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

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 6JDK entry

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

Chain ID	Initial residue	Terminal residue
A	GLU 16	ASP 544
B	GLU 16	ASP 544

There are 46 helices in PDB entry 6JDK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	26	39	Right-handed alpha
Helix 2	AA2	A	54	59	Right-handed alpha
Helix 3	AA3	A	77	82	Right-handed alpha
Helix 4	AA4	A	92	108	Right-handed alpha
Helix 5	AA5	A	109	111	Right-handed 310
Helix 6	AA6	A	126	129	Right-handed 310
Helix 7	AA7	A	163	167	Right-handed 310
Helix 8	AA8	A	175	177	Right-handed 310
Helix 9	AA9	A	195	209	Right-handed alpha
Helix 10	AB1	A	231	239	Right-handed alpha
Helix 11	AB2	A	241	250	Right-handed alpha
Helix 12	AB3	A	269	284	Right-handed alpha
Helix 13	AB4	A	286	291	Right-handed alpha
Helix 14	AB5	A	299	318	Right-handed alpha
Helix 15	AB6	A	320	328	Right-handed alpha
Helix 16	AB7	A	346	351	Right-handed alpha
Helix 17	AB8	A	394	400	Right-handed alpha
Helix 18	AB9	A	411	416	Right-handed alpha
Helix 19	AC1	A	443	447	Right-handed 310
Helix 20	AC2	A	448	470	Right-handed alpha
Helix 21	AC3	A	478	494	Right-handed alpha
Helix 22	AC4	A	495	496	Right-handed 310
Helix 23	AC5	A	497	501	Right-handed 310
Helix 24	AC6	A	522	536	Right-handed alpha
Helix 25	AC7	B	26	39	Right-handed alpha
Helix 26	AC8	B	54	59	Right-handed alpha
Helix 27	AC9	B	77	82	Right-handed alpha
Helix 28	AD1	B	92	108	Right-handed alpha
Helix 29	AD2	B	109	111	Right-handed 310
Helix 30	AD3	B	175	177	Right-handed 310
Helix 31	AD4	B	195	207	Right-handed alpha
Helix 32	AD5	B	231	239	Right-handed alpha
Helix 33	AD6	B	241	250	Right-handed alpha
Helix 34	AD7	B	269	284	Right-handed alpha
Helix 35	AD8	B	286	291	Right-handed alpha
Helix 36	AD9	B	299	318	Right-handed alpha
Helix 37	AE1	B	320	328	Right-handed alpha
Helix 38	AE2	B	346	351	Right-handed alpha
Helix 39	AE3	B	394	401	Right-handed alpha
Helix 40	AE4	B	411	416	Right-handed alpha
Helix 41	AE5	B	443	447	Right-handed 310
Helix 42	AE6	B	448	470	Right-handed alpha
Helix 43	AE7	B	478	494	Right-handed alpha
Helix 44	AE8	B	495	496	Right-handed 310
Helix 45	AE9	B	497	501	Right-handed 310
Helix 46	AF1	B	522	536	Right-handed alpha

There are 12 sheets in PDB entry 6JDK. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

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	113	115	first strand
Strand 2	A	43	47	parallel
Strand 3	A	17	23	parallel
Strand 4	A	140	148	parallel
Strand 5	A	130	135	anti-parallel
Strand 6	A	119	125	anti-parallel
Strand 7	A	403	405	parallel

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There are 5 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	113	115	first strand
Strand 2	A	43	47	parallel
Strand 3	A	17	23	parallel
Strand 4	A	140	148	parallel
Strand 5	A	434	436	parallel

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There are 5 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	170	173	first strand
Strand 2	A	385	388	parallel
Strand 3	A	188	192	parallel
Strand 4	A	211	216	parallel
Strand 5	A	356	360	parallel

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There are 2 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	223	224	first strand
Strand 2	A	343	344	parallel

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There are 3 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	366	370	first strand
Strand 2	A	373	376	anti-parallel
Strand 3	A	379	382	anti-parallel

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There are 2 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	475	477	first strand
Strand 2	A	541	543	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	113	115	first strand
Strand 2	B	43	47	parallel
Strand 3	B	17	23	parallel
Strand 4	B	140	148	parallel
Strand 5	B	130	135	anti-parallel
Strand 6	B	119	125	anti-parallel
Strand 7	B	403	405	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	113	115	first strand
Strand 2	B	43	47	parallel
Strand 3	B	17	23	parallel
Strand 4	B	140	148	parallel
Strand 5	B	434	436	parallel

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There are 5 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	170	173	first strand
Strand 2	B	385	388	parallel
Strand 3	B	188	192	parallel
Strand 4	B	211	216	parallel
Strand 5	B	356	360	parallel

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There are 2 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	223	224	first strand
Strand 2	B	343	344	parallel

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There are 3 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	366	370	first strand
Strand 2	B	373	376	anti-parallel
Strand 3	B	379	382	anti-parallel

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There are 2 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	475	477	first strand
Strand 2	B	541	543	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: 6JDK

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