Analysis of interatomic Contacts of Structural Units in PDB entry:
5DK3

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 5DK3 entry

There are 4 chains in PDB entry 5DK3 (CSU analysis of residue contacts immediately below table)

Chain ID	Initial residue	Terminal residue
A	GLU 1	CYS 218
B	GLN 1	SER 444
F	GLU 1	CYS 218
G	GLN 1	SER 444

There are 25 helices in PDB entry 5DK3. Click on helix of interest for CSU analysis.

Helix number	Helix ID	Chain ID	Initial residue	Terminal residue	Helix class
Helix 1	AA1	A	83	87	Right-handed 310
Helix 2	AA2	A	125	131	Right-handed alpha
Helix 3	AA3	A	187	192	Right-handed alpha
Helix 4	AA4	B	28	30	Right-handed 310
Helix 5	AA5	B	87	91	Right-handed 310
Helix 6	AA6	B	163	165	Right-handed 310
Helix 7	AA7	B	194	196	Right-handed 310
Helix 8	AA8	B	208	211	Right-handed 310
Helix 9	AA9	B	311	316	Right-handed alpha
Helix 10	AB1	B	354	360	Right-handed 310
Helix 11	AB2	B	414	419	Right-handed alpha
Helix 12	AB3	B	432	436	Right-handed 310
Helix 13	AB4	F	83	87	Right-handed 310
Helix 14	AB5	F	125	130	Right-handed alpha
Helix 15	AB6	F	187	193	Right-handed alpha
Helix 16	AB7	G	28	30	Right-handed 310
Helix 17	AB8	G	87	91	Right-handed 310
Helix 18	AB9	G	163	165	Right-handed 310
Helix 19	AC1	G	194	196	Right-handed 310
Helix 20	AC2	G	208	211	Right-handed 310
Helix 21	AC3	G	246	252	Right-handed alpha
Helix 22	AC4	G	309	315	Right-handed alpha
Helix 23	AC5	G	354	360	Right-handed 310
Helix 24	AC6	G	414	419	Right-handed alpha
Helix 25	AC7	G	432	436	Right-handed 310

There are 34 sheets in PDB entry 5DK3. 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, AC9, AD1, AD2, AD3, AD4, AD5, AD6, AD7,

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	4	7	first strand
Strand 2	A	19	25	anti-parallel
Strand 3	A	74	79	anti-parallel
Strand 4	A	66	71	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	10	13	first strand
Strand 2	A	106	110	parallel
Strand 3	A	88	94	anti-parallel
Strand 4	A	37	42	anti-parallel
Strand 5	A	49	53	anti-parallel
Strand 6	A	57	58	anti-parallel

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There are 4 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	10	13	first strand
Strand 2	A	106	110	parallel
Strand 3	A	88	94	anti-parallel
Strand 4	A	101	102	anti-parallel

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There are 2 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	30	31	first strand
Strand 2	A	34	35	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	118	122	first strand
Strand 2	A	133	143	anti-parallel
Strand 3	A	177	186	anti-parallel
Strand 4	A	163	167	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	157	158	first strand
Strand 2	A	149	154	anti-parallel
Strand 3	A	195	201	anti-parallel
Strand 4	A	209	214	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	B	3	6	first strand
Strand 2	B	18	25	anti-parallel
Strand 3	B	78	83	anti-parallel
Strand 4	B	68	73	anti-parallel

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There are 6 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	10	12	first strand
Strand 2	B	114	118	parallel
Strand 3	B	92	100	anti-parallel
Strand 4	B	32	39	anti-parallel
Strand 5	B	45	51	anti-parallel
Strand 6	B	58	60	anti-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	B	10	12	first strand
Strand 2	B	114	118	parallel
Strand 3	B	92	100	anti-parallel
Strand 4	B	107	110	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	B	127	131	first strand
Strand 2	B	142	152	anti-parallel
Strand 3	B	183	192	anti-parallel
Strand 4	B	170	172	anti-parallel

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There are 4 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	127	131	first strand
Strand 2	B	142	152	anti-parallel
Strand 3	B	183	192	anti-parallel
Strand 4	B	176	177	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	B	158	161	first strand
Strand 2	B	201	207	anti-parallel
Strand 3	B	212	219	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	B	239	243	first strand
Strand 2	B	258	266	anti-parallel
Strand 3	B	300	307	anti-parallel
Strand 4	B	288	289	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	282	284	first strand
Strand 2	B	273	279	anti-parallel
Strand 3	B	319	325	anti-parallel
Strand 4	B	332	336	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	B	347	351	first strand
Strand 2	B	362	372	anti-parallel
Strand 3	B	404	413	anti-parallel
Strand 4	B	391	393	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	B	347	351	first strand
Strand 2	B	362	372	anti-parallel
Strand 3	B	404	413	anti-parallel
Strand 4	B	397	398	anti-parallel

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There are 4 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	386	387	first strand
Strand 2	B	378	383	anti-parallel
Strand 3	B	423	428	anti-parallel
Strand 4	B	437	441	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	F	4	7	first strand
Strand 2	F	19	25	anti-parallel
Strand 3	F	74	79	anti-parallel
Strand 4	F	66	71	anti-parallel

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There are 6 strands in AC1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	10	13	first strand
Strand 2	F	106	110	parallel
Strand 3	F	89	94	anti-parallel
Strand 4	F	37	42	anti-parallel
Strand 5	F	49	53	anti-parallel
Strand 6	F	57	58	anti-parallel

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There are 4 strands in AC2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	10	13	first strand
Strand 2	F	106	110	parallel
Strand 3	F	89	94	anti-parallel
Strand 4	F	101	102	anti-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	F	30	31	first strand
Strand 2	F	34	35	anti-parallel

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There are 4 strands in AC4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	F	118	122	first strand
Strand 2	F	133	143	anti-parallel
Strand 3	F	177	186	anti-parallel
Strand 4	F	163	167	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	F	157	158	first strand
Strand 2	F	149	154	anti-parallel
Strand 3	F	195	201	anti-parallel
Strand 4	F	209	214	anti-parallel

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There are 4 strands in AC6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	3	6	first strand
Strand 2	G	18	25	anti-parallel
Strand 3	G	78	83	anti-parallel
Strand 4	G	68	73	anti-parallel

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There are 6 strands in AC7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	10	12	first strand
Strand 2	G	114	118	parallel
Strand 3	G	92	100	anti-parallel
Strand 4	G	32	39	anti-parallel
Strand 5	G	45	51	anti-parallel
Strand 6	G	58	60	anti-parallel

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There are 4 strands in AC8 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	127	131	first strand
Strand 2	G	142	152	anti-parallel
Strand 3	G	183	192	anti-parallel
Strand 4	G	170	172	anti-parallel

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There are 4 strands in AC9 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	127	131	first strand
Strand 2	G	142	152	anti-parallel
Strand 3	G	183	192	anti-parallel
Strand 4	G	176	177	anti-parallel

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There are 3 strands in AD1 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	158	161	first strand
Strand 2	G	201	207	anti-parallel
Strand 3	G	212	219	anti-parallel

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There are 4 strands in AD2 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	239	243	first strand
Strand 2	G	258	266	anti-parallel
Strand 3	G	300	307	anti-parallel
Strand 4	G	288	289	anti-parallel

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There are 4 strands in AD3 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	239	243	first strand
Strand 2	G	258	266	anti-parallel
Strand 3	G	300	307	anti-parallel
Strand 4	G	293	294	anti-parallel

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There are 4 strands in AD4 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	282	284	first strand
Strand 2	G	274	279	anti-parallel
Strand 3	G	319	324	anti-parallel
Strand 4	G	332	336	anti-parallel

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There are 4 strands in AD5 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	347	351	first strand
Strand 2	G	362	372	anti-parallel
Strand 3	G	404	413	anti-parallel
Strand 4	G	391	393	anti-parallel

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There are 4 strands in AD6 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	347	351	first strand
Strand 2	G	362	372	anti-parallel
Strand 3	G	404	413	anti-parallel
Strand 4	G	397	398	anti-parallel

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There are 4 strands in AD7 sheet. Click on strand of interest for CSU analysis.

Strand number	Chain ID	Initial residue	Terminal residue	Strand sense
Strand 1	G	386	387	first strand
Strand 2	G	378	383	anti-parallel
Strand 3	G	423	428	anti-parallel
Strand 4	G	437	441	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: 5DK3

Analysis of interatomic Contacts of Structural Units in PDB entry:
5DK3