Analysis of interatomic Contacts of Structural Units in PDB entry:
5Y39

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 5Y39 entry

There are 10 chains in PDB entry 5Y39 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	HIS 79	GLN 145
B	LYS 5	THR 120
C	ASP 3	VAL 123
D	GLY 0	ASP 98
E	MET 83	ALA 172
F	GLN 114	GLN 145
G	ALA 6	VAL 122
H	ASP 3	GLN 119
I	ALA 4	LYS 88
J	MET 83	MET 171

There are 36 helices in PDB entry 5Y39. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	81	97	Right-handed alpha
Helix 2	AA2	A	114	121	Right-handed alpha
Helix 3	AA3	A	125	145	Right-handed alpha
Helix 4	AA4	B	6	13	Right-handed alpha
Helix 5	AA5	B	41	62	Right-handed alpha
Helix 6	AA6	B	100	117	Right-handed alpha
Helix 7	AA7	B	118	120	Right-handed 310
Helix 8	AA8	C	4	13	Right-handed alpha
Helix 9	AA9	C	14	16	Right-handed 310
Helix 10	AB1	C	41	45	Right-handed 310
Helix 11	AB2	C	46	51	Right-handed alpha
Helix 12	AB3	C	51	61	Right-handed alpha
Helix 13	AB4	C	99	116	Right-handed alpha
Helix 14	AB5	C	117	121	Right-handed 310
Helix 15	AB6	D	1	11	Right-handed alpha
Helix 16	AB7	D	36	52	Right-handed alpha
Helix 17	AB8	E	84	97	Right-handed alpha
Helix 18	AB9	E	120	122	Right-handed 310
Helix 19	AC1	E	123	136	Right-handed alpha
Helix 20	AC2	F	115	119	Right-handed alpha
Helix 21	AC3	F	125	143	Right-handed alpha
Helix 22	AC4	G	7	13	Right-handed alpha
Helix 23	AC5	G	41	59	Right-handed alpha
Helix 24	AC6	G	59	64	Right-handed alpha
Helix 25	AC7	G	100	122	Right-handed alpha
Helix 26	AC8	H	4	11	Right-handed alpha
Helix 27	AC9	H	12	16	Right-handed 310
Helix 28	AD1	H	41	45	Right-handed 310
Helix 29	AD2	H	46	51	Right-handed alpha
Helix 30	AD3	H	51	61	Right-handed alpha
Helix 31	AD4	H	99	116	Right-handed alpha
Helix 32	AD5	I	6	11	Right-handed alpha
Helix 33	AD6	I	39	53	Right-handed alpha
Helix 34	AD7	J	84	95	Right-handed alpha
Helix 35	AD8	J	123	135	Right-handed alpha
Helix 36	AD9	J	136	138	Right-handed 310

There are 5 sheets in PDB entry 5Y39. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5,

There are 10 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	31	36	first strand
Strand 2	B	19	25	anti-parallel
Strand 3	B	89	95	anti-parallel
Strand 4	B	79	86	anti-parallel
Strand 5	B	69	76	anti-parallel
Strand 6	C	68	75	anti-parallel
Strand 7	C	78	85	anti-parallel
Strand 8	C	88	95	anti-parallel
Strand 9	C	19	25	anti-parallel
Strand 10	C	31	36	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	D	25	31	first strand
Strand 2	D	15	22	anti-parallel
Strand 3	D	83	90	anti-parallel
Strand 4	D	73	80	anti-parallel
Strand 5	D	65	69	anti-parallel
Strand 6	E	146	150	anti-parallel
Strand 7	E	154	160	anti-parallel
Strand 8	E	164	171	anti-parallel
Strand 9	E	100	107	anti-parallel
Strand 10	E	112	117	anti-parallel

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There are 10 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	31	36	first strand
Strand 2	G	19	26	anti-parallel
Strand 3	G	89	95	anti-parallel
Strand 4	G	79	86	anti-parallel
Strand 5	G	69	76	anti-parallel
Strand 6	H	68	75	anti-parallel
Strand 7	H	78	85	anti-parallel
Strand 8	H	88	95	anti-parallel
Strand 9	H	19	25	anti-parallel
Strand 10	H	31	36	anti-parallel

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There are 4 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	20	21	first strand
Strand 2	I	84	87	anti-parallel
Strand 3	I	76	78	anti-parallel
Strand 4	I	66	67	anti-parallel

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There are 5 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	112	117	first strand
Strand 2	J	102	106	anti-parallel
Strand 3	J	165	169	anti-parallel
Strand 4	J	156	160	anti-parallel
Strand 5	J	147	149	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: 5Y39

Analysis of interatomic Contacts of Structural Units in PDB entry:
5Y39