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

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 8AMD entry

There are 5 chains in PDB entry 8AMD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 9	ARG 341
D	T 1002	T 1013
B	GLU 9	ARG 341
F	GLU 9	ARG 341
G	GLU 9	ARG 341

There are 53 helices in PDB entry 8AMD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	20	25	Right-handed alpha
Helix 2	AA2	A	25	30	Right-handed alpha
Helix 3	AA3	A	43	49	Right-handed 310
Helix 4	AA4	A	57	65	Right-handed alpha
Helix 5	AA5	A	84	99	Right-handed alpha
Helix 6	AA6	A	113	118	Right-handed alpha
Helix 7	AA7	A	135	147	Right-handed alpha
Helix 8	AA8	A	164	168	Right-handed 310
Helix 9	AA9	A	180	192	Right-handed alpha
Helix 10	AB1	A	225	232	Right-handed alpha
Helix 11	AB2	A	247	251	Right-handed 310
Helix 12	AB3	A	286	297	Right-handed alpha
Helix 13	AB4	A	322	327	Right-handed alpha
Helix 14	AB5	A	333	338	Right-handed alpha
Helix 15	AB6	B	20	25	Right-handed alpha
Helix 16	AB7	B	25	30	Right-handed alpha
Helix 17	AB8	B	43	49	Right-handed 310
Helix 18	AB9	B	57	65	Right-handed alpha
Helix 19	AC1	B	84	99	Right-handed alpha
Helix 20	AC2	B	113	118	Right-handed alpha
Helix 21	AC3	B	134	147	Right-handed alpha
Helix 22	AC4	B	164	168	Right-handed 310
Helix 23	AC5	B	180	192	Right-handed alpha
Helix 24	AC6	B	226	232	Right-handed alpha
Helix 25	AC7	B	286	297	Right-handed alpha
Helix 26	AC8	B	333	341	Right-handed alpha
Helix 27	AC9	F	20	25	Right-handed alpha
Helix 28	AD1	F	25	30	Right-handed alpha
Helix 29	AD2	F	45	49	Right-handed 310
Helix 30	AD3	F	57	64	Right-handed alpha
Helix 31	AD4	F	84	99	Right-handed alpha
Helix 32	AD5	F	113	121	Right-handed alpha
Helix 33	AD6	F	134	147	Right-handed alpha
Helix 34	AD7	F	164	168	Right-handed 310
Helix 35	AD8	F	180	192	Right-handed alpha
Helix 36	AD9	F	226	232	Right-handed alpha
Helix 37	AE1	F	247	251	Right-handed 310
Helix 38	AE2	F	286	297	Right-handed alpha
Helix 39	AE3	F	322	327	Right-handed alpha
Helix 40	AE4	F	333	338	Right-handed alpha
Helix 41	AE5	G	19	25	Right-handed alpha
Helix 42	AE6	G	25	30	Right-handed alpha
Helix 43	AE7	G	41	45	Right-handed 310
Helix 44	AE8	G	57	64	Right-handed alpha
Helix 45	AE9	G	84	99	Right-handed alpha
Helix 46	AF1	G	113	121	Right-handed alpha
Helix 47	AF2	G	134	149	Right-handed alpha
Helix 48	AF3	G	164	168	Right-handed 310
Helix 49	AF4	G	180	192	Right-handed alpha
Helix 50	AF5	G	226	232	Right-handed alpha
Helix 51	AF6	G	247	251	Right-handed 310
Helix 52	AF7	G	286	298	Right-handed alpha
Helix 53	AF8	G	333	338	Right-handed alpha

There are 15 sheets in PDB entry 8AMD. 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 2 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	39	41	first strand
Strand 2	B	128	130	anti-parallel

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There are 2 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	52	53	first strand
Strand 2	A	69	70	anti-parallel

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There are 8 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	103	106	first strand
Strand 2	A	153	156	parallel
Strand 3	A	201	206	parallel
Strand 4	A	74	78	parallel
Strand 5	A	234	245	parallel
Strand 6	A	254	265	anti-parallel
Strand 7	A	277	280	anti-parallel
Strand 8	A	284	285	anti-parallel

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There are 2 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	209	210	first strand
Strand 2	A	220	221	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	B	39	41	first strand
Strand 2	F	128	130	anti-parallel

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There are 2 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	52	53	first strand
Strand 2	B	69	70	anti-parallel

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There are 6 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	153	156	first strand
Strand 2	B	201	205	parallel
Strand 3	B	74	78	parallel
Strand 4	B	234	248	parallel
Strand 5	B	251	263	anti-parallel
Strand 6	B	275	280	anti-parallel

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There are 2 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	209	210	first strand
Strand 2	B	220	221	anti-parallel

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There are 2 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	39	41	first strand
Strand 2	G	128	130	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	F	52	53	first strand
Strand 2	F	69	70	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	F	153	156	first strand
Strand 2	F	201	205	parallel
Strand 3	F	74	78	parallel
Strand 4	F	234	245	parallel
Strand 5	F	254	265	anti-parallel
Strand 6	F	277	280	anti-parallel

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There are 2 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	209	210	first strand
Strand 2	F	220	221	anti-parallel

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There are 2 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	52	53	first strand
Strand 2	G	69	70	anti-parallel

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There are 8 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	103	106	first strand
Strand 2	G	153	156	parallel
Strand 3	G	201	204	parallel
Strand 4	G	74	78	parallel
Strand 5	G	234	245	parallel
Strand 6	G	254	266	anti-parallel
Strand 7	G	275	280	anti-parallel
Strand 8	G	284	285	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	G	209	210	first strand
Strand 2	G	220	221	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: 8AMD

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