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

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 5GYD entry

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

Chain ID	Initial residue	Terminal residue
A	GLY 0	ASN 267
B	GLY 0	PHE 266
C	GLY 0	ASN 267
D	GLY 0	ASP 265

There are 29 helices in PDB entry 5GYD. 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	12	Right-handed 310
Helix 2	AA2	A	15	30	Right-handed alpha
Helix 3	AA3	A	63	73	Right-handed alpha
Helix 4	AA4	A	185	189	Right-handed 310
Helix 5	AA5	A	199	204	Right-handed alpha
Helix 6	AA6	A	206	210	Right-handed 310
Helix 7	AA7	A	224	228	Right-handed 310
Helix 8	AA8	A	230	257	Right-handed alpha
Helix 9	AA9	B	15	30	Right-handed alpha
Helix 10	AB1	B	63	72	Right-handed alpha
Helix 11	AB2	B	185	189	Right-handed 310
Helix 12	AB3	B	199	204	Right-handed alpha
Helix 13	AB4	B	206	210	Right-handed 310
Helix 14	AB5	B	230	256	Right-handed alpha
Helix 15	AB6	C	8	12	Right-handed 310
Helix 16	AB7	C	15	30	Right-handed alpha
Helix 17	AB8	C	63	73	Right-handed alpha
Helix 18	AB9	C	185	189	Right-handed 310
Helix 19	AC1	C	199	204	Right-handed alpha
Helix 20	AC2	C	206	210	Right-handed 310
Helix 21	AC3	C	224	228	Right-handed 310
Helix 22	AC4	C	230	256	Right-handed alpha
Helix 23	AC5	D	14	30	Right-handed alpha
Helix 24	AC6	D	63	73	Right-handed alpha
Helix 25	AC7	D	185	189	Right-handed 310
Helix 26	AC8	D	199	204	Right-handed alpha
Helix 27	AC9	D	206	210	Right-handed 310
Helix 28	AD1	D	224	228	Right-handed 310
Helix 29	AD2	D	230	256	Right-handed alpha

There are 6 sheets in PDB entry 5GYD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6,

There are 5 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	37	46	first strand
Strand 2	A	132	141	anti-parallel
Strand 3	A	149	171	anti-parallel
Strand 4	A	174	182	anti-parallel
Strand 5	A	262	264	anti-parallel

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There are 10 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	214	222	first strand
Strand 2	A	149	171	anti-parallel
Strand 3	A	119	128	anti-parallel
Strand 4	A	50	60	anti-parallel
Strand 5	B	1	6	parallel
Strand 6	A	1	6	anti-parallel
Strand 7	B	50	60	parallel
Strand 8	B	119	127	anti-parallel
Strand 9	B	147	170	anti-parallel
Strand 10	B	214	222	anti-parallel

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There are 5 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	37	46	first strand
Strand 2	B	132	143	anti-parallel
Strand 3	B	147	170	anti-parallel
Strand 4	B	175	182	anti-parallel
Strand 5	B	262	263	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	C	37	46	first strand
Strand 2	C	132	141	anti-parallel
Strand 3	C	149	171	anti-parallel
Strand 4	C	174	182	anti-parallel
Strand 5	C	262	265	anti-parallel

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There are 10 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	214	222	first strand
Strand 2	C	149	171	anti-parallel
Strand 3	C	119	127	anti-parallel
Strand 4	C	50	60	anti-parallel
Strand 5	D	1	6	parallel
Strand 6	C	1	6	anti-parallel
Strand 7	D	50	60	parallel
Strand 8	D	119	127	anti-parallel
Strand 9	D	149	171	anti-parallel
Strand 10	D	214	222	anti-parallel

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There are 5 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	37	46	first strand
Strand 2	D	132	141	anti-parallel
Strand 3	D	149	171	anti-parallel
Strand 4	D	174	182	anti-parallel
Strand 5	D	262	264	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: 5GYD

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