425	parallel
Strand 5	F	543	546	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	507	511	first strand
Strand 2	F	514	519	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: 4GDF

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