Analysis of interatomic Contacts of Structural Units in PDB entry:
5GKD

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 5GKD entry

There are 4 chains in PDB entry 5GKD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ALA 2	LEU 727
B	ALA 2	LEU 727
C	ALA 2	LEU 727
D	ALA 2	LEU 727

There are 26 helices in PDB entry 5GKD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	8	19	Right-handed alpha
Helix 2	AA2	A	191	194	Right-handed 310
Helix 3	AA3	A	284	288	Right-handed 310
Helix 4	AA4	A	403	409	Right-handed 310
Helix 5	AA5	A	419	423	Right-handed 310
Helix 6	AA6	A	450	459	Right-handed alpha
Helix 7	AA7	B	8	19	Right-handed alpha
Helix 8	AA8	B	157	161	Right-handed 310
Helix 9	AA9	B	190	194	Right-handed 310
Helix 10	AB1	B	284	288	Right-handed 310
Helix 11	AB2	B	403	407	Right-handed 310
Helix 12	AB3	B	419	423	Right-handed 310
Helix 13	AB4	B	450	459	Right-handed alpha
Helix 14	AB5	C	8	18	Right-handed alpha
Helix 15	AB6	C	190	194	Right-handed 310
Helix 16	AB7	C	284	288	Right-handed 310
Helix 17	AB8	C	403	407	Right-handed 310
Helix 18	AB9	C	419	423	Right-handed 310
Helix 19	AC1	C	450	459	Right-handed alpha
Helix 20	AC2	D	8	19	Right-handed alpha
Helix 21	AC3	D	157	161	Right-handed 310
Helix 22	AC4	D	190	194	Right-handed 310
Helix 23	AC5	D	284	288	Right-handed 310
Helix 24	AC6	D	403	409	Right-handed 310
Helix 25	AC7	D	419	423	Right-handed 310
Helix 26	AC8	D	450	459	Right-handed alpha

There are 32 sheets in PDB entry 5GKD. 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, AD2, AD3, AD4, AD5,

There are 14 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	3	6	first strand
Strand 2	A	24	27	parallel
Strand 3	A	49	53	parallel
Strand 4	A	74	84	parallel
Strand 5	A	106	113	parallel
Strand 6	A	135	137	parallel
Strand 7	A	166	168	parallel
Strand 8	A	201	203	parallel
Strand 9	A	225	227	parallel
Strand 10	A	247	249	parallel
Strand 11	A	272	274	parallel
Strand 12	A	311	313	parallel
Strand 13	A	340	343	parallel
Strand 14	A	365	368	parallel

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There are 14 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	30	33	first strand
Strand 2	A	59	63	parallel
Strand 3	A	74	84	parallel
Strand 4	A	106	113	parallel
Strand 5	A	140	142	parallel
Strand 6	A	171	172	parallel
Strand 7	A	206	208	parallel
Strand 8	A	230	232	parallel
Strand 9	A	252	254	parallel
Strand 10	A	277	279	parallel
Strand 11	A	316	318	parallel
Strand 12	A	346	348	parallel
Strand 13	A	370	373	parallel
Strand 14	A	384	387	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	36	42	first strand
Strand 2	A	66	72	parallel
Strand 3	A	100	103	parallel
Strand 4	A	95	97	anti-parallel

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There are 12 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	36	42	first strand
Strand 2	A	66	72	parallel
Strand 3	A	90	93	parallel
Strand 4	A	125	129	parallel
Strand 5	A	151	153	parallel
Strand 6	A	186	189	parallel
Strand 7	A	215	220	parallel
Strand 8	A	237	242	parallel
Strand 9	A	264	266	parallel
Strand 10	A	290	293	parallel
Strand 11	A	323	327	parallel
Strand 12	A	356	358	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	391	393	first strand
Strand 2	A	399	401	anti-parallel

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There are 11 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	442	445	first strand
Strand 2	A	463	467	parallel
Strand 3	A	483	488	parallel
Strand 4	A	511	515	parallel
Strand 5	A	544	549	parallel
Strand 6	A	573	579	parallel
Strand 7	A	607	611	parallel
Strand 8	A	638	642	parallel
Strand 9	A	668	672	parallel
Strand 10	A	692	696	parallel
Strand 11	A	718	722	parallel

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There are 11 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	448	449	first strand
Strand 2	A	470	474	parallel
Strand 3	A	494	498	parallel
Strand 4	A	518	520	parallel
Strand 5	A	552	556	parallel
Strand 6	A	582	586	parallel
Strand 7	A	614	618	parallel
Strand 8	A	645	649	parallel
Strand 9	A	675	677	parallel
Strand 10	A	699	701	parallel
Strand 11	A	725	726	parallel

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There are 9 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	478	480	first strand
Strand 2	A	504	506	parallel
Strand 3	A	531	535	parallel
Strand 4	A	563	566	parallel
Strand 5	A	591	593	parallel
Strand 6	A	623	626	parallel
Strand 7	A	661	664	parallel
Strand 8	A	682	686	parallel
Strand 9	A	707	710	parallel

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There are 14 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	3	6	first strand
Strand 2	B	24	27	parallel
Strand 3	B	49	53	parallel
Strand 4	B	74	77	parallel
Strand 5	B	106	108	parallel
Strand 6	B	135	137	parallel
Strand 7	B	166	168	parallel
Strand 8	B	201	203	parallel
Strand 9	B	225	227	parallel
Strand 10	B	247	249	parallel
Strand 11	B	272	274	parallel
Strand 12	B	311	313	parallel
Strand 13	B	340	343	parallel
Strand 14	B	365	368	parallel

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There are 14 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	30	33	first strand
Strand 2	B	59	63	parallel
Strand 3	B	80	84	parallel
Strand 4	B	111	113	parallel
Strand 5	B	140	142	parallel
Strand 6	B	171	172	parallel
Strand 7	B	206	208	parallel
Strand 8	B	230	232	parallel
Strand 9	B	252	254	parallel
Strand 10	B	277	279	parallel
Strand 11	B	316	318	parallel
Strand 12	B	346	348	parallel
Strand 13	B	370	373	parallel
Strand 14	B	384	387	parallel

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There are 4 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	36	42	first strand
Strand 2	B	66	72	parallel
Strand 3	B	100	103	parallel
Strand 4	B	95	97	anti-parallel

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There are 12 strands in AB3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	36	42	first strand
Strand 2	B	66	72	parallel
Strand 3	B	90	93	parallel
Strand 4	B	125	129	parallel
Strand 5	B	151	153	parallel
Strand 6	B	186	188	parallel
Strand 7	B	215	220	parallel
Strand 8	B	237	242	parallel
Strand 9	B	264	266	parallel
Strand 10	B	290	293	parallel
Strand 11	B	323	327	parallel
Strand 12	B	356	358	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	B	391	393	first strand
Strand 2	B	399	401	anti-parallel

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There are 11 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	442	445	first strand
Strand 2	B	463	467	parallel
Strand 3	B	483	488	parallel
Strand 4	B	511	515	parallel
Strand 5	B	544	549	parallel
Strand 6	B	573	579	parallel
Strand 7	B	605	611	parallel
Strand 8	B	638	642	parallel
Strand 9	B	668	672	parallel
Strand 10	B	692	696	parallel
Strand 11	B	718	722	parallel

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There are 11 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	448	449	first strand
Strand 2	B	470	474	parallel
Strand 3	B	494	498	parallel
Strand 4	B	518	520	parallel
Strand 5	B	552	556	parallel
Strand 6	B	582	586	parallel
Strand 7	B	614	618	parallel
Strand 8	B	645	649	parallel
Strand 9	B	675	677	parallel
Strand 10	B	699	701	parallel
Strand 11	B	725	726	parallel

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There are 9 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	478	480	first strand
Strand 2	B	502	506	parallel
Strand 3	B	531	535	parallel
Strand 4	B	563	566	parallel
Strand 5	B	591	593	parallel
Strand 6	B	623	626	parallel
Strand 7	B	661	664	parallel
Strand 8	B	682	686	parallel
Strand 9	B	707	710	parallel

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There are 14 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	3	6	first strand
Strand 2	C	24	27	parallel
Strand 3	C	49	53	parallel
Strand 4	C	74	77	parallel
Strand 5	C	106	108	parallel
Strand 6	C	135	137	parallel
Strand 7	C	166	168	parallel
Strand 8	C	201	203	parallel
Strand 9	C	225	227	parallel
Strand 10	C	247	249	parallel
Strand 11	C	272	274	parallel
Strand 12	C	311	313	parallel
Strand 13	C	340	343	parallel
Strand 14	C	365	368	parallel

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There are 14 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	30	33	first strand
Strand 2	C	59	63	parallel
Strand 3	C	80	84	parallel
Strand 4	C	111	113	parallel
Strand 5	C	140	142	parallel
Strand 6	C	171	172	parallel
Strand 7	C	206	208	parallel
Strand 8	C	230	232	parallel
Strand 9	C	252	254	parallel
Strand 10	C	277	279	parallel
Strand 11	C	316	318	parallel
Strand 12	C	346	348	parallel
Strand 13	C	370	373	parallel
Strand 14	C	384	387	parallel

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There are 4 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	36	42	first strand
Strand 2	C	66	72	parallel
Strand 3	C	100	103	parallel
Strand 4	C	95	97	anti-parallel

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There are 12 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	36	42	first strand
Strand 2	C	66	72	parallel
Strand 3	C	90	93	parallel
Strand 4	C	125	129	parallel
Strand 5	C	151	153	parallel
Strand 6	C	186	188	parallel
Strand 7	C	215	220	parallel
Strand 8	C	237	242	parallel
Strand 9	C	264	266	parallel
Strand 10	C	290	293	parallel
Strand 11	C	323	327	parallel
Strand 12	C	356	358	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	391	393	first strand
Strand 2	C	399	401	anti-parallel

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There are 11 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	442	445	first strand
Strand 2	C	463	467	parallel
Strand 3	C	483	488	parallel
Strand 4	C	511	515	parallel
Strand 5	C	544	549	parallel
Strand 6	C	573	579	parallel
Strand 7	C	607	611	parallel
Strand 8	C	638	642	parallel
Strand 9	C	668	672	parallel
Strand 10	C	692	696	parallel
Strand 11	C	718	722	parallel

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There are 11 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	448	449	first strand
Strand 2	C	470	474	parallel
Strand 3	C	494	498	parallel
Strand 4	C	518	520	parallel
Strand 5	C	552	556	parallel
Strand 6	C	582	586	parallel
Strand 7	C	614	618	parallel
Strand 8	C	645	649	parallel
Strand 9	C	675	677	parallel
Strand 10	C	699	701	parallel
Strand 11	C	725	726	parallel

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There are 9 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	478	480	first strand
Strand 2	C	502	506	parallel
Strand 3	C	531	535	parallel
Strand 4	C	563	566	parallel
Strand 5	C	591	593	parallel
Strand 6	C	623	626	parallel
Strand 7	C	661	664	parallel
Strand 8	C	682	686	parallel
Strand 9	C	707	710	parallel

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There are 14 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	3	6	first strand
Strand 2	D	24	27	parallel
Strand 3	D	49	53	parallel
Strand 4	D	74	84	parallel
Strand 5	D	106	113	parallel
Strand 6	D	135	137	parallel
Strand 7	D	166	168	parallel
Strand 8	D	201	203	parallel
Strand 9	D	225	227	parallel
Strand 10	D	247	249	parallel
Strand 11	D	272	274	parallel
Strand 12	D	311	313	parallel
Strand 13	D	340	343	parallel
Strand 14	D	365	368	parallel

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There are 14 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	30	33	first strand
Strand 2	D	59	63	parallel
Strand 3	D	74	84	parallel
Strand 4	D	106	113	parallel
Strand 5	D	140	142	parallel
Strand 6	D	171	172	parallel
Strand 7	D	206	208	parallel
Strand 8	D	230	232	parallel
Strand 9	D	252	254	parallel
Strand 10	D	277	279	parallel
Strand 11	D	316	318	parallel
Strand 12	D	346	348	parallel
Strand 13	D	370	373	parallel
Strand 14	D	384	387	parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	36	42	first strand
Strand 2	D	66	72	parallel
Strand 3	D	100	103	parallel
Strand 4	D	95	97	anti-parallel

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There are 12 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	36	42	first strand
Strand 2	D	66	72	parallel
Strand 3	D	90	93	parallel
Strand 4	D	125	129	parallel
Strand 5	D	151	153	parallel
Strand 6	D	186	188	parallel
Strand 7	D	215	220	parallel
Strand 8	D	237	242	parallel
Strand 9	D	264	266	parallel
Strand 10	D	290	293	parallel
Strand 11	D	323	327	parallel
Strand 12	D	356	358	parallel

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There are 2 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	391	393	first strand
Strand 2	D	399	401	anti-parallel

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There are 11 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	442	445	first strand
Strand 2	D	463	467	parallel
Strand 3	D	483	488	parallel
Strand 4	D	511	515	parallel
Strand 5	D	544	549	parallel
Strand 6	D	573	579	parallel
Strand 7	D	607	611	parallel
Strand 8	D	638	642	parallel
Strand 9	D	668	672	parallel
Strand 10	D	692	696	parallel
Strand 11	D	718	722	parallel

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There are 11 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	448	449	first strand
Strand 2	D	470	474	parallel
Strand 3	D	494	498	parallel
Strand 4	D	518	520	parallel
Strand 5	D	552	556	parallel
Strand 6	D	582	586	parallel
Strand 7	D	614	618	parallel
Strand 8	D	645	649	parallel
Strand 9	D	675	677	parallel
Strand 10	D	699	701	parallel
Strand 11	D	725	727	parallel

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There are 9 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	478	480	first strand
Strand 2	D	502	506	parallel
Strand 3	D	531	535	parallel
Strand 4	D	563	566	parallel
Strand 5	D	591	593	parallel
Strand 6	D	623	626	parallel
Strand 7	D	661	664	parallel
Strand 8	D	682	686	parallel
Strand 9	D	707	710	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: 5GKD

Analysis of interatomic Contacts of Structural Units in PDB entry:
5GKD