Analysis of interatomic Contacts of Structural Units in PDB entry:
4YPJ

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 4YPJ entry

There are 2 chains in PDB entry 4YPJ (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	SER 38	PRO 847
B	SER 38	PRO 847

There are 29 helices in PDB entry 4YPJ. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	85	89	Right-handed 310
Helix 2	AA2	A	118	122	Right-handed 310
Helix 3	AA3	A	217	222	Right-handed alpha
Helix 4	AA4	A	348	352	Right-handed 310
Helix 5	AA5	A	356	371	Right-handed alpha
Helix 6	AA6	A	383	394	Right-handed alpha
Helix 7	AA7	A	413	416	Right-handed 310
Helix 8	AA8	A	417	434	Right-handed alpha
Helix 9	AA9	A	448	452	Right-handed 310
Helix 10	AB1	A	453	471	Right-handed alpha
Helix 11	AB2	A	494	504	Right-handed alpha
Helix 12	AB3	A	512	514	Right-handed 310
Helix 13	AB4	A	515	523	Right-handed alpha
Helix 14	AB5	A	573	583	Right-handed alpha
Helix 15	AB6	A	626	637	Right-handed alpha
Helix 16	AB7	B	85	89	Right-handed 310
Helix 17	AB8	B	118	122	Right-handed 310
Helix 18	AB9	B	217	222	Right-handed alpha
Helix 19	AC1	B	348	352	Right-handed 310
Helix 20	AC2	B	356	371	Right-handed alpha
Helix 21	AC3	B	383	394	Right-handed alpha
Helix 22	AC4	B	414	434	Right-handed alpha
Helix 23	AC5	B	448	452	Right-handed 310
Helix 24	AC6	B	453	469	Right-handed alpha
Helix 25	AC7	B	494	504	Right-handed alpha
Helix 26	AC8	B	512	516	Right-handed 310
Helix 27	AC9	B	517	523	Right-handed alpha
Helix 28	AD1	B	573	583	Right-handed alpha
Helix 29	AD2	B	626	637	Right-handed alpha

There are 26 sheets in PDB entry 4YPJ. 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,

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	46	48	first strand
Strand 2	A	196	201	anti-parallel
Strand 3	A	125	130	anti-parallel
Strand 4	A	156	159	anti-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	77	79	first strand
Strand 2	A	53	57	anti-parallel
Strand 3	A	107	115	anti-parallel
Strand 4	A	171	179	anti-parallel
Strand 5	A	137	141	anti-parallel
Strand 6	A	144	149	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	204	214	first strand
Strand 2	A	226	237	anti-parallel
Strand 3	A	273	284	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	258	263	first strand
Strand 2	A	243	252	anti-parallel
Strand 3	A	267	269	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	A	258	263	first strand
Strand 2	A	243	252	anti-parallel
Strand 3	A	297	305	anti-parallel
Strand 4	A	308	317	anti-parallel

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There are 3 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	322	325	first strand
Strand 2	A	329	332	anti-parallel
Strand 3	A	335	336	anti-parallel

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There are 9 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	339	344	first strand
Strand 2	A	374	377	parallel
Strand 3	A	396	400	parallel
Strand 4	A	439	446	parallel
Strand 5	A	476	480	parallel
Strand 6	A	506	510	parallel
Strand 7	A	528	534	parallel
Strand 8	A	587	593	parallel
Strand 9	A	339	344	parallel

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There are 2 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	550	551	first strand
Strand 2	A	566	567	parallel

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There are 3 strands in AA9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	642	645	first strand
Strand 2	A	655	662	anti-parallel
Strand 3	A	702	707	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	A	674	680	first strand
Strand 2	A	666	671	anti-parallel
Strand 3	A	712	718	anti-parallel
Strand 4	A	724	731	anti-parallel

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There are 2 strands in AB2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	682	685	first strand
Strand 2	A	691	694	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	A	736	743	first strand
Strand 2	A	755	764	anti-parallel
Strand 3	A	812	819	anti-parallel
Strand 4	A	785	791	anti-parallel

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There are 5 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	747	749	first strand
Strand 2	A	838	845	parallel
Strand 3	A	824	831	anti-parallel
Strand 4	A	776	783	anti-parallel
Strand 5	A	805	807	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	B	46	48	first strand
Strand 2	B	196	201	anti-parallel
Strand 3	B	125	130	anti-parallel
Strand 4	B	156	159	anti-parallel

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There are 6 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	77	79	first strand
Strand 2	B	53	57	anti-parallel
Strand 3	B	107	115	anti-parallel
Strand 4	B	171	179	anti-parallel
Strand 5	B	137	141	anti-parallel
Strand 6	B	144	149	anti-parallel

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There are 3 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	204	214	first strand
Strand 2	B	226	237	anti-parallel
Strand 3	B	273	284	anti-parallel

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There are 3 strands in AB8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	258	263	first strand
Strand 2	B	243	252	anti-parallel
Strand 3	B	267	269	anti-parallel

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There are 4 strands in AB9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	258	263	first strand
Strand 2	B	243	252	anti-parallel
Strand 3	B	296	305	anti-parallel
Strand 4	B	308	318	anti-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	B	322	325	first strand
Strand 2	B	329	332	anti-parallel
Strand 3	B	335	336	anti-parallel

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There are 9 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	339	344	first strand
Strand 2	B	374	377	parallel
Strand 3	B	396	400	parallel
Strand 4	B	439	446	parallel
Strand 5	B	476	480	parallel
Strand 6	B	506	510	parallel
Strand 7	B	528	533	parallel
Strand 8	B	587	592	parallel
Strand 9	B	339	344	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	B	550	551	first strand
Strand 2	B	566	567	parallel

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There are 3 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	642	645	first strand
Strand 2	B	655	662	anti-parallel
Strand 3	B	702	707	anti-parallel

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There are 4 strands in AC5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	674	680	first strand
Strand 2	B	666	671	anti-parallel
Strand 3	B	712	718	anti-parallel
Strand 4	B	724	731	anti-parallel

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There are 2 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	682	685	first strand
Strand 2	B	691	694	anti-parallel

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There are 4 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	736	743	first strand
Strand 2	B	755	764	anti-parallel
Strand 3	B	812	819	anti-parallel
Strand 4	B	785	791	anti-parallel

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There are 5 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	747	749	first strand
Strand 2	B	838	845	parallel
Strand 3	B	824	831	anti-parallel
Strand 4	B	776	783	anti-parallel
Strand 5	B	805	807	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: 4YPJ

Analysis of interatomic Contacts of Structural Units in PDB entry:
4YPJ