Analysis of interatomic Contacts of Structural Units in PDB entry:
5YBB

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 5YBB entry

There are 4 chains in PDB entry 5YBB (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	PRO 4	GLY 496
C	SER 465	GLU 494
D	PRO 5	LEU 398
B	PRO 4	PHE 347

There are 73 helices in PDB entry 5YBB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	6	24	Right-handed alpha
Helix 2	AA2	A	29	58	Right-handed alpha
Helix 3	AA3	A	73	80	Right-handed alpha
Helix 4	AA4	A	83	94	Right-handed alpha
Helix 5	AA5	A	94	101	Right-handed alpha
Helix 6	AA6	A	108	116	Right-handed alpha
Helix 7	AA7	A	125	138	Right-handed alpha
Helix 8	AA8	A	143	165	Right-handed alpha
Helix 9	AA9	A	174	186	Right-handed alpha
Helix 10	AB1	A	203	214	Right-handed alpha
Helix 11	AB2	A	217	226	Right-handed alpha
Helix 12	AB3	A	235	250	Right-handed alpha
Helix 13	AB4	A	289	294	Right-handed 310
Helix 14	AB5	A	300	313	Right-handed alpha
Helix 15	AB6	A	327	332	Right-handed alpha
Helix 16	AB7	A	334	347	Right-handed alpha
Helix 17	AB8	A	405	422	Right-handed alpha
Helix 18	AB9	A	426	431	Right-handed 310
Helix 19	AC1	A	440	446	Right-handed alpha
Helix 20	AC2	A	465	494	Right-handed alpha
Helix 21	AC3	C	466	492	Right-handed alpha
Helix 22	AC4	D	18	20	Right-handed 310
Helix 23	AC5	D	28	32	Right-handed 310
Helix 24	AC6	D	41	43	Right-handed 310
Helix 25	AC7	D	61	63	Right-handed 310
Helix 26	AC8	D	92	96	Right-handed 310
Helix 27	AC9	D	115	125	Right-handed alpha
Helix 28	AD1	D	125	135	Right-handed alpha
Helix 29	AD2	D	146	151	Right-handed alpha
Helix 30	AD3	D	162	203	Right-handed alpha
Helix 31	AD4	D	219	222	Right-handed alpha
Helix 32	AD5	D	232	234	Right-handed 310
Helix 33	AD6	D	248	252	Right-handed 310
Helix 34	AD7	D	309	325	Right-handed alpha
Helix 35	AD8	D	337	343	Right-handed alpha
Helix 36	AD9	D	350	394	Right-handed alpha
Helix 37	AE1	B	6	24	Right-handed alpha
Helix 38	AE2	B	29	56	Right-handed alpha
Helix 39	AE3	B	69	72	Right-handed 310
Helix 40	AE4	B	73	80	Right-handed alpha
Helix 41	AE5	B	83	94	Right-handed alpha
Helix 42	AE6	B	95	100	Right-handed alpha
Helix 43	AE7	B	105	117	Right-handed alpha
Helix 44	AE8	B	125	138	Right-handed alpha
Helix 45	AE9	B	143	165	Right-handed alpha
Helix 46	AF1	B	174	186	Right-handed alpha
Helix 47	AF2	B	203	214	Right-handed alpha
Helix 48	AF3	B	217	226	Right-handed alpha
Helix 49	AF4	B	235	250	Right-handed alpha
Helix 50	AF5	B	289	294	Right-handed 310
Helix 51	AF6	B	300	313	Right-handed alpha
Helix 52	AF7	B	327	332	Right-handed alpha
Helix 53	AF8	B	334	347	Right-handed alpha
Helix 54	AF9	B	403	422	Right-handed alpha
Helix 55	AG1	B	426	430	Right-handed 310
Helix 56	AG2	B	440	446	Right-handed alpha
Helix 57	AG3	B	465	494	Right-handed alpha
Helix 58	AG4	E	466	491	Right-handed alpha
Helix 59	AG5	G	28	32	Right-handed 310
Helix 60	AG6	G	41	43	Right-handed 310
Helix 61	AG7	G	61	63	Right-handed 310
Helix 62	AG8	G	92	96	Right-handed 310
Helix 63	AG9	G	115	125	Right-handed alpha
Helix 64	AH1	G	125	135	Right-handed alpha
Helix 65	AH2	G	146	153	Right-handed alpha
Helix 66	AH3	G	162	165	Right-handed 310
Helix 67	AH4	G	166	203	Right-handed alpha
Helix 68	AH5	G	219	222	Right-handed alpha
Helix 69	AH6	G	232	234	Right-handed 310
Helix 70	AH7	G	248	252	Right-handed 310
Helix 71	AH8	G	309	325	Right-handed alpha
Helix 72	AH9	G	337	343	Right-handed alpha
Helix 73	AI1	G	350	394	Right-handed alpha

There are 19 sheets in PDB entry 5YBB. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AC1,

There are 7 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	193	194	first strand
Strand 2	A	275	278	parallel
Strand 3	A	319	326	parallel
Strand 4	A	368	375	anti-parallel
Strand 5	A	348	355	anti-parallel
Strand 6	A	381	386	parallel
Strand 7	A	435	439	anti-parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	230	233	first strand
Strand 2	A	255	258	parallel

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There are 2 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	13	16	first strand
Strand 2	D	154	157	anti-parallel

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There are 2 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	36	39	first strand
Strand 2	D	56	59	anti-parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	45	46	first strand
Strand 2	D	51	52	anti-parallel

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There are 2 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	67	71	first strand
Strand 2	D	98	101	anti-parallel

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There are 3 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	88	90	first strand
Strand 2	D	76	79	anti-parallel
Strand 3	D	104	107	anti-parallel

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There are 2 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	215	218	first strand
Strand 2	D	345	348	anti-parallel

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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	223	226	first strand
Strand 2	D	299	304	anti-parallel
Strand 3	D	275	278	anti-parallel
Strand 4	D	286	288	anti-parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	236	237	first strand
Strand 2	D	262	263	anti-parallel
Strand 3	D	243	246	anti-parallel
Strand 4	D	293	295	parallel
Strand 5	D	269	270	anti-parallel

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There are 7 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	193	194	first strand
Strand 2	B	275	278	parallel
Strand 3	B	319	326	parallel
Strand 4	B	368	375	anti-parallel
Strand 5	B	348	355	anti-parallel
Strand 6	B	381	386	parallel
Strand 7	B	435	439	anti-parallel

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There are 2 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	232	233	first strand
Strand 2	B	257	258	parallel

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There are 2 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	13	16	first strand
Strand 2	G	154	157	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	56	59	first strand
Strand 2	G	36	40	anti-parallel
Strand 3	G	98	101	parallel
Strand 4	G	67	71	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	45	46	first strand
Strand 2	G	51	52	anti-parallel

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There are 3 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	88	90	first strand
Strand 2	G	76	79	anti-parallel
Strand 3	G	104	107	anti-parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	215	218	first strand
Strand 2	G	345	348	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	223	226	first strand
Strand 2	G	299	304	anti-parallel
Strand 3	G	275	278	anti-parallel
Strand 4	G	286	288	anti-parallel

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There are 5 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	236	237	first strand
Strand 2	G	262	263	anti-parallel
Strand 3	G	243	246	anti-parallel
Strand 4	G	293	295	parallel
Strand 5	G	269	270	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: 5YBB

Analysis of interatomic Contacts of Structural Units in PDB entry:
5YBB