Analysis of interatomic Contacts of Structural Units in PDB entry:
5D13

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 5D13 entry

There are 9 chains in PDB entry 5D13 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 307	VAL 406
B	ILE 307	VAL 406
C	ASP 306	VAL 406
D	ILE 307	VAL 406
G	LYS 420	VAL 425
E	LYS 420	VAL 425
H	LYS 420	VAL 425
F	LYS 420	VAL 425
I	LYS 502	LYS 502

There are 12 helices in PDB entry 5D13. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	345	351	Right-handed alpha
Helix 2	AA2	A	371	381	Right-handed alpha
Helix 3	AA3	A	393	406	Right-handed alpha
Helix 4	AA4	B	345	351	Right-handed alpha
Helix 5	AA5	B	371	381	Right-handed alpha
Helix 6	AA6	B	393	405	Right-handed alpha
Helix 7	AA7	C	345	351	Right-handed alpha
Helix 8	AA8	C	371	381	Right-handed alpha
Helix 9	AA9	C	393	405	Right-handed alpha
Helix 10	AB1	D	345	351	Right-handed alpha
Helix 11	AB2	D	371	381	Right-handed alpha
Helix 12	AB3	D	393	406	Right-handed alpha

There are 8 sheets in PDB entry 5D13. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

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	312	317	first strand
Strand 2	A	385	392	anti-parallel
Strand 3	A	357	362	anti-parallel
Strand 4	A	365	366	anti-parallel

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There are 3 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	336	341	first strand
Strand 2	A	325	329	anti-parallel
Strand 3	E	423	424	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	B	312	317	first strand
Strand 2	B	385	392	anti-parallel
Strand 3	B	357	362	anti-parallel
Strand 4	B	365	366	anti-parallel

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There are 3 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	336	341	first strand
Strand 2	B	325	329	anti-parallel
Strand 3	G	423	424	anti-parallel

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There are 4 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	312	317	first strand
Strand 2	C	385	392	anti-parallel
Strand 3	C	357	362	anti-parallel
Strand 4	C	365	366	anti-parallel

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There are 6 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	312	317	first strand
Strand 2	C	385	392	anti-parallel
Strand 3	C	357	362	anti-parallel
Strand 4	C	336	341	anti-parallel
Strand 5	C	325	329	anti-parallel
Strand 6	H	422	424	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	D	312	317	first strand
Strand 2	D	385	392	anti-parallel
Strand 3	D	357	362	anti-parallel
Strand 4	D	365	366	anti-parallel

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There are 3 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	336	341	first strand
Strand 2	D	325	329	anti-parallel
Strand 3	F	422	424	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: 5D13

Analysis of interatomic Contacts of Structural Units in PDB entry:
5D13