Analysis of interatomic Contacts of Structural Units in PDB entry:
9PDA

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 9PDA entry

There are 4 chains in PDB entry 9PDA (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 16	ASN 238
B	ILE 16	ASN 238
C	ILE 16	ASN 238
D	ILE 16	ASN 34

There are 12 helices in PDB entry 9PDA. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	53	57	Right-handed 310
Helix 2	AA2	A	159	167	Right-handed alpha
Helix 3	AA3	A	227	237	Right-handed alpha
Helix 4	AA4	B	53	57	Right-handed 310
Helix 5	AA5	B	159	167	Right-handed alpha
Helix 6	AA6	B	227	238	Right-handed alpha
Helix 7	AA7	C	53	57	Right-handed 310
Helix 8	AA8	C	159	167	Right-handed alpha
Helix 9	AA9	C	227	237	Right-handed alpha
Helix 10	AB1	D	53	57	Right-handed 310
Helix 11	AB2	D	159	167	Right-handed alpha
Helix 12	AB3	D	227	238	Right-handed alpha

There are 8 sheets in PDB entry 9PDA. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

There are 7 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	20	21	first strand
Strand 2	A	151	156	anti-parallel
Strand 3	A	130	135	anti-parallel
Strand 4	A	195	198	anti-parallel
Strand 5	A	201	208	anti-parallel
Strand 6	A	219	223	anti-parallel
Strand 7	A	175	178	anti-parallel

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There are 7 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	30	34	first strand
Strand 2	A	38	46	anti-parallel
Strand 3	A	49	52	anti-parallel
Strand 4	A	101	105	anti-parallel
Strand 5	A	78	87	anti-parallel
Strand 6	A	62	65	anti-parallel
Strand 7	A	30	34	anti-parallel

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There are 7 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	20	21	first strand
Strand 2	B	151	156	anti-parallel
Strand 3	B	130	135	anti-parallel
Strand 4	B	195	198	anti-parallel
Strand 5	B	201	208	anti-parallel
Strand 6	B	219	223	anti-parallel
Strand 7	B	175	178	anti-parallel

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There are 7 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	30	34	first strand
Strand 2	B	38	46	anti-parallel
Strand 3	B	49	52	anti-parallel
Strand 4	B	101	105	anti-parallel
Strand 5	B	78	87	anti-parallel
Strand 6	B	62	65	anti-parallel
Strand 7	B	30	34	anti-parallel

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There are 7 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	20	21	first strand
Strand 2	C	151	156	anti-parallel
Strand 3	C	130	135	anti-parallel
Strand 4	C	195	198	anti-parallel
Strand 5	C	201	208	anti-parallel
Strand 6	C	219	223	anti-parallel
Strand 7	C	175	178	anti-parallel

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There are 7 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	30	34	first strand
Strand 2	C	38	46	anti-parallel
Strand 3	C	49	52	anti-parallel
Strand 4	C	101	105	anti-parallel
Strand 5	C	78	87	anti-parallel
Strand 6	C	62	65	anti-parallel
Strand 7	C	30	34	anti-parallel

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There are 7 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	20	21	first strand
Strand 2	D	151	156	anti-parallel
Strand 3	D	130	135	anti-parallel
Strand 4	D	195	198	anti-parallel
Strand 5	D	201	208	anti-parallel
Strand 6	D	219	223	anti-parallel
Strand 7	D	175	178	anti-parallel

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There are 7 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	30	34	first strand
Strand 2	D	38	46	anti-parallel
Strand 3	D	49	52	anti-parallel
Strand 4	D	101	105	anti-parallel
Strand 5	D	78	87	anti-parallel
Strand 6	D	62	65	anti-parallel
Strand 7	D	30	34	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: 9PDA

Analysis of interatomic Contacts of Structural Units in PDB entry:
9PDA