Analysis of interatomic Contacts of Structural Units in PDB entry:
3GD3

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 3GD3 entry

There are 3 chains in PDB entry 3GD3 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	PRO 128	HIS 610
B	ALA 127	HIS 610
C	PRO 128	VAL 489

There are 65 helices in PDB entry 3GD3. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	139	153	Right-handed alpha
Helix 2	2	A	171	180	Right-handed 310
Helix 3	3	A	184	190	Right-handed alpha
Helix 4	4	A	206	210	Right-handed 310
Helix 5	5	A	215	219	Right-handed 310
Helix 6	6	A	266	272	Right-handed alpha
Helix 7	7	A	273	279	Right-handed alpha
Helix 8	8	A	285	297	Right-handed alpha
Helix 9	9	A	308	326	Right-handed alpha
Helix 10	10	A	344	358	Right-handed alpha
Helix 11	11	A	405	410	Right-handed alpha
Helix 12	12	A	453	469	Right-handed alpha
Helix 13	13	A	515	524	Right-handed alpha
Helix 14	14	A	527	532	Right-handed alpha
Helix 15	15	A	583	594	Right-handed alpha
Helix 16	16	A	599	605	Right-handed alpha
Helix 17	17	A	606	608	Right-handed 310
Helix 18	18	B	139	153	Right-handed alpha
Helix 19	19	B	171	176	Right-handed 310
Helix 20	20	B	185	190	Right-handed alpha
Helix 21	21	B	206	210	Right-handed 310
Helix 22	22	B	266	271	Right-handed alpha
Helix 23	23	B	273	279	Right-handed alpha
Helix 24	24	B	285	296	Right-handed alpha
Helix 25	25	B	308	326	Right-handed alpha
Helix 26	26	B	344	357	Right-handed alpha
Helix 27	27	B	404	410	Right-handed alpha
Helix 28	28	B	453	469	Right-handed alpha
Helix 29	29	B	515	524	Right-handed alpha
Helix 30	30	B	527	533	Right-handed alpha
Helix 31	31	B	583	594	Right-handed alpha
Helix 32	32	B	600	605	Right-handed alpha
Helix 33	33	B	606	608	Right-handed 310
Helix 34	34	C	139	153	Right-handed alpha
Helix 35	35	C	171	175	Right-handed 310
Helix 36	36	C	176	180	Right-handed 310
Helix 37	37	C	184	190	Right-handed alpha
Helix 38	38	C	206	210	Right-handed 310
Helix 39	39	C	215	219	Right-handed 310
Helix 40	40	C	266	272	Right-handed alpha
Helix 41	41	C	273	278	Right-handed alpha
Helix 42	42	C	285	297	Right-handed alpha
Helix 43	43	C	308	326	Right-handed alpha
Helix 44	44	C	344	357	Right-handed alpha
Helix 45	45	C	405	410	Right-handed alpha
Helix 46	46	C	453	469	Right-handed alpha
Helix 47	47	C	516	524	Right-handed alpha
Helix 48	48	C	527	533	Right-handed alpha
Helix 49	49	C	583	593	Right-handed alpha
Helix 50	50	C	602	608	Right-handed 310
Helix 51	51	D	139	153	Right-handed alpha
Helix 52	52	D	171	176	Right-handed 310
Helix 53	53	D	185	190	Right-handed alpha
Helix 54	54	D	206	210	Right-handed 310
Helix 55	55	D	266	272	Right-handed alpha
Helix 56	56	D	273	278	Right-handed alpha
Helix 57	57	D	285	296	Right-handed alpha
Helix 58	58	D	308	321	Right-handed alpha
Helix 59	59	D	321	326	Right-handed alpha
Helix 60	60	D	344	356	Right-handed alpha
Helix 61	61	D	403	410	Right-handed alpha
Helix 62	62	D	453	469	Right-handed alpha
Helix 63	63	D	515	524	Right-handed alpha
Helix 64	64	D	586	594	Right-handed alpha
Helix 65	65	D	604	608	Right-handed 310

There are 32 sheets in PDB entry 3GD3. 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, AA, AB, AC, AD, AE, AF,

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	223	228	first strand
Strand 2	A	157	162	parallel
Strand 3	A	129	136	parallel
Strand 4	A	249	257	parallel
Strand 5	A	241	244	anti-parallel
Strand 6	A	232	236	anti-parallel

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There are 6 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	223	228	first strand
Strand 2	A	157	162	parallel
Strand 3	A	129	136	parallel
Strand 4	A	249	257	parallel
Strand 5	A	432	434	parallel
Strand 6	A	427	429	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	191	193	first strand
Strand 2	A	199	201	anti-parallel

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There are 2 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	261	263	first strand
Strand 2	A	399	401	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	280	281	first strand
Strand 2	A	392	395	parallel
Strand 3	A	301	305	parallel
Strand 4	A	328	332	parallel
Strand 5	A	360	363	parallel

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There are 3 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	368	374	first strand
Strand 2	A	377	382	anti-parallel
Strand 3	A	387	390	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	420	421	first strand
Strand 2	A	439	440	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	A	480	485	first strand
Strand 2	A	489	495	anti-parallel
Strand 3	A	572	578	anti-parallel
Strand 4	A	561	567	anti-parallel
Strand 5	A	503	508	anti-parallel
Strand 6	F	2	6	anti-parallel
Strand 7	E	5	6	anti-parallel

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There are 6 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	223	227	first strand
Strand 2	B	157	161	parallel
Strand 3	B	133	136	parallel
Strand 4	B	254	257	parallel
Strand 5	B	432	434	parallel
Strand 6	B	427	429	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	B	191	193	first strand
Strand 2	B	199	201	anti-parallel

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There are 3 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	232	236	first strand
Strand 2	B	241	244	anti-parallel
Strand 3	B	249	251	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	B	261	263	first strand
Strand 2	B	399	401	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	280	282	first strand
Strand 2	B	392	395	parallel
Strand 3	B	301	305	parallel
Strand 4	B	328	333	parallel
Strand 5	B	361	364	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	368	374	first strand
Strand 2	B	377	382	anti-parallel
Strand 3	B	387	390	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	420	422	first strand
Strand 2	B	439	442	parallel
Strand 3	B	448	450	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	481	485	first strand
Strand 2	B	489	495	anti-parallel
Strand 3	B	571	578	anti-parallel
Strand 4	B	561	568	anti-parallel
Strand 5	B	503	508	anti-parallel

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There are 6 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	224	227	first strand
Strand 2	C	158	161	parallel
Strand 3	C	129	136	parallel
Strand 4	C	249	257	parallel
Strand 5	C	241	244	anti-parallel
Strand 6	C	232	236	anti-parallel

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There are 5 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	224	227	first strand
Strand 2	C	158	161	parallel
Strand 3	C	129	136	parallel
Strand 4	C	249	257	parallel
Strand 5	C	432	434	parallel

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There are 2 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	191	194	first strand
Strand 2	C	197	201	anti-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	C	261	263	first strand
Strand 2	C	399	401	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	C	280	282	first strand
Strand 2	C	393	395	parallel
Strand 3	C	301	305	parallel
Strand 4	C	328	332	parallel
Strand 5	C	361	363	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	368	374	first strand
Strand 2	C	377	382	anti-parallel
Strand 3	C	387	390	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	420	422	first strand
Strand 2	C	439	442	parallel
Strand 3	C	448	449	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	480	485	first strand
Strand 2	C	489	495	anti-parallel
Strand 3	C	571	578	anti-parallel
Strand 4	C	561	568	anti-parallel
Strand 5	C	503	508	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	D	223	227	first strand
Strand 2	D	157	161	parallel
Strand 3	D	130	136	parallel
Strand 4	D	249	257	parallel
Strand 5	D	241	244	anti-parallel
Strand 6	D	232	236	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	223	227	first strand
Strand 2	D	157	161	parallel
Strand 3	D	130	136	parallel
Strand 4	D	249	257	parallel
Strand 5	D	432	434	parallel
Strand 6	D	427	429	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	191	194	first strand
Strand 2	D	197	201	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	261	263	first strand
Strand 2	D	399	401	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	280	282	first strand
Strand 2	D	392	395	parallel
Strand 3	D	301	305	parallel
Strand 4	D	328	333	parallel
Strand 5	D	361	364	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	368	374	first strand
Strand 2	D	377	382	anti-parallel
Strand 3	D	387	390	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	420	421	first strand
Strand 2	D	439	443	parallel
Strand 3	D	447	449	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	480	484	first strand
Strand 2	D	490	495	anti-parallel
Strand 3	D	571	578	anti-parallel
Strand 4	D	561	568	anti-parallel
Strand 5	D	503	508	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: 3GD3

Analysis of interatomic Contacts of Structural Units in PDB entry:
3GD3