Analysis of interatomic Contacts of Structural Units in PDB entry:
2PMD


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 2PMD entry

There are 2 chains in PDB entry 2PMD (CSU analysis of residue contacts immediately below table)
Chain ID Initial residueTerminal residue
A
 ALA 2ILE 415
B
 ALA 2ILE 415
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 20 helices in PDB entry 2PMD. Click on helix of interest for CSU analysis.
Helix
number 		Helix
ID		Chain
ID		 Initial
residue		Terminal
residue		 Helix class
Helix 1
1
A
21 31Right-handed alpha
Helix 2
2
A
74 78Right-handed 310
Helix 3
3
A
102 107Right-handed alpha
Helix 4
4
A
126 140Right-handed alpha
Helix 5
5
A
150 154Right-handed 310
Helix 6
6
A
155 168Right-handed alpha
Helix 7
7
A
173 178Right-handed 310
Helix 8
8
A
190 202Right-handed alpha
Helix 9
9
A
229 233Right-handed 310
Helix 10
10
A
302 306Right-handed 310
Helix 11
11
B
21 30Right-handed alpha
Helix 12
12
B
38 43Right-handed alpha
Helix 13
13
B
104 109Right-handed alpha
Helix 14
14
B
126 139Right-handed alpha
Helix 15
15
B
150 154Right-handed 310
Helix 16
16
B
155 170Right-handed alpha
Helix 17
17
B
173 178Right-handed 310
Helix 18
18
B
190 202Right-handed alpha
Helix 19
19
B
229 233Right-handed 310
Helix 20
20
B
302 307Right-handed alpha
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There are 8 sheets in PDB entry 2PMD. Click on sheet of interest to get list of strands forming it: A, B, C, D, E, F, G, H,

There are 7 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
68 69first strand
Strand 2
A
50 58anti-parallel
Strand 3
A
84 93anti-parallel
Strand 4
A
11 16parallel
Strand 5
A
113 119parallel
Strand 6
A
143 149parallel
Strand 7
A
180 182parallel
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There are 8 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
266 275first strand
Strand 2
A
252 263anti-parallel
Strand 3
A
315 318anti-parallel
Strand 4
A
214 221anti-parallel
Strand 5
A
237 244anti-parallel
Strand 6
A
295 298anti-parallel
Strand 7
A
278 281anti-parallel
Strand 8
A
284 286anti-parallel
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There are 2 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
247 248first strand
Strand 2
A
288 289anti-parallel
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There are 7 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
325 335first strand
Strand 2
A
377 387anti-parallel
Strand 3
A
364 373anti-parallel
Strand 4
A
356 361anti-parallel
Strand 5
A
394 399anti-parallel
Strand 6
A
406 414anti-parallel
Strand 7
A
325 335anti-parallel
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There are 7 strands in E sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
68 69first strand
Strand 2
B
50 58anti-parallel
Strand 3
B
84 93anti-parallel
Strand 4
B
11 16parallel
Strand 5
B
113 119parallel
Strand 6
B
144 149parallel
Strand 7
B
180 182parallel
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There are 8 strands in F sheet. Click on strand of interest for CSU analysis.
Strand
number 		Chain
ID		 Initial
residue		Terminal
residue		 Strand sense
Strand 1
B
268 275first strand
Strand 2
B
252 261anti-parallel
Strand 3
B
315 318anti-parallel
Strand 4
B
214 221anti-parallel
Strand 5
B
237 244anti-parallel
Strand 6
B
295 298anti-parallel
Strand 7
B
278 281anti-parallel
Strand 8
B
284 286anti-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
247 248first strand
Strand 2
B
288 289anti-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
325 335first strand
Strand 2
B
377 387anti-parallel
Strand 3
B
364 373anti-parallel
Strand 4
B
356 361anti-parallel
Strand 5
B
394 399anti-parallel
Strand 6
B
406 414anti-parallel
Strand 7
B
325 335anti-parallel
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Please mail questions/suggestions concerning this page to Vladimir.Sobolev@weizmann. ac.il