Analysis of interatomic Contacts of Structural Units in PDB entry:
6KDO

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 6KDO entry

There are 6 chains in PDB entry 6KDO (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	ILE 2	SER 553
B	ILE 5	TYR 427
E	T -1	C 1
E	C 3	C 3
E	C 5	G 33
C	ILE 2	TYR 181

There are 67 helices in PDB entry 6KDO. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	27	44	Right-handed alpha
Helix 2	AA2	A	77	84	Right-handed alpha
Helix 3	AA3	A	96	100	Right-handed 310
Helix 4	AA4	A	114	118	Right-handed 310
Helix 5	AA5	A	121	129	Right-handed 310
Helix 6	AA6	A	134	138	Right-handed 310
Helix 7	AA7	A	155	175	Right-handed alpha
Helix 8	AA8	A	194	212	Right-handed alpha
Helix 9	AA9	A	217	221	Right-handed 310
Helix 10	AB1	A	253	268	Right-handed alpha
Helix 11	AB2	A	276	282	Right-handed alpha
Helix 12	AB3	A	296	312	Right-handed alpha
Helix 13	AB4	A	363	384	Right-handed alpha
Helix 14	AB5	A	394	405	Right-handed alpha
Helix 15	AB6	A	473	489	Right-handed alpha
Helix 16	AB7	A	499	508	Right-handed alpha
Helix 17	AB8	A	515	528	Right-handed alpha
Helix 18	AB9	A	542	553	Right-handed alpha
Helix 19	AC1	B	27	44	Right-handed alpha
Helix 20	AC2	B	77	84	Right-handed alpha
Helix 21	AC3	B	112	118	Right-handed 310
Helix 22	AC4	B	124	129	Right-handed 310
Helix 23	AC5	B	134	138	Right-handed 310
Helix 24	AC6	B	154	160	Right-handed alpha
Helix 25	AC7	B	160	174	Right-handed alpha
Helix 26	AC8	B	194	213	Right-handed alpha
Helix 27	AC9	B	235	239	Right-handed 310
Helix 28	AD1	B	253	268	Right-handed alpha
Helix 29	AD2	B	276	282	Right-handed alpha
Helix 30	AD3	B	296	310	Right-handed alpha
Helix 31	AD4	B	363	383	Right-handed alpha
Helix 32	AD5	B	394	402	Right-handed alpha
Helix 33	AD6	B	403	405	Right-handed 310
Helix 34	AD7	C	28	44	Right-handed alpha
Helix 35	AD8	C	77	84	Right-handed alpha
Helix 36	AD9	C	96	100	Right-handed 310
Helix 37	AE1	C	114	118	Right-handed 310
Helix 38	AE2	C	121	126	Right-handed alpha
Helix 39	AE3	C	127	129	Right-handed 310
Helix 40	AE4	C	155	175	Right-handed alpha
Helix 41	AE5	C	194	212	Right-handed alpha
Helix 42	AE6	C	217	219	Right-handed 310
Helix 43	AE7	C	253	268	Right-handed alpha
Helix 44	AE8	C	276	282	Right-handed alpha
Helix 45	AE9	C	296	312	Right-handed alpha
Helix 46	AF1	C	363	384	Right-handed alpha
Helix 47	AF2	C	394	405	Right-handed alpha
Helix 48	AF3	C	473	488	Right-handed alpha
Helix 49	AF4	C	499	508	Right-handed alpha
Helix 50	AF5	C	515	528	Right-handed alpha
Helix 51	AF6	C	544	553	Right-handed alpha
Helix 52	AF7	D	27	44	Right-handed alpha
Helix 53	AF8	D	77	84	Right-handed alpha
Helix 54	AF9	D	87	92	Right-handed alpha
Helix 55	AG1	D	99	103	Right-handed 310
Helix 56	AG2	D	112	118	Right-handed 310
Helix 57	AG3	D	121	129	Right-handed 310
Helix 58	AG4	D	134	138	Right-handed 310
Helix 59	AG5	D	154	175	Right-handed alpha
Helix 60	AG6	D	194	211	Right-handed alpha
Helix 61	AG7	D	235	239	Right-handed 310
Helix 62	AG8	D	253	268	Right-handed alpha
Helix 63	AG9	D	276	282	Right-handed alpha
Helix 64	AH1	D	296	312	Right-handed alpha
Helix 65	AH2	D	363	383	Right-handed alpha
Helix 66	AH3	D	394	402	Right-handed alpha
Helix 67	AH4	D	403	406	Right-handed 310

There are 22 sheets in PDB entry 6KDO. 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,

There are 3 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	47	50	first strand
Strand 2	A	142	146	anti-parallel
Strand 3	A	130	132	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	60	64	first strand
Strand 2	A	71	75	anti-parallel

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There are 3 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	105	110	first strand
Strand 2	A	186	191	anti-parallel
Strand 3	A	179	183	anti-parallel

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There are 3 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	227	229	first strand
Strand 2	A	232	234	anti-parallel
Strand 3	A	239	241	anti-parallel

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There are 5 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	347	354	first strand
Strand 2	A	336	344	anti-parallel
Strand 3	A	326	333	anti-parallel
Strand 4	A	388	391	parallel
Strand 5	A	414	416	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	361	362	first strand
Strand 2	A	512	513	anti-parallel

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There are 5 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	464	470	first strand
Strand 2	A	452	459	anti-parallel
Strand 3	A	438	447	anti-parallel
Strand 4	A	492	497	parallel
Strand 5	A	530	535	parallel

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There are 3 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	47	50	first strand
Strand 2	B	142	146	anti-parallel
Strand 3	B	130	132	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	B	60	65	first strand
Strand 2	B	68	75	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	B	179	183	first strand
Strand 2	B	186	191	anti-parallel
Strand 3	B	105	110	anti-parallel
Strand 4	B	233	234	anti-parallel

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There are 5 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	348	355	first strand
Strand 2	B	336	342	anti-parallel
Strand 3	B	326	333	anti-parallel
Strand 4	B	388	391	parallel
Strand 5	B	414	416	parallel

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There are 3 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	47	49	first strand
Strand 2	C	142	146	anti-parallel
Strand 3	C	130	132	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	C	60	64	first strand
Strand 2	C	71	75	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	C	179	183	first strand
Strand 2	C	186	191	anti-parallel
Strand 3	C	105	110	anti-parallel
Strand 4	C	221	222	anti-parallel

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There are 3 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	227	229	first strand
Strand 2	C	232	234	anti-parallel
Strand 3	C	239	241	anti-parallel

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There are 5 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	348	354	first strand
Strand 2	C	336	342	anti-parallel
Strand 3	C	326	333	anti-parallel
Strand 4	C	388	391	parallel
Strand 5	C	414	416	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	361	362	first strand
Strand 2	C	512	513	anti-parallel

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There are 5 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	464	469	first strand
Strand 2	C	453	459	anti-parallel
Strand 3	C	438	446	anti-parallel
Strand 4	C	492	497	parallel
Strand 5	C	530	535	parallel

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There are 3 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	47	50	first strand
Strand 2	D	142	146	anti-parallel
Strand 3	D	130	132	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	D	60	64	first strand
Strand 2	D	71	75	anti-parallel

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There are 4 strands in AC3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	D	179	183	first strand
Strand 2	D	186	191	anti-parallel
Strand 3	D	105	110	anti-parallel
Strand 4	D	233	234	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	D	348	355	first strand
Strand 2	D	336	342	anti-parallel
Strand 3	D	326	333	anti-parallel
Strand 4	D	388	391	parallel
Strand 5	D	414	416	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: 6KDO

Analysis of interatomic Contacts of Structural Units in PDB entry:
6KDO