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

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 5YKB entry

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

Chain ID	Initial residue	Terminal residue
A	PRO 6	ASN 552
B	PRO 6	ASN 552
C	PRO 6	ASN 552
D	PRO 6	ASN 552

There are101 helices in PDB entry 5YKB. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	7	11	Right-handed 310
Helix 2	AA2	A	18	23	Right-handed alpha
Helix 3	AA3	A	32	38	Right-handed alpha
Helix 4	AA4	A	39	47	Right-handed alpha
Helix 5	AA5	A	75	79	Right-handed 310
Helix 6	AA6	A	80	94	Right-handed alpha
Helix 7	AA7	A	111	118	Right-handed alpha
Helix 8	AA8	A	129	135	Right-handed 310
Helix 9	AA9	A	184	202	Right-handed alpha
Helix 10	AB1	A	210	214	Right-handed 310
Helix 11	AB2	A	225	243	Right-handed alpha
Helix 12	AB3	A	255	260	Right-handed alpha
Helix 13	AB4	A	261	264	Right-handed 310
Helix 14	AB5	A	278	290	Right-handed alpha
Helix 15	AB6	A	292	301	Right-handed alpha
Helix 16	AB7	A	327	339	Right-handed alpha
Helix 17	AB8	A	341	343	Right-handed 310
Helix 18	AB9	A	353	358	Right-handed alpha
Helix 19	AC1	A	361	375	Right-handed alpha
Helix 20	AC2	A	398	402	Right-handed 310
Helix 21	AC3	A	419	423	Right-handed 310
Helix 22	AC4	A	439	446	Right-handed alpha
Helix 23	AC5	A	449	463	Right-handed alpha
Helix 24	AC6	A	464	470	Right-handed alpha
Helix 25	AC7	A	512	515	Right-handed 310
Helix 26	AC8	B	7	11	Right-handed 310
Helix 27	AC9	B	18	23	Right-handed alpha
Helix 28	AD1	B	32	38	Right-handed alpha
Helix 29	AD2	B	39	47	Right-handed alpha
Helix 30	AD3	B	75	79	Right-handed 310
Helix 31	AD4	B	80	94	Right-handed alpha
Helix 32	AD5	B	111	118	Right-handed alpha
Helix 33	AD6	B	131	135	Right-handed 310
Helix 34	AD7	B	184	202	Right-handed alpha
Helix 35	AD8	B	211	214	Right-handed 310
Helix 36	AD9	B	225	243	Right-handed alpha
Helix 37	AE1	B	255	260	Right-handed alpha
Helix 38	AE2	B	261	264	Right-handed 310
Helix 39	AE3	B	278	290	Right-handed alpha
Helix 40	AE4	B	292	301	Right-handed alpha
Helix 41	AE5	B	327	339	Right-handed alpha
Helix 42	AE6	B	341	343	Right-handed 310
Helix 43	AE7	B	353	358	Right-handed alpha
Helix 44	AE8	B	361	375	Right-handed alpha
Helix 45	AE9	B	384	388	Right-handed 310
Helix 46	AF1	B	398	402	Right-handed 310
Helix 47	AF2	B	419	423	Right-handed 310
Helix 48	AF3	B	439	446	Right-handed alpha
Helix 49	AF4	B	449	463	Right-handed alpha
Helix 50	AF5	B	464	470	Right-handed alpha
Helix 51	AF6	B	512	515	Right-handed 310
Helix 52	AF7	C	7	11	Right-handed 310
Helix 53	AF8	C	18	23	Right-handed alpha
Helix 54	AF9	C	32	38	Right-handed alpha
Helix 55	AG1	C	39	47	Right-handed alpha
Helix 56	AG2	C	75	79	Right-handed 310
Helix 57	AG3	C	80	94	Right-handed alpha
Helix 58	AG4	C	111	118	Right-handed alpha
Helix 59	AG5	C	131	135	Right-handed 310
Helix 60	AG6	C	184	202	Right-handed alpha
Helix 61	AG7	C	211	214	Right-handed 310
Helix 62	AG8	C	225	243	Right-handed alpha
Helix 63	AG9	C	255	260	Right-handed alpha
Helix 64	AH1	C	261	264	Right-handed 310
Helix 65	AH2	C	278	290	Right-handed alpha
Helix 66	AH3	C	292	301	Right-handed alpha
Helix 67	AH4	C	327	339	Right-handed alpha
Helix 68	AH5	C	341	343	Right-handed 310
Helix 69	AH6	C	353	358	Right-handed alpha
Helix 70	AH7	C	361	375	Right-handed alpha
Helix 71	AH8	C	419	423	Right-handed 310
Helix 72	AH9	C	439	446	Right-handed alpha
Helix 73	AI1	C	449	463	Right-handed alpha
Helix 74	AI2	C	464	470	Right-handed alpha
Helix 75	AI3	C	512	515	Right-handed 310
Helix 76	AI4	D	7	11	Right-handed 310
Helix 77	AI5	D	18	23	Right-handed alpha
Helix 78	AI6	D	32	39	Right-handed alpha
Helix 79	AI7	D	39	47	Right-handed alpha
Helix 80	AI8	D	75	79	Right-handed 310
Helix 81	AI9	D	80	94	Right-handed alpha
Helix 82	AJ1	D	111	118	Right-handed alpha
Helix 83	AJ2	D	131	135	Right-handed 310
Helix 84	AJ3	D	184	202	Right-handed alpha
Helix 85	AJ4	D	210	214	Right-handed 310
Helix 86	AJ5	D	225	243	Right-handed alpha
Helix 87	AJ6	D	255	260	Right-handed alpha
Helix 88	AJ7	D	261	264	Right-handed 310
Helix 89	AJ8	D	278	290	Right-handed alpha
Helix 90	AJ9	D	292	300	Right-handed alpha
Helix 91	AK1	D	327	339	Right-handed alpha
Helix 92	AK2	D	341	343	Right-handed 310
Helix 93	AK3	D	353	358	Right-handed alpha
Helix 94	AK4	D	361	375	Right-handed alpha
Helix 95	AK5	D	384	388	Right-handed 310
Helix 96	AK6	D	398	402	Right-handed 310
Helix 97	AK7	D	419	423	Right-handed 310
Helix 98	AK8	D	439	446	Right-handed alpha
Helix 99	AK9	D	449	463	Right-handed alpha
Helix 100	AL1	D	465	470	Right-handed alpha
Helix 101	AL2	D	512	515	Right-handed 310

There are 21 sheets in PDB entry 5YKB. 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, AC2, AC3,

There are 9 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	14	17	first strand
Strand 2	A	50	53	parallel
Strand 3	A	97	103	parallel
Strand 4	A	205	209	parallel
Strand 5	A	247	250	parallel
Strand 6	A	273	275	parallel
Strand 7	A	310	314	parallel
Strand 8	A	378	382	parallel
Strand 9	A	14	17	parallel

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There are 3 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	137	138	first strand
Strand 2	A	168	170	anti-parallel
Strand 3	A	159	161	anti-parallel

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There are 3 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	321	322	first strand
Strand 2	A	349	350	anti-parallel
Strand 3	A	345	346	anti-parallel

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There are 5 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	471	474	first strand
Strand 2	A	482	489	anti-parallel
Strand 3	A	492	499	anti-parallel
Strand 4	A	546	552	anti-parallel
Strand 5	A	518	521	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	A	505	510	first strand
Strand 2	A	536	541	anti-parallel

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There are 9 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	14	17	first strand
Strand 2	B	50	53	parallel
Strand 3	B	97	103	parallel
Strand 4	B	205	209	parallel
Strand 5	B	247	251	parallel
Strand 6	B	273	275	parallel
Strand 7	B	310	314	parallel
Strand 8	B	378	382	parallel
Strand 9	B	14	17	parallel

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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	159	161	first strand
Strand 2	B	168	170	anti-parallel

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There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	321	322	first strand
Strand 2	B	349	350	anti-parallel
Strand 3	B	345	346	anti-parallel

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There are 5 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	471	475	first strand
Strand 2	B	482	489	anti-parallel
Strand 3	B	492	499	anti-parallel
Strand 4	B	546	552	anti-parallel
Strand 5	B	518	521	anti-parallel

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There are 2 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	505	510	first strand
Strand 2	B	536	541	anti-parallel

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There are 9 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	14	17	first strand
Strand 2	C	50	53	parallel
Strand 3	C	97	103	parallel
Strand 4	C	205	209	parallel
Strand 5	C	247	251	parallel
Strand 6	C	273	275	parallel
Strand 7	C	310	314	parallel
Strand 8	C	378	382	parallel
Strand 9	C	14	17	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	C	122	123	first strand
Strand 2	C	127	128	anti-parallel

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There are 3 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	137	138	first strand
Strand 2	C	168	170	anti-parallel
Strand 3	C	159	161	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	321	322	first strand
Strand 2	C	349	350	anti-parallel
Strand 3	C	345	346	anti-parallel

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There are 5 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	471	475	first strand
Strand 2	C	482	489	anti-parallel
Strand 3	C	492	499	anti-parallel
Strand 4	C	546	552	anti-parallel
Strand 5	C	518	521	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	505	510	first strand
Strand 2	C	536	541	anti-parallel

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There are 9 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	14	17	first strand
Strand 2	D	50	53	parallel
Strand 3	D	97	103	parallel
Strand 4	D	205	209	parallel
Strand 5	D	247	250	parallel
Strand 6	D	273	275	parallel
Strand 7	D	310	314	parallel
Strand 8	D	378	382	parallel
Strand 9	D	14	17	parallel

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There are 3 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	137	138	first strand
Strand 2	D	168	170	anti-parallel
Strand 3	D	159	161	anti-parallel

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There are 3 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	321	322	first strand
Strand 2	D	349	350	anti-parallel
Strand 3	D	345	346	anti-parallel

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There are 5 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	473	475	first strand
Strand 2	D	482	489	anti-parallel
Strand 3	D	492	499	anti-parallel
Strand 4	D	546	552	anti-parallel
Strand 5	D	518	521	anti-parallel

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There are 2 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	505	510	first strand
Strand 2	D	536	541	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: 5YKB

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