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

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 1VDM entry

There are 12 chains in PDB entry 1VDM (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	MET 1	GLU 153
B	MET 1	GLU 153
C	MET 1	LYS 152
D	MET 1	LYS 152
E	MET 1	GLU 153
F	MET 1	LYS 152
G	MET 1	LYS 152
H	MET 1	GLU 153
I	MET 1	LYS 152
J	MET 1	LYS 152
K	MET 1	LYS 152
L	MET 1	GLU 153

There are 38 helices in PDB entry 1VDM. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	7	26	Right-handed alpha
Helix 2	2	A	37	48	Right-handed alpha
Helix 3	3	A	96	108	Right-handed alpha
Helix 4	4	B	7	26	Right-handed alpha
Helix 5	5	B	37	48	Right-handed alpha
Helix 6	6	B	96	108	Right-handed alpha
Helix 7	7	C	7	23	Right-handed alpha
Helix 8	8	C	37	48	Right-handed alpha
Helix 9	9	C	96	108	Right-handed alpha
Helix 10	10	D	7	23	Right-handed alpha
Helix 11	11	D	24	26	Right-handed 310
Helix 12	12	D	37	48	Right-handed alpha
Helix 13	13	D	96	109	Right-handed alpha
Helix 14	14	E	7	26	Right-handed alpha
Helix 15	15	E	37	48	Right-handed alpha
Helix 16	16	E	96	108	Right-handed alpha
Helix 17	17	F	7	23	Right-handed alpha
Helix 18	18	F	37	48	Right-handed alpha
Helix 19	19	F	96	109	Right-handed alpha
Helix 20	20	G	7	24	Right-handed alpha
Helix 21	21	G	37	48	Right-handed alpha
Helix 22	22	G	96	108	Right-handed alpha
Helix 23	23	H	7	24	Right-handed alpha
Helix 24	24	H	37	48	Right-handed alpha
Helix 25	25	H	96	108	Right-handed alpha
Helix 26	26	I	7	26	Right-handed alpha
Helix 27	27	I	37	48	Right-handed alpha
Helix 28	28	I	96	108	Right-handed alpha
Helix 29	29	J	7	23	Right-handed alpha
Helix 30	30	J	24	26	Right-handed 310
Helix 31	31	J	37	48	Right-handed alpha
Helix 32	32	J	96	108	Right-handed alpha
Helix 33	33	K	7	26	Right-handed alpha
Helix 34	34	K	37	48	Right-handed alpha
Helix 35	35	K	96	108	Right-handed alpha
Helix 36	36	L	7	23	Right-handed alpha
Helix 37	37	L	37	48	Right-handed alpha
Helix 38	38	L	96	109	Right-handed alpha

There are 31 sheets in PDB entry 1VDM. 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,

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	3	5	first strand
Strand 2	A	139	141	parallel

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There are 6 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	72	75	first strand
Strand 2	A	53	59	anti-parallel
Strand 3	A	29	33	parallel
Strand 4	A	85	93	parallel
Strand 5	A	113	121	parallel
Strand 6	A	134	135	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	150	151	first strand
Strand 2	E	131	132	anti-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	B	3	5	first strand
Strand 2	B	139	141	parallel

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There are 6 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	70	75	first strand
Strand 2	B	53	61	anti-parallel
Strand 3	B	29	33	parallel
Strand 4	B	85	93	parallel
Strand 5	B	113	121	parallel
Strand 6	B	134	135	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	B	131	132	first strand
Strand 2	F	150	151	anti-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	150	151	first strand
Strand 2	D	131	132	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	C	3	5	first strand
Strand 2	C	139	141	parallel

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There are 6 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	72	75	first strand
Strand 2	C	53	59	anti-parallel
Strand 3	C	29	33	parallel
Strand 4	C	85	93	parallel
Strand 5	C	113	121	parallel
Strand 6	C	134	135	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	5	first strand
Strand 2	D	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	70	75	first strand
Strand 2	D	53	61	anti-parallel
Strand 3	D	29	33	parallel
Strand 4	D	85	93	parallel
Strand 5	D	113	121	parallel
Strand 6	D	134	135	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	D	150	151	first strand
Strand 2	F	131	132	anti-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	E	3	5	first strand
Strand 2	E	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	E	70	75	first strand
Strand 2	E	53	61	anti-parallel
Strand 3	E	29	33	parallel
Strand 4	E	85	93	parallel
Strand 5	E	113	121	parallel
Strand 6	E	134	135	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	F	3	5	first strand
Strand 2	F	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	69	75	first strand
Strand 2	F	53	62	anti-parallel
Strand 3	F	29	33	parallel
Strand 4	F	85	93	parallel
Strand 5	F	113	121	parallel
Strand 6	F	134	135	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	G	3	5	first strand
Strand 2	G	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	70	75	first strand
Strand 2	G	53	61	anti-parallel
Strand 3	G	29	33	parallel
Strand 4	G	85	93	parallel
Strand 5	G	113	121	parallel
Strand 6	G	134	135	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	G	150	151	first strand
Strand 2	K	131	132	anti-parallel

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There are 2 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	3	5	first strand
Strand 2	H	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	70	75	first strand
Strand 2	H	53	61	anti-parallel
Strand 3	H	29	34	parallel
Strand 4	H	85	93	parallel
Strand 5	H	113	121	parallel
Strand 6	H	131	135	parallel
Strand 7	L	150	151	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	H	150	151	first strand
Strand 2	J	131	132	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	3	5	first strand
Strand 2	I	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	70	75	first strand
Strand 2	I	53	61	anti-parallel
Strand 3	I	29	33	parallel
Strand 4	I	85	93	parallel
Strand 5	I	113	121	parallel
Strand 6	I	134	135	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	3	5	first strand
Strand 2	J	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	70	75	first strand
Strand 2	J	53	61	anti-parallel
Strand 3	J	29	33	parallel
Strand 4	J	85	93	parallel
Strand 5	J	113	121	parallel
Strand 6	J	134	135	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	J	150	151	first strand
Strand 2	L	131	132	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	4	5	first strand
Strand 2	K	140	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	K	70	75	first strand
Strand 2	K	53	61	anti-parallel
Strand 3	K	29	33	parallel
Strand 4	K	85	93	parallel
Strand 5	K	113	121	parallel
Strand 6	K	134	135	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	3	5	first strand
Strand 2	L	139	141	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	70	75	first strand
Strand 2	L	53	61	anti-parallel
Strand 3	L	29	33	parallel
Strand 4	L	85	93	parallel
Strand 5	L	113	121	parallel
Strand 6	L	134	135	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: 1VDM

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