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

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 5YPK entry

There are 8 chains in PDB entry 5YPK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 43	ARG 270
B	ASP 43	ARG 270
C	ASP 43	ARG 270
D	GLY 42	ARG 270
E	ASP 43	ARG 270
F	ASP 43	ARG 270
G	GLY 42	ARG 270
H	ASP 43	ARG 270

There are 55 helices in PDB entry 5YPK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	94	109	Right-handed alpha
Helix 2	AA2	A	122	127	Right-handed alpha
Helix 3	AA3	A	128	135	Right-handed alpha
Helix 4	AA4	A	143	149	Right-handed alpha
Helix 5	AA5	A	228	240	Right-handed alpha
Helix 6	AA6	A	256	268	Right-handed alpha
Helix 7	AA7	B	94	109	Right-handed alpha
Helix 8	AA8	B	122	127	Right-handed alpha
Helix 9	AA9	B	128	135	Right-handed alpha
Helix 10	AB1	B	143	149	Right-handed alpha
Helix 11	AB2	B	228	240	Right-handed alpha
Helix 12	AB3	B	256	267	Right-handed alpha
Helix 13	AB4	B	268	270	Right-handed 310
Helix 14	AB5	C	94	109	Right-handed alpha
Helix 15	AB6	C	122	127	Right-handed alpha
Helix 16	AB7	C	128	135	Right-handed alpha
Helix 17	AB8	C	143	149	Right-handed alpha
Helix 18	AB9	C	170	174	Right-handed 310
Helix 19	AC1	C	228	240	Right-handed alpha
Helix 20	AC2	C	256	268	Right-handed alpha
Helix 21	AC3	D	94	109	Right-handed alpha
Helix 22	AC4	D	122	127	Right-handed alpha
Helix 23	AC5	D	128	135	Right-handed alpha
Helix 24	AC6	D	143	149	Right-handed alpha
Helix 25	AC7	D	228	240	Right-handed alpha
Helix 26	AC8	D	256	268	Right-handed alpha
Helix 27	AC9	E	94	109	Right-handed alpha
Helix 28	AD1	E	122	127	Right-handed alpha
Helix 29	AD2	E	128	135	Right-handed alpha
Helix 30	AD3	E	143	149	Right-handed alpha
Helix 31	AD4	E	170	174	Right-handed 310
Helix 32	AD5	E	228	240	Right-handed alpha
Helix 33	AD6	E	256	268	Right-handed alpha
Helix 34	AD7	F	94	109	Right-handed alpha
Helix 35	AD8	F	122	127	Right-handed alpha
Helix 36	AD9	F	128	135	Right-handed alpha
Helix 37	AE1	F	143	149	Right-handed alpha
Helix 38	AE2	F	170	174	Right-handed 310
Helix 39	AE3	F	228	240	Right-handed alpha
Helix 40	AE4	F	256	268	Right-handed alpha
Helix 41	AE5	G	94	109	Right-handed alpha
Helix 42	AE6	G	122	127	Right-handed alpha
Helix 43	AE7	G	128	135	Right-handed alpha
Helix 44	AE8	G	143	149	Right-handed alpha
Helix 45	AE9	G	170	174	Right-handed 310
Helix 46	AF1	G	228	240	Right-handed alpha
Helix 47	AF2	G	256	267	Right-handed alpha
Helix 48	AF3	G	268	270	Right-handed 310
Helix 49	AF4	H	94	109	Right-handed alpha
Helix 50	AF5	H	122	127	Right-handed alpha
Helix 51	AF6	H	128	135	Right-handed alpha
Helix 52	AF7	H	143	149	Right-handed alpha
Helix 53	AF8	H	150	153	Right-handed 310
Helix 54	AF9	H	228	240	Right-handed alpha
Helix 55	AG1	H	256	268	Right-handed alpha

There are 16 sheets in PDB entry 5YPK. 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,

There are 8 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	44	46	first strand
Strand 2	A	49	55	anti-parallel
Strand 3	A	58	67	anti-parallel
Strand 4	A	71	82	anti-parallel
Strand 5	A	85	89	anti-parallel
Strand 6	A	113	118	parallel
Strand 7	A	138	142	parallel
Strand 8	A	159	161	parallel

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There are 4 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	180	183	first strand
Strand 2	A	195	198	anti-parallel
Strand 3	A	203	207	anti-parallel
Strand 4	A	245	248	parallel

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There are 8 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	44	46	first strand
Strand 2	B	49	55	anti-parallel
Strand 3	B	58	65	anti-parallel
Strand 4	B	73	82	anti-parallel
Strand 5	B	85	89	anti-parallel
Strand 6	B	113	117	parallel
Strand 7	B	138	142	parallel
Strand 8	B	159	161	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	B	180	183	first strand
Strand 2	B	195	198	anti-parallel
Strand 3	B	203	207	anti-parallel
Strand 4	B	245	248	parallel
Strand 5	B	251	254	anti-parallel

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There are 8 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	44	46	first strand
Strand 2	C	49	55	anti-parallel
Strand 3	C	58	67	anti-parallel
Strand 4	C	71	82	anti-parallel
Strand 5	C	85	89	anti-parallel
Strand 6	C	113	117	parallel
Strand 7	C	138	142	parallel
Strand 8	C	159	161	parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	180	183	first strand
Strand 2	C	195	198	anti-parallel
Strand 3	C	203	207	anti-parallel
Strand 4	C	245	248	parallel

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There are 8 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	44	46	first strand
Strand 2	D	49	55	anti-parallel
Strand 3	D	58	67	anti-parallel
Strand 4	D	71	82	anti-parallel
Strand 5	D	85	89	anti-parallel
Strand 6	D	113	117	parallel
Strand 7	D	138	142	parallel
Strand 8	D	159	161	parallel

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There are 5 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	180	183	first strand
Strand 2	D	195	198	anti-parallel
Strand 3	D	203	207	anti-parallel
Strand 4	D	245	248	parallel
Strand 5	D	251	254	anti-parallel

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There are 8 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	44	46	first strand
Strand 2	E	49	55	anti-parallel
Strand 3	E	58	67	anti-parallel
Strand 4	E	71	82	anti-parallel
Strand 5	E	85	89	anti-parallel
Strand 6	E	113	118	parallel
Strand 7	E	138	142	parallel
Strand 8	E	159	161	parallel

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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	180	183	first strand
Strand 2	E	195	198	anti-parallel
Strand 3	E	203	207	anti-parallel
Strand 4	E	245	248	parallel

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There are 8 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	44	46	first strand
Strand 2	F	49	55	anti-parallel
Strand 3	F	58	67	anti-parallel
Strand 4	F	71	82	anti-parallel
Strand 5	F	85	89	anti-parallel
Strand 6	F	113	117	parallel
Strand 7	F	138	142	parallel
Strand 8	F	159	161	parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	180	183	first strand
Strand 2	F	195	198	anti-parallel
Strand 3	F	203	207	anti-parallel
Strand 4	F	245	248	parallel
Strand 5	F	251	254	anti-parallel

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There are 8 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	44	46	first strand
Strand 2	G	49	55	anti-parallel
Strand 3	G	58	67	anti-parallel
Strand 4	G	71	82	anti-parallel
Strand 5	G	85	89	anti-parallel
Strand 6	G	113	117	parallel
Strand 7	G	138	142	parallel
Strand 8	G	159	161	parallel

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There are 5 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	180	183	first strand
Strand 2	G	195	198	anti-parallel
Strand 3	G	203	207	anti-parallel
Strand 4	G	245	248	parallel
Strand 5	G	251	254	anti-parallel

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There are 8 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	44	46	first strand
Strand 2	H	49	55	anti-parallel
Strand 3	H	58	67	anti-parallel
Strand 4	H	71	82	anti-parallel
Strand 5	H	85	89	anti-parallel
Strand 6	H	113	117	parallel
Strand 7	H	138	142	parallel
Strand 8	H	159	161	parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	180	183	first strand
Strand 2	H	195	198	anti-parallel
Strand 3	H	203	207	anti-parallel
Strand 4	H	245	248	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: 5YPK

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