Analysis of interatomic Contacts of Structural Units in PDB entry:
3NDY

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 3NDY entry

There are 8 chains in PDB entry 3NDY (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 4	SER 348
E	SER 381	LYS 487
B	SER 4	SER 348
F	SER 381	LYS 487
C	THR 8	SER 348
G	SER 381	LYS 487
D	SER 4	SER 348
H	SER 381	LYS 487

There are 61 helices in PDB entry 3NDY. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	14	23	Right-handed alpha
Helix 2	2	A	47	58	Right-handed alpha
Helix 3	3	A	81	97	Right-handed alpha
Helix 4	4	A	119	138	Right-handed alpha
Helix 5	5	A	157	161	Right-handed 310
Helix 6	6	A	166	187	Right-handed alpha
Helix 7	7	A	188	193	Right-handed 310
Helix 8	8	A	201	204	Right-handed 310
Helix 9	9	A	206	212	Right-handed alpha
Helix 10	10	A	215	219	Right-handed 310
Helix 11	11	A	231	236	Right-handed alpha
Helix 12	12	A	246	264	Right-handed alpha
Helix 13	13	A	265	268	Right-handed 310
Helix 14	14	A	283	300	Right-handed alpha
Helix 15	15	A	333	345	Right-handed alpha
Helix 16	16	B	14	23	Right-handed alpha
Helix 17	17	B	47	58	Right-handed alpha
Helix 18	18	B	81	97	Right-handed alpha
Helix 19	19	B	116	118	Right-handed 310
Helix 20	20	B	119	138	Right-handed alpha
Helix 21	21	B	157	161	Right-handed 310
Helix 22	22	B	166	187	Right-handed alpha
Helix 23	23	B	188	193	Right-handed 310
Helix 24	24	B	201	204	Right-handed 310
Helix 25	25	B	206	213	Right-handed alpha
Helix 26	26	B	215	219	Right-handed 310
Helix 27	27	B	231	236	Right-handed alpha
Helix 28	28	B	246	264	Right-handed alpha
Helix 29	29	B	265	268	Right-handed 310
Helix 30	30	B	283	300	Right-handed alpha
Helix 31	31	B	333	345	Right-handed alpha
Helix 32	32	C	14	23	Right-handed alpha
Helix 33	33	C	47	58	Right-handed alpha
Helix 34	34	C	81	97	Right-handed alpha
Helix 35	35	C	119	139	Right-handed alpha
Helix 36	36	C	157	161	Right-handed 310
Helix 37	37	C	166	187	Right-handed alpha
Helix 38	38	C	188	193	Right-handed 310
Helix 39	39	C	201	204	Right-handed 310
Helix 40	40	C	206	213	Right-handed alpha
Helix 41	41	C	215	219	Right-handed 310
Helix 42	42	C	231	236	Right-handed alpha
Helix 43	43	C	246	264	Right-handed alpha
Helix 44	44	C	265	268	Right-handed 310
Helix 45	45	C	283	300	Right-handed alpha
Helix 46	46	C	333	345	Right-handed alpha
Helix 47	47	D	14	23	Right-handed alpha
Helix 48	48	D	47	58	Right-handed alpha
Helix 49	49	D	81	97	Right-handed alpha
Helix 50	50	D	116	138	Right-handed alpha
Helix 51	51	D	157	161	Right-handed 310
Helix 52	52	D	166	187	Right-handed alpha
Helix 53	53	D	188	193	Right-handed 310
Helix 54	54	D	201	204	Right-handed 310
Helix 55	55	D	206	213	Right-handed alpha
Helix 56	56	D	215	219	Right-handed 310
Helix 57	57	D	231	236	Right-handed alpha
Helix 58	58	D	246	264	Right-handed alpha
Helix 59	59	D	265	268	Right-handed 310
Helix 60	60	D	283	300	Right-handed alpha
Helix 61	61	D	333	345	Right-handed alpha

There are 20 sheets in PDB entry 3NDY. 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,

There are 9 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	25	27	first strand
Strand 2	A	61	64	parallel
Strand 3	A	101	104	parallel
Strand 4	A	145	148	parallel
Strand 5	A	196	199	parallel
Strand 6	A	222	227	parallel
Strand 7	A	271	276	parallel
Strand 8	A	304	307	parallel
Strand 9	A	25	27	parallel

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There are 2 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	324	325	first strand
Strand 2	A	330	331	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	425	430	first strand
Strand 2	E	457	466	anti-parallel
Strand 3	E	396	405	anti-parallel
Strand 4	E	383	392	anti-parallel
Strand 5	E	485	486	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	411	412	first strand
Strand 2	E	451	452	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	432	437	first strand
Strand 2	E	440	445	anti-parallel
Strand 3	E	415	419	anti-parallel
Strand 4	E	478	479	anti-parallel
Strand 5	E	482	483	anti-parallel

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There are 9 strands in F sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	25	28	first strand
Strand 2	B	61	64	parallel
Strand 3	B	101	105	parallel
Strand 4	B	145	148	parallel
Strand 5	B	196	199	parallel
Strand 6	B	222	227	parallel
Strand 7	B	271	276	parallel
Strand 8	B	304	309	parallel
Strand 9	B	25	28	parallel

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There are 2 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	324	325	first strand
Strand 2	B	330	331	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	424	430	first strand
Strand 2	F	457	467	anti-parallel
Strand 3	F	396	405	anti-parallel
Strand 4	F	383	392	anti-parallel
Strand 5	F	485	486	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	F	411	412	first strand
Strand 2	F	451	452	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	432	437	first strand
Strand 2	F	440	445	anti-parallel
Strand 3	F	415	419	anti-parallel
Strand 4	F	478	479	anti-parallel
Strand 5	F	482	483	anti-parallel

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There are 9 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	25	28	first strand
Strand 2	C	61	64	parallel
Strand 3	C	101	105	parallel
Strand 4	C	145	148	parallel
Strand 5	C	196	199	parallel
Strand 6	C	222	227	parallel
Strand 7	C	271	276	parallel
Strand 8	C	304	309	parallel
Strand 9	C	25	28	parallel

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There are 2 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	324	325	first strand
Strand 2	C	330	331	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	424	430	first strand
Strand 2	G	457	467	anti-parallel
Strand 3	G	396	405	anti-parallel
Strand 4	G	383	392	anti-parallel
Strand 5	G	485	486	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	G	411	412	first strand
Strand 2	G	451	452	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	432	437	first strand
Strand 2	G	440	445	anti-parallel
Strand 3	G	415	419	anti-parallel
Strand 4	G	478	479	anti-parallel
Strand 5	G	482	483	anti-parallel

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There are 9 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	25	28	first strand
Strand 2	D	61	64	parallel
Strand 3	D	101	105	parallel
Strand 4	D	145	148	parallel
Strand 5	D	196	199	parallel
Strand 6	D	222	227	parallel
Strand 7	D	271	276	parallel
Strand 8	D	304	309	parallel
Strand 9	D	25	28	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	D	324	325	first strand
Strand 2	D	330	331	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	424	430	first strand
Strand 2	H	457	467	anti-parallel
Strand 3	H	396	405	anti-parallel
Strand 4	H	383	392	anti-parallel
Strand 5	H	485	486	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	H	411	412	first strand
Strand 2	H	451	452	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	432	437	first strand
Strand 2	H	440	445	anti-parallel
Strand 3	H	415	419	anti-parallel
Strand 4	H	478	479	anti-parallel
Strand 5	H	482	483	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: 3NDY

Analysis of interatomic Contacts of Structural Units in PDB entry:
3NDY