Analysis of interatomic Contacts of Structural Units in PDB entry:
6VDK

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 6VDK entry

There are 12 chains in PDB entry 6VDK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	PHE 1	ASP 270
B	PHE 1	ASP 270
C	PHE 1	ASP 270
D	LEU 2	ASP 270
E	A 15	T 41
F	A -3	A 21
G	A 15	T 41
H	A -3	A 21
I	GLN 221	ALA 276
J	GLN 221	ALA 276
M	ASN 222	ASP 270
P	ASN 222	ILE 268

There are 38 helices in PDB entry 6VDK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	2	16	Right-handed alpha
Helix 2	AA2	A	18	27	Right-handed alpha
Helix 3	AA3	A	29	40	Right-handed alpha
Helix 4	AA4	A	93	108	Right-handed alpha
Helix 5	AA5	A	119	122	Right-handed 310
Helix 6	AA6	A	123	134	Right-handed alpha
Helix 7	AA7	A	149	166	Right-handed alpha
Helix 8	AA8	A	171	186	Right-handed alpha
Helix 9	AA9	A	195	219	Right-handed alpha
Helix 10	AB1	B	4	15	Right-handed alpha
Helix 11	AB2	B	18	26	Right-handed alpha
Helix 12	AB3	B	29	40	Right-handed alpha
Helix 13	AB4	B	93	108	Right-handed alpha
Helix 14	AB5	B	123	134	Right-handed alpha
Helix 15	AB6	B	147	166	Right-handed alpha
Helix 16	AB7	B	167	169	Right-handed 310
Helix 17	AB8	B	171	186	Right-handed alpha
Helix 18	AB9	B	196	221	Right-handed alpha
Helix 19	AC1	C	2	16	Right-handed alpha
Helix 20	AC2	C	18	26	Right-handed alpha
Helix 21	AC3	C	29	40	Right-handed alpha
Helix 22	AC4	C	93	108	Right-handed alpha
Helix 23	AC5	C	119	122	Right-handed 310
Helix 24	AC6	C	123	134	Right-handed alpha
Helix 25	AC7	C	148	166	Right-handed alpha
Helix 26	AC8	C	171	186	Right-handed alpha
Helix 27	AC9	C	195	221	Right-handed alpha
Helix 28	AD1	D	2	5	Right-handed 310
Helix 29	AD2	D	6	15	Right-handed alpha
Helix 30	AD3	D	18	26	Right-handed alpha
Helix 31	AD4	D	29	39	Right-handed alpha
Helix 32	AD5	D	93	108	Right-handed alpha
Helix 33	AD6	D	118	122	Right-handed 310
Helix 34	AD7	D	123	134	Right-handed alpha
Helix 35	AD8	D	147	166	Right-handed alpha
Helix 36	AD9	D	171	186	Right-handed alpha
Helix 37	AE1	D	196	221	Right-handed alpha
Helix 38	AE2	J	271	275	Right-handed 310

There are 12 sheets in PDB entry 6VDK. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 4 strands in AA1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	84	88	first strand
Strand 2	A	71	78	anti-parallel
Strand 3	A	60	68	anti-parallel
Strand 4	A	112	114	parallel

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There are 5 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	257	261	first strand
Strand 2	A	248	252	anti-parallel
Strand 3	A	235	243	anti-parallel
Strand 4	A	224	228	anti-parallel
Strand 5	A	267	268	anti-parallel

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There are 5 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	83	89	first strand
Strand 2	B	71	78	anti-parallel
Strand 3	B	60	68	anti-parallel
Strand 4	B	112	115	parallel
Strand 5	B	136	139	parallel

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There are 5 strands in AA4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	257	261	first strand
Strand 2	B	248	252	anti-parallel
Strand 3	B	232	243	anti-parallel
Strand 4	B	224	229	anti-parallel
Strand 5	B	265	268	anti-parallel

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There are 4 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	84	88	first strand
Strand 2	C	71	78	anti-parallel
Strand 3	C	60	68	anti-parallel
Strand 4	C	112	114	parallel

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There are 5 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	257	261	first strand
Strand 2	C	248	252	anti-parallel
Strand 3	C	236	243	anti-parallel
Strand 4	C	224	227	anti-parallel
Strand 5	C	265	268	anti-parallel

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There are 5 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	83	89	first strand
Strand 2	D	71	78	anti-parallel
Strand 3	D	60	68	anti-parallel
Strand 4	D	112	115	parallel
Strand 5	D	136	139	parallel

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There are 4 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	225	228	first strand
Strand 2	D	235	243	anti-parallel
Strand 3	D	248	252	anti-parallel
Strand 4	D	257	261	anti-parallel

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There are 5 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	I	258	261	first strand
Strand 2	I	248	252	anti-parallel
Strand 3	I	236	244	anti-parallel
Strand 4	I	224	227	anti-parallel
Strand 5	I	265	268	anti-parallel

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There are 5 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	J	257	261	first strand
Strand 2	J	248	252	anti-parallel
Strand 3	J	236	244	anti-parallel
Strand 4	J	224	227	anti-parallel
Strand 5	J	265	268	anti-parallel

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There are 5 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	M	257	261	first strand
Strand 2	M	248	252	anti-parallel
Strand 3	M	235	243	anti-parallel
Strand 4	M	224	228	anti-parallel
Strand 5	M	265	267	anti-parallel

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There are 5 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	P	257	261	first strand
Strand 2	P	248	252	anti-parallel
Strand 3	P	236	243	anti-parallel
Strand 4	P	224	227	anti-parallel
Strand 5	P	265	267	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: 6VDK

Analysis of interatomic Contacts of Structural Units in PDB entry:
6VDK