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

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 6NJD entry

There are 4 chains in PDB entry 6NJD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLY -4	ARG 148
B	PHE 8	LYS 198
C	MET 1	ARG 148
D	ASN 12	THR 194

There are 25 helices in PDB entry 6NJD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	22	35	Right-handed alpha
Helix 2	AA2	A	37	39	Right-handed 310
Helix 3	AA3	A	56	60	Right-handed 310
Helix 4	AA4	A	98	111	Right-handed alpha
Helix 5	AA5	A	113	115	Right-handed 310
Helix 6	AA6	A	132	136	Right-handed 310
Helix 7	AA7	B	12	27	Right-handed alpha
Helix 8	AA8	B	45	50	Right-handed 310
Helix 9	AA9	B	53	55	Right-handed 310
Helix 10	AB1	B	65	75	Right-handed alpha
Helix 11	AB2	B	127	132	Right-handed alpha
Helix 12	AB3	B	155	172	Right-handed alpha
Helix 13	AB4	B	173	184	Right-handed alpha
Helix 14	AB5	C	22	35	Right-handed alpha
Helix 15	AB6	C	37	39	Right-handed 310
Helix 16	AB7	C	98	111	Right-handed alpha
Helix 17	AB8	C	113	115	Right-handed 310
Helix 18	AB9	C	132	136	Right-handed 310
Helix 19	AC1	D	13	27	Right-handed alpha
Helix 20	AC2	D	45	50	Right-handed 310
Helix 21	AC3	D	53	55	Right-handed 310
Helix 22	AC4	D	65	75	Right-handed alpha
Helix 23	AC5	D	127	132	Right-handed alpha
Helix 24	AC6	D	155	172	Right-handed alpha
Helix 25	AC7	D	173	184	Right-handed alpha

There are 8 sheets in PDB entry 6NJD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8,

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	12	17	first strand
Strand 2	A	1	6	anti-parallel
Strand 3	A	66	71	parallel
Strand 4	A	41	45	anti-parallel
Strand 5	A	48	49	anti-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	88	93	first strand
Strand 2	A	77	83	anti-parallel
Strand 3	A	142	147	parallel
Strand 4	A	117	121	anti-parallel
Strand 5	A	124	125	anti-parallel

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There are 2 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	28	32	first strand
Strand 2	B	191	195	anti-parallel

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There are 6 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	57	60	first strand
Strand 2	B	147	153	anti-parallel
Strand 3	B	82	88	anti-parallel
Strand 4	B	93	100	anti-parallel
Strand 5	B	107	112	anti-parallel
Strand 6	B	115	118	anti-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	C	48	49	first strand
Strand 2	C	41	45	anti-parallel
Strand 3	C	68	71	anti-parallel

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There are 5 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	88	93	first strand
Strand 2	C	77	82	anti-parallel
Strand 3	C	142	147	parallel
Strand 4	C	117	121	anti-parallel
Strand 5	C	124	125	anti-parallel

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There are 2 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	30	32	first strand
Strand 2	D	191	193	anti-parallel

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There are 6 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	57	60	first strand
Strand 2	D	149	153	anti-parallel
Strand 3	D	82	87	anti-parallel
Strand 4	D	93	101	anti-parallel
Strand 5	D	106	112	anti-parallel
Strand 6	D	115	118	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: 6NJD

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