Analysis of interatomic Contacts of Structural Units in PDB entry:
5YD8

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 5YD8 entry

There are 6 chains in PDB entry 5YD8 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
Y	MET 1	LYS 254
X	MET 1	ILE 255
Z	MET 1	ILE 255
W	SER 1070	VAL 1077
U	GLY 1069	LYS 1079
V	ASP 1071	VAL 1077

There are 21 helices in PDB entry 5YD8. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	Y	9	20	Right-handed alpha
Helix 2	AA2	Y	55	57	Right-handed 310
Helix 3	AA3	Y	72	80	Right-handed alpha
Helix 4	AA4	Y	141	152	Right-handed alpha
Helix 5	AA5	Y	190	194	Right-handed 310
Helix 6	AA6	Y	209	216	Right-handed alpha
Helix 7	AA7	Y	217	222	Right-handed 310
Helix 8	AA8	X	9	18	Right-handed alpha
Helix 9	AA9	X	55	57	Right-handed 310
Helix 10	AB1	X	72	80	Right-handed alpha
Helix 11	AB2	X	141	153	Right-handed alpha
Helix 12	AB3	X	209	216	Right-handed alpha
Helix 13	AB4	X	217	222	Right-handed 310
Helix 14	AB5	Z	9	21	Right-handed alpha
Helix 15	AB6	Z	72	80	Right-handed alpha
Helix 16	AB7	Z	141	152	Right-handed alpha
Helix 17	AB8	Z	209	216	Right-handed alpha
Helix 18	AB9	Z	217	222	Right-handed 310
Helix 19	AC1	W	1072	1076	Right-handed 310
Helix 20	AC2	U	1072	1076	Right-handed 310
Helix 21	AC3	V	1072	1076	Right-handed 310

There are 7 sheets in PDB entry 5YD8. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7,

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	Y	59	62	first strand
Strand 2	Y	2	6	anti-parallel
Strand 3	Y	88	92	anti-parallel
Strand 4	Y	98	103	anti-parallel
Strand 5	Y	110	117	anti-parallel
Strand 6	Z	176	183	anti-parallel
Strand 7	Z	166	173	anti-parallel
Strand 8	Z	157	162	anti-parallel
Strand 9	Z	203	208	anti-parallel

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There are 9 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Y	66	71	first strand
Strand 2	Y	25	31	anti-parallel
Strand 3	Y	34	40	anti-parallel
Strand 4	Y	46	53	anti-parallel
Strand 5	Y	245	251	anti-parallel
Strand 6	Y	235	241	anti-parallel
Strand 7	Y	224	229	anti-parallel
Strand 8	Y	135	140	anti-parallel
Strand 9	Y	196	199	anti-parallel

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There are 9 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Y	203	208	first strand
Strand 2	Y	157	163	anti-parallel
Strand 3	Y	166	172	anti-parallel
Strand 4	Y	176	183	anti-parallel
Strand 5	X	110	117	anti-parallel
Strand 6	X	98	104	anti-parallel
Strand 7	X	87	92	anti-parallel
Strand 8	X	2	6	anti-parallel
Strand 9	X	59	62	anti-parallel

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There are 9 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	X	66	71	first strand
Strand 2	X	25	31	anti-parallel
Strand 3	X	34	40	anti-parallel
Strand 4	X	46	53	anti-parallel
Strand 5	X	245	251	anti-parallel
Strand 6	X	235	241	anti-parallel
Strand 7	X	224	229	anti-parallel
Strand 8	X	135	140	anti-parallel
Strand 9	X	196	199	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	X	126	127	first strand
Strand 2	U	1077	1078	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	X	203	208	first strand
Strand 2	X	157	162	anti-parallel
Strand 3	X	166	172	anti-parallel
Strand 4	X	176	183	anti-parallel
Strand 5	Z	110	117	anti-parallel
Strand 6	Z	98	104	anti-parallel
Strand 7	Z	87	92	anti-parallel
Strand 8	Z	2	6	anti-parallel
Strand 9	Z	57	62	anti-parallel

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There are 9 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	Z	66	71	first strand
Strand 2	Z	25	31	anti-parallel
Strand 3	Z	34	40	anti-parallel
Strand 4	Z	46	53	anti-parallel
Strand 5	Z	245	251	anti-parallel
Strand 6	Z	235	240	anti-parallel
Strand 7	Z	224	229	anti-parallel
Strand 8	Z	135	140	anti-parallel
Strand 9	Z	196	199	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: 5YD8

Analysis of interatomic Contacts of Structural Units in PDB entry:
5YD8