Analysis of interatomic Contacts of Structural Units in PDB entry:
5Y28

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 5Y28 entry

There are 4 chains in PDB entry 5Y28 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 21	THR 362
B	ILE 20	ARG 273
C	ILE 22	LEU 363
G	ALA 1	ALA 4

There are 14 helices in PDB entry 5Y28. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	44	49	Right-handed alpha
Helix 2	AA2	A	50	53	Right-handed 310
Helix 3	AA3	A	114	119	Right-handed alpha
Helix 4	AA4	A	255	268	Right-handed alpha
Helix 5	AA5	A	329	337	Right-handed alpha
Helix 6	AA6	B	44	53	Right-handed alpha
Helix 7	AA7	B	114	119	Right-handed alpha
Helix 8	AA8	B	165	169	Right-handed 310
Helix 9	AA9	B	255	268	Right-handed alpha
Helix 10	AB1	C	44	53	Right-handed alpha
Helix 11	AB2	C	144	147	Right-handed 310
Helix 12	AB3	C	255	268	Right-handed alpha
Helix 13	AB4	C	306	312	Right-handed alpha
Helix 14	AB5	C	329	340	Right-handed alpha

There are 12 sheets in PDB entry 5Y28. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 2 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	30	32	first strand
Strand 2	B	40	42	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	40	42	first strand
Strand 2	C	30	32	parallel

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There are 7 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	55	59	first strand
Strand 2	A	98	104	anti-parallel
Strand 3	A	110	113	anti-parallel
Strand 4	A	148	152	anti-parallel
Strand 5	A	134	143	anti-parallel
Strand 6	A	124	127	anti-parallel
Strand 7	A	55	59	anti-parallel

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There are 7 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	174	179	first strand
Strand 2	A	187	195	anti-parallel
Strand 3	A	210	212	anti-parallel
Strand 4	A	250	254	anti-parallel
Strand 5	A	232	237	anti-parallel
Strand 6	A	224	226	anti-parallel
Strand 7	A	174	179	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	324	325	first strand
Strand 2	A	356	357	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	B	30	32	first strand
Strand 2	C	40	42	parallel

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There are 7 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	135	136	first strand
Strand 2	B	125	127	anti-parallel
Strand 3	B	55	59	anti-parallel
Strand 4	B	98	104	anti-parallel
Strand 5	B	110	113	anti-parallel
Strand 6	B	148	152	anti-parallel
Strand 7	B	138	143	anti-parallel

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There are 7 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	174	179	first strand
Strand 2	B	187	195	anti-parallel
Strand 3	B	210	212	anti-parallel
Strand 4	B	250	254	anti-parallel
Strand 5	B	232	237	anti-parallel
Strand 6	B	224	226	anti-parallel
Strand 7	B	174	179	anti-parallel

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There are 7 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	55	59	first strand
Strand 2	C	101	104	anti-parallel
Strand 3	C	110	113	anti-parallel
Strand 4	C	148	153	anti-parallel
Strand 5	C	135	143	anti-parallel
Strand 6	C	125	127	anti-parallel
Strand 7	C	55	59	anti-parallel

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There are 7 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	174	178	first strand
Strand 2	C	189	196	anti-parallel
Strand 3	C	210	212	anti-parallel
Strand 4	C	250	254	anti-parallel
Strand 5	C	232	237	anti-parallel
Strand 6	C	224	226	anti-parallel
Strand 7	C	174	178	anti-parallel

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There are 3 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	297	298	first strand
Strand 2	C	318	322	anti-parallel
Strand 3	C	325	326	anti-parallel

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There are 4 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	297	298	first strand
Strand 2	C	318	322	anti-parallel
Strand 3	C	345	351	anti-parallel
Strand 4	C	355	361	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: 5Y28

Analysis of interatomic Contacts of Structural Units in PDB entry:
5Y28