Analysis of interatomic Contacts of Structural Units in PDB entry:
4NKD

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 4NKD entry

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

Chain ID	Initial residue	Terminal residue
A	ASP 1	SER 254
B	ASP 1	SER 254
C	ASP 1	SER 254
D	ASP 1	SER 254

There are 12 helices in PDB entry 4NKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	196	199	Right-handed 310
Helix 2	2	A	221	225	Right-handed 310
Helix 3	3	A	84	88	Right-handed 310
Helix 4	4	B	196	199	Right-handed 310
Helix 5	5	B	221	225	Right-handed 310
Helix 6	6	B	84	88	Right-handed 310
Helix 7	7	C	196	199	Right-handed 310
Helix 8	8	C	221	225	Right-handed 310
Helix 9	9	C	84	88	Right-handed 310
Helix 10	10	D	196	199	Right-handed 310
Helix 11	11	D	221	225	Right-handed 310
Helix 12	12	D	84	88	Right-handed 310

There are 24 sheets in PDB entry 4NKD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	136	139	first strand
Strand 2	A	151	158	anti-parallel
Strand 3	A	212	217	anti-parallel
Strand 4	A	202	207	anti-parallel

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There are 6 strands in B sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	143	145	first strand
Strand 2	A	249	253	parallel
Strand 3	A	226	233	anti-parallel
Strand 4	A	168	175	anti-parallel
Strand 5	A	179	187	anti-parallel
Strand 6	A	192	194	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	143	145	first strand
Strand 2	A	249	253	parallel
Strand 3	A	226	233	anti-parallel
Strand 4	A	242	245	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	4	6	first strand
Strand 2	A	19	25	anti-parallel
Strand 3	A	75	80	anti-parallel
Strand 4	A	67	68	anti-parallel

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There are 2 strands in E sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	12	13	first strand
Strand 2	A	110	111	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	58	59	first strand
Strand 2	A	50	54	anti-parallel
Strand 3	A	38	43	anti-parallel
Strand 4	A	90	95	anti-parallel
Strand 5	A	107	108	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	136	139	first strand
Strand 2	B	151	158	anti-parallel
Strand 3	B	212	217	anti-parallel
Strand 4	B	202	207	anti-parallel

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There are 6 strands in H sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	143	145	first strand
Strand 2	B	249	253	parallel
Strand 3	B	226	233	anti-parallel
Strand 4	B	168	175	anti-parallel
Strand 5	B	179	187	anti-parallel
Strand 6	B	192	194	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	143	145	first strand
Strand 2	B	249	253	parallel
Strand 3	B	226	233	anti-parallel
Strand 4	B	242	245	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	4	6	first strand
Strand 2	B	19	25	anti-parallel
Strand 3	B	75	80	anti-parallel
Strand 4	B	67	68	anti-parallel

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There are 2 strands in K sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	12	13	first strand
Strand 2	B	110	111	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	58	59	first strand
Strand 2	B	50	54	anti-parallel
Strand 3	B	38	43	anti-parallel
Strand 4	B	90	95	anti-parallel
Strand 5	B	107	108	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	136	139	first strand
Strand 2	C	151	158	anti-parallel
Strand 3	C	212	217	anti-parallel
Strand 4	C	202	207	anti-parallel

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There are 6 strands in N sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	143	145	first strand
Strand 2	C	249	253	parallel
Strand 3	C	226	233	anti-parallel
Strand 4	C	168	175	anti-parallel
Strand 5	C	179	187	anti-parallel
Strand 6	C	192	194	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	143	145	first strand
Strand 2	C	249	253	parallel
Strand 3	C	226	233	anti-parallel
Strand 4	C	242	245	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	4	6	first strand
Strand 2	C	19	25	anti-parallel
Strand 3	C	75	80	anti-parallel
Strand 4	C	67	68	anti-parallel

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There are 2 strands in Q sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	12	13	first strand
Strand 2	C	110	111	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	58	59	first strand
Strand 2	C	50	54	anti-parallel
Strand 3	C	38	43	anti-parallel
Strand 4	C	90	95	anti-parallel
Strand 5	C	107	108	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	136	139	first strand
Strand 2	D	151	158	anti-parallel
Strand 3	D	212	217	anti-parallel
Strand 4	D	202	207	anti-parallel

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There are 6 strands in T sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	143	145	first strand
Strand 2	D	249	253	parallel
Strand 3	D	226	233	anti-parallel
Strand 4	D	168	175	anti-parallel
Strand 5	D	179	187	anti-parallel
Strand 6	D	192	194	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	143	145	first strand
Strand 2	D	249	253	parallel
Strand 3	D	226	233	anti-parallel
Strand 4	D	242	245	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	4	6	first strand
Strand 2	D	19	25	anti-parallel
Strand 3	D	75	80	anti-parallel
Strand 4	D	67	68	anti-parallel

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There are 2 strands in W sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	12	13	first strand
Strand 2	D	110	111	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	58	59	first strand
Strand 2	D	50	54	anti-parallel
Strand 3	D	38	43	anti-parallel
Strand 4	D	90	95	anti-parallel
Strand 5	D	107	108	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: 4NKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
4NKD