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

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 1NFD entry

There are 8 chains in PDB entry 1NFD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 1	CYS 213
B	ASP 1	CYS 247
C	ASP 1	CYS 213
D	ASP 1	CYS 247
E	TYR 2	LEU 215
F	GLU 1	ARG 228
G	TYR 2	LEU 215
H	GLU 1	ARG 228

There are 28 helices in PDB entry 1NFD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	82	84	Right-handed 310
Helix 2	2	A	191	194	Right-handed alpha
Helix 3	3	B	84	86	Right-handed 310
Helix 4	4	B	119	121	Right-handed 310
Helix 5	5	B	134	140	Right-handed alpha
Helix 6	6	B	200	204	Right-handed alpha
Helix 7	7	C	82	84	Right-handed 310
Helix 8	8	C	191	194	Right-handed alpha
Helix 9	9	D	84	86	Right-handed 310
Helix 10	10	D	119	121	Right-handed 310
Helix 11	11	D	134	139	Right-handed alpha
Helix 12	12	D	200	204	Right-handed alpha
Helix 13	13	E	28	30	Right-handed 310
Helix 14	14	E	80	82	Right-handed 310
Helix 15	15	E	122	127	Right-handed alpha
Helix 16	16	E	183	187	Right-handed alpha
Helix 17	17	F	29	31	Right-handed 310
Helix 18	18	F	61	63	Right-handed 310
Helix 19	19	F	84	86	Right-handed 310
Helix 20	20	F	162	164	Right-handed 310
Helix 21	21	F	195	199	Right-handed alpha
Helix 22	22	G	80	82	Right-handed 310
Helix 23	23	G	122	126	Right-handed alpha
Helix 24	24	G	183	186	Right-handed alpha
Helix 25	25	H	29	31	Right-handed 310
Helix 26	26	H	61	63	Right-handed 310
Helix 27	27	H	84	86	Right-handed 310
Helix 28	28	H	162	164	Right-handed 310

There are 39 sheets in PDB entry 1NFD. 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, Y, Z, AA, AB, AC, AD, AE, AF, AG, AH, AI, AJ, AK, AL, AM,

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	2	5	first strand
Strand 2	A	22	25	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	18	20	first strand
Strand 2	A	72	77	anti-parallel
Strand 3	A	62	67	anti-parallel
Strand 4	A	54	57	anti-parallel

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There are 4 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	110	112	first strand
Strand 2	A	86	94	anti-parallel
Strand 3	A	30	37	anti-parallel
Strand 4	A	43	49	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	124	128	first strand
Strand 2	A	139	144	anti-parallel
Strand 3	A	181	184	anti-parallel

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There are 2 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	166	169	first strand
Strand 2	A	176	179	anti-parallel

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There are 3 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	5	7	first strand
Strand 2	B	20	24	anti-parallel
Strand 3	B	75	78	anti-parallel

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There are 3 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	10	14	first strand
Strand 2	B	112	116	parallel
Strand 3	B	88	90	anti-parallel

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There are 4 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	92	95	first strand
Strand 2	B	31	36	anti-parallel
Strand 3	B	44	50	anti-parallel
Strand 4	B	54	57	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	126	130	first strand
Strand 2	B	142	152	anti-parallel
Strand 3	B	190	199	anti-parallel
Strand 4	B	172	174	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	157	163	first strand
Strand 2	B	210	216	anti-parallel
Strand 3	B	235	241	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	B	179	182	first strand
Strand 2	B	189	191	anti-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	11	13	first strand
Strand 2	C	113	115	parallel

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There are 2 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	18	20	first strand
Strand 2	C	75	77	anti-parallel

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There are 4 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	124	126	first strand
Strand 2	C	139	144	anti-parallel
Strand 3	C	179	184	anti-parallel
Strand 4	C	160	162	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	166	168	first strand
Strand 2	C	177	179	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	86	94	first strand
Strand 2	C	30	38	anti-parallel
Strand 3	C	43	49	anti-parallel

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There are 4 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	5	7	first strand
Strand 2	D	18	24	anti-parallel
Strand 3	D	75	80	anti-parallel
Strand 4	D	66	69	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	D	10	14	first strand
Strand 2	D	112	116	parallel
Strand 3	D	88	95	anti-parallel
Strand 4	D	31	37	anti-parallel
Strand 5	D	43	50	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	142	149	first strand
Strand 2	D	192	199	anti-parallel
Strand 3	D	172	174	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	166	168	first strand
Strand 2	D	158	163	anti-parallel
Strand 3	D	210	216	anti-parallel
Strand 4	D	235	241	anti-parallel

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There are 4 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	4	6	first strand
Strand 2	E	21	25	anti-parallel
Strand 3	E	70	75	anti-parallel
Strand 4	E	62	67	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	9	14	first strand
Strand 2	E	103	106	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	95	98	first strand
Strand 2	E	85	92	anti-parallel
Strand 3	E	34	38	anti-parallel
Strand 4	E	44	48	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	114	116	first strand
Strand 2	E	134	139	anti-parallel
Strand 3	E	173	177	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	153	155	first strand
Strand 2	E	145	150	anti-parallel
Strand 3	E	192	197	anti-parallel
Strand 4	E	209	211	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	3	7	first strand
Strand 2	F	17	25	anti-parallel
Strand 3	F	77	82	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	10	12	first strand
Strand 2	F	109	111	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	91	96	first strand
Strand 2	F	32	39	anti-parallel
Strand 3	F	45	51	anti-parallel
Strand 4	F	57	59	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	137	139	first strand
Strand 2	F	192	194	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	152	157	first strand
Strand 2	F	206	212	anti-parallel
Strand 3	F	219	222	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	171	173	first strand
Strand 2	F	189	191	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	9	14	first strand
Strand 2	G	103	106	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	19	24	first strand
Strand 2	G	70	75	anti-parallel
Strand 3	G	62	67	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	95	98	first strand
Strand 2	G	85	92	anti-parallel
Strand 3	G	33	38	anti-parallel
Strand 4	G	44	48	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	134	136	first strand
Strand 2	G	175	177	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	3	7	first strand
Strand 2	H	18	25	anti-parallel
Strand 3	H	77	82	anti-parallel
Strand 4	H	67	72	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	91	95	first strand
Strand 2	H	33	39	anti-parallel
Strand 3	H	45	51	anti-parallel
Strand 4	H	57	59	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	120	125	first strand
Strand 2	H	137	147	anti-parallel
Strand 3	H	185	194	anti-parallel
Strand 4	H	171	173	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	153	157	first strand
Strand 2	H	208	211	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: 1NFD

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