Analysis of interatomic Contacts of Structural Units in PDB entry:
1JDY


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).
For CSU analysis of other PDB entry

This page provides analyses of contacts formed by:
For analysis of ligand-protein contacts, use: 3D structure can be seen in additional window with STING software for 1JDY entry


Note, this PDB entry contains modified residue(s) PHOSPHOSERINE (SEP) . This residue is treated as heterogroup (ligand) both in the PDB entry and in LPC/CSU analysis.

There are 4 chains in PDB entry 1JDY (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 VAL 1ALA 115
A
 HIS 117THR 561
B
 VAL 1ALA 115
B
 HIS 117THR 561
Residue contacts

1. List of contacts for up to 10 consecutive residues:
Chain ID from residue number to residue number


2. Detailed analyses of contacts for any single residue:
Residue number chain ID
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There are 47 helices in PDB entry 1JDY. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
25 30Right-handed alpha
Helix 2
2
A
34 45Right-handed alpha
Helix 3
3
A
48 50Right-handed 310
Helix 4
4
A
66 79Right-handed alpha
Helix 5
5
A
89 91Right-handed 310
Helix 6
6
A
95 105Right-handed alpha
Helix 7
7
A
140 152Right-handed alpha
Helix 8
8
A
192 199Right-handed alpha
Helix 9
9
A
204 212Right-handed alpha
Helix 10
10
A
229 236Right-handed alpha
Helix 11
11
A
244 246Right-handed 310
Helix 12
12
A
256 258Right-handed 310
Helix 13
13
A
269 277Right-handed alpha
Helix 14
14
A
298 300Right-handed 310
Helix 15
15
A
305 314Right-handed alpha
Helix 16
16
A
316 318Right-handed 310
Helix 17
17
A
320 325Right-handed alpha
Helix 18
18
A
339 346Right-handed alpha
Helix 19
19
A
358 366Right-handed alpha
Helix 20
20
A
390 404Right-handed alpha
Helix 21
21
A
408 419Right-handed alpha
Helix 22
22
A
434 449Right-handed alpha
Helix 23
23
A
531 546Right-handed alpha
Helix 24
24
A
548 552Right-handed alpha
Helix 25
25
B
25 30Right-handed alpha
Helix 26
26
B
34 45Right-handed alpha
Helix 27
27
B
48 50Right-handed 310
Helix 28
28
B
66 79Right-handed alpha
Helix 29
29
B
89 91Right-handed 310
Helix 30
30
B
95 105Right-handed alpha
Helix 31
31
B
140 152Right-handed alpha
Helix 32
32
B
192 201Right-handed alpha
Helix 33
33
B
204 212Right-handed alpha
Helix 34
34
B
227 236Right-handed 310
Helix 35
35
B
244 246Right-handed 310
Helix 36
36
B
256 258Right-handed 310
Helix 37
37
B
269 276Right-handed alpha
Helix 38
38
B
298 300Right-handed 310
Helix 39
39
B
305 318Right-handed alpha
Helix 40
40
B
320 325Right-handed alpha
Helix 41
41
B
338 347Right-handed 310
Helix 42
42
B
359 366Right-handed alpha
Helix 43
43
B
390 404Right-handed alpha
Helix 44
44
B
408 419Right-handed alpha
Helix 45
45
B
434 448Right-handed alpha
Helix 46
46
B
531 546Right-handed alpha
Helix 47
47
B
548 552Right-handed alpha
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There are 12 sheets in PDB entry 1JDY. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H, I, J, K, L,

There are 2 strands in A sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
4 7first strand
Strand 2
A
155 158anti-parallel
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There are 7 strands in B sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
21 24first strand
Strand 2
A
125 132anti-parallel
Strand 3
A
109 113anti-parallel
Strand 4
A
55 60parallel
Strand 5
A
84 88parallel
Strand 6
A
183 188parallel
Strand 7
A
170 174anti-parallel
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There are 3 strands in C sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
219 222first strand
Strand 2
A
282 286parallel
Strand 3
A
293 297anti-parallel
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There are 4 strands in D sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
351 354first strand
Strand 2
A
330 333parallel
Strand 3
A
372 375parallel
Strand 4
A
379 382anti-parallel
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There are 6 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
559 561first strand
Strand 2
A
421 429anti-parallel
Strand 3
A
511 521anti-parallel
Strand 4
A
498 505anti-parallel
Strand 5
A
489 493anti-parallel
Strand 6
A
467 472anti-parallel
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There are 2 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
A
457 460first strand
Strand 2
A
463 466anti-parallel
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There are 2 strands in G sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
4 7first strand
Strand 2
B
155 158anti-parallel
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There are 7 strands in H sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
21 24first strand
Strand 2
B
125 132anti-parallel
Strand 3
B
109 113anti-parallel
Strand 4
B
55 60parallel
Strand 5
B
84 88parallel
Strand 6
B
183 188parallel
Strand 7
B
170 174anti-parallel
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There are 3 strands in I sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
219 222first strand
Strand 2
B
282 286parallel
Strand 3
B
293 297anti-parallel
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There are 4 strands in J sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
351 354first strand
Strand 2
B
330 333parallel
Strand 3
B
372 375parallel
Strand 4
B
379 382anti-parallel
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There are 6 strands in K sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
559 561first strand
Strand 2
B
421 429anti-parallel
Strand 3
B
513 521anti-parallel
Strand 4
B
498 503anti-parallel
Strand 5
B
489 493anti-parallel
Strand 6
B
467 472anti-parallel
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There are 2 strands in L sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
457 459first strand
Strand 2
B
464 466anti-parallel
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