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

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 1VKD entry

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

Chain ID	Initial residue	Terminal residue
A	HIS 0	MSE 326
B	MSE 1	MSE 326
C	MSE 1	MSE 326
D	MSE 1	MSE 326
E	MSE 1	SER 325
F	MSE 1	MSE 326

There are 18 helices in PDB entry 1VKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	206	210	Right-handed 310
Helix 2	2	A	270	275	Right-handed alpha
Helix 3	3	A	314	324	Right-handed alpha
Helix 4	4	B	206	210	Right-handed 310
Helix 5	5	B	270	275	Right-handed alpha
Helix 6	6	B	314	324	Right-handed alpha
Helix 7	7	C	206	210	Right-handed 310
Helix 8	8	C	270	275	Right-handed alpha
Helix 9	9	C	314	324	Right-handed alpha
Helix 10	10	D	206	210	Right-handed 310
Helix 11	11	D	270	275	Right-handed alpha
Helix 12	12	D	314	324	Right-handed alpha
Helix 13	13	E	206	210	Right-handed 310
Helix 14	14	E	270	275	Right-handed alpha
Helix 15	15	E	314	324	Right-handed alpha
Helix 16	16	F	206	210	Right-handed 310
Helix 17	17	F	270	275	Right-handed alpha
Helix 18	18	F	314	324	Right-handed alpha

There are 36 sheets in PDB entry 1VKD. 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,

There are 4 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	24	26	first strand
Strand 2	A	306	313	anti-parallel
Strand 3	A	295	302	anti-parallel
Strand 4	A	282	289	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	41	52	first strand
Strand 2	A	55	64	anti-parallel
Strand 3	A	69	76	anti-parallel
Strand 4	A	83	84	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	A	91	92	first strand
Strand 2	A	140	143	parallel
Strand 3	A	127	134	anti-parallel
Strand 4	A	115	123	anti-parallel
Strand 5	A	104	112	anti-parallel

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There are 4 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	151	156	first strand
Strand 2	A	165	171	anti-parallel
Strand 3	A	182	187	anti-parallel
Strand 4	A	194	200	anti-parallel

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There are 3 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	212	215	first strand
Strand 2	A	225	236	anti-parallel
Strand 3	A	220	222	anti-parallel

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There are 4 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	212	215	first strand
Strand 2	A	225	236	anti-parallel
Strand 3	A	239	249	anti-parallel
Strand 4	A	257	260	anti-parallel

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There are 4 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	24	26	first strand
Strand 2	B	306	313	anti-parallel
Strand 3	B	295	302	anti-parallel
Strand 4	B	282	289	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	41	52	first strand
Strand 2	B	55	64	anti-parallel
Strand 3	B	69	76	anti-parallel
Strand 4	B	83	84	anti-parallel

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There are 5 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	91	92	first strand
Strand 2	B	140	143	parallel
Strand 3	B	127	134	anti-parallel
Strand 4	B	115	123	anti-parallel
Strand 5	B	104	112	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	B	151	156	first strand
Strand 2	B	165	171	anti-parallel
Strand 3	B	182	187	anti-parallel
Strand 4	B	194	200	anti-parallel

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There are 3 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	212	215	first strand
Strand 2	B	225	236	anti-parallel
Strand 3	B	220	222	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	212	215	first strand
Strand 2	B	225	236	anti-parallel
Strand 3	B	239	249	anti-parallel
Strand 4	B	257	260	anti-parallel

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There are 4 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	24	26	first strand
Strand 2	C	306	313	anti-parallel
Strand 3	C	295	302	anti-parallel
Strand 4	C	282	289	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	41	52	first strand
Strand 2	C	55	64	anti-parallel
Strand 3	C	69	76	anti-parallel
Strand 4	C	83	84	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	C	91	92	first strand
Strand 2	C	140	143	parallel
Strand 3	C	127	134	anti-parallel
Strand 4	C	115	123	anti-parallel
Strand 5	C	104	112	anti-parallel

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There are 4 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	151	156	first strand
Strand 2	C	165	171	anti-parallel
Strand 3	C	182	187	anti-parallel
Strand 4	C	194	200	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	212	215	first strand
Strand 2	C	225	236	anti-parallel
Strand 3	C	220	222	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	C	212	215	first strand
Strand 2	C	225	236	anti-parallel
Strand 3	C	239	249	anti-parallel
Strand 4	C	257	260	anti-parallel

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There are 4 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	24	26	first strand
Strand 2	D	306	313	anti-parallel
Strand 3	D	295	302	anti-parallel
Strand 4	D	282	289	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	41	52	first strand
Strand 2	D	55	64	anti-parallel
Strand 3	D	69	76	anti-parallel
Strand 4	D	83	84	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	91	92	first strand
Strand 2	D	140	143	parallel
Strand 3	D	127	134	anti-parallel
Strand 4	D	115	123	anti-parallel
Strand 5	D	104	112	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	151	156	first strand
Strand 2	D	165	171	anti-parallel
Strand 3	D	182	187	anti-parallel
Strand 4	D	194	200	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	212	215	first strand
Strand 2	D	225	236	anti-parallel
Strand 3	D	220	222	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	212	215	first strand
Strand 2	D	225	236	anti-parallel
Strand 3	D	239	249	anti-parallel
Strand 4	D	257	260	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	24	26	first strand
Strand 2	E	306	313	anti-parallel
Strand 3	E	295	302	anti-parallel
Strand 4	E	282	289	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	41	52	first strand
Strand 2	E	55	64	anti-parallel
Strand 3	E	69	76	anti-parallel
Strand 4	E	83	84	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	91	92	first strand
Strand 2	E	140	143	parallel
Strand 3	E	127	134	anti-parallel
Strand 4	E	115	123	anti-parallel
Strand 5	E	104	112	anti-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	E	151	156	first strand
Strand 2	E	165	171	anti-parallel
Strand 3	E	182	187	anti-parallel
Strand 4	E	194	200	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	212	215	first strand
Strand 2	E	225	236	anti-parallel
Strand 3	E	220	222	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	212	215	first strand
Strand 2	E	225	236	anti-parallel
Strand 3	E	239	249	anti-parallel
Strand 4	E	257	260	anti-parallel

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There are 4 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	24	26	first strand
Strand 2	F	306	313	anti-parallel
Strand 3	F	295	302	anti-parallel
Strand 4	F	282	289	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	41	52	first strand
Strand 2	F	55	64	anti-parallel
Strand 3	F	69	76	anti-parallel
Strand 4	F	83	84	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	91	92	first strand
Strand 2	F	140	143	parallel
Strand 3	F	127	134	anti-parallel
Strand 4	F	115	123	anti-parallel
Strand 5	F	104	112	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	F	151	156	first strand
Strand 2	F	165	171	anti-parallel
Strand 3	F	182	187	anti-parallel
Strand 4	F	194	200	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	212	215	first strand
Strand 2	F	225	236	anti-parallel
Strand 3	F	220	222	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	F	212	215	first strand
Strand 2	F	225	236	anti-parallel
Strand 3	F	239	249	anti-parallel
Strand 4	F	257	260	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: 1VKD

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