Analysis of interatomic Contacts of Structural Units in PDB entry:
7NKD

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 7NKD entry

There are 8 chains in PDB entry 7NKD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 5	ALA 125
B	THR 5	GLN 90
C	THR 5	VAL 74
D	LYS 7	ASP 81
E	THR 8	ASP 81
F	ARG 11	VAL 77
d	MET 109	PRO 444
b	ASP 130	SER 166

There are 21 helices in PDB entry 7NKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	7	21	Right-handed alpha
Helix 2	AA2	B	10	22	Right-handed alpha
Helix 3	AA3	C	7	23	Right-handed alpha
Helix 4	AA4	d	110	138	Right-handed alpha
Helix 5	AA5	d	139	157	Right-handed alpha
Helix 6	AA6	d	173	192	Right-handed alpha
Helix 7	AA7	d	195	216	Right-handed alpha
Helix 8	AA8	d	216	225	Right-handed alpha
Helix 9	AA9	d	230	242	Right-handed alpha
Helix 10	AB1	d	246	259	Right-handed alpha
Helix 11	AB2	d	263	286	Right-handed alpha
Helix 12	AB3	d	288	306	Right-handed alpha
Helix 13	AB4	d	306	314	Right-handed alpha
Helix 14	AB5	d	319	331	Right-handed alpha
Helix 15	AB6	d	338	351	Right-handed alpha
Helix 16	AB7	d	356	372	Right-handed alpha
Helix 17	AB8	d	386	402	Right-handed alpha
Helix 18	AB9	d	412	416	Right-handed 310
Helix 19	AC1	d	431	442	Right-handed alpha
Helix 20	AC2	b	131	145	Right-handed alpha
Helix 21	AC3	b	147	161	Right-handed alpha

There are 5 sheets in PDB entry 7NKD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5,

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	44	46	first strand
Strand 2	A	29	34	anti-parallel
Strand 3	A	90	93	anti-parallel
Strand 4	A	55	58	anti-parallel
Strand 5	A	62	65	anti-parallel

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There are 6 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	44	46	first strand
Strand 2	A	29	34	anti-parallel
Strand 3	d	426	429	anti-parallel
Strand 4	d	419	423	anti-parallel
Strand 5	d	375	381	anti-parallel
Strand 6	d	405	409	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	33	36	first strand
Strand 2	B	43	45	anti-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	D	11	14	first strand
Strand 2	D	21	23	anti-parallel
Strand 3	D	61	63	anti-parallel
Strand 4	D	56	58	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	E	56	58	first strand
Strand 2	E	61	64	anti-parallel
Strand 3	E	20	23	anti-parallel
Strand 4	E	10	14	anti-parallel
Strand 5	E	78	79	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: 7NKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
7NKD