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

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 1NDO entry

There are 6 chains in PDB entry 1NDO (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	THR 447
B	MET 502	LEU 694
C	MET 1	THR 447
D	MET 502	LEU 694
E	MET 1	LYS 445
F	MET 502	LEU 694

There are 71 helices in PDB entry 1NDO. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	11	13	Right-handed 310
Helix 2	2	A	18	21	Right-handed 310
Helix 3	3	A	24	33	Right-handed alpha
Helix 4	4	A	45	47	Right-handed 310
Helix 5	5	A	120	123	Right-handed alpha
Helix 6	6	A	130	132	Right-handed 310
Helix 7	7	A	159	174	Right-handed alpha
Helix 8	8	A	195	204	Right-handed alpha
Helix 9	9	A	209	212	Right-handed alpha
Helix 10	10	A	214	220	Right-handed alpha
Helix 11	11	A	225	230	Right-handed 310
Helix 12	12	A	263	284	Right-handed alpha
Helix 13	13	A	286	293	Right-handed alpha
Helix 14	14	A	338	352	Right-handed alpha
Helix 15	15	A	357	374	Right-handed alpha
Helix 16	16	A	411	424	Right-handed alpha
Helix 17	17	A	429	436	Right-handed alpha
Helix 18	18	A	439	443	Right-handed alpha
Helix 19	19	B	513	523	Right-handed alpha
Helix 20	20	B	528	546	Right-handed alpha
Helix 21	21	B	550	557	Right-handed alpha
Helix 22	22	B	592	603	Right-handed alpha
Helix 23	23	B	608	610	Right-handed 310
Helix 24	24	C	11	13	Right-handed 310
Helix 25	25	C	18	21	Right-handed 310
Helix 26	26	C	24	33	Right-handed alpha
Helix 27	27	C	45	47	Right-handed 310
Helix 28	28	C	120	123	Right-handed alpha
Helix 29	29	C	130	132	Right-handed 310
Helix 30	30	C	159	174	Right-handed alpha
Helix 31	31	C	195	204	Right-handed alpha
Helix 32	32	C	209	212	Right-handed alpha
Helix 33	33	C	214	220	Right-handed alpha
Helix 34	34	C	225	230	Right-handed 310
Helix 35	35	C	263	284	Right-handed alpha
Helix 36	36	C	286	293	Right-handed alpha
Helix 37	37	C	338	352	Right-handed alpha
Helix 38	38	C	357	374	Right-handed alpha
Helix 39	39	C	376	379	Right-handed alpha
Helix 40	40	C	411	424	Right-handed alpha
Helix 41	41	C	429	436	Right-handed alpha
Helix 42	42	C	439	444	Right-handed alpha
Helix 43	43	D	513	523	Right-handed alpha
Helix 44	44	D	528	546	Right-handed alpha
Helix 45	45	D	550	557	Right-handed alpha
Helix 46	46	D	592	603	Right-handed alpha
Helix 47	47	D	608	610	Right-handed 310
Helix 48	48	D	667	669	Right-handed 310
Helix 49	49	E	11	13	Right-handed 310
Helix 50	50	E	18	21	Right-handed 310
Helix 51	51	E	24	33	Right-handed alpha
Helix 52	52	E	120	123	Right-handed alpha
Helix 53	53	E	130	132	Right-handed 310
Helix 54	54	E	159	174	Right-handed alpha
Helix 55	55	E	195	204	Right-handed alpha
Helix 56	56	E	209	212	Right-handed alpha
Helix 57	57	E	214	220	Right-handed alpha
Helix 58	58	E	225	230	Right-handed 310
Helix 59	59	E	263	284	Right-handed alpha
Helix 60	60	E	286	293	Right-handed alpha
Helix 61	61	E	338	352	Right-handed alpha
Helix 62	62	E	357	374	Right-handed alpha
Helix 63	63	E	411	424	Right-handed alpha
Helix 64	64	E	429	436	Right-handed alpha
Helix 65	65	E	439	443	Right-handed alpha
Helix 66	66	F	513	523	Right-handed alpha
Helix 67	67	F	528	546	Right-handed alpha
Helix 68	68	F	550	557	Right-handed alpha
Helix 69	69	F	592	603	Right-handed alpha
Helix 70	70	F	608	610	Right-handed 310
Helix 71	71	F	667	669	Right-handed 310

There are 24 sheets in PDB entry 1NDO. 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 2 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	15	17	first strand
Strand 2	A	382	384	anti-parallel

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There are 4 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	93	95	first strand
Strand 2	A	53	59	anti-parallel
Strand 3	A	62	68	anti-parallel
Strand 4	A	74	78	anti-parallel

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There are 2 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	98	100	first strand
Strand 2	A	107	109	anti-parallel

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There are 3 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	140	144	first strand
Strand 2	A	147	151	anti-parallel
Strand 3	A	40	44	anti-parallel

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There are 8 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	180	183	first strand
Strand 2	A	323	333	anti-parallel
Strand 3	A	312	320	anti-parallel
Strand 4	A	304	307	anti-parallel
Strand 5	A	295	300	anti-parallel
Strand 6	A	249	253	anti-parallel
Strand 7	A	239	243	anti-parallel
Strand 8	A	402	404	anti-parallel

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There are 2 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	187	191	first strand
Strand 2	A	324	328	anti-parallel

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There are 6 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	584	590	first strand
Strand 2	B	563	569	anti-parallel
Strand 3	B	671	679	parallel
Strand 4	B	651	665	anti-parallel
Strand 5	B	634	647	anti-parallel
Strand 6	B	615	621	anti-parallel

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There are 2 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	624	627	first strand
Strand 2	B	635	638	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	15	17	first strand
Strand 2	C	382	384	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	C	93	95	first strand
Strand 2	C	53	59	anti-parallel
Strand 3	C	62	68	anti-parallel
Strand 4	C	74	78	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	C	98	100	first strand
Strand 2	C	107	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	140	144	first strand
Strand 2	C	147	151	anti-parallel
Strand 3	C	40	44	anti-parallel

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There are 8 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	180	183	first strand
Strand 2	C	323	333	anti-parallel
Strand 3	C	312	320	anti-parallel
Strand 4	C	304	307	anti-parallel
Strand 5	C	295	300	anti-parallel
Strand 6	C	249	253	anti-parallel
Strand 7	C	239	243	anti-parallel
Strand 8	C	402	404	anti-parallel

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There are 2 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	187	191	first strand
Strand 2	C	324	328	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	584	590	first strand
Strand 2	D	563	569	anti-parallel
Strand 3	D	671	679	parallel
Strand 4	D	651	665	anti-parallel
Strand 5	D	634	647	anti-parallel
Strand 6	D	615	621	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	624	627	first strand
Strand 2	D	635	638	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	E	15	17	first strand
Strand 2	E	382	384	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	93	95	first strand
Strand 2	E	53	59	anti-parallel
Strand 3	E	62	68	anti-parallel
Strand 4	E	74	78	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	98	100	first strand
Strand 2	E	107	109	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	140	144	first strand
Strand 2	E	147	151	anti-parallel
Strand 3	E	40	44	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	180	183	first strand
Strand 2	E	323	333	anti-parallel
Strand 3	E	312	320	anti-parallel
Strand 4	E	304	307	anti-parallel
Strand 5	E	295	300	anti-parallel
Strand 6	E	249	253	anti-parallel
Strand 7	E	239	243	anti-parallel
Strand 8	E	402	404	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	187	191	first strand
Strand 2	E	324	328	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	584	590	first strand
Strand 2	F	563	569	anti-parallel
Strand 3	F	671	679	parallel
Strand 4	F	651	665	anti-parallel
Strand 5	F	634	647	anti-parallel
Strand 6	F	615	621	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	624	627	first strand
Strand 2	F	635	638	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: 1NDO

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