Contacts of the helix formed by residues 302 - 327 (chain O) in PDB entry 3EXG
Residue contacts within the protein 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). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 302 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1O PHE* 3.8 11.7 - - - -
296O VAL* 4.0 4.0 - - - -
301O ALA* 1.4 70.9 - - - +
303O VAL* 1.3 55.8 + - - +
304O GLU* 3.1 11.0 - - - +
305O GLU* 2.8 41.1 + - - +
306O LEU* 2.8 35.7 + - - +
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Residues in contact with VAL 303 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292O LYS* 3.5 21.5 - - - +
296O VAL* 3.5 24.0 - - + +
302O SER* 1.3 72.1 - - - +
304O GLU* 1.3 85.2 + - + +
306O LEU* 4.2 5.0 - - - +
307O LYS* 3.2 30.7 + - + +
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Residues in contact with GLU 304 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302O SER* 3.1 8.2 - - - +
303O VAL* 1.3 107.4 + - + +
305O GLU* 1.3 66.6 + - - +
306O LEU 3.4 0.2 - - - -
307O LYS* 3.7 8.5 - - + +
308O GLU* 2.7 37.0 + - - +
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Residues in contact with GLU 305 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1O PHE* 3.1 23.0 - - + -
29O ARG* 4.7 9.9 + - - -
33O LEU* 4.8 12.2 - - + +
301O ALA* 2.9 22.0 - - + +
302O SER* 2.8 45.3 + - - +
304O GLU* 1.3 77.4 - - - +
306O LEU* 1.3 59.1 + - + +
308O GLU* 2.9 24.1 + - - +
309O ILE* 3.2 16.0 + - + +
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Residues in contact with LEU 306 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O TYR* 3.6 41.5 - - + +
292O LYS* 3.5 49.6 - - + +
295O MET* 4.7 19.3 - - + -
296O VAL* 4.3 13.5 - - + -
301O ALA* 4.7 7.9 - - + -
302O SER 2.8 21.7 + - - +
303O VAL* 4.2 3.6 - - - +
305O GLU* 1.3 71.8 - - + +
307O LYS* 1.3 60.6 + - - +
308O GLU 2.8 7.1 + - - -
309O ILE* 2.9 17.6 + - + +
310O ASP* 2.9 26.7 + - - +
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Residues in contact with LYS 307 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292O LYS* 4.9 12.5 - - - +
303O VAL* 3.2 24.7 + - + +
304O GLU* 3.7 13.0 - - + +
306O LEU* 1.3 78.1 - - - +
308O GLU* 1.3 59.1 + - + +
310O ASP* 3.4 39.6 + - - +
311O VAL* 3.2 18.9 - - + +
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Residues in contact with GLU 308 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304O GLU* 2.7 26.4 - - - +
305O GLU* 2.9 9.0 + - - +
306O LEU 2.8 3.8 + - - -
307O LYS* 1.3 77.0 - - + +
309O ILE* 1.3 62.4 + - - +
310O ASP 3.2 0.4 - - - -
311O VAL* 3.3 19.0 + - + +
312O GLU* 3.1 29.4 + - - +
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Residues in contact with ILE 309 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33O LEU* 4.6 28.5 - - + +
36O TYR* 3.7 27.4 - - + -
37O ARG* 2.9 53.6 - - + +
40O GLN* 6.3 0.2 - - - -
305O GLU* 3.2 15.7 + - + +
306O LEU* 2.9 17.9 + - + +
308O GLU* 1.3 76.2 - - - +
310O ASP* 1.3 63.4 + - - +
312O GLU* 3.4 3.9 + - - +
313O VAL* 3.2 24.0 + - + +
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Residues in contact with ASP 310 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36O TYR* 2.6 31.2 + - - -
40O GLN* 3.1 24.7 - - - +
44O ARG* 5.9 0.3 - - - +
292O LYS* 4.9 2.9 - - - -
306O LEU* 2.9 18.4 + - - +
307O LYS* 3.4 41.2 + - - +
309O ILE* 1.3 76.7 - - - +
311O VAL* 1.3 57.4 + - + +
312O GLU 3.3 0.2 + - - -
313O VAL* 3.3 4.6 + - - +
314O ARG* 2.9 31.6 + - - +
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Residues in contact with VAL 311 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307O LYS* 3.2 18.2 - - + +
308O GLU* 3.3 19.2 + - + +
309O ILE 3.2 0.4 - - - -
310O ASP* 1.3 77.0 - - + +
312O GLU* 1.3 62.3 + - + +
314O ARG* 3.2 10.1 + - - +
315O LYS* 3.1 30.2 + - + +
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Residues in contact with GLU 312 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ARG* 3.4 25.7 + - - +
308O GLU* 3.1 21.6 + - - +
309O ILE* 4.0 4.9 - - - +
310O ASP 3.2 0.6 - - - -
311O VAL* 1.3 78.6 - - + +
313O VAL* 1.3 56.5 + - - +
315O LYS* 3.6 6.6 + - - +
316O GLU* 2.8 34.1 + - - +
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Residues in contact with VAL 313 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ARG* 3.9 20.9 - - - +
40O GLN* 3.8 16.6 - - + +
41O THR* 3.7 30.7 - - - +
44O ARG* 3.3 36.8 - - + -
309O ILE* 3.2 14.2 + - + +
310O ASP* 3.5 9.0 - - - +
312O GLU* 1.3 76.3 - - - +
314O ARG* 1.3 66.9 + - - +
316O GLU* 2.8 18.2 + - + +
317O ILE* 2.8 19.0 + - + +
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Residues in contact with ARG 314 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44O ARG* 3.1 46.5 - - - +
310O ASP 2.9 14.5 + - - +
311O VAL* 3.2 13.9 + - - +
313O VAL* 1.3 76.7 - - - +
315O LYS* 1.3 57.4 + - - +
317O ILE* 3.6 6.1 + - - +
318O GLU* 3.0 49.0 + - + +
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Residues in contact with LYS 315 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311O VAL* 3.1 19.2 + - + +
312O GLU* 4.1 5.8 - - - +
314O ARG* 1.3 73.2 - - - +
316O GLU* 1.3 66.5 + - - +
318O GLU* 3.9 7.6 - - + +
319O ASP* 3.0 50.1 + - - +
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Residues in contact with GLU 316 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ARG* 5.3 8.4 + - - +
41O THR* 5.6 6.1 - - + +
102O VAL* 4.9 17.9 - - + -
312O GLU 2.8 20.4 + - - +
313O VAL* 2.8 15.6 + - + +
315O LYS* 1.3 74.6 - - - +
317O ILE* 1.3 66.0 + - + +
319O ASP* 3.9 4.6 - - - +
320O ALA* 3.0 23.1 + - - +
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Residues in contact with ILE 317 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41O THR* 4.1 8.3 - - + +
44O ARG* 3.6 31.0 - - + +
45O MET* 3.9 18.4 - - + +
48O LYS* 3.7 42.6 - - + -
102O VAL* 3.5 31.4 - - + -
106O LEU* 4.7 1.5 - - + +
313O VAL* 2.8 20.0 + - + +
314O ARG* 3.9 5.4 - - - +
316O GLU* 1.3 73.1 - - + +
318O GLU* 1.3 71.1 + - - +
320O ALA* 2.9 5.7 + - - +
321O ALA* 2.8 22.5 + - - +
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Residues in contact with GLU 318 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LYS* 3.6 28.3 + - - -
314O ARG* 3.0 36.1 + - + +
315O LYS* 3.9 10.1 - - + +
317O ILE* 1.3 78.3 - - - +
319O ASP* 1.3 63.9 + - - +
321O ALA* 3.4 3.9 + - - +
322O GLN* 3.2 25.0 + - - +
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Residues in contact with ASP 319 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O ARG* 5.2 4.1 + - - -
315O LYS* 3.0 48.7 + - - +
316O GLU* 4.0 4.7 - - - +
318O GLU* 1.3 75.1 - - - +
320O ALA* 1.3 64.8 + - - +
322O GLN* 4.0 12.9 + - - +
323O PHE* 3.5 19.1 + - - +
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Residues in contact with ALA 320 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O VAL* 3.9 34.5 - - + +
103O ARG* 4.1 17.3 - - + +
106O LEU* 4.1 4.2 - - + +
316O GLU 3.0 12.9 + - - +
317O ILE 2.9 7.5 + - - +
319O ASP* 1.3 76.3 - - - +
321O ALA* 1.3 59.7 + - - +
323O PHE* 3.0 10.4 + - - +
324O ALA* 2.8 28.8 + - - +
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Residues in contact with ALA 321 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48O LYS* 3.5 42.2 - - + -
52O LEU* 4.8 9.9 - - + -
106O LEU* 4.1 9.1 - - + +
317O ILE 2.8 16.9 + - - +
318O GLU* 4.2 3.6 - - - +
320O ALA* 1.3 73.3 - - - +
322O GLN* 1.3 56.5 + - - +
324O ALA* 3.2 5.4 + - - +
325O THR* 3.0 36.1 + - + +
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Residues in contact with GLN 322 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318O GLU 3.2 17.2 + - - +
319O ASP* 4.0 15.0 - - - +
321O ALA* 1.3 78.3 - - - +
323O PHE* 1.3 64.4 + - + +
325O THR* 3.4 7.8 + - - -
326O ALA* 3.2 32.2 + - - +
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Residues in contact with PHE 323 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103O ARG* 3.1 68.0 - - + +
107O ALA* 3.7 22.7 - - + -
114O GLY* 4.2 21.8 - - - -
319O ASP 3.5 11.6 + - - +
320O ALA* 3.0 10.7 + - - +
322O GLN* 1.3 82.9 - - + +
324O ALA* 1.3 70.5 + - - +
326O ALA* 4.0 1.1 - - - -
327O ASP* 3.1 45.6 + - + +
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Residues in contact with ALA 324 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O LEU* 5.5 1.1 - - + -
106O LEU* 3.5 39.0 - - + +
107O ALA* 3.8 7.9 - - + +
110O THR* 3.3 23.4 + - + +
112O ARG* 3.3 18.4 + - - +
320O ALA 2.8 15.2 + - - +
321O ALA* 3.2 6.3 + - - +
323O PHE* 1.3 85.4 - - + +
325O THR* 1.3 59.5 - - + +
326O ALA 3.6 0.2 + - - -
327O ASP* 3.9 1.5 + - - -
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Residues in contact with THR 325 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52O LEU* 4.3 20.2 - - + -
57O ILE* 4.1 26.2 - - + -
110O THR* 4.3 5.4 - - + -
112O ARG* 2.9 21.8 + - - +
321O ALA 3.0 17.3 + - - +
322O GLN* 3.4 10.7 + - - -
323O PHE 3.3 0.2 - - - -
324O ALA* 1.3 79.6 - - - +
326O ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 326 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O ARG* 4.4 0.4 - - - -
322O GLN* 3.2 29.7 + - - +
323O PHE* 4.6 0.9 - - - +
325O THR* 1.3 77.9 - - - +
327O ASP* 1.3 64.6 + - - +
328O PRO* 3.7 4.3 - - - +
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Residues in contact with ASP 327 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O ALA* 5.5 0.2 - - + -
112O ARG* 3.0 34.3 + - + +
113O LYS* 3.8 6.5 + - - +
114O GLY* 2.8 38.7 + - - -
323O PHE* 3.1 38.9 + - + +
324O ALA* 3.9 2.4 + - - +
325O THR 3.5 0.8 - - - -
326O ALA* 1.3 78.3 - - - +
328O PRO* 1.4 82.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il