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

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 8KDI entry

There are 4 chains in PDB entry 8KDI (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 162	ALA 630
B	THR 51	THR 507
L	ASP 1	ARG 217
H	GLU 1	ARG 220

There are 55 helices in PDB entry 8KDI. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	165	173	Right-handed alpha
Helix 2	AA2	A	177	207	Right-handed alpha
Helix 3	AA3	A	217	222	Right-handed 310
Helix 4	AA4	A	240	255	Right-handed alpha
Helix 5	AA5	A	281	285	Right-handed 310
Helix 6	AA6	A	286	300	Right-handed alpha
Helix 7	AA7	A	322	341	Right-handed alpha
Helix 8	AA8	A	349	353	Right-handed 310
Helix 9	AA9	A	355	371	Right-handed alpha
Helix 10	AB1	A	384	395	Right-handed alpha
Helix 11	AB2	A	403	407	Right-handed 310
Helix 12	AB3	A	414	427	Right-handed alpha
Helix 13	AB4	A	440	444	Right-handed 310
Helix 14	AB5	A	449	458	Right-handed alpha
Helix 15	AB6	A	469	473	Right-handed 310
Helix 16	AB7	A	504	507	Right-handed 310
Helix 17	AB8	A	508	514	Right-handed alpha
Helix 18	AB9	A	518	533	Right-handed alpha
Helix 19	AC1	A	533	539	Right-handed alpha
Helix 20	AC2	A	612	614	Right-handed 310
Helix 21	AC3	B	52	64	Right-handed alpha
Helix 22	AC4	B	66	70	Right-handed 310
Helix 23	AC5	B	71	80	Right-handed alpha
Helix 24	AC6	B	81	110	Right-handed alpha
Helix 25	AC7	B	115	124	Right-handed alpha
Helix 26	AC8	B	125	139	Right-handed alpha
Helix 27	AC9	B	139	158	Right-handed alpha
Helix 28	AD1	B	159	161	Right-handed 310
Helix 29	AD2	B	167	189	Right-handed alpha
Helix 30	AD3	B	189	222	Right-handed alpha
Helix 31	AD4	B	239	254	Right-handed alpha
Helix 32	AD5	B	256	261	Right-handed alpha
Helix 33	AD6	B	262	267	Right-handed 310
Helix 34	AD7	B	272	298	Right-handed alpha
Helix 35	AD8	B	301	306	Right-handed alpha
Helix 36	AD9	B	310	320	Right-handed alpha
Helix 37	AE1	B	322	325	Right-handed 310
Helix 38	AE2	B	326	345	Right-handed alpha
Helix 39	AE3	B	346	356	Right-handed alpha
Helix 40	AE4	B	360	365	Right-handed 310
Helix 41	AE5	B	373	387	Right-handed alpha
Helix 42	AE6	B	388	390	Right-handed 310
Helix 43	AE7	B	392	422	Right-handed alpha
Helix 44	AE8	B	435	454	Right-handed alpha
Helix 45	AE9	B	454	467	Right-handed alpha
Helix 46	AF1	B	467	476	Right-handed alpha
Helix 47	AF2	B	482	501	Right-handed alpha
Helix 48	AF3	L	85	89	Right-handed 310
Helix 49	AF4	L	129	133	Right-handed 310
Helix 50	AF5	L	189	194	Right-handed alpha
Helix 51	AF6	H	28	32	Right-handed 310
Helix 52	AF7	H	62	65	Right-handed 310
Helix 53	AF8	H	87	91	Right-handed 310
Helix 54	AF9	H	136	140	Right-handed 310
Helix 55	AG1	H	194	198	Right-handed 310

There are 13 sheets in PDB entry 8KDI. 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,

There are 7 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	399	401	first strand
Strand 2	A	375	379	parallel
Strand 3	A	344	347	parallel
Strand 4	A	305	307	parallel
Strand 5	A	260	261	parallel
Strand 6	A	224	227	parallel
Strand 7	A	465	467	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	540	544	first strand
Strand 2	A	551	556	anti-parallel
Strand 3	A	562	567	anti-parallel
Strand 4	A	622	626	anti-parallel
Strand 5	A	592	598	anti-parallel
Strand 6	A	608	610	anti-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	573	574	first strand
Strand 2	L	99	100	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	L	4	7	first strand
Strand 2	L	19	25	anti-parallel
Strand 3	L	76	81	anti-parallel
Strand 4	L	68	73	anti-parallel

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There are 6 strands in AA5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	10	14	first strand
Strand 2	L	108	113	parallel
Strand 3	L	90	96	anti-parallel
Strand 4	L	39	44	anti-parallel
Strand 5	L	51	55	anti-parallel
Strand 6	L	59	60	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	L	10	14	first strand
Strand 2	L	108	113	parallel
Strand 3	L	90	96	anti-parallel
Strand 4	L	103	104	anti-parallel

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There are 4 strands in AA7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	L	120	124	first strand
Strand 2	L	135	145	anti-parallel
Strand 3	L	179	188	anti-parallel
Strand 4	L	165	169	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	L	159	161	first strand
Strand 2	L	150	156	anti-parallel
Strand 3	L	197	204	anti-parallel
Strand 4	L	211	216	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	H	3	6	first strand
Strand 2	H	18	25	anti-parallel
Strand 3	H	78	83	anti-parallel
Strand 4	H	68	73	anti-parallel

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There are 6 strands in AB1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	9	12	first strand
Strand 2	H	114	118	parallel
Strand 3	H	92	98	anti-parallel
Strand 4	H	34	39	anti-parallel
Strand 5	H	45	51	anti-parallel
Strand 6	H	58	60	anti-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	H	9	12	first strand
Strand 2	H	114	118	parallel
Strand 3	H	92	98	anti-parallel
Strand 4	H	109	110	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	H	127	131	first strand
Strand 2	H	142	152	anti-parallel
Strand 3	H	181	191	anti-parallel
Strand 4	H	170	178	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	H	201	205	first strand
Strand 2	H	212	216	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: 8KDI

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