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

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 5NMD entry

There are 4 chains in PDB entry 5NMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	LYS 2	SER 201
B	ASP 1	ASP 242
C	LYS 2	SER 201
D	ASP 1	ASP 242

There are 14 helices in PDB entry 5NMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	80	84	Right-handed 310
Helix 2	AA2	A	164	167	Right-handed 310
Helix 3	AA3	A	183	188	Right-handed alpha
Helix 4	AA4	B	82	86	Right-handed 310
Helix 5	AA5	B	114	118	Right-handed 310
Helix 6	AA6	B	129	137	Right-handed alpha
Helix 7	AA7	B	196	200	Right-handed alpha
Helix 8	AA8	C	80	84	Right-handed 310
Helix 9	AA9	C	164	167	Right-handed 310
Helix 10	AB1	C	183	188	Right-handed alpha
Helix 11	AB2	D	82	86	Right-handed 310
Helix 12	AB3	D	114	118	Right-handed 310
Helix 13	AB4	D	129	137	Right-handed alpha
Helix 14	AB5	D	196	200	Right-handed alpha

There are 18 sheets in PDB entry 5NMD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6, AB7, AB8, AB9,

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	4	5	first strand
Strand 2	A	19	25	anti-parallel
Strand 3	A	71	76	anti-parallel
Strand 4	A	61	66	anti-parallel
Strand 5	A	54	58	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	11	14	first strand
Strand 2	A	105	110	parallel
Strand 3	A	85	93	anti-parallel
Strand 4	A	30	38	anti-parallel
Strand 5	A	45	50	anti-parallel

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There are 4 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	11	14	first strand
Strand 2	A	105	110	parallel
Strand 3	A	85	93	anti-parallel
Strand 4	A	100	101	anti-parallel

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There are 8 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	153	155	first strand
Strand 2	A	168	177	anti-parallel
Strand 3	A	132	137	anti-parallel
Strand 4	A	119	125	anti-parallel
Strand 5	B	122	127	anti-parallel
Strand 6	B	138	148	anti-parallel
Strand 7	B	186	195	anti-parallel
Strand 8	B	168	170	anti-parallel

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There are 8 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	159	163	first strand
Strand 2	A	168	177	anti-parallel
Strand 3	A	132	137	anti-parallel
Strand 4	A	119	125	anti-parallel
Strand 5	B	122	127	anti-parallel
Strand 6	B	138	148	anti-parallel
Strand 7	B	186	195	anti-parallel
Strand 8	B	175	176	anti-parallel

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There are 4 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	5	7	first strand
Strand 2	B	19	24	anti-parallel
Strand 3	B	74	78	anti-parallel
Strand 4	B	64	68	anti-parallel

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There are 6 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	10	14	first strand
Strand 2	B	107	112	parallel
Strand 3	B	87	94	anti-parallel
Strand 4	B	31	37	anti-parallel
Strand 5	B	44	50	anti-parallel
Strand 6	B	53	57	anti-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	10	14	first strand
Strand 2	B	107	112	parallel
Strand 3	B	87	94	anti-parallel
Strand 4	B	102	103	anti-parallel

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There are 4 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	162	164	first strand
Strand 2	B	153	159	anti-parallel
Strand 3	B	205	212	anti-parallel
Strand 4	B	231	238	anti-parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	4	5	first strand
Strand 2	C	19	25	anti-parallel
Strand 3	C	71	76	anti-parallel
Strand 4	C	61	66	anti-parallel
Strand 5	C	54	58	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	11	14	first strand
Strand 2	C	105	110	parallel
Strand 3	C	85	93	anti-parallel
Strand 4	C	30	38	anti-parallel
Strand 5	C	45	50	anti-parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	11	14	first strand
Strand 2	C	105	110	parallel
Strand 3	C	85	93	anti-parallel
Strand 4	C	100	101	anti-parallel

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There are 8 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	153	155	first strand
Strand 2	C	168	177	anti-parallel
Strand 3	C	132	137	anti-parallel
Strand 4	C	119	125	anti-parallel
Strand 5	D	122	127	anti-parallel
Strand 6	D	138	148	anti-parallel
Strand 7	D	186	195	anti-parallel
Strand 8	D	168	170	anti-parallel

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There are 8 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	159	163	first strand
Strand 2	C	168	177	anti-parallel
Strand 3	C	132	137	anti-parallel
Strand 4	C	119	125	anti-parallel
Strand 5	D	122	127	anti-parallel
Strand 6	D	138	148	anti-parallel
Strand 7	D	186	195	anti-parallel
Strand 8	D	175	176	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	5	7	first strand
Strand 2	D	19	24	anti-parallel
Strand 3	D	74	78	anti-parallel
Strand 4	D	64	68	anti-parallel

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There are 6 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	10	14	first strand
Strand 2	D	107	112	parallel
Strand 3	D	87	94	anti-parallel
Strand 4	D	31	37	anti-parallel
Strand 5	D	44	50	anti-parallel
Strand 6	D	53	57	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	10	14	first strand
Strand 2	D	107	112	parallel
Strand 3	D	87	94	anti-parallel
Strand 4	D	102	103	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	162	164	first strand
Strand 2	D	153	159	anti-parallel
Strand 3	D	205	212	anti-parallel
Strand 4	D	231	238	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: 5NMD

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