Contacts of the helix formed by residues 274 - 299 (chain F) in PDB entry 5UHE
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 PRO 274 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272F LYS 4.5 0.9 - - - +
273F LEU* 1.3 93.3 - - + +
275F ALA* 1.3 60.9 + - - +
276F ALA* 3.1 6.5 - - + +
277F GLN* 3.3 36.5 + - + +
278F ARG* 2.9 28.7 + - - +
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Residues in contact with ALA 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PRO* 1.3 74.1 - - - +
276F ALA* 1.3 56.8 + - - +
278F ARG* 4.2 16.7 - - - +
279F ARG* 3.1 38.2 - - - +
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Residues in contact with ALA 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274F PRO* 3.1 5.2 - - + +
275F ALA* 1.3 80.7 - - - +
277F GLN* 1.3 64.4 + - + +
279F ARG* 4.4 2.1 - - - +
280F ASP* 3.5 21.5 + - - +
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Residues in contact with GLN 277 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273F LEU* 3.3 35.4 - - + +
274F PRO* 3.3 29.0 + - + +
276F ALA* 1.3 78.7 - - + +
278F ARG* 1.3 54.3 + - - +
280F ASP* 3.3 5.1 + - - +
281F MET* 2.8 41.3 + - + +
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Residues in contact with ARG 278 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F MET* 4.9 15.3 - - + -
272F LYS* 3.8 31.8 - - + +
273F LEU* 3.1 35.9 + - + +
274F PRO 2.9 18.4 + - - +
275F ALA* 4.2 16.8 + - - +
277F GLN* 1.3 77.3 - - - +
279F ARG* 1.3 59.2 + - - +
281F MET* 3.4 6.4 - - - +
282F MET* 2.6 44.4 + - + +
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Residues in contact with ARG 279 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275F ALA* 3.1 30.1 + - - +
276F ALA* 4.4 2.9 - - - +
277F GLN 3.3 0.6 - - - -
278F ARG* 1.3 83.1 - - - +
280F ASP* 1.3 61.5 + - - +
282F MET* 3.5 6.8 + - - +
283F TRP* 3.2 22.2 + - - +
286F ARG* 4.7 2.4 + - - -
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Residues in contact with ASP 280 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276F ALA 3.5 16.8 + - - +
277F GLN* 3.3 5.3 + - - +
278F ARG 3.3 0.2 - - - -
279F ARG* 1.3 77.1 - - - +
281F MET* 1.3 65.5 + - + +
283F TRP* 3.5 14.2 + - - +
284F ILE* 3.3 26.3 + - - +
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Residues in contact with MET 281 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259F ALA* 3.9 24.5 - - + +
262F LEU* 3.5 26.9 - - + -
263F MET* 3.9 22.9 - - + -
273F LEU* 3.6 22.4 - - + -
277F GLN* 2.8 21.4 + - + +
278F ARG* 3.4 9.2 - - - +
280F ASP* 1.3 76.9 - - - +
282F MET* 1.3 62.9 + - - +
284F ILE* 3.4 10.3 + - - +
285F CYS* 3.4 15.8 + - - +
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Residues in contact with MET 282 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263F MET* 3.8 29.1 - - + +
278F ARG* 2.6 26.9 + - + +
279F ARG* 3.8 7.6 - - - +
281F MET* 1.3 74.0 - - - +
283F TRP* 1.3 58.4 + - - +
285F CYS* 3.2 12.3 + - - +
286F ARG* 3.0 54.3 + - + +
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Residues in contact with TRP 283 (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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279F ARG 3.2 17.2 + - - +
280F ASP* 3.9 11.0 - - - +
281F MET 3.3 0.6 - - - -
282F MET* 1.3 74.0 - - - +
284F ILE* 1.3 84.4 + - + +
286F ARG* 3.4 24.0 + - + +
287F ASP* 2.9 51.9 + - + -
290F ARG* 5.1 7.8 - - - +
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Residues in contact with ILE 284 (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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252F ARG 5.1 0.7 - - - +
255F ALA* 3.6 42.6 - - + +
256F GLY* 3.6 2.3 - - - +
259F ALA* 4.3 6.1 - - + -
280F ASP* 3.3 21.3 - - - +
281F MET* 3.4 9.6 + - - +
282F MET 3.2 0.4 - - - -
283F TRP* 1.3 101.2 - - + +
285F CYS* 1.3 52.4 + - - +
287F ASP* 3.1 6.1 + - - +
288F GLY* 2.6 35.2 + - - -
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Residues in contact with CYS 285 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256F GLY* 4.1 12.8 - - - +
259F ALA* 4.4 3.8 - - + +
260F THR* 3.1 34.0 + - - +
263F MET* 4.3 16.4 - - + -
281F MET 3.4 9.0 + - - +
282F MET* 3.2 19.9 + - - +
284F ILE* 1.3 79.3 - - - +
286F ARG* 1.3 59.4 + - - +
289F ASP* 3.3 23.5 + - - +
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Residues in contact with ARG 286 (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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279F ARG 4.7 2.0 + - - -
282F MET* 3.0 36.6 + - + +
283F TRP* 3.6 44.8 - - + +
284F ILE 3.2 0.2 - - - -
285F CYS* 1.3 75.0 - - + +
287F ASP* 1.3 53.7 + - - +
289F ASP* 3.1 5.7 + - - +
290F ARG* 2.7 54.2 + - - +
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Residues in contact with ASP 287 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ARG* 2.4 51.3 + - - +
283F TRP* 2.9 48.5 + - + +
284F ILE* 3.8 5.3 - - - +
286F ARG* 1.3 76.4 - - - +
288F GLY* 1.3 58.5 + - - +
290F ARG* 3.3 22.6 + - - +
291F ALA* 2.8 26.7 + - - +
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Residues in contact with GLY 288 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ARG 3.8 12.8 - - - -
253F ILE* 3.9 9.9 - - - +
256F GLY* 3.7 20.2 - - - -
257F LEU 5.5 0.2 - - - -
284F ILE 2.6 21.4 + - - -
287F ASP* 1.3 70.2 + - - +
289F ASP* 1.3 62.8 + - - +
290F ARG 3.1 1.6 - - - -
291F ALA* 3.2 4.0 + - - +
292F LYS* 3.1 23.4 + - - +
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Residues in contact with ASP 289 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D GLY 5.1 3.1 - - - +
256F GLY* 5.1 0.6 - - - -
285F CYS* 3.3 20.9 + - - +
286F ARG* 3.1 5.9 + - - +
288F GLY* 1.3 75.7 - - - +
290F ARG* 1.3 61.2 + - - +
292F LYS* 3.9 22.8 + - - +
293F ASN* 3.5 29.1 + - - +
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Residues in contact with ARG 290 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ARG* 5.4 3.4 - - - +
283F TRP* 5.1 8.9 - - - +
286F ARG* 2.7 33.6 + - - +
287F ASP* 3.3 46.4 + - - +
289F ASP* 1.3 77.5 - - - +
291F ALA* 1.3 65.7 + - - +
293F ASN* 3.2 9.4 + - + +
294F HIS* 3.1 20.0 + - + +
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Residues in contact with ALA 291 (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 LEU* 4.1 12.4 - - + +
252F ARG* 4.0 33.0 - - + +
253F ILE* 3.8 16.2 - - + -
287F ASP 2.8 17.4 + - - +
288F GLY 3.2 5.8 + - - +
290F ARG* 1.3 78.7 - - - +
292F LYS* 1.3 62.1 + - - +
294F HIS* 2.9 9.8 + - - +
295F LEU* 2.9 23.7 + - - +
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Residues in contact with LYS 292 (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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360D LEU 4.4 11.0 - - - -
361D GLY 2.9 23.7 + - - -
362D ALA* 4.5 1.0 - - - +
253F ILE* 3.6 27.2 - - + +
288F GLY 3.1 14.8 + - - +
289F ASP* 3.9 22.4 + - - +
290F ARG 3.3 0.2 - - - -
291F ALA* 1.3 75.6 - - - +
293F ASN* 1.3 86.1 + - - +
294F HIS 3.2 0.2 + - - -
295F LEU* 3.3 3.2 + - - +
296F LEU* 3.1 46.1 + - + +
329F ILE* 4.8 7.9 - - - -
332F VAL* 4.4 8.9 - - + +
333F GLU* 3.5 26.7 - - - +
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Residues in contact with ASN 293 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D GLY 3.9 4.6 + - - +
362D ALA 4.6 0.4 + - - -
363D PRO* 3.6 37.4 - - + +
364D GLU 5.0 0.4 - - - +
289F ASP* 3.5 15.0 + - - +
290F ARG* 3.2 12.4 + - + +
292F LYS* 1.3 110.2 + - - +
294F HIS* 1.3 57.5 + - - +
296F LEU 4.1 0.9 - - - -
297F GLU* 2.9 34.7 + - - +
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Residues in contact with HIS 294 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F VAL* 4.4 18.0 - - + +
239F ALA 5.8 0.2 - - - -
241F LEU* 3.9 24.9 - - + -
249F LEU* 3.3 28.3 - - + +
252F ARG* 5.6 2.5 - - - +
290F ARG* 3.1 11.8 + - + +
291F ALA* 2.9 13.2 + - - +
293F ASN* 1.3 78.4 - - - +
295F LEU* 1.3 63.3 + - - +
296F LEU 3.3 0.4 - - - -
297F GLU* 3.4 12.5 + - - +
298F ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 295 (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* 3.6 26.5 - - + -
246F GLU* 4.6 13.2 - - + +
249F LEU* 3.7 24.4 - - + +
250F ALA* 4.7 6.5 - - + +
253F ILE* 4.2 9.2 - - + -
291F ALA 2.9 12.3 + - - +
292F LYS 3.8 4.3 - - - +
294F HIS* 1.3 78.3 - - - +
296F LEU* 1.3 61.8 + - - +
298F ALA* 3.2 2.0 + - + -
299F ASN* 3.2 50.3 + - - +
332F VAL* 3.6 28.3 - - + -
335F PHE* 5.7 1.8 - - + -
343F PHE* 4.2 17.2 - - + -
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Residues in contact with LEU 296 (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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363D PRO* 3.6 37.5 - - + -
366D ILE* 4.7 7.4 - - + -
292F LYS* 3.1 39.5 + - + +
293F ASN 4.3 0.2 - - - +
295F LEU* 1.3 77.0 - - - +
297F GLU* 1.3 60.1 + - - +
299F ASN 3.7 1.7 - - - -
300F LEU* 3.1 27.4 + - - +
328F LEU* 3.7 26.7 - - + +
329F ILE* 3.8 32.5 - - + -
332F VAL* 3.7 25.6 - - + -
343F PHE* 5.9 0.4 - - + -
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Residues in contact with GLU 297 (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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363D PRO* 4.5 7.3 - - + +
364D GLU 5.7 0.2 + - - -
365D ILE* 3.5 36.1 + - + +
366D ILE* 6.2 0.2 - - + -
235F ILE* 4.4 6.6 - - - +
238F VAL* 3.9 34.2 - - + +
293F ASN* 2.9 25.3 + - - +
294F HIS* 3.4 12.7 + - - +
295F LEU 3.3 0.6 - - - -
296F LEU* 1.3 79.9 - - - +
298F ALA* 1.3 64.4 + - - +
300F LEU* 3.2 21.8 - - + +
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Residues in contact with ALA 298 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238F VAL* 4.1 13.2 - - + +
239F ALA 4.3 6.2 - - - +
240F LEU* 4.2 16.4 - - - +
241F LEU* 3.6 35.9 - - + +
294F HIS 3.1 13.9 + - - +
295F LEU* 3.5 11.7 - - - +
296F LEU 3.2 0.4 - - - -
297F GLU* 1.3 79.1 - - - +
299F ASN* 1.3 65.6 + - - +
300F LEU 3.1 4.9 + - - -
301F ARG* 4.0 5.7 + - - +
6H T 3.7 6.3 - - - +
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Residues in contact with ASN 299 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241F LEU* 5.0 5.1 + - - +
246F GLU* 4.1 6.3 + - - +
295F LEU* 3.2 36.6 + - - +
296F LEU 3.7 3.1 - - - -
298F ALA* 1.3 74.9 - - - +
300F LEU* 1.3 61.2 + - - +
301F ARG 3.2 2.5 - - - -
302F LEU* 3.4 18.6 + - + +
303F VAL* 4.0 1.2 + - - +
328F LEU* 3.4 16.9 - - + +
343F PHE* 3.1 40.4 - - + +
6H T 2.5 46.2 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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