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

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 5NER entry

There are 6 chains in PDB entry 5NER (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
1	THR 1	LYS 210
2	GLU 5	GLU 218
3	GLY 1	GLN 220
4	SER 15	ALA 85
A	PHE 1	LEU 594
B	GLY 5	GLU 471

There are 38 helices in PDB entry 5NER. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	1	14	19	Right-handed 310
Helix 2	AA2	1	31	36	Right-handed alpha
Helix 3	AA3	1	52	56	Right-handed 310
Helix 4	AA4	1	60	67	Right-handed alpha
Helix 5	AA5	1	95	100	Right-handed 310
Helix 6	AA6	1	146	152	Right-handed alpha
Helix 7	AA7	1	153	156	Right-handed 310
Helix 8	AA8	2	56	59	Right-handed 310
Helix 9	AA9	2	91	95	Right-handed 310
Helix 10	AB1	2	135	143	Right-handed 310
Helix 11	AB2	3	43	51	Right-handed alpha
Helix 12	AB3	3	84	88	Right-handed 310
Helix 13	AB4	3	89	95	Right-handed alpha
Helix 14	AB5	3	135	140	Right-handed alpha
Helix 15	AB6	4	27	32	Right-handed alpha
Helix 16	AB7	4	66	74	Right-handed alpha
Helix 17	AB8	A	175	180	Right-handed alpha
Helix 18	AB9	A	188	194	Right-handed alpha
Helix 19	AC1	A	214	218	Right-handed 310
Helix 20	AC2	A	245	250	Right-handed alpha
Helix 21	AC3	A	366	370	Right-handed 310
Helix 22	AC4	A	427	429	Right-handed 310
Helix 23	AC5	A	544	548	Right-handed 310
Helix 24	AC6	A	564	569	Right-handed alpha
Helix 25	AC7	B	14	20	Right-handed alpha
Helix 26	AC8	B	77	81	Right-handed 310
Helix 27	AC9	B	127	131	Right-handed 310
Helix 28	AD1	B	135	145	Right-handed alpha
Helix 29	AD2	B	169	175	Right-handed alpha
Helix 30	AD3	B	199	210	Right-handed alpha
Helix 31	AD4	B	221	232	Right-handed alpha
Helix 32	AD5	B	232	237	Right-handed alpha
Helix 33	AD6	B	256	264	Right-handed 310
Helix 34	AD7	B	281	286	Right-handed 310
Helix 35	AD8	B	291	302	Right-handed alpha
Helix 36	AD9	B	314	325	Right-handed alpha
Helix 37	AE1	B	339	351	Right-handed alpha
Helix 38	AE2	B	434	438	Right-handed 310

There are 29 sheets in PDB entry 5NER. 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, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1, AD2,

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	1	2	3	first strand
Strand 2	3	154	159	anti-parallel
Strand 3	3	105	111	anti-parallel
Strand 4	3	199	205	anti-parallel
Strand 5	3	53	54	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	1	2	3	first strand
Strand 2	3	154	159	anti-parallel
Strand 3	3	105	111	anti-parallel
Strand 4	3	199	205	anti-parallel
Strand 5	3	63	64	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	1	39	42	first strand
Strand 2	1	172	188	anti-parallel
Strand 3	1	69	83	anti-parallel
Strand 4	1	126	127	anti-parallel

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There are 5 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	1	39	42	first strand
Strand 2	1	172	188	anti-parallel
Strand 3	1	69	83	anti-parallel
Strand 4	1	113	117	anti-parallel
Strand 5	3	23	24	parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	1	48	50	first strand
Strand 2	1	166	169	anti-parallel
Strand 3	1	86	90	anti-parallel
Strand 4	1	105	106	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	2	15	19	first strand
Strand 2	2	22	26	anti-parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	2	32	34	first strand
Strand 2	2	155	160	parallel
Strand 3	2	98	111	anti-parallel
Strand 4	2	197	213	anti-parallel
Strand 5	2	52	54	anti-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	2	32	34	first strand
Strand 2	2	155	160	parallel
Strand 3	2	98	111	anti-parallel
Strand 4	2	197	213	anti-parallel
Strand 5	2	62	69	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	2	80	83	first strand
Strand 2	2	177	189	anti-parallel
Strand 3	2	117	127	anti-parallel
Strand 4	2	145	148	anti-parallel

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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	3	73	78	first strand
Strand 2	3	183	192	anti-parallel
Strand 3	3	118	126	anti-parallel
Strand 4	3	143	148	anti-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	3	168	169	first strand
Strand 2	3	98	102	anti-parallel
Strand 3	3	210	214	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	A	9	12	first strand
Strand 2	A	431	435	anti-parallel
Strand 3	A	421	426	anti-parallel
Strand 4	A	407	412	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	23	26	first strand
Strand 2	A	35	40	anti-parallel
Strand 3	A	55	60	anti-parallel
Strand 4	A	67	70	anti-parallel

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There are 2 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	79	81	first strand
Strand 2	A	84	85	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	87	88	first strand
Strand 2	A	113	114	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	98	101	first strand
Strand 2	A	104	109	anti-parallel
Strand 3	A	127	132	anti-parallel
Strand 4	A	135	139	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	A	161	163	first strand
Strand 2	A	168	173	anti-parallel
Strand 3	A	182	187	anti-parallel
Strand 4	A	207	209	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	A	226	229	first strand
Strand 2	A	238	243	anti-parallel
Strand 3	A	252	256	anti-parallel
Strand 4	A	266	268	anti-parallel

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There are 4 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	280	283	first strand
Strand 2	A	292	297	anti-parallel
Strand 3	A	314	320	anti-parallel
Strand 4	A	326	332	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	301	303	first strand
Strand 2	A	309	311	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	344	348	first strand
Strand 2	A	357	362	anti-parallel
Strand 3	A	372	377	anti-parallel
Strand 4	A	389	392	anti-parallel

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There are 3 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	481	482	first strand
Strand 2	A	440	443	anti-parallel
Strand 3	A	577	578	parallel

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There are 4 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	446	450	first strand
Strand 2	A	472	479	anti-parallel
Strand 3	A	534	542	anti-parallel
Strand 4	A	511	513	anti-parallel

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There are 5 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	453	454	first strand
Strand 2	A	585	592	parallel
Strand 3	A	555	563	anti-parallel
Strand 4	A	490	499	anti-parallel
Strand 5	A	520	528	anti-parallel

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There are 3 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	39	40	first strand
Strand 2	B	25	27	anti-parallel
Strand 3	B	55	56	anti-parallel

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There are 6 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	61	66	first strand
Strand 2	B	88	93	anti-parallel
Strand 3	B	424	430	parallel
Strand 4	B	411	417	anti-parallel
Strand 5	B	355	360	anti-parallel
Strand 6	B	385	386	anti-parallel

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There are 5 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	84	85	first strand
Strand 2	B	99	106	anti-parallel
Strand 3	B	394	402	anti-parallel
Strand 4	B	367	373	anti-parallel
Strand 5	B	379	381	anti-parallel

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There are 6 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	190	197	first strand
Strand 2	B	150	157	anti-parallel
Strand 3	B	113	120	parallel
Strand 4	B	243	250	parallel
Strand 5	B	305	311	parallel
Strand 6	B	329	333	parallel

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There are 2 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	452	455	first strand
Strand 2	B	458	461	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: 5NER

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