Analysis of interatomic Contacts of Structural Units in PDB entry:
8GKD

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 8GKD entry

There are 3 chains in PDB entry 8GKD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 40	TYR 392
B	SER 40	TYR 392
C	HIS 37	TYR 392

There are 36 helices in PDB entry 8GKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	48	62	Right-handed alpha
Helix 2	AA2	A	72	77	Right-handed alpha
Helix 3	AA3	A	78	88	Right-handed alpha
Helix 4	AA4	A	124	128	Right-handed 310
Helix 5	AA5	A	241	246	Right-handed 310
Helix 6	AA6	A	247	258	Right-handed alpha
Helix 7	AA7	A	268	274	Right-handed alpha
Helix 8	AA8	A	278	297	Right-handed alpha
Helix 9	AA9	A	322	338	Right-handed alpha
Helix 10	AB1	A	345	352	Right-handed alpha
Helix 11	AB2	A	353	361	Right-handed alpha
Helix 12	AB3	A	371	387	Right-handed alpha
Helix 13	AB4	B	48	62	Right-handed alpha
Helix 14	AB5	B	72	77	Right-handed alpha
Helix 15	AB6	B	78	88	Right-handed alpha
Helix 16	AB7	B	124	128	Right-handed 310
Helix 17	AB8	B	241	246	Right-handed 310
Helix 18	AB9	B	247	256	Right-handed alpha
Helix 19	AC1	B	268	274	Right-handed alpha
Helix 20	AC2	B	278	297	Right-handed alpha
Helix 21	AC3	B	323	339	Right-handed alpha
Helix 22	AC4	B	345	352	Right-handed alpha
Helix 23	AC5	B	354	361	Right-handed alpha
Helix 24	AC6	B	371	387	Right-handed alpha
Helix 25	AC7	C	48	62	Right-handed alpha
Helix 26	AC8	C	72	77	Right-handed alpha
Helix 27	AC9	C	78	88	Right-handed alpha
Helix 28	AD1	C	124	128	Right-handed 310
Helix 29	AD2	C	241	246	Right-handed 310
Helix 30	AD3	C	247	258	Right-handed alpha
Helix 31	AD4	C	268	274	Right-handed alpha
Helix 32	AD5	C	278	297	Right-handed alpha
Helix 33	AD6	C	323	338	Right-handed alpha
Helix 34	AD7	C	345	352	Right-handed alpha
Helix 35	AD8	C	354	361	Right-handed alpha
Helix 36	AD9	C	371	386	Right-handed alpha

There are 15 sheets in PDB entry 8GKD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3, AB4, AB5, AB6,

There are 6 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	43	45	first strand
Strand 2	A	341	344	anti-parallel
Strand 3	A	301	306	parallel
Strand 4	A	262	266	parallel
Strand 5	A	65	71	parallel
Strand 6	A	228	234	parallel

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There are 4 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	95	97	first strand
Strand 2	A	215	222	anti-parallel
Strand 3	A	137	141	anti-parallel
Strand 4	A	117	121	anti-parallel

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There are 4 strands in AA3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	95	97	first strand
Strand 2	A	215	222	anti-parallel
Strand 3	A	158	166	anti-parallel
Strand 4	A	195	202	anti-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	A	110	115	first strand
Strand 2	A	147	152	anti-parallel
Strand 3	A	205	209	anti-parallel
Strand 4	A	172	177	anti-parallel
Strand 5	A	183	187	anti-parallel

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There are 2 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	311	313	first strand
Strand 2	A	318	320	anti-parallel

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There are 6 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	43	45	first strand
Strand 2	B	341	344	anti-parallel
Strand 3	B	301	306	parallel
Strand 4	B	262	266	parallel
Strand 5	B	65	71	parallel
Strand 6	B	228	234	parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	95	97	first strand
Strand 2	B	215	222	anti-parallel
Strand 3	B	137	141	anti-parallel
Strand 4	B	117	121	anti-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	B	95	97	first strand
Strand 2	B	215	222	anti-parallel
Strand 3	B	158	166	anti-parallel
Strand 4	B	195	202	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	B	110	115	first strand
Strand 2	B	147	152	anti-parallel
Strand 3	B	205	209	anti-parallel
Strand 4	B	172	177	anti-parallel
Strand 5	B	183	187	anti-parallel

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There are 2 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	311	313	first strand
Strand 2	B	318	320	anti-parallel

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There are 6 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	43	45	first strand
Strand 2	C	341	344	anti-parallel
Strand 3	C	301	306	parallel
Strand 4	C	262	266	parallel
Strand 5	C	65	71	parallel
Strand 6	C	228	234	parallel

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There are 4 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	95	97	first strand
Strand 2	C	215	222	anti-parallel
Strand 3	C	137	141	anti-parallel
Strand 4	C	117	121	anti-parallel

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There are 4 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	95	97	first strand
Strand 2	C	215	222	anti-parallel
Strand 3	C	158	166	anti-parallel
Strand 4	C	195	202	anti-parallel

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There are 5 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	110	115	first strand
Strand 2	C	147	152	anti-parallel
Strand 3	C	205	209	anti-parallel
Strand 4	C	172	177	anti-parallel
Strand 5	C	183	187	anti-parallel

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There are 2 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	311	313	first strand
Strand 2	C	318	320	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: 8GKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
8GKD