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

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 6DGD entry

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

Chain ID	Initial residue	Terminal residue
A	MET 1	GLU 730
B	SER 2	GLU 730
W	A 2	T 13
X	G 2	C 13
Y	G 1	T 13
Z	G 2	C 13

There are 48 helices in PDB entry 6DGD. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	73	88	Right-handed alpha
Helix 2	AA2	A	90	98	Right-handed alpha
Helix 3	AA3	A	100	105	Right-handed alpha
Helix 4	AA4	A	120	126	Right-handed alpha
Helix 5	AA5	A	127	132	Right-handed 310
Helix 6	AA6	A	136	145	Right-handed alpha
Helix 7	AA7	A	152	157	Right-handed 310
Helix 8	AA8	A	160	170	Right-handed alpha
Helix 9	AA9	A	199	211	Right-handed alpha
Helix 10	AB1	A	228	243	Right-handed alpha
Helix 11	AB2	A	257	268	Right-handed alpha
Helix 12	AB3	A	280	293	Right-handed alpha
Helix 13	AB4	A	302	308	Right-handed 310
Helix 14	AB5	A	323	327	Right-handed 310
Helix 15	AB6	A	335	348	Right-handed alpha
Helix 16	AB7	A	359	369	Right-handed alpha
Helix 17	AB8	A	403	416	Right-handed alpha
Helix 18	AB9	A	455	457	Right-handed 310
Helix 19	AC1	A	492	498	Right-handed alpha
Helix 20	AC2	A	557	563	Right-handed alpha
Helix 21	AC3	A	568	586	Right-handed alpha
Helix 22	AC4	A	602	612	Right-handed alpha
Helix 23	AC5	A	612	627	Right-handed alpha
Helix 24	AC6	A	646	661	Right-handed alpha
Helix 25	AC7	A	696	710	Right-handed alpha
Helix 26	AC8	A	711	719	Right-handed 310
Helix 27	AC9	B	55	59	Right-handed 310
Helix 28	AD1	B	73	87	Right-handed alpha
Helix 29	AD2	B	90	98	Right-handed alpha
Helix 30	AD3	B	100	105	Right-handed alpha
Helix 31	AD4	B	138	143	Right-handed alpha
Helix 32	AD5	B	160	170	Right-handed alpha
Helix 33	AD6	B	199	212	Right-handed alpha
Helix 34	AD7	B	228	243	Right-handed alpha
Helix 35	AD8	B	257	266	Right-handed alpha
Helix 36	AD9	B	280	293	Right-handed alpha
Helix 37	AE1	B	302	308	Right-handed 310
Helix 38	AE2	B	335	347	Right-handed alpha
Helix 39	AE3	B	359	368	Right-handed alpha
Helix 40	AE4	B	403	416	Right-handed alpha
Helix 41	AE5	B	454	458	Right-handed 310
Helix 42	AE6	B	492	501	Right-handed alpha
Helix 43	AE7	B	557	563	Right-handed alpha
Helix 44	AE8	B	568	584	Right-handed alpha
Helix 45	AE9	B	602	611	Right-handed alpha
Helix 46	AF1	B	612	628	Right-handed alpha
Helix 47	AF2	B	646	661	Right-handed alpha
Helix 48	AF3	B	696	714	Right-handed alpha

There are 14 sheets in PDB entry 6DGD. 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,

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	16	19	first strand
Strand 2	A	3	7	anti-parallel
Strand 3	A	39	49	anti-parallel
Strand 4	A	31	36	anti-parallel
Strand 5	A	64	65	anti-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	149	150	first strand
Strand 2	A	114	119	anti-parallel
Strand 3	A	173	178	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	272	274	first strand
Strand 2	A	298	301	parallel
Strand 3	A	246	250	parallel
Strand 4	A	313	319	parallel
Strand 5	A	350	355	parallel
Strand 6	A	217	222	parallel
Strand 7	A	372	375	parallel

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There are 6 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	388	392	first strand
Strand 2	A	592	597	parallel
Strand 3	A	550	555	parallel
Strand 4	A	419	423	parallel
Strand 5	A	533	537	parallel
Strand 6	A	506	508	parallel

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There are 2 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	433	435	first strand
Strand 2	A	483	485	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	452	454	first strand
Strand 2	A	459	461	anti-parallel
Strand 3	A	468	470	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	A	670	676	first strand
Strand 2	A	686	694	anti-parallel
Strand 3	A	634	642	anti-parallel
Strand 4	A	721	726	anti-parallel

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There are 5 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	16	19	first strand
Strand 2	B	3	7	anti-parallel
Strand 3	B	39	49	anti-parallel
Strand 4	B	31	36	anti-parallel
Strand 5	B	64	65	anti-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	B	149	150	first strand
Strand 2	B	114	117	anti-parallel
Strand 3	B	177	178	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	272	274	first strand
Strand 2	B	298	301	parallel
Strand 3	B	246	250	parallel
Strand 4	B	313	319	parallel
Strand 5	B	351	355	parallel
Strand 6	B	218	223	parallel
Strand 7	B	372	376	parallel

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There are 6 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	387	392	first strand
Strand 2	B	592	597	parallel
Strand 3	B	552	555	parallel
Strand 4	B	420	423	parallel
Strand 5	B	534	537	parallel
Strand 6	B	506	508	parallel

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There are 2 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	433	435	first strand
Strand 2	B	483	485	anti-parallel

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There are 2 strands in AB4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	B	460	461	first strand
Strand 2	B	468	469	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	670	681	first strand
Strand 2	B	686	694	anti-parallel
Strand 3	B	634	642	anti-parallel
Strand 4	B	721	726	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: 6DGD

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