Analysis of interatomic Contacts of Structural Units in PDB entry:
5ND1

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 5ND1 entry

There are 2 chains in PDB entry 5ND1 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 2	GLY 973
B	MET 1	LYS 1005

There are 67 helices in PDB entry 5ND1. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	3	7	Right-handed 310
Helix 2	AA2	A	10	28	Right-handed alpha
Helix 3	AA3	A	42	46	Right-handed 310
Helix 4	AA4	A	52	58	Right-handed alpha
Helix 5	AA5	A	129	136	Right-handed alpha
Helix 6	AA6	A	144	152	Right-handed alpha
Helix 7	AA7	A	153	175	Right-handed alpha
Helix 8	AA8	A	188	203	Right-handed alpha
Helix 9	AA9	A	249	254	Right-handed alpha
Helix 10	AB1	A	260	273	Right-handed alpha
Helix 11	AB2	A	319	327	Right-handed alpha
Helix 12	AB3	A	346	350	Right-handed alpha
Helix 13	AB4	A	377	385	Right-handed alpha
Helix 14	AB5	A	398	411	Right-handed alpha
Helix 15	AB6	A	432	437	Right-handed alpha
Helix 16	AB7	A	440	447	Right-handed alpha
Helix 17	AB8	A	450	466	Right-handed alpha
Helix 18	AB9	A	492	498	Right-handed alpha
Helix 19	AC1	A	515	540	Right-handed alpha
Helix 20	AC2	A	554	564	Right-handed alpha
Helix 21	AC3	A	589	592	Right-handed 310
Helix 22	AC4	A	593	598	Right-handed alpha
Helix 23	AC5	A	599	603	Right-handed 310
Helix 24	AC6	A	606	615	Right-handed alpha
Helix 25	AC7	A	643	648	Right-handed alpha
Helix 26	AC8	A	703	707	Right-handed 310
Helix 27	AC9	A	738	748	Right-handed alpha
Helix 28	AD1	A	757	761	Right-handed alpha
Helix 29	AD2	A	766	782	Right-handed alpha
Helix 30	AD3	A	807	812	Right-handed alpha
Helix 31	AD4	A	837	847	Right-handed alpha
Helix 32	AD5	A	892	896	Right-handed 310
Helix 33	AD6	A	898	904	Right-handed alpha
Helix 34	AD7	A	939	943	Right-handed 310
Helix 35	AD8	A	963	971	Right-handed alpha
Helix 36	AD9	B	5	10	Right-handed alpha
Helix 37	AE1	B	22	26	Right-handed 310
Helix 38	AE2	B	67	78	Right-handed alpha
Helix 39	AE3	B	95	108	Right-handed alpha
Helix 40	AE4	B	174	187	Right-handed alpha
Helix 41	AE5	B	204	212	Right-handed alpha
Helix 42	AE6	B	219	237	Right-handed alpha
Helix 43	AE7	B	246	253	Right-handed alpha
Helix 44	AE8	B	272	284	Right-handed alpha
Helix 45	AE9	B	296	298	Right-handed 310
Helix 46	AF1	B	304	309	Right-handed alpha
Helix 47	AF2	B	335	346	Right-handed alpha
Helix 48	AF3	B	357	367	Right-handed alpha
Helix 49	AF4	B	389	404	Right-handed alpha
Helix 50	AF5	B	405	408	Right-handed 310
Helix 51	AF6	B	410	422	Right-handed alpha
Helix 52	AF7	B	451	458	Right-handed alpha
Helix 53	AF8	B	470	505	Right-handed alpha
Helix 54	AF9	B	513	527	Right-handed alpha
Helix 55	AG1	B	537	544	Right-handed alpha
Helix 56	AG2	B	553	562	Right-handed alpha
Helix 57	AG3	B	608	618	Right-handed alpha
Helix 58	AG4	B	667	681	Right-handed alpha
Helix 59	AG5	B	691	704	Right-handed alpha
Helix 60	AG6	B	706	716	Right-handed alpha
Helix 61	AG7	B	762	767	Right-handed alpha
Helix 62	AG8	B	770	785	Right-handed alpha
Helix 63	AG9	B	787	794	Right-handed alpha
Helix 64	AH1	B	817	831	Right-handed alpha
Helix 65	AH2	B	859	873	Right-handed alpha
Helix 66	AH3	B	923	929	Right-handed alpha
Helix 67	AH4	B	957	962	Right-handed alpha

There are 17 sheets in PDB entry 5ND1. 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,

There are 3 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	100	103	first strand
Strand 2	A	75	79	anti-parallel
Strand 3	A	856	860	anti-parallel

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There are 4 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	94	97	first strand
Strand 2	A	82	85	anti-parallel
Strand 3	A	851	854	anti-parallel
Strand 4	A	755	756	anti-parallel

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There are 7 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	216	217	first strand
Strand 2	A	206	209	anti-parallel
Strand 3	A	228	234	anti-parallel
Strand 4	A	340	345	anti-parallel
Strand 5	A	330	334	anti-parallel
Strand 6	A	280	285	anti-parallel
Strand 7	A	298	303	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	A	243	245	first strand
Strand 2	A	629	631	anti-parallel
Strand 3	A	725	728	anti-parallel
Strand 4	A	688	691	anti-parallel

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There are 2 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	367	370	first strand
Strand 2	A	417	420	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	A	547	549	first strand
Strand 2	A	679	681	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	652	657	first strand
Strand 2	A	798	803	parallel
Strand 3	A	786	788	anti-parallel
Strand 4	A	822	823	anti-parallel

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There are 3 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	669	670	first strand
Strand 2	A	684	686	parallel
Strand 3	A	731	732	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	928	929	first strand
Strand 2	B	599	600	parallel

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There are 3 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	952	953	first strand
Strand 2	B	291	294	anti-parallel
Strand 3	B	300	301	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	35	36	first strand
Strand 2	B	978	979	anti-parallel

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There are 3 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	137	140	first strand
Strand 2	B	121	134	anti-parallel
Strand 3	B	145	151	anti-parallel

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There are 3 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	137	140	first strand
Strand 2	B	121	134	anti-parallel
Strand 3	B	933	941	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	160	163	first strand
Strand 2	B	438	442	parallel
Strand 3	B	580	581	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	B	263	264	first strand
Strand 2	B	267	268	anti-parallel

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There are 2 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	641	644	first strand
Strand 2	B	810	813	anti-parallel

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There are 3 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	886	889	first strand
Strand 2	B	875	880	anti-parallel
Strand 3	B	908	913	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: 5ND1

Analysis of interatomic Contacts of Structural Units in PDB entry:
5ND1