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

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 5KOD entry

There are 3 chains in PDB entry 5KOD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ASP 18	GLN 608
B	THR 16	PRO 604
C	THR 16	ILE 123

There are102 helices in PDB entry 5KOD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	18	34	Right-handed alpha
Helix 2	AA2	A	34	50	Right-handed alpha
Helix 3	AA3	A	53	59	Right-handed alpha
Helix 4	AA4	A	66	74	Right-handed alpha
Helix 5	AA5	A	78	91	Right-handed alpha
Helix 6	AA6	A	125	142	Right-handed alpha
Helix 7	AA7	A	147	151	Right-handed 310
Helix 8	AA8	A	173	180	Right-handed alpha
Helix 9	AA9	A	181	186	Right-handed alpha
Helix 10	AB1	A	190	194	Right-handed 310
Helix 11	AB2	A	198	203	Right-handed alpha
Helix 12	AB3	A	206	221	Right-handed alpha
Helix 13	AB4	A	233	257	Right-handed alpha
Helix 14	AB5	A	266	274	Right-handed alpha
Helix 15	AB6	A	279	291	Right-handed alpha
Helix 16	AB7	A	297	303	Right-handed alpha
Helix 17	AB8	A	314	319	Right-handed 310
Helix 18	AB9	A	320	329	Right-handed alpha
Helix 19	AC1	A	354	358	Right-handed 310
Helix 20	AC2	A	402	404	Right-handed 310
Helix 21	AC3	A	459	472	Right-handed alpha
Helix 22	AC4	A	473	477	Right-handed 310
Helix 23	AC5	A	512	527	Right-handed alpha
Helix 24	AC6	A	528	537	Right-handed alpha
Helix 25	AC7	A	552	564	Right-handed alpha
Helix 26	AC8	A	579	588	Right-handed alpha
Helix 27	AC9	B	17	34	Right-handed alpha
Helix 28	AD1	B	34	50	Right-handed alpha
Helix 29	AD2	B	53	59	Right-handed alpha
Helix 30	AD3	B	66	74	Right-handed alpha
Helix 31	AD4	B	78	92	Right-handed alpha
Helix 32	AD5	B	125	135	Right-handed alpha
Helix 33	AD6	B	136	142	Right-handed alpha
Helix 34	AD7	B	147	151	Right-handed 310
Helix 35	AD8	B	173	180	Right-handed alpha
Helix 36	AD9	B	198	203	Right-handed alpha
Helix 37	AE1	B	206	221	Right-handed alpha
Helix 38	AE2	B	233	257	Right-handed alpha
Helix 39	AE3	B	265	276	Right-handed alpha
Helix 40	AE4	B	279	291	Right-handed alpha
Helix 41	AE5	B	297	303	Right-handed alpha
Helix 42	AE6	B	314	319	Right-handed 310
Helix 43	AE7	B	320	329	Right-handed alpha
Helix 44	AE8	B	354	358	Right-handed 310
Helix 45	AE9	B	402	404	Right-handed 310
Helix 46	AF1	B	459	471	Right-handed alpha
Helix 47	AF2	B	472	477	Right-handed 310
Helix 48	AF3	B	512	527	Right-handed alpha
Helix 49	AF4	B	528	537	Right-handed alpha
Helix 50	AF5	B	552	565	Right-handed alpha
Helix 51	AF6	B	579	588	Right-handed alpha
Helix 52	AF7	C	17	34	Right-handed alpha
Helix 53	AF8	C	34	50	Right-handed alpha
Helix 54	AF9	C	53	59	Right-handed alpha
Helix 55	AG1	C	66	74	Right-handed alpha
Helix 56	AG2	C	78	92	Right-handed alpha
Helix 57	AG3	C	125	142	Right-handed alpha
Helix 58	AG4	C	147	151	Right-handed 310
Helix 59	AG5	C	173	180	Right-handed alpha
Helix 60	AG6	C	198	203	Right-handed alpha
Helix 61	AG7	C	206	221	Right-handed alpha
Helix 62	AG8	C	233	257	Right-handed alpha
Helix 63	AG9	C	265	274	Right-handed alpha
Helix 64	AH1	C	279	291	Right-handed alpha
Helix 65	AH2	C	297	303	Right-handed alpha
Helix 66	AH3	C	314	319	Right-handed 310
Helix 67	AH4	C	320	329	Right-handed alpha
Helix 68	AH5	C	354	358	Right-handed 310
Helix 69	AH6	C	391	397	Right-handed alpha
Helix 70	AH7	C	402	404	Right-handed 310
Helix 71	AH8	C	460	472	Right-handed alpha
Helix 72	AH9	C	473	478	Right-handed 310
Helix 73	AI1	C	513	525	Right-handed alpha
Helix 74	AI2	C	528	537	Right-handed alpha
Helix 75	AI3	C	552	565	Right-handed alpha
Helix 76	AI4	C	579	588	Right-handed alpha
Helix 77	AI5	D	17	34	Right-handed alpha
Helix 78	AI6	D	34	50	Right-handed alpha
Helix 79	AI7	D	53	59	Right-handed alpha
Helix 80	AI8	D	66	74	Right-handed alpha
Helix 81	AI9	D	78	91	Right-handed alpha
Helix 82	AJ1	D	125	142	Right-handed alpha
Helix 83	AJ2	D	147	151	Right-handed 310
Helix 84	AJ3	D	173	180	Right-handed alpha
Helix 85	AJ4	D	181	186	Right-handed alpha
Helix 86	AJ5	D	190	194	Right-handed 310
Helix 87	AJ6	D	198	203	Right-handed alpha
Helix 88	AJ7	D	206	221	Right-handed alpha
Helix 89	AJ8	D	233	257	Right-handed alpha
Helix 90	AJ9	D	265	274	Right-handed alpha
Helix 91	AK1	D	279	292	Right-handed alpha
Helix 92	AK2	D	297	303	Right-handed alpha
Helix 93	AK3	D	314	319	Right-handed 310
Helix 94	AK4	D	320	329	Right-handed alpha
Helix 95	AK5	D	354	358	Right-handed 310
Helix 96	AK6	D	402	404	Right-handed 310
Helix 97	AK7	D	459	472	Right-handed alpha
Helix 98	AK8	D	473	478	Right-handed 310
Helix 99	AK9	D	512	526	Right-handed alpha
Helix 100	AL1	D	528	537	Right-handed alpha
Helix 101	AL2	D	552	564	Right-handed alpha
Helix 102	AL3	D	579	588	Right-handed alpha

There are 17 sheets in PDB entry 5KOD. 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,

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	116	122	first strand
Strand 2	A	105	113	anti-parallel
Strand 3	A	170	172	parallel
Strand 4	A	163	164	anti-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	152	155	first strand
Strand 2	A	225	232	parallel
Strand 3	A	309	312	parallel
Strand 4	A	333	334	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	337	339	first strand
Strand 2	A	344	347	anti-parallel
Strand 3	A	360	362	anti-parallel
Strand 4	A	438	446	anti-parallel
Strand 5	A	423	435	anti-parallel
Strand 6	A	409	415	anti-parallel
Strand 7	A	368	373	anti-parallel
Strand 8	A	399	400	anti-parallel

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There are 4 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	479	489	first strand
Strand 2	A	496	505	anti-parallel
Strand 3	A	545	549	parallel
Strand 4	A	590	595	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	B	116	122	first strand
Strand 2	B	105	113	anti-parallel
Strand 3	B	170	172	parallel
Strand 4	B	163	164	anti-parallel

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There are 4 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	152	155	first strand
Strand 2	B	225	232	parallel
Strand 3	B	308	312	parallel
Strand 4	B	333	334	parallel

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There are 8 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	337	339	first strand
Strand 2	B	344	347	anti-parallel
Strand 3	B	360	362	anti-parallel
Strand 4	B	438	446	anti-parallel
Strand 5	B	423	435	anti-parallel
Strand 6	B	409	415	anti-parallel
Strand 7	B	368	373	anti-parallel
Strand 8	B	399	400	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	479	489	first strand
Strand 2	B	496	505	anti-parallel
Strand 3	B	545	549	parallel
Strand 4	B	590	595	anti-parallel

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There are 4 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	116	122	first strand
Strand 2	C	105	113	anti-parallel
Strand 3	C	170	172	parallel
Strand 4	C	163	164	anti-parallel

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There are 4 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	152	155	first strand
Strand 2	C	225	232	parallel
Strand 3	C	309	312	parallel
Strand 4	C	333	334	parallel

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There are 8 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	337	339	first strand
Strand 2	C	344	347	anti-parallel
Strand 3	C	360	362	anti-parallel
Strand 4	C	438	446	anti-parallel
Strand 5	C	423	435	anti-parallel
Strand 6	C	409	415	anti-parallel
Strand 7	C	368	373	anti-parallel
Strand 8	C	399	400	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	C	449	451	first strand
Strand 2	C	458	459	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	480	489	first strand
Strand 2	C	496	504	anti-parallel
Strand 3	C	545	549	parallel
Strand 4	C	590	595	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	D	116	122	first strand
Strand 2	D	105	113	anti-parallel
Strand 3	D	170	172	parallel
Strand 4	D	163	164	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	152	156	first strand
Strand 2	D	225	232	parallel
Strand 3	D	309	312	parallel
Strand 4	D	333	334	parallel

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There are 8 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	337	339	first strand
Strand 2	D	344	347	anti-parallel
Strand 3	D	360	362	anti-parallel
Strand 4	D	438	446	anti-parallel
Strand 5	D	423	435	anti-parallel
Strand 6	D	409	415	anti-parallel
Strand 7	D	368	374	anti-parallel
Strand 8	D	399	400	anti-parallel

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There are 4 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	481	489	first strand
Strand 2	D	496	503	anti-parallel
Strand 3	D	545	549	parallel
Strand 4	D	590	595	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: 5KOD

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