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

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 4UPK entry

There are 3 chains in PDB entry 4UPK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLN 4	ASP 509
B	GLN 4	ASP 509
C	GLN 4	PHE 250

There are 78 helices in PDB entry 4UPK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	1	A	16	21	Right-handed alpha
Helix 2	2	A	24	28	Right-handed 310
Helix 3	3	A	30	39	Right-handed alpha
Helix 4	4	A	52	63	Right-handed alpha
Helix 5	5	A	65	70	Right-handed alpha
Helix 6	6	A	84	92	Right-handed alpha
Helix 7	7	A	107	111	Right-handed 310
Helix 8	8	A	115	119	Right-handed 310
Helix 9	9	A	139	149	Right-handed alpha
Helix 10	10	A	155	161	Right-handed 310
Helix 11	11	A	179	182	Right-handed 310
Helix 12	12	A	183	196	Right-handed alpha
Helix 13	13	A	197	200	Right-handed 310
Helix 14	14	A	228	232	Right-handed 310
Helix 15	15	A	240	247	Right-handed alpha
Helix 16	16	A	250	258	Right-handed alpha
Helix 17	17	A	259	263	Right-handed 310
Helix 18	18	A	273	305	Right-handed alpha
Helix 19	19	A	324	328	Right-handed 310
Helix 20	20	A	335	339	Right-handed 310
Helix 21	21	A	364	374	Right-handed alpha
Helix 22	22	A	386	391	Right-handed alpha
Helix 23	23	A	415	422	Right-handed alpha
Helix 24	24	A	459	461	Right-handed 310
Helix 25	25	A	466	468	Right-handed 310
Helix 26	26	A	469	487	Right-handed alpha
Helix 27	27	B	16	21	Right-handed alpha
Helix 28	28	B	24	28	Right-handed 310
Helix 29	29	B	30	39	Right-handed alpha
Helix 30	30	B	52	63	Right-handed alpha
Helix 31	31	B	65	70	Right-handed alpha
Helix 32	32	B	84	92	Right-handed alpha
Helix 33	33	B	107	111	Right-handed 310
Helix 34	34	B	115	119	Right-handed 310
Helix 35	35	B	139	150	Right-handed alpha
Helix 36	36	B	155	161	Right-handed 310
Helix 37	37	B	179	182	Right-handed 310
Helix 38	38	B	183	196	Right-handed alpha
Helix 39	39	B	197	200	Right-handed 310
Helix 40	40	B	228	232	Right-handed 310
Helix 41	41	B	240	246	Right-handed alpha
Helix 42	42	B	250	258	Right-handed alpha
Helix 43	43	B	259	263	Right-handed 310
Helix 44	44	B	273	305	Right-handed alpha
Helix 45	45	B	324	328	Right-handed 310
Helix 46	46	B	335	339	Right-handed 310
Helix 47	47	B	364	374	Right-handed alpha
Helix 48	48	B	386	391	Right-handed alpha
Helix 49	49	B	415	422	Right-handed alpha
Helix 50	50	B	459	461	Right-handed 310
Helix 51	51	B	466	468	Right-handed 310
Helix 52	52	B	469	487	Right-handed alpha
Helix 53	53	C	16	21	Right-handed alpha
Helix 54	54	C	24	28	Right-handed 310
Helix 55	55	C	30	39	Right-handed alpha
Helix 56	56	C	52	63	Right-handed alpha
Helix 57	57	C	65	70	Right-handed alpha
Helix 58	58	C	84	92	Right-handed alpha
Helix 59	59	C	107	111	Right-handed 310
Helix 60	60	C	115	119	Right-handed 310
Helix 61	61	C	139	149	Right-handed alpha
Helix 62	62	C	155	161	Right-handed 310
Helix 63	63	C	179	182	Right-handed 310
Helix 64	64	C	183	196	Right-handed alpha
Helix 65	65	C	197	200	Right-handed 310
Helix 66	66	C	228	232	Right-handed 310
Helix 67	67	C	240	248	Right-handed alpha
Helix 68	68	C	250	258	Right-handed alpha
Helix 69	69	C	259	263	Right-handed 310
Helix 70	70	C	273	305	Right-handed alpha
Helix 71	71	C	324	328	Right-handed 310
Helix 72	72	C	335	339	Right-handed 310
Helix 73	73	C	364	374	Right-handed alpha
Helix 74	74	C	386	391	Right-handed alpha
Helix 75	75	C	415	422	Right-handed alpha
Helix 76	76	C	459	461	Right-handed 310
Helix 77	77	C	466	468	Right-handed 310
Helix 78	78	C	469	487	Right-handed alpha

There are 9 sheets in PDB entry 4UPK. Click on sheet of interest to get list of strands forming it: AA, AB, AC, BA, BB, BC, CA, CB, CC,

There are 8 strands in AA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	129	133	first strand
Strand 2	A	96	100	parallel
Strand 3	A	205	210	parallel
Strand 4	A	6	12	parallel
Strand 5	A	311	317	parallel
Strand 6	A	343	346	anti-parallel
Strand 7	A	41	47	anti-parallel
Strand 8	A	355	361	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	402	407	first strand
Strand 2	A	429	434	anti-parallel
Strand 3	A	438	443	anti-parallel
Strand 4	A	450	453	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	A	495	498	first strand
Strand 2	A	501	504	anti-parallel

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There are 8 strands in BA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	129	133	first strand
Strand 2	B	96	100	parallel
Strand 3	B	205	210	parallel
Strand 4	B	6	12	parallel
Strand 5	B	311	317	parallel
Strand 6	B	343	346	anti-parallel
Strand 7	B	41	47	anti-parallel
Strand 8	B	355	361	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	402	407	first strand
Strand 2	B	429	434	anti-parallel
Strand 3	B	438	443	anti-parallel
Strand 4	B	450	453	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	495	498	first strand
Strand 2	B	501	504	anti-parallel

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There are 8 strands in CA sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	129	133	first strand
Strand 2	C	96	100	parallel
Strand 3	C	205	210	parallel
Strand 4	C	6	12	parallel
Strand 5	C	311	317	parallel
Strand 6	C	343	346	anti-parallel
Strand 7	C	41	47	anti-parallel
Strand 8	C	355	361	parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	402	407	first strand
Strand 2	C	429	434	anti-parallel
Strand 3	C	438	443	anti-parallel
Strand 4	C	450	453	anti-parallel

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

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	495	498	first strand
Strand 2	C	501	504	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: 4UPK

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