Analysis of interatomic Contacts of Structural Units in PDB entry:
1NDA

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 1NDA entry

There are 4 chains in PDB entry 1NDA (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 4	GLU 484
B	ILE 4	GLU 484
C	ILE 4	GLU 484
D	ILE 4	GLU 484

There are 56 helices in PDB entry 1NDA. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1B	A	13	27	Right-handed alpha
Helix 2	2B	A	49	80	Right-handed alpha
Helix 3	3B	A	91	117	Right-handed alpha
Helix 4	4B	A	171	175	Right-handed 310
Helix 5	5B	A	177	182	Right-handed alpha
Helix 6	6B	A	197	211	Right-handed alpha
Helix 7	7B	A	231	245	Right-handed alpha
Helix 8	8B	A	295	299	Right-handed 310
Helix 9	9B	A	333	349	Right-handed alpha
Helix 10	10B	A	377	385	Right-handed alpha
Helix 11	11B	A	397	402	Right-handed alpha
Helix 12	12B	A	432	447	Right-handed alpha
Helix 13	13B	A	450	455	Right-handed alpha
Helix 14	14B	A	463	470	Right-handed 310
Helix 15	1B	B	13	27	Right-handed alpha
Helix 16	2B	B	49	80	Right-handed alpha
Helix 17	3B	B	91	117	Right-handed alpha
Helix 18	4B	B	171	175	Right-handed 310
Helix 19	5B	B	177	182	Right-handed alpha
Helix 20	6B	B	197	211	Right-handed alpha
Helix 21	7B	B	231	245	Right-handed alpha
Helix 22	8B	B	295	299	Right-handed 310
Helix 23	9B	B	333	349	Right-handed alpha
Helix 24	10B	B	377	385	Right-handed alpha
Helix 25	11B	B	397	402	Right-handed alpha
Helix 26	12B	B	432	447	Right-handed alpha
Helix 27	13B	B	450	455	Right-handed alpha
Helix 28	14B	B	463	470	Right-handed 310
Helix 29	1B	C	13	27	Right-handed alpha
Helix 30	2B	C	49	80	Right-handed alpha
Helix 31	3B	C	91	117	Right-handed alpha
Helix 32	4B	C	171	175	Right-handed 310
Helix 33	5B	C	177	182	Right-handed alpha
Helix 34	6B	C	197	211	Right-handed alpha
Helix 35	7B	C	231	245	Right-handed alpha
Helix 36	8B	C	295	299	Right-handed 310
Helix 37	9B	C	333	349	Right-handed alpha
Helix 38	10B	C	377	385	Right-handed alpha
Helix 39	11B	C	397	402	Right-handed alpha
Helix 40	12B	C	432	447	Right-handed alpha
Helix 41	13B	C	450	455	Right-handed alpha
Helix 42	14B	C	463	470	Right-handed 310
Helix 43	1B	D	13	27	Right-handed alpha
Helix 44	2B	D	49	80	Right-handed alpha
Helix 45	3B	D	91	117	Right-handed alpha
Helix 46	4B	D	171	175	Right-handed 310
Helix 47	5B	D	177	182	Right-handed alpha
Helix 48	6B	D	197	211	Right-handed alpha
Helix 49	7B	D	231	245	Right-handed alpha
Helix 50	8B	D	295	299	Right-handed 310
Helix 51	9B	D	333	349	Right-handed alpha
Helix 52	10B	D	377	385	Right-handed alpha
Helix 53	11B	D	397	402	Right-handed alpha
Helix 54	12B	D	432	447	Right-handed alpha
Helix 55	13B	D	450	455	Right-handed alpha
Helix 56	14B	D	463	470	Right-handed 310

There are 24 sheets in PDB entry 1NDA. Click on sheet of interest to get list of strands forming it: AA, BA, CA, A, EA, FA, AB, BB, CB, DB, EB, FB, AC, BC, CC, C, EC, FC, AD, BD, CD, DD, ED, FD,

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	120	124	first strand
Strand 2	A	31	35	parallel
Strand 3	A	7	10	parallel
Strand 4	A	156	158	parallel
Strand 5	A	321	323	parallel
Strand 6	A	315	315	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	5	5	first strand
Strand 2	A	147	153	parallel
Strand 3	A	134	138	anti-parallel
Strand 4	A	126	129	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	176	176	first strand
Strand 2	A	280	283	parallel
Strand 3	A	190	194	parallel
Strand 4	A	216	221	anti-parallel
Strand 5	A	248	251	anti-parallel

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There are 3 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	255	260	first strand
Strand 2	A	266	270	anti-parallel
Strand 3	A	275	278	anti-parallel

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There are 7 strands in EA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	363	365	first strand
Strand 2	A	371	375	anti-parallel
Strand 3	A	422	429	anti-parallel
Strand 4	A	410	417	anti-parallel
Strand 5	A	388	395	anti-parallel
Strand 6	A	475	477	anti-parallel
Strand 7	A	481	483	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	162	165	first strand
Strand 2	A	286	289	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	120	124	first strand
Strand 2	B	31	35	parallel
Strand 3	B	7	10	parallel
Strand 4	B	156	158	parallel
Strand 5	B	321	323	parallel
Strand 6	B	315	315	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	5	5	first strand
Strand 2	B	147	153	parallel
Strand 3	B	134	138	anti-parallel
Strand 4	B	126	129	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	176	176	first strand
Strand 2	B	280	283	parallel
Strand 3	B	190	194	parallel
Strand 4	B	216	221	anti-parallel
Strand 5	B	248	251	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	255	260	first strand
Strand 2	B	266	270	anti-parallel
Strand 3	B	275	278	anti-parallel

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There are 7 strands in EB sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	363	365	first strand
Strand 2	B	371	375	anti-parallel
Strand 3	B	422	429	anti-parallel
Strand 4	B	410	417	anti-parallel
Strand 5	B	388	395	anti-parallel
Strand 6	B	475	477	anti-parallel
Strand 7	B	481	483	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	162	165	first strand
Strand 2	B	286	289	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	120	124	first strand
Strand 2	C	31	35	parallel
Strand 3	C	7	10	parallel
Strand 4	C	156	158	parallel
Strand 5	C	321	323	parallel
Strand 6	C	315	315	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	5	5	first strand
Strand 2	C	147	153	parallel
Strand 3	C	134	138	anti-parallel
Strand 4	C	126	129	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	176	176	first strand
Strand 2	C	280	283	parallel
Strand 3	C	190	194	parallel
Strand 4	C	216	221	anti-parallel
Strand 5	C	248	251	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	255	260	first strand
Strand 2	C	266	270	anti-parallel
Strand 3	C	275	278	anti-parallel

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There are 7 strands in EC sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	363	365	first strand
Strand 2	C	371	375	anti-parallel
Strand 3	C	422	429	anti-parallel
Strand 4	C	410	417	anti-parallel
Strand 5	C	388	395	anti-parallel
Strand 6	C	475	477	anti-parallel
Strand 7	C	481	483	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	162	165	first strand
Strand 2	C	286	289	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	120	124	first strand
Strand 2	D	31	35	parallel
Strand 3	D	7	10	parallel
Strand 4	D	156	158	parallel
Strand 5	D	321	323	parallel
Strand 6	D	315	315	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	5	5	first strand
Strand 2	D	147	153	parallel
Strand 3	D	134	138	anti-parallel
Strand 4	D	126	129	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	176	176	first strand
Strand 2	D	280	283	parallel
Strand 3	D	190	194	parallel
Strand 4	D	216	221	anti-parallel
Strand 5	D	248	251	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	255	260	first strand
Strand 2	D	266	270	anti-parallel
Strand 3	D	275	278	anti-parallel

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There are 7 strands in ED sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	363	365	first strand
Strand 2	D	371	375	anti-parallel
Strand 3	D	422	429	anti-parallel
Strand 4	D	410	417	anti-parallel
Strand 5	D	388	395	anti-parallel
Strand 6	D	475	477	anti-parallel
Strand 7	D	481	483	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	162	165	first strand
Strand 2	D	286	289	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: 1NDA

Analysis of interatomic Contacts of Structural Units in PDB entry:
1NDA