Analysis of interatomic Contacts of Structural Units in PDB entry:
6UPK

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 6UPK entry

There are 10 chains in PDB entry 6UPK (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 59	ARG 134
B	ASN 25	GLY 102
C	ARG 11	LYS 118
D	ARG 31	SER 124
E	PRO 38	ALA 135
F	ARG 23	GLY 102
G	VAL 510	UNK 960
H	MET 1	ASN 427
I	T -39	A 32
J	T -32	A 39

There are 35 helices in PDB entry 6UPK. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	63	79	Right-handed alpha
Helix 2	AA2	A	85	114	Right-handed alpha
Helix 3	AA3	A	120	131	Right-handed alpha
Helix 4	AA4	B	25	29	Right-handed 310
Helix 5	AA5	B	30	41	Right-handed alpha
Helix 6	AA6	B	48	77	Right-handed alpha
Helix 7	AA7	B	82	94	Right-handed alpha
Helix 8	AA8	C	26	38	Right-handed alpha
Helix 9	AA9	C	45	74	Right-handed alpha
Helix 10	AB1	C	81	87	Right-handed alpha
Helix 11	AB2	C	91	97	Right-handed alpha
Helix 12	AB3	C	112	116	Right-handed 310
Helix 13	AB4	D	40	45	Right-handed alpha
Helix 14	AB5	D	55	84	Right-handed alpha
Helix 15	AB6	D	90	102	Right-handed alpha
Helix 16	AB7	D	103	124	Right-handed alpha
Helix 17	AB8	E	44	57	Right-handed alpha
Helix 18	AB9	E	64	79	Right-handed alpha
Helix 19	AC1	E	85	115	Right-handed alpha
Helix 20	AC2	E	121	132	Right-handed alpha
Helix 21	AC3	F	24	29	Right-handed 310
Helix 22	AC4	F	30	41	Right-handed alpha
Helix 23	AC5	F	49	76	Right-handed alpha
Helix 24	AC6	F	83	94	Right-handed alpha
Helix 25	AC7	G	617	636	Right-handed alpha
Helix 26	AC8	G	763	788	Right-handed alpha
Helix 27	AC9	G	878	890	Right-handed alpha
Helix 28	AD1	G	901	910	Right-handed alpha
Helix 29	AD2	G	916	924	Right-handed 310
Helix 30	AD3	H	80	90	Right-handed alpha
Helix 31	AD4	H	176	180	Right-handed 310
Helix 32	AD5	H	292	299	Right-handed alpha
Helix 33	AD6	H	309	323	Right-handed alpha
Helix 34	AD7	H	334	338	Right-handed 310
Helix 35	AD8	H	407	421	Right-handed alpha

There are 16 sheets in PDB entry 6UPK. 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,

There are 2 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	83	84	first strand
Strand 2	B	80	81	parallel

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There are 2 strands in AA2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	C	77	78	first strand
Strand 2	D	53	54	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	E	83	84	first strand
Strand 2	F	80	81	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	G	530	532	first strand
Strand 2	G	537	541	anti-parallel
Strand 3	G	546	550	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	G	554	562	first strand
Strand 2	G	565	572	anti-parallel
Strand 3	G	597	601	anti-parallel
Strand 4	H	159	164	anti-parallel
Strand 5	H	146	149	anti-parallel
Strand 6	H	138	141	anti-parallel

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There are 7 strands in AA6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	698	700	first strand
Strand 2	G	686	691	anti-parallel
Strand 3	G	677	683	anti-parallel
Strand 4	G	661	668	anti-parallel
Strand 5	G	733	743	anti-parallel
Strand 6	G	717	730	anti-parallel
Strand 7	G	704	710	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	G	806	808	first strand
Strand 2	G	815	819	anti-parallel
Strand 3	G	824	826	anti-parallel
Strand 4	G	833	834	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	G	870	874	first strand
Strand 2	G	855	861	anti-parallel
Strand 3	G	840	846	anti-parallel
Strand 4	G	894	895	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	6	7	first strand
Strand 2	H	22	25	anti-parallel
Strand 3	H	30	33	anti-parallel
Strand 4	H	40	42	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	H	11	12	first strand
Strand 2	H	71	75	anti-parallel
Strand 3	H	62	66	anti-parallel
Strand 4	H	48	53	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	H	111	114	first strand
Strand 2	H	119	122	anti-parallel
Strand 3	H	127	130	anti-parallel

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There are 3 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	200	201	first strand
Strand 2	H	212	218	anti-parallel
Strand 3	H	205	207	anti-parallel

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There are 4 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	200	201	first strand
Strand 2	H	212	218	anti-parallel
Strand 3	H	222	226	anti-parallel
Strand 4	H	232	235	anti-parallel

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There are 3 strands in AB5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	239	246	first strand
Strand 2	H	252	264	anti-parallel
Strand 3	H	269	278	anti-parallel

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There are 4 strands in AB6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	342	344	first strand
Strand 2	H	349	354	anti-parallel
Strand 3	H	358	361	anti-parallel
Strand 4	H	367	370	anti-parallel

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There are 4 strands in AB7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	H	400	406	first strand
Strand 2	H	389	395	anti-parallel
Strand 3	H	374	378	anti-parallel
Strand 4	H	425	426	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: 6UPK

Analysis of interatomic Contacts of Structural Units in PDB entry:
6UPK