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

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 9KPD entry

There are 5 chains in PDB entry 9KPD (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 9	PHE 249
B	GLU 3	SER 343
G	THR 6	ARG 62
N	GLN 1	SER 128
R	ILE 2	ARG 285

There are 24 helices in PDB entry 9KPD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	9	39	Right-handed alpha
Helix 2	AA2	A	52	64	Right-handed alpha
Helix 3	AA3	A	99	104	Right-handed 310
Helix 4	AA4	A	120	133	Right-handed alpha
Helix 5	AA5	A	148	158	Right-handed alpha
Helix 6	AA6	A	186	207	Right-handed alpha
Helix 7	AA7	A	222	247	Right-handed alpha
Helix 8	AA8	B	4	26	Right-handed alpha
Helix 9	AA9	B	29	34	Right-handed alpha
Helix 10	AB1	G	7	24	Right-handed alpha
Helix 11	AB2	G	29	44	Right-handed alpha
Helix 12	AB3	N	62	65	Right-handed 310
Helix 13	AB4	N	87	91	Right-handed 310
Helix 14	AB5	R	3	39	Right-handed alpha
Helix 15	AB6	R	43	71	Right-handed alpha
Helix 16	AB7	R	81	107	Right-handed alpha
Helix 17	AB8	R	112	125	Right-handed alpha
Helix 18	AB9	R	125	141	Right-handed alpha
Helix 19	AC1	R	141	156	Right-handed alpha
Helix 20	AC2	R	173	210	Right-handed alpha
Helix 21	AC3	R	211	214	Right-handed 310
Helix 22	AC4	R	215	249	Right-handed alpha
Helix 23	AC5	R	258	280	Right-handed alpha
Helix 24	AC6	R	280	285	Right-handed alpha

There are 10 sheets in PDB entry 9KPD. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1,

There are 6 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	72	79	first strand
Strand 2	A	82	89	anti-parallel
Strand 3	A	40	47	parallel
Strand 4	A	108	114	parallel
Strand 5	A	141	147	parallel
Strand 6	A	214	215	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	B	45	51	first strand
Strand 2	B	336	341	anti-parallel
Strand 3	B	327	331	anti-parallel
Strand 4	B	315	320	anti-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	B	58	63	first strand
Strand 2	B	69	74	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	88	94	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	B	100	105	first strand
Strand 2	B	111	116	anti-parallel
Strand 3	B	120	125	anti-parallel
Strand 4	B	134	140	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	146	151	first strand
Strand 2	B	156	161	anti-parallel
Strand 3	B	166	170	anti-parallel
Strand 4	B	175	180	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	187	192	first strand
Strand 2	B	198	203	anti-parallel
Strand 3	B	208	212	anti-parallel
Strand 4	B	218	222	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	B	229	234	first strand
Strand 2	B	240	245	anti-parallel
Strand 3	B	249	254	anti-parallel
Strand 4	B	259	265	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	273	278	first strand
Strand 2	B	284	289	anti-parallel
Strand 3	B	294	298	anti-parallel
Strand 4	B	304	308	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	N	3	5	first strand
Strand 2	N	18	25	anti-parallel
Strand 3	N	78	83	anti-parallel
Strand 4	N	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	N	11	12	first strand
Strand 2	N	122	126	parallel
Strand 3	N	92	98	anti-parallel
Strand 4	N	34	39	anti-parallel
Strand 5	N	45	51	anti-parallel
Strand 6	N	58	60	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: 9KPD

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