Contacts of the helix formed by residues 260 - 284 (chain F) in PDB entry 2GPV
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 260 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257F VAL* 5.4 1.0 - - - +
258F PRO* 3.3 12.1 + - - -
259F ASP* 1.3 76.0 - - - +
261F ASP* 1.3 69.3 + - - +
262F ILE* 3.3 9.5 + - - +
263F LYS* 3.4 16.7 + - - +
264F ALA* 3.1 22.4 + - - +
339F LEU* 4.9 9.2 - - - -
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Residues in contact with ASP 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F SER* 1.3 75.4 - - - +
262F ILE* 1.3 97.1 + - - +
264F ALA* 3.3 2.8 + - - +
265F LEU* 3.2 34.2 + - + +
339F LEU* 3.2 27.1 + - - +
340F ALA* 4.0 16.8 - - - +
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Residues in contact with ILE 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F SER* 3.2 7.3 - - - +
261F ASP* 1.3 103.6 + - - +
263F LYS* 1.3 55.4 + - - +
265F LEU* 3.5 11.0 + - + +
266F THR* 2.5 45.3 + - - +
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Residues in contact with LYS 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253F PRO* 4.0 14.3 - - - +
254F ASP* 2.7 41.9 + - + +
255F PRO* 4.2 7.3 + - - +
257F VAL* 3.1 44.0 + - + +
259F ASP* 3.2 35.2 + - - +
260F SER* 3.4 19.6 + - - +
261F ASP 3.3 0.4 - - - -
262F ILE* 1.3 76.9 - - - +
264F ALA* 1.3 59.1 + - - +
266F THR* 3.5 6.8 - - - -
267F THR* 2.8 39.9 + - - +
330F TYR* 6.3 0.9 - - - -
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Residues in contact with ALA 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260F SER 3.1 12.6 + - - +
261F ASP 3.3 9.1 + - - +
263F LYS* 1.3 76.5 - - - +
265F LEU* 1.3 61.9 + - - +
267F THR* 3.5 2.4 + - - -
268F LEU* 3.1 33.3 + - + +
330F TYR* 3.4 22.9 + - - +
332F MET* 5.0 3.6 - - + -
336F GLN 5.6 0.4 - - - +
340F ALA* 3.8 25.6 - - + -
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Residues in contact with LEU 265 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261F ASP* 3.2 25.0 + - + +
262F ILE* 4.0 11.9 - - + +
264F ALA* 1.3 74.6 - - + +
266F THR* 1.3 56.6 + - - +
268F LEU* 3.1 6.8 + - - +
269F CYS* 2.7 45.4 + - - +
340F ALA* 4.3 15.3 - - + +
342F LEU* 4.3 17.5 - - + -
438F ILE* 3.8 24.5 - - + -
505F OHT 3.8 28.9 - - + -
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Residues in contact with THR 266 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262F ILE* 2.5 33.6 + - - +
263F LYS* 3.5 7.8 - - - -
265F LEU* 1.3 76.7 - - - +
267F THR* 1.3 62.8 + - - +
269F CYS* 3.7 7.4 - - - +
270F ASP* 3.0 24.8 + - + +
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Residues in contact with THR 267 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251F ALA* 3.6 41.3 - - + +
253F PRO* 4.0 25.4 - - + +
263F LYS* 2.8 33.7 + - - +
264F ALA* 3.7 5.2 - - - -
266F THR* 1.3 72.3 - - - +
268F LEU* 1.3 55.0 + - - +
270F ASP* 3.0 8.3 + - - +
271F LEU* 2.7 35.5 + - + +
274F ARG* 5.1 0.2 + - - -
330F TYR* 4.4 17.5 + - + -
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Residues in contact with LEU 268 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264F ALA* 3.1 22.2 + - + +
265F LEU* 3.1 6.8 + - - +
267F THR* 1.3 75.6 - - - +
269F CYS* 1.3 53.8 + - - +
271F LEU* 3.0 7.4 + - + +
272F ALA* 2.6 37.4 + - - +
326F TYR* 3.6 46.9 - - + -
330F TYR* 4.0 13.9 - - + -
332F MET* 4.4 9.6 - - - -
342F LEU* 3.9 28.5 - - + -
505F OHT 4.0 32.7 - - + -
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Residues in contact with CYS 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265F LEU* 2.7 31.2 + - - +
266F THR* 3.7 7.9 - - - +
268F LEU* 1.3 72.7 - - - +
270F ASP* 1.3 57.4 + - - +
272F ALA* 3.3 1.6 + - - +
273F ASP* 3.0 37.1 + - - +
435F PHE* 3.6 33.2 - - - -
505F OHT 3.8 23.5 - - - +
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Residues in contact with ASP 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251F ALA 4.2 5.5 - - - +
252F MET 5.2 1.9 - - - +
266F THR* 3.0 19.2 + - + +
267F THR* 3.0 6.7 + - - +
269F CYS* 1.3 74.2 - - - +
271F LEU* 1.3 67.0 + - - +
273F ASP* 3.5 8.3 + - - +
274F ARG* 3.1 53.3 + - - +
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Residues in contact with LEU 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249F ILE* 3.6 33.7 - - + +
250F TYR 4.0 17.5 - - - +
251F ALA* 4.1 17.3 - - + -
267F THR 2.7 16.7 + - - +
268F LEU* 3.3 14.4 - - + +
270F ASP* 1.3 74.9 - - - +
272F ALA* 1.3 57.5 + - - +
274F ARG* 3.2 11.3 + - - +
275F GLU* 2.9 46.0 + - - +
326F TYR* 3.5 41.3 - - + +
327F ALA* 4.2 0.4 - - + -
330F TYR* 5.2 0.4 - - + -
505F OHT 4.5 7.0 - - + -
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Residues in contact with ALA 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268F LEU 2.6 20.2 + - - +
269F CYS 3.6 4.0 - - - +
271F LEU* 1.3 74.8 - - - +
273F ASP* 1.3 56.0 + - - +
275F GLU* 3.4 2.5 + - - +
276F LEU* 3.0 34.0 + - - +
309F LEU* 4.0 15.7 - - + +
505F OHT 3.7 49.4 - - + -
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Residues in contact with ASP 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269F CYS* 3.0 21.8 + - - +
270F ASP* 3.8 8.5 - - - +
271F LEU 3.3 0.2 - - - -
272F ALA* 1.3 72.3 - - - +
274F ARG* 1.3 67.0 + - + +
276F LEU* 3.3 10.5 + - - +
277F VAL* 3.2 26.0 + - - +
505F OHT 2.9 39.3 + - - +
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Residues in contact with ARG 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ILE* 3.2 34.2 - - + +
250F TYR 3.0 29.8 + - - +
251F ALA* 3.3 13.3 + - - +
252F MET* 5.3 2.3 - - - +
270F ASP* 3.1 44.1 + - - +
271F LEU* 3.2 22.9 + - - +
273F ASP* 1.3 75.0 - - + +
275F GLU* 1.3 66.1 + - - +
277F VAL* 3.3 18.0 + - - +
278F VAL* 3.5 12.5 + - - +
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Residues in contact with GLU 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249F ILE* 4.0 16.7 - - + +
271F LEU* 2.9 43.8 + - + +
272F ALA 3.6 0.7 - - - +
273F ASP 3.3 0.2 - - - -
274F ARG* 1.3 76.6 - - - +
276F LEU* 1.3 56.4 + - - +
278F VAL* 2.8 28.0 - - + +
279F ILE* 2.9 21.4 + - + +
309F LEU* 3.6 25.6 - - + +
312F GLY* 5.6 0.9 - - - -
316F ARG* 3.7 21.9 + - - -
326F TYR 3.8 3.3 - - - +
505F OHT 3.2 27.6 + - - -
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Residues in contact with LEU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F ALA 3.0 24.4 + - - +
273F ASP* 3.4 14.8 - - - +
275F GLU* 1.3 74.2 - - - +
277F VAL* 1.3 66.5 + - + +
279F ILE* 3.6 19.9 - - + +
280F ILE* 3.0 39.2 + - + +
305F TRP* 3.8 48.2 - - + -
309F LEU* 4.5 7.9 - - + -
505F OHT 4.3 17.9 - - - +
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Residues in contact with VAL 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F ASP 3.2 14.6 + - - +
274F ARG* 3.6 11.4 - - - +
275F GLU 3.3 0.4 - - - -
276F LEU* 1.3 78.8 - - + +
278F VAL* 1.3 65.5 + - + +
280F ILE* 3.7 11.6 + - + +
281F GLY* 3.4 14.9 + - - -
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Residues in contact with VAL 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F PRO* 4.1 27.7 - - + +
247F GLU 6.1 0.2 - - - +
249F ILE* 3.3 33.4 - - + -
274F ARG 3.5 2.7 + - - +
275F GLU* 2.8 24.5 - - + +
277F VAL* 1.3 80.8 - - + +
279F ILE* 1.3 60.7 + - + +
281F GLY* 3.5 2.7 + - - +
282F TRP* 2.8 28.3 + - - +
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Residues in contact with ILE 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246F PRO* 5.5 3.8 - - + -
275F GLU* 2.9 26.6 + - + +
276F LEU* 3.2 18.1 + - + +
278F VAL* 1.3 76.8 - - + +
280F ILE* 1.3 60.6 + - + +
282F TRP* 3.2 18.5 + - + +
283F ALA* 2.8 26.7 + - - +
301F LEU* 4.6 15.3 - - + -
305F TRP* 5.0 2.7 - - - +
308F ILE* 3.8 39.0 - - + +
309F LEU* 3.9 32.1 - - + +
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Residues in contact with ILE 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276F LEU* 3.0 31.2 + - + +
277F VAL* 4.2 9.2 - - + +
278F VAL 3.4 0.2 - - - -
279F ILE* 1.3 73.5 - - + +
281F GLY* 1.3 66.4 + - - +
283F ALA* 3.2 15.2 + - - +
284F LYS* 3.3 24.6 + - + +
289F PHE* 6.2 0.9 - - + -
301F LEU* 4.0 27.8 - - + -
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Residues in contact with GLY 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277F VAL 3.4 11.7 + - - -
278F VAL* 3.7 4.9 - - - -
279F ILE 3.4 0.4 - - - -
280F ILE* 1.3 77.8 - - - +
282F TRP* 1.3 57.5 + - - +
284F LYS* 3.6 17.1 + - - +
285F HIS* 3.0 27.1 + - - -
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Residues in contact with TRP 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F LEU* 4.4 16.1 + - + +
244F ALA* 3.4 32.5 - - + +
245F GLU* 4.3 9.3 + - - -
246F PRO* 4.3 17.0 - - + -
278F VAL 2.8 18.6 + - - +
279F ILE* 3.3 23.8 - - + +
280F ILE 3.1 0.2 - - - -
281F GLY* 1.3 72.3 - - - +
283F ALA* 1.3 78.8 + - + +
284F LYS 3.1 1.6 - - - -
285F HIS* 2.8 24.8 + - + +
286F ILE* 3.5 31.3 + - + +
308F ILE* 4.0 26.9 - - + -
367F VAL* 4.5 6.4 - - - +
370F LYS* 3.5 52.0 - - + +
371F ALA* 4.1 5.2 - - - -
374F LEU* 4.4 5.4 - - + -
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Residues in contact with ALA 283 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279F ILE 2.8 16.7 + - - +
280F ILE* 3.2 11.2 + - - +
282F TRP* 1.3 80.3 - - + +
284F LYS* 1.3 61.7 + - - +
286F ILE* 3.0 24.2 + - - +
289F PHE* 3.1 40.7 - - + -
301F LEU* 4.2 12.1 - - + -
374F LEU* 4.2 11.2 - - + -
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Residues in contact with LYS 284 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280F ILE* 3.3 21.9 + - + +
281F GLY* 3.7 15.3 - - - +
282F TRP 3.1 1.0 - - - -
283F ALA* 1.3 76.6 - - - +
285F HIS* 1.3 64.9 + - + +
286F ILE 3.6 3.7 + - - +
289F PHE* 4.0 8.5 - - + -
290F SER* 2.9 30.2 + - - +
297F GLN* 5.4 5.4 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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