Analysis of interatomic Contacts of Structural Units in PDB entry:
2DKF

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 2DKF entry

There are 4 chains in PDB entry 2DKF (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MSE 1	VAL 431
B	MSE 1	VAL 431
C	MSE 1	VAL 431
D	MSE 1	VAL 431

There are 62 helices in PDB entry 2DKF. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	34	38	Right-handed 310
Helix 2	2	A	48	52	Right-handed 310
Helix 3	3	A	67	74	Right-handed alpha
Helix 4	4	A	83	101	Right-handed alpha
Helix 5	5	A	107	116	Right-handed alpha
Helix 6	6	A	196	214	Right-handed alpha
Helix 7	7	A	225	237	Right-handed alpha
Helix 8	8	A	251	261	Right-handed alpha
Helix 9	9	A	262	268	Right-handed 310
Helix 10	10	A	269	278	Right-handed alpha
Helix 11	11	A	293	303	Right-handed alpha
Helix 12	12	A	320	327	Right-handed alpha
Helix 13	13	A	348	353	Right-handed alpha
Helix 14	14	A	382	391	Right-handed alpha
Helix 15	15	A	402	415	Right-handed alpha
Helix 16	16	B	61	66	Right-handed alpha
Helix 17	17	B	67	74	Right-handed alpha
Helix 18	18	B	83	101	Right-handed alpha
Helix 19	19	B	107	117	Right-handed alpha
Helix 20	20	B	196	213	Right-handed alpha
Helix 21	21	B	226	237	Right-handed alpha
Helix 22	22	B	251	259	Right-handed alpha
Helix 23	23	B	260	268	Right-handed 310
Helix 24	24	B	269	278	Right-handed alpha
Helix 25	25	B	293	303	Right-handed alpha
Helix 26	26	B	319	327	Right-handed alpha
Helix 27	27	B	348	354	Right-handed alpha
Helix 28	28	B	382	391	Right-handed alpha
Helix 29	29	B	402	417	Right-handed alpha
Helix 30	30	C	48	52	Right-handed 310
Helix 31	31	C	61	66	Right-handed alpha
Helix 32	32	C	67	74	Right-handed alpha
Helix 33	33	C	83	100	Right-handed alpha
Helix 34	34	C	107	117	Right-handed alpha
Helix 35	35	C	196	213	Right-handed alpha
Helix 36	36	C	226	237	Right-handed alpha
Helix 37	37	C	251	261	Right-handed alpha
Helix 38	38	C	264	268	Right-handed 310
Helix 39	39	C	269	278	Right-handed alpha
Helix 40	40	C	293	303	Right-handed alpha
Helix 41	41	C	322	327	Right-handed alpha
Helix 42	42	C	382	391	Right-handed alpha
Helix 43	43	C	402	416	Right-handed alpha
Helix 44	44	D	34	38	Right-handed 310
Helix 45	45	D	39	43	Right-handed 310
Helix 46	46	D	61	66	Right-handed alpha
Helix 47	47	D	67	74	Right-handed alpha
Helix 48	48	D	83	98	Right-handed alpha
Helix 49	49	D	107	116	Right-handed alpha
Helix 50	50	D	196	213	Right-handed alpha
Helix 51	51	D	226	237	Right-handed alpha
Helix 52	52	D	238	242	Right-handed 310
Helix 53	53	D	256	261	Right-handed alpha
Helix 54	54	D	263	268	Right-handed 310
Helix 55	55	D	269	278	Right-handed alpha
Helix 56	56	D	293	299	Right-handed alpha
Helix 57	57	D	300	302	Right-handed 310
Helix 58	58	D	319	321	Right-handed 310
Helix 59	59	D	322	327	Right-handed alpha
Helix 60	60	D	350	354	Right-handed 310
Helix 61	61	D	382	391	Right-handed alpha
Helix 62	62	D	402	416	Right-handed alpha

There are 17 sheets in PDB entry 2DKF. 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,

There are 7 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	118	120	first strand
Strand 2	A	80	82	parallel
Strand 3	A	54	56	parallel
Strand 4	A	24	30	parallel
Strand 5	A	16	21	anti-parallel
Strand 6	A	2	5	anti-parallel
Strand 7	A	429	430	anti-parallel

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There are 7 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	127	128	first strand
Strand 2	A	133	138	anti-parallel
Strand 3	A	146	152	anti-parallel
Strand 4	A	155	159	anti-parallel
Strand 5	A	182	186	parallel
Strand 6	A	396	399	parallel
Strand 7	A	420	421	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	A	247	250	first strand
Strand 2	A	307	312	parallel
Strand 3	A	217	222	parallel
Strand 4	A	335	338	parallel
Strand 5	A	370	373	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	A	357	360	first strand
Strand 2	A	363	366	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	118	120	first strand
Strand 2	B	80	82	parallel
Strand 3	B	54	56	parallel
Strand 4	B	24	28	parallel
Strand 5	B	17	21	anti-parallel
Strand 6	B	2	5	anti-parallel
Strand 7	B	429	430	anti-parallel

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There are 7 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	126	129	first strand
Strand 2	B	132	138	anti-parallel
Strand 3	B	146	152	anti-parallel
Strand 4	B	155	159	anti-parallel
Strand 5	B	182	186	parallel
Strand 6	B	396	399	parallel
Strand 7	B	420	422	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	287	288	first strand
Strand 2	B	246	250	parallel
Strand 3	B	307	311	parallel
Strand 4	B	217	221	parallel
Strand 5	B	335	338	parallel
Strand 6	B	370	373	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	357	360	first strand
Strand 2	B	363	366	anti-parallel

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There are 7 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	118	120	first strand
Strand 2	C	80	82	parallel
Strand 3	C	54	56	parallel
Strand 4	C	24	28	parallel
Strand 5	C	17	21	anti-parallel
Strand 6	C	2	5	anti-parallel
Strand 7	C	429	430	anti-parallel

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There are 7 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	127	128	first strand
Strand 2	C	133	138	anti-parallel
Strand 3	C	146	152	anti-parallel
Strand 4	C	155	159	anti-parallel
Strand 5	C	182	186	parallel
Strand 6	C	396	399	parallel
Strand 7	C	420	422	parallel

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There are 5 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	247	250	first strand
Strand 2	C	307	311	parallel
Strand 3	C	217	221	parallel
Strand 4	C	335	338	parallel
Strand 5	C	370	373	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	357	359	first strand
Strand 2	C	364	366	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	118	120	first strand
Strand 2	D	80	82	parallel
Strand 3	D	54	56	parallel
Strand 4	D	24	28	parallel
Strand 5	D	17	21	anti-parallel
Strand 6	D	2	5	anti-parallel
Strand 7	D	429	430	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	126	129	first strand
Strand 2	D	132	138	anti-parallel
Strand 3	D	146	152	anti-parallel
Strand 4	D	155	159	anti-parallel
Strand 5	D	182	186	parallel
Strand 6	D	396	399	parallel
Strand 7	D	421	422	parallel

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There are 3 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	217	221	first strand
Strand 2	D	307	311	parallel
Strand 3	D	247	250	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	337	338	first strand
Strand 2	D	372	373	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	357	359	first strand
Strand 2	D	364	366	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: 2DKF

Analysis of interatomic Contacts of Structural Units in PDB entry:
2DKF