Analysis of interatomic Contacts of Structural Units in PDB entry:
9RKD

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 9RKD entry

There are 4 chains in PDB entry 9RKD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	HIS 1	ASN 713
B	HIS 758	GLU 810
C	HIS 1	ASN 713
D	HIS 758	GLU 810

There are 22 helices in PDB entry 9RKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	16	24	Right-handed 310
Helix 2	AA2	A	42	46	Right-handed 310
Helix 3	AA3	A	132	136	Right-handed 310
Helix 4	AA4	A	161	165	Right-handed 310
Helix 5	AA5	A	255	268	Right-handed alpha
Helix 6	AA6	A	323	330	Right-handed alpha
Helix 7	AA7	A	352	359	Right-handed alpha
Helix 8	AA8	A	435	447	Right-handed alpha
Helix 9	AA9	A	496	498	Right-handed 310
Helix 10	AB1	A	640	644	Right-handed 310
Helix 11	AB2	A	692	711	Right-handed alpha
Helix 12	AB3	C	16	24	Right-handed 310
Helix 13	AB4	C	42	46	Right-handed 310
Helix 14	AB5	C	132	136	Right-handed 310
Helix 15	AB6	C	161	165	Right-handed 310
Helix 16	AB7	C	255	268	Right-handed alpha
Helix 17	AB8	C	323	330	Right-handed alpha
Helix 18	AB9	C	352	359	Right-handed alpha
Helix 19	AC1	C	435	447	Right-handed alpha
Helix 20	AC2	C	496	498	Right-handed 310
Helix 21	AC3	C	640	644	Right-handed 310
Helix 22	AC4	C	692	711	Right-handed alpha

There are 28 sheets in PDB entry 9RKD. 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, AB7, AB8, AB9, AC1, AC2, AC3, AC4, AC5, AC6, AC7, AC8, AC9, AD1,

There are 5 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	6	14	first strand
Strand 2	A	26	38	parallel
Strand 3	A	56	57	parallel
Strand 4	A	81	82	parallel
Strand 5	A	111	112	parallel

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There are 6 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	6	14	first strand
Strand 2	A	26	38	parallel
Strand 3	A	61	66	parallel
Strand 4	A	91	96	parallel
Strand 5	A	116	120	parallel
Strand 6	A	144	146	parallel

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There are 2 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	171	172	first strand
Strand 2	A	179	180	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	231	233	first strand
Strand 2	A	236	238	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	246	248	first strand
Strand 2	A	252	254	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	A	278	280	first strand
Strand 2	A	283	285	anti-parallel

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There are 2 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	292	294	first strand
Strand 2	A	301	303	anti-parallel

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There are 5 strands in AA8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	311	321	first strand
Strand 2	A	335	342	parallel
Strand 3	A	363	364	parallel
Strand 4	A	387	388	parallel
Strand 5	A	420	421	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	A	311	321	first strand
Strand 2	A	335	342	parallel
Strand 3	A	368	371	parallel
Strand 4	A	398	403	parallel
Strand 5	A	425	429	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	A	471	473	first strand
Strand 2	A	583	585	parallel

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There are 3 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	475	480	first strand
Strand 2	A	485	489	anti-parallel
Strand 3	A	552	555	anti-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	A	530	534	first strand
Strand 2	A	500	509	anti-parallel
Strand 3	A	563	572	anti-parallel
Strand 4	A	588	591	anti-parallel

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There are 3 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	604	607	first strand
Strand 2	A	613	616	anti-parallel
Strand 3	B	769	772	anti-parallel

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There are 4 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	761	764	first strand
Strand 2	A	629	637	anti-parallel
Strand 3	B	780	788	anti-parallel
Strand 4	B	801	806	anti-parallel

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There are 5 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	6	14	first strand
Strand 2	C	26	38	parallel
Strand 3	C	56	57	parallel
Strand 4	C	81	82	parallel
Strand 5	C	111	112	parallel

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There are 6 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	6	14	first strand
Strand 2	C	26	38	parallel
Strand 3	C	61	66	parallel
Strand 4	C	91	96	parallel
Strand 5	C	116	120	parallel
Strand 6	C	144	146	parallel

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There are 2 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	171	172	first strand
Strand 2	C	179	180	anti-parallel

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There are 2 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	231	233	first strand
Strand 2	C	236	238	anti-parallel

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There are 2 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	246	248	first strand
Strand 2	C	252	254	anti-parallel

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There are 2 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	278	280	first strand
Strand 2	C	283	285	anti-parallel

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There are 2 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	292	294	first strand
Strand 2	C	301	303	anti-parallel

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There are 5 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	311	321	first strand
Strand 2	C	335	342	parallel
Strand 3	C	363	364	parallel
Strand 4	C	387	388	parallel
Strand 5	C	420	421	parallel

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There are 5 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	311	321	first strand
Strand 2	C	335	342	parallel
Strand 3	C	368	371	parallel
Strand 4	C	398	403	parallel
Strand 5	C	425	429	parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	471	473	first strand
Strand 2	C	583	585	parallel

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There are 3 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	475	480	first strand
Strand 2	C	485	489	anti-parallel
Strand 3	C	552	555	anti-parallel

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There are 4 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	530	534	first strand
Strand 2	C	500	509	anti-parallel
Strand 3	C	563	572	anti-parallel
Strand 4	C	588	591	anti-parallel

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There are 3 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	604	607	first strand
Strand 2	C	613	616	anti-parallel
Strand 3	D	769	772	anti-parallel

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There are 4 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	761	764	first strand
Strand 2	C	629	637	anti-parallel
Strand 3	D	780	788	anti-parallel
Strand 4	D	801	806	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: 9RKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
9RKD