Analysis of interatomic Contacts of Structural Units in PDB entry:
6PD4

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 6PD4 entry

There are 2 chains in PDB entry 6PD4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 176	ARG 611
B	GLN 176	SER 604

There are 7 helices in PDB entry 6PD4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	373	375	Right-handed 310
Helix 2	AA2	A	378	382	Right-handed 310
Helix 3	AA3	A	393	398	Right-handed alpha
Helix 4	AA4	B	204	207	Right-handed 310
Helix 5	AA5	B	373	375	Right-handed 310
Helix 6	AA6	B	378	382	Right-handed 310
Helix 7	AA7	B	393	398	Right-handed alpha

There are 14 sheets in PDB entry 6PD4. 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,

There are 5 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	178	180	first strand
Strand 2	A	558	568	anti-parallel
Strand 3	A	571	582	anti-parallel
Strand 4	A	587	596	anti-parallel
Strand 5	A	201	202	anti-parallel

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There are 4 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	215	225	first strand
Strand 2	A	228	237	anti-parallel
Strand 3	A	244	257	anti-parallel
Strand 4	A	263	271	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	279	287	first strand
Strand 2	A	290	297	anti-parallel
Strand 3	A	314	320	anti-parallel
Strand 4	A	332	337	anti-parallel

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There are 5 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	339	341	first strand
Strand 2	A	425	430	parallel
Strand 3	A	407	417	anti-parallel
Strand 4	A	361	371	anti-parallel
Strand 5	A	347	350	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	A	339	341	first strand
Strand 2	A	425	430	parallel
Strand 3	A	407	417	anti-parallel
Strand 4	A	361	371	anti-parallel
Strand 5	A	356	358	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	442	447	first strand
Strand 2	A	450	455	anti-parallel
Strand 3	A	465	471	anti-parallel
Strand 4	A	476	479	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	A	511	515	first strand
Strand 2	A	520	526	anti-parallel
Strand 3	A	535	541	anti-parallel
Strand 4	A	544	550	anti-parallel

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There are 5 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	178	180	first strand
Strand 2	B	558	568	anti-parallel
Strand 3	B	571	582	anti-parallel
Strand 4	B	587	596	anti-parallel
Strand 5	B	201	202	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	B	215	225	first strand
Strand 2	B	228	237	anti-parallel
Strand 3	B	244	257	anti-parallel
Strand 4	B	263	271	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	B	279	287	first strand
Strand 2	B	290	297	anti-parallel
Strand 3	B	314	320	anti-parallel
Strand 4	B	332	337	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	339	341	first strand
Strand 2	B	425	430	parallel
Strand 3	B	407	417	anti-parallel
Strand 4	B	361	371	anti-parallel
Strand 5	B	347	350	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	339	341	first strand
Strand 2	B	425	430	parallel
Strand 3	B	407	417	anti-parallel
Strand 4	B	361	371	anti-parallel
Strand 5	B	356	358	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	B	442	447	first strand
Strand 2	B	450	455	anti-parallel
Strand 3	B	465	471	anti-parallel
Strand 4	B	476	479	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	511	515	first strand
Strand 2	B	520	526	anti-parallel
Strand 3	B	535	541	anti-parallel
Strand 4	B	544	550	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: 6PD4

Analysis of interatomic Contacts of Structural Units in PDB entry:
6PD4