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

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 5JOD entry

There are 2 chains in PDB entry 5JOD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 78	LEU 328
B	LYS 78	LEU 328

There are 22 helices in PDB entry 5JOD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	88	100	Right-handed alpha
Helix 2	AA2	A	102	115	Right-handed alpha
Helix 3	AA3	A	7	12	Right-handed 310
Helix 4	AA4	A	49	55	Right-handed 310
Helix 5	AA5	A	59	63	Right-handed 310
Helix 6	AA6	A	108	112	Right-handed 310
Helix 7	AA7	A	138	146	Right-handed alpha
Helix 8	AA8	A	174	176	Right-handed 310
Helix 9	AA9	A	223	234	Right-handed alpha
Helix 10	AB1	A	269	273	Right-handed alpha
Helix 11	AB2	A	302	308	Right-handed alpha
Helix 12	AB3	B	88	100	Right-handed alpha
Helix 13	AB4	B	102	115	Right-handed alpha
Helix 14	AB5	B	7	12	Right-handed alpha
Helix 15	AB6	B	49	55	Right-handed 310
Helix 16	AB7	B	59	63	Right-handed 310
Helix 17	AB8	B	108	112	Right-handed 310
Helix 18	AB9	B	138	146	Right-handed alpha
Helix 19	AC1	B	174	176	Right-handed 310
Helix 20	AC2	B	223	234	Right-handed alpha
Helix 21	AC3	B	269	273	Right-handed alpha
Helix 22	AC4	B	302	308	Right-handed alpha

There are 8 sheets in PDB entry 5JOD. 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	27	28	first strand
Strand 2	A	21	22	anti-parallel
Strand 3	A	80	93	anti-parallel
Strand 4	A	67	77	anti-parallel

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There are 14 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	27	28	first strand
Strand 2	A	21	22	anti-parallel
Strand 3	A	80	93	anti-parallel
Strand 4	A	96	107	anti-parallel
Strand 5	A	40	43	parallel
Strand 6	A	122	125	anti-parallel
Strand 7	A	31	34	parallel
Strand 8	A	14	17	anti-parallel
Strand 9	A	80	87	anti-parallel
Strand 10	A	165	170	anti-parallel
Strand 11	A	153	157	anti-parallel
Strand 12	A	309	314	anti-parallel
Strand 13	A	319	325	anti-parallel
Strand 14	A	178	186	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	A	265	268	first strand
Strand 2	A	257	260	anti-parallel
Strand 3	A	194	201	anti-parallel
Strand 4	A	204	213	anti-parallel
Strand 5	A	298	301	parallel
Strand 6	A	220	222	anti-parallel
Strand 7	A	289	291	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	237	238	first strand
Strand 2	A	245	248	anti-parallel
Strand 3	A	281	287	anti-parallel
Strand 4	A	274	277	anti-parallel

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There are 9 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	67	77	first strand
Strand 2	B	80	93	anti-parallel
Strand 3	B	15	22	anti-parallel
Strand 4	B	80	87	anti-parallel
Strand 5	B	165	170	anti-parallel
Strand 6	B	153	157	anti-parallel
Strand 7	B	309	314	anti-parallel
Strand 8	B	319	325	anti-parallel
Strand 9	B	178	186	anti-parallel

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There are 13 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	67	77	first strand
Strand 2	B	80	93	anti-parallel
Strand 3	B	96	107	anti-parallel
Strand 4	B	40	43	parallel
Strand 5	B	122	125	anti-parallel
Strand 6	B	27	34	parallel
Strand 7	B	15	22	anti-parallel
Strand 8	B	80	87	anti-parallel
Strand 9	B	165	170	anti-parallel
Strand 10	B	153	157	anti-parallel
Strand 11	B	309	314	anti-parallel
Strand 12	B	319	325	anti-parallel
Strand 13	B	178	186	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	B	265	268	first strand
Strand 2	B	257	260	anti-parallel
Strand 3	B	194	201	anti-parallel
Strand 4	B	204	213	anti-parallel
Strand 5	B	298	301	parallel
Strand 6	B	220	222	anti-parallel
Strand 7	B	289	291	parallel

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There are 4 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	237	238	first strand
Strand 2	B	245	248	anti-parallel
Strand 3	B	281	287	anti-parallel
Strand 4	B	274	277	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: 5JOD

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