Analysis of interatomic Contacts of Structural Units in PDB entry:
8UP4

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 8UP4 entry

There are 4 chains in PDB entry 8UP4 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	THR 20	ALA 298
A	ALA 300	THR 487
B	THR 20	ALA 298
B	ALA 300	THR 487

There are 43 helices in PDB entry 8UP4. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	29	40	Right-handed alpha
Helix 2	AA2	A	64	69	Right-handed 310
Helix 3	AA3	A	75	85	Right-handed alpha
Helix 4	AA4	A	87	95	Right-handed alpha
Helix 5	AA5	A	128	141	Right-handed alpha
Helix 6	AA6	A	194	203	Right-handed alpha
Helix 7	AA7	A	226	230	Right-handed 310
Helix 8	AA8	A	276	287	Right-handed alpha
Helix 9	AA9	A	291	298	Right-handed alpha
Helix 10	AB1	A	319	322	Right-handed 310
Helix 11	AB2	A	333	335	Right-handed 310
Helix 12	AB3	A	340	344	Right-handed 310
Helix 13	AB4	A	345	365	Right-handed alpha
Helix 14	AB5	A	369	382	Right-handed alpha
Helix 15	AB6	A	382	394	Right-handed alpha
Helix 16	AB7	A	405	410	Right-handed alpha
Helix 17	AB8	A	411	427	Right-handed alpha
Helix 18	AB9	A	429	441	Right-handed alpha
Helix 19	AC1	A	445	450	Right-handed 310
Helix 20	AC2	A	451	461	Right-handed alpha
Helix 21	AC3	A	473	478	Right-handed alpha
Helix 22	AC4	A	479	481	Right-handed 310
Helix 23	AC5	B	29	40	Right-handed alpha
Helix 24	AC6	B	64	69	Right-handed 310
Helix 25	AC7	B	75	85	Right-handed alpha
Helix 26	AC8	B	87	95	Right-handed alpha
Helix 27	AC9	B	128	141	Right-handed alpha
Helix 28	AD1	B	194	203	Right-handed alpha
Helix 29	AD2	B	226	230	Right-handed 310
Helix 30	AD3	B	276	287	Right-handed alpha
Helix 31	AD4	B	291	298	Right-handed alpha
Helix 32	AD5	B	319	322	Right-handed 310
Helix 33	AD6	B	333	335	Right-handed 310
Helix 34	AD7	B	340	344	Right-handed 310
Helix 35	AD8	B	345	365	Right-handed alpha
Helix 36	AD9	B	369	394	Right-handed alpha
Helix 37	AE1	B	405	409	Right-handed 310
Helix 38	AE2	B	411	427	Right-handed alpha
Helix 39	AE3	B	429	441	Right-handed alpha
Helix 40	AE4	B	445	450	Right-handed 310
Helix 41	AE5	B	451	461	Right-handed alpha
Helix 42	AE6	B	473	478	Right-handed alpha
Helix 43	AE7	B	479	481	Right-handed 310

There are 12 sheets in PDB entry 8UP4. Click on sheet of interest to get list of strands forming it: AA1, AA2, AA3, AA4, AA5, AA6, AA7, AA8, AA9, AB1, AB2, AB3,

There are 5 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	146	149	first strand
Strand 2	A	45	49	parallel
Strand 3	A	22	26	parallel
Strand 4	A	184	187	parallel
Strand 5	A	329	331	parallel

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There are 3 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	72	74	first strand
Strand 2	A	122	126	anti-parallel
Strand 3	A	98	102	anti-parallel

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There are 7 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	113	114	first strand
Strand 2	A	106	110	anti-parallel
Strand 3	A	235	238	parallel
Strand 4	A	249	256	anti-parallel
Strand 5	A	260	267	anti-parallel
Strand 6	A	217	224	anti-parallel
Strand 7	A	301	302	anti-parallel

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There are 7 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	113	114	first strand
Strand 2	A	106	110	anti-parallel
Strand 3	A	235	238	parallel
Strand 4	A	249	256	anti-parallel
Strand 5	A	260	267	anti-parallel
Strand 6	A	217	224	anti-parallel
Strand 7	A	307	309	anti-parallel

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There are 3 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	152	160	first strand
Strand 2	A	163	171	anti-parallel
Strand 3	A	177	181	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	A	337	338	first strand
Strand 2	A	314	317	anti-parallel
Strand 3	A	209	213	anti-parallel
Strand 4	A	400	402	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	B	146	149	first strand
Strand 2	B	45	49	parallel
Strand 3	B	22	26	parallel
Strand 4	B	184	187	parallel
Strand 5	B	329	331	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	72	74	first strand
Strand 2	B	122	126	anti-parallel
Strand 3	B	98	102	anti-parallel

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There are 7 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	113	114	first strand
Strand 2	B	106	110	anti-parallel
Strand 3	B	235	238	parallel
Strand 4	B	249	256	anti-parallel
Strand 5	B	260	267	anti-parallel
Strand 6	B	217	224	anti-parallel
Strand 7	B	301	302	anti-parallel

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There are 7 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	113	114	first strand
Strand 2	B	106	110	anti-parallel
Strand 3	B	235	238	parallel
Strand 4	B	249	256	anti-parallel
Strand 5	B	260	267	anti-parallel
Strand 6	B	217	224	anti-parallel
Strand 7	B	307	309	anti-parallel

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There are 3 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	152	160	first strand
Strand 2	B	163	171	anti-parallel
Strand 3	B	177	181	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	B	337	338	first strand
Strand 2	B	314	317	anti-parallel
Strand 3	B	209	213	anti-parallel
Strand 4	B	400	402	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: 8UP4

Analysis of interatomic Contacts of Structural Units in PDB entry:
8UP4