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

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 5YDZ entry

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

Chain ID	Initial residue	Terminal residue
A	ARG 61	GLY 529
B	ARG 61	GLY 529
C	ARG 61	GLY 529
D	ARG 61	GLY 529

There are 48 helices in PDB entry 5YDZ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	61	106	Right-handed alpha
Helix 2	AA2	A	112	116	Right-handed 310
Helix 3	AA3	A	121	143	Right-handed alpha
Helix 4	AA4	A	242	246	Right-handed 310
Helix 5	AA5	A	297	333	Right-handed alpha
Helix 6	AA6	A	355	373	Right-handed alpha
Helix 7	AA7	A	374	378	Right-handed 310
Helix 8	AA8	A	379	405	Right-handed alpha
Helix 9	AA9	A	412	447	Right-handed alpha
Helix 10	AB1	A	456	469	Right-handed alpha
Helix 11	AB2	A	472	483	Right-handed alpha
Helix 12	AB3	A	488	526	Right-handed alpha
Helix 13	AB4	B	62	106	Right-handed alpha
Helix 14	AB5	B	112	116	Right-handed 310
Helix 15	AB6	B	121	143	Right-handed alpha
Helix 16	AB7	B	242	246	Right-handed 310
Helix 17	AB8	B	297	333	Right-handed alpha
Helix 18	AB9	B	355	373	Right-handed alpha
Helix 19	AC1	B	374	378	Right-handed 310
Helix 20	AC2	B	379	405	Right-handed alpha
Helix 21	AC3	B	412	447	Right-handed alpha
Helix 22	AC4	B	456	469	Right-handed alpha
Helix 23	AC5	B	472	483	Right-handed alpha
Helix 24	AC6	B	488	526	Right-handed alpha
Helix 25	AC7	C	62	106	Right-handed alpha
Helix 26	AC8	C	112	116	Right-handed 310
Helix 27	AC9	C	121	143	Right-handed alpha
Helix 28	AD1	C	242	246	Right-handed 310
Helix 29	AD2	C	297	333	Right-handed alpha
Helix 30	AD3	C	355	373	Right-handed alpha
Helix 31	AD4	C	374	378	Right-handed 310
Helix 32	AD5	C	379	405	Right-handed alpha
Helix 33	AD6	C	412	447	Right-handed alpha
Helix 34	AD7	C	456	469	Right-handed alpha
Helix 35	AD8	C	472	483	Right-handed alpha
Helix 36	AD9	C	488	526	Right-handed alpha
Helix 37	AE1	D	62	106	Right-handed alpha
Helix 38	AE2	D	112	116	Right-handed 310
Helix 39	AE3	D	121	143	Right-handed alpha
Helix 40	AE4	D	242	246	Right-handed 310
Helix 41	AE5	D	297	333	Right-handed alpha
Helix 42	AE6	D	355	373	Right-handed alpha
Helix 43	AE7	D	374	378	Right-handed 310
Helix 44	AE8	D	379	405	Right-handed alpha
Helix 45	AE9	D	412	447	Right-handed alpha
Helix 46	AF1	D	456	469	Right-handed alpha
Helix 47	AF2	D	472	483	Right-handed alpha
Helix 48	AF3	D	488	526	Right-handed alpha

There are 8 sheets in PDB entry 5YDZ. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

There are 6 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	118	119	first strand
Strand 2	A	271	282	anti-parallel
Strand 3	A	253	263	anti-parallel
Strand 4	A	230	240	anti-parallel
Strand 5	A	163	170	anti-parallel
Strand 6	A	188	195	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	174	176	first strand
Strand 2	A	181	183	anti-parallel

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There are 6 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	118	119	first strand
Strand 2	B	271	282	anti-parallel
Strand 3	B	253	263	anti-parallel
Strand 4	B	230	240	anti-parallel
Strand 5	B	163	170	anti-parallel
Strand 6	B	188	195	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	B	174	176	first strand
Strand 2	B	181	183	anti-parallel

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There are 6 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	118	119	first strand
Strand 2	C	271	282	anti-parallel
Strand 3	C	253	263	anti-parallel
Strand 4	C	230	240	anti-parallel
Strand 5	C	163	170	anti-parallel
Strand 6	C	188	195	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	C	174	176	first strand
Strand 2	C	181	183	anti-parallel

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There are 6 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	118	119	first strand
Strand 2	D	271	282	anti-parallel
Strand 3	D	253	263	anti-parallel
Strand 4	D	230	240	anti-parallel
Strand 5	D	163	170	anti-parallel
Strand 6	D	188	195	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	174	176	first strand
Strand 2	D	181	183	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: 5YDZ

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