Analysis of interatomic Contacts of Structural Units in PDB entry:
1YP4

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 1YP4 entry

There are 4 chains in PDB entry 1YP4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 11	ILE 451
B	CYS 12	ILE 451
C	THR 11	ILE 451
D	CYS 12	ILE 451

There are 67 helices in PDB entry 1YP4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	16	20	Right-handed alpha
Helix 2	2	A	42	45	Right-handed 310
Helix 3	3	A	55	65	Right-handed alpha
Helix 4	4	A	78	89	Right-handed alpha
Helix 5	5	A	119	132	Right-handed alpha
Helix 6	6	A	151	162	Right-handed alpha
Helix 7	7	A	174	179	Right-handed alpha
Helix 8	8	A	200	206	Right-handed alpha
Helix 9	9	A	210	215	Right-handed 310
Helix 10	10	A	217	224	Right-handed alpha
Helix 11	11	A	237	246	Right-handed alpha
Helix 12	12	A	257	265	Right-handed alpha
Helix 13	13	A	283	293	Right-handed alpha
Helix 14	14	A	294	296	Right-handed 310
Helix 15	15	A	374	385	Right-handed alpha
Helix 16	16	A	426	428	Right-handed 310
Helix 17	17	B	16	20	Right-handed alpha
Helix 18	18	B	42	45	Right-handed 310
Helix 19	19	B	55	64	Right-handed alpha
Helix 20	20	B	78	89	Right-handed alpha
Helix 21	21	B	90	93	Right-handed 310
Helix 22	22	B	119	127	Right-handed alpha
Helix 23	23	B	127	132	Right-handed alpha
Helix 24	24	B	151	162	Right-handed alpha
Helix 25	25	B	177	180	Right-handed 310
Helix 26	26	B	201	206	Right-handed alpha
Helix 27	27	B	237	246	Right-handed alpha
Helix 28	28	B	257	265	Right-handed alpha
Helix 29	29	B	283	293	Right-handed alpha
Helix 30	30	B	376	384	Right-handed alpha
Helix 31	31	B	426	428	Right-handed 310
Helix 32	32	C	16	20	Right-handed alpha
Helix 33	33	C	31	35	Right-handed 310
Helix 34	34	C	42	45	Right-handed 310
Helix 35	35	C	55	64	Right-handed alpha
Helix 36	36	C	78	89	Right-handed alpha
Helix 37	37	C	119	127	Right-handed alpha
Helix 38	38	C	127	132	Right-handed alpha
Helix 39	39	C	151	162	Right-handed alpha
Helix 40	40	C	174	179	Right-handed alpha
Helix 41	41	C	200	206	Right-handed alpha
Helix 42	42	C	210	215	Right-handed 310
Helix 43	43	C	217	224	Right-handed alpha
Helix 44	44	C	237	246	Right-handed alpha
Helix 45	45	C	257	265	Right-handed alpha
Helix 46	46	C	283	292	Right-handed alpha
Helix 47	47	C	293	296	Right-handed 310
Helix 48	48	C	374	384	Right-handed alpha
Helix 49	49	C	426	428	Right-handed 310
Helix 50	50	D	16	20	Right-handed alpha
Helix 51	51	D	42	45	Right-handed 310
Helix 52	52	D	55	64	Right-handed alpha
Helix 53	53	D	78	89	Right-handed alpha
Helix 54	54	D	119	127	Right-handed alpha
Helix 55	55	D	127	132	Right-handed alpha
Helix 56	56	D	151	162	Right-handed alpha
Helix 57	57	D	174	179	Right-handed alpha
Helix 58	58	D	200	208	Right-handed alpha
Helix 59	59	D	210	215	Right-handed 310
Helix 60	60	D	217	224	Right-handed alpha
Helix 61	61	D	237	246	Right-handed alpha
Helix 62	62	D	257	265	Right-handed alpha
Helix 63	63	D	283	293	Right-handed alpha
Helix 64	64	D	294	296	Right-handed 310
Helix 65	65	D	374	379	Right-handed alpha
Helix 66	66	D	380	385	Right-handed 310
Helix 67	67	D	426	428	Right-handed 310

There are 26 sheets in PDB entry 1YP4. 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,

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	101	108	first strand
Strand 2	A	69	76	parallel
Strand 3	A	21	28	parallel
Strand 4	A	138	143	parallel
Strand 5	A	226	236	anti-parallel
Strand 6	A	182	186	anti-parallel
Strand 7	A	192	197	anti-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	A	101	108	first strand
Strand 2	A	69	76	parallel
Strand 3	A	21	28	parallel
Strand 4	A	138	143	parallel
Strand 5	A	226	236	anti-parallel
Strand 6	A	166	173	anti-parallel
Strand 7	A	269	273	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	47	48	first strand
Strand 2	A	52	53	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	146	147	first strand
Strand 2	A	279	280	anti-parallel

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There are 14 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	423	424	first strand
Strand 2	A	430	433	anti-parallel
Strand 3	A	436	439	anti-parallel
Strand 4	A	400	402	parallel
Strand 5	A	365	366	parallel
Strand 6	A	348	349	parallel
Strand 7	A	321	333	parallel
Strand 8	B	321	333	anti-parallel
Strand 9	B	348	349	parallel
Strand 10	B	365	366	parallel
Strand 11	B	400	402	parallel
Strand 12	B	436	439	parallel
Strand 13	B	430	433	anti-parallel
Strand 14	B	423	425	anti-parallel

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There are 10 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	413	414	first strand
Strand 2	A	396	398	parallel
Strand 3	A	359	362	parallel
Strand 4	A	338	345	parallel
Strand 5	A	321	333	parallel
Strand 6	B	321	333	anti-parallel
Strand 7	B	338	345	parallel
Strand 8	B	360	362	parallel
Strand 9	B	396	398	parallel
Strand 10	B	413	414	parallel

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There are 6 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	354	355	first strand
Strand 2	A	338	345	parallel
Strand 3	A	321	333	parallel
Strand 4	B	321	333	anti-parallel
Strand 5	B	338	345	parallel
Strand 6	B	354	355	parallel

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There are 2 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	407	408	first strand
Strand 2	A	444	445	parallel

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There are 7 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	101	106	first strand
Strand 2	B	69	74	parallel
Strand 3	B	21	26	parallel
Strand 4	B	138	143	parallel
Strand 5	B	226	236	anti-parallel
Strand 6	B	166	173	anti-parallel
Strand 7	B	269	273	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	47	48	first strand
Strand 2	B	52	53	anti-parallel

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There are 2 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	146	147	first strand
Strand 2	B	279	280	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	182	186	first strand
Strand 2	B	192	197	anti-parallel

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There are 3 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	390	391	first strand
Strand 2	B	407	408	parallel
Strand 3	B	444	445	parallel

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There are 7 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	101	108	first strand
Strand 2	C	69	76	parallel
Strand 3	C	21	28	parallel
Strand 4	C	138	143	parallel
Strand 5	C	226	236	anti-parallel
Strand 6	C	166	173	anti-parallel
Strand 7	C	269	273	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	47	48	first strand
Strand 2	C	52	53	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	C	146	147	first strand
Strand 2	C	279	280	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	C	182	186	first strand
Strand 2	C	192	197	anti-parallel

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There are 14 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	422	425	first strand
Strand 2	C	430	433	anti-parallel
Strand 3	C	436	439	anti-parallel
Strand 4	C	400	402	parallel
Strand 5	C	365	366	parallel
Strand 6	C	348	349	parallel
Strand 7	C	321	333	parallel
Strand 8	D	321	333	anti-parallel
Strand 9	D	348	349	parallel
Strand 10	D	365	366	parallel
Strand 11	D	400	402	parallel
Strand 12	D	436	439	parallel
Strand 13	D	430	433	anti-parallel
Strand 14	D	423	425	anti-parallel

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There are 11 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	413	414	first strand
Strand 2	C	396	398	parallel
Strand 3	C	360	362	parallel
Strand 4	C	338	345	parallel
Strand 5	C	321	333	parallel
Strand 6	D	321	333	anti-parallel
Strand 7	D	338	345	parallel
Strand 8	D	360	362	parallel
Strand 9	D	396	398	parallel
Strand 10	D	413	414	parallel
Strand 11	D	450	451	parallel

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There are 6 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	354	355	first strand
Strand 2	C	338	345	parallel
Strand 3	C	321	333	parallel
Strand 4	D	321	333	anti-parallel
Strand 5	D	338	345	parallel
Strand 6	D	354	355	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	C	390	391	first strand
Strand 2	C	407	408	parallel
Strand 3	C	444	445	parallel

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There are 7 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	101	106	first strand
Strand 2	D	69	74	parallel
Strand 3	D	21	26	parallel
Strand 4	D	138	143	parallel
Strand 5	D	226	236	anti-parallel
Strand 6	D	182	185	anti-parallel
Strand 7	D	194	197	anti-parallel

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There are 7 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	101	106	first strand
Strand 2	D	69	74	parallel
Strand 3	D	21	26	parallel
Strand 4	D	138	143	parallel
Strand 5	D	226	236	anti-parallel
Strand 6	D	166	173	anti-parallel
Strand 7	D	269	273	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	47	48	first strand
Strand 2	D	52	53	anti-parallel

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There are 2 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	146	147	first strand
Strand 2	D	279	280	anti-parallel

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There are 3 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	390	391	first strand
Strand 2	D	407	408	parallel
Strand 3	D	444	445	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: 1YP4

Analysis of interatomic Contacts of Structural Units in PDB entry:
1YP4