Analysis of interatomic Contacts of Structural Units in PDB entry:
5YD3

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 5YD3 entry

There are 8 chains in PDB entry 5YD3 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 3	LYS 252
B	ILE 2	PRO 9
C	GLU 3	LYS 252
D	ILE 2	PRO 9
E	GLU 3	VAL 253
F	ASP 1	PRO 9
G	VAL 4	LEU 251
H	ASN 3	PRO 9

There are 15 helices in PDB entry 5YD3. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	30	34	Right-handed 310
Helix 2	AA2	A	64	67	Right-handed 310
Helix 3	AA3	A	89	93	Right-handed 310
Helix 4	AA4	A	224	228	Right-handed 310
Helix 5	AA5	C	64	67	Right-handed 310
Helix 6	AA6	C	89	93	Right-handed 310
Helix 7	AA7	C	224	228	Right-handed 310
Helix 8	AA8	E	30	34	Right-handed 310
Helix 9	AA9	E	64	67	Right-handed 310
Helix 10	AB1	E	89	93	Right-handed 310
Helix 11	AB2	E	224	228	Right-handed 310
Helix 12	AB3	G	64	67	Right-handed 310
Helix 13	AB4	G	76	78	Right-handed 310
Helix 14	AB5	G	89	93	Right-handed 310
Helix 15	AB6	G	224	228	Right-handed 310

There are 25 sheets in PDB entry 5YD3. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7,

There are 4 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	5	8	first strand
Strand 2	A	20	27	anti-parallel
Strand 3	A	80	85	anti-parallel
Strand 4	A	70	75	anti-parallel

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There are 6 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	12	14	first strand
Strand 2	A	113	117	parallel
Strand 3	A	94	102	anti-parallel
Strand 4	A	36	41	anti-parallel
Strand 5	A	47	53	anti-parallel
Strand 6	A	60	62	anti-parallel

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There are 4 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	12	14	first strand
Strand 2	A	113	117	parallel
Strand 3	A	94	102	anti-parallel
Strand 4	A	105	109	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	A	144	145	first strand
Strand 2	A	159	165	anti-parallel
Strand 3	A	215	220	anti-parallel
Strand 4	A	207	211	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	A	150	153	first strand
Strand 2	A	247	251	parallel
Strand 3	A	229	235	anti-parallel
Strand 4	A	178	183	anti-parallel
Strand 5	A	189	194	anti-parallel
Strand 6	A	198	199	anti-parallel

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There are 4 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	150	153	first strand
Strand 2	A	247	251	parallel
Strand 3	A	229	235	anti-parallel
Strand 4	A	242	243	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	5	8	first strand
Strand 2	C	20	27	anti-parallel
Strand 3	C	80	85	anti-parallel
Strand 4	C	70	75	anti-parallel

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There are 6 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	12	14	first strand
Strand 2	C	113	117	parallel
Strand 3	C	94	102	anti-parallel
Strand 4	C	36	41	anti-parallel
Strand 5	C	47	53	anti-parallel
Strand 6	C	60	62	anti-parallel

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There are 4 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	12	14	first strand
Strand 2	C	113	117	parallel
Strand 3	C	94	102	anti-parallel
Strand 4	C	105	109	anti-parallel

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There are 4 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	144	145	first strand
Strand 2	C	159	165	anti-parallel
Strand 3	C	215	220	anti-parallel
Strand 4	C	207	211	anti-parallel

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There are 6 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	150	153	first strand
Strand 2	C	247	251	parallel
Strand 3	C	229	235	anti-parallel
Strand 4	C	178	183	anti-parallel
Strand 5	C	190	194	anti-parallel
Strand 6	C	198	199	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	150	153	first strand
Strand 2	C	247	251	parallel
Strand 3	C	229	235	anti-parallel
Strand 4	C	242	243	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	5	8	first strand
Strand 2	E	20	27	anti-parallel
Strand 3	E	80	85	anti-parallel
Strand 4	E	70	75	anti-parallel

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There are 6 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	12	14	first strand
Strand 2	E	113	117	parallel
Strand 3	E	94	102	anti-parallel
Strand 4	E	36	41	anti-parallel
Strand 5	E	47	53	anti-parallel
Strand 6	E	60	62	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	12	14	first strand
Strand 2	E	113	117	parallel
Strand 3	E	94	102	anti-parallel
Strand 4	E	105	109	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	144	145	first strand
Strand 2	E	159	165	anti-parallel
Strand 3	E	215	220	anti-parallel
Strand 4	E	207	211	anti-parallel

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There are 6 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	150	153	first strand
Strand 2	E	247	251	parallel
Strand 3	E	229	235	anti-parallel
Strand 4	E	178	183	anti-parallel
Strand 5	E	190	194	anti-parallel
Strand 6	E	198	199	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	150	153	first strand
Strand 2	E	247	251	parallel
Strand 3	E	229	235	anti-parallel
Strand 4	E	242	243	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	5	8	first strand
Strand 2	G	20	27	anti-parallel
Strand 3	G	80	85	anti-parallel
Strand 4	G	70	75	anti-parallel

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There are 6 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	12	14	first strand
Strand 2	G	113	117	parallel
Strand 3	G	94	102	anti-parallel
Strand 4	G	36	41	anti-parallel
Strand 5	G	47	53	anti-parallel
Strand 6	G	60	62	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	12	14	first strand
Strand 2	G	113	117	parallel
Strand 3	G	94	102	anti-parallel
Strand 4	G	105	109	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	144	145	first strand
Strand 2	G	159	165	anti-parallel
Strand 3	G	215	220	anti-parallel
Strand 4	G	207	211	anti-parallel

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There are 5 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	150	152	first strand
Strand 2	G	247	250	parallel
Strand 3	G	229	235	anti-parallel
Strand 4	G	178	183	anti-parallel
Strand 5	G	190	191	anti-parallel

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There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	150	152	first strand
Strand 2	G	247	250	parallel
Strand 3	G	229	235	anti-parallel
Strand 4	G	242	243	anti-parallel

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There are 2 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	193	194	first strand
Strand 2	G	198	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: 5YD3

Analysis of interatomic Contacts of Structural Units in PDB entry:
5YD3