Contacts of the helix formed by residues 234 - 255 (chain F) in PDB entry 6OY5
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 LYS 234 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F LEU 5.8 2.0 + - - -
96F LEU* 4.7 27.7 - - + +
99F GLU* 3.4 25.3 + - - +
227F PHE* 4.2 1.6 - - - -
232F ARG 3.8 2.3 + - - +
233F PHE* 1.3 78.8 - - - +
235F PHE* 1.3 66.6 + - - +
236F SER* 3.3 3.6 - - - +
237F THR* 3.3 15.5 + - - +
238F TYR 3.9 1.9 + - - -
4H A 2.7 30.7 + - - +
5H T 3.1 41.3 + - - +
6H G 5.4 8.0 + - - -
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Residues in contact with PHE 235 (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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99F GLU* 2.6 32.1 + - + +
103F ALA* 6.0 0.4 - - + -
187F LEU* 4.6 11.2 - - + -
191F ASN* 3.3 41.5 - - - +
220F LEU* 3.7 13.5 - - + -
223F ALA* 4.0 6.7 - - + -
224F VAL* 3.4 34.5 - - + -
227F PHE* 3.7 48.4 - + + -
233F PHE 3.7 0.8 + - - -
234F LYS* 1.3 73.0 - - - +
236F SER* 1.3 66.0 + - - +
237F THR 3.0 1.7 + - - -
238F TYR* 3.1 4.6 + + - +
239F ALA* 3.0 41.2 + - + -
6H G 5.1 0.2 - - - +
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Residues in contact with SER 236 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLU* 5.0 0.2 + - - -
194F LEU* 4.1 19.9 - - - +
234F LYS* 4.1 1.8 - - - +
235F PHE* 1.3 80.4 - - - +
237F THR* 1.3 63.5 + - - +
239F ALA* 4.0 3.0 - - - +
240F THR* 3.0 30.0 + - - -
4H A 3.5 9.0 - - - +
5H T 2.6 44.3 + - - -
6H G 4.2 20.8 + - - -
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Residues in contact with THR 237 (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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233F PHE* 4.9 2.0 - - + -
234F LYS 3.3 10.5 + - - -
235F PHE 3.0 1.0 + - - -
236F SER* 1.3 81.6 + - - +
238F TYR* 1.3 63.0 + - - +
240F THR* 3.8 3.6 + - - -
241F TRP* 4.2 4.2 + - - +
2H T 4.0 15.1 - - - +
3H A 3.6 36.6 - - - +
4H A 2.9 52.6 + - + +
5H T 3.2 17.4 - - + +
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Residues in contact with TYR 238 (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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223F ALA* 3.7 10.5 - - + -
226F LYS* 3.0 47.0 + - + +
227F PHE* 3.5 34.3 - + + -
234F LYS 3.9 1.2 + - - -
235F PHE* 3.1 5.7 + + + +
237F THR* 1.3 77.1 - - - +
239F ALA* 1.3 69.8 + - - +
241F TRP* 3.2 19.6 + - + +
242F TRP* 3.3 23.0 + + - -
1H A 3.1 35.7 + - - -
2H T 3.2 61.6 + + + +
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Residues in contact with ALA 239 (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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194F LEU* 4.6 5.2 - - + -
220F LEU* 4.3 2.5 - - + -
223F ALA* 3.7 15.3 - - + -
235F PHE* 3.0 43.5 + - + +
236F SER* 4.0 5.4 - - - +
238F TYR* 1.3 76.4 - - - +
240F THR* 1.3 65.1 + - - +
242F TRP* 2.8 17.3 + - - +
243F ILE* 3.1 28.3 + - + +
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Residues in contact with THR 240 (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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194F LEU* 3.8 14.1 - - - +
198F ILE* 3.9 18.3 - - + +
236F SER 3.0 13.0 + - - -
237F THR 4.0 0.4 - - - -
238F TYR 3.3 0.4 + - - -
239F ALA* 1.3 76.7 - - - +
241F TRP* 1.3 63.3 + - - +
243F ILE* 3.9 2.1 - - - +
244F ARG* 3.0 59.8 + - - +
5H T 3.2 37.3 - - + +
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Residues in contact with TRP 241 (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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237F THR 4.2 3.6 + - - +
238F TYR* 3.2 13.5 + - + +
239F ALA 3.0 1.0 + - - -
240F THR* 1.3 79.8 - - - +
242F TRP* 1.3 110.4 + + + +
244F ARG* 3.4 6.2 + - - +
245F GLN* 2.8 63.4 + - + +
1H A 3.6 51.1 + - - +
2H T 4.6 11.2 + - - -
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Residues in contact with TRP 242 (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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219F GLY* 3.5 20.5 - - - +
222F ARG* 3.6 33.7 - - + -
223F ALA* 3.8 17.9 - - + -
226F LYS* 4.1 31.0 - - + -
238F TYR* 3.3 44.6 + + - -
239F ALA 2.8 10.1 + - - +
241F TRP* 1.3 104.3 - + - +
243F ILE* 1.3 60.9 + - - +
245F GLN* 3.5 8.2 - - + +
246F ALA* 2.9 28.2 + - - +
1H A 4.3 10.7 - + - -
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Residues in contact with ILE 243 (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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191F ASN 5.7 0.4 - - - +
194F LEU* 4.6 9.2 - - + -
195F VAL* 3.6 26.0 - - + -
198F ILE* 3.8 33.0 - - + -
216F GLY* 3.7 24.9 - - - +
219F GLY* 4.3 0.9 - - - -
220F LEU* 3.7 28.7 - - + +
239F ALA* 3.1 31.5 + - + +
240F THR* 3.9 4.5 - - - +
242F TRP* 1.3 73.2 - - - +
244F ARG* 1.3 65.3 + - - +
246F ALA* 3.1 2.8 + - - +
247F ILE* 3.0 27.8 + - + +
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Residues in contact with ARG 244 (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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361C MET* 4.3 10.6 - - - -
198F ILE* 3.9 23.6 - - + +
201F LYS* 3.3 34.8 - - - +
202F TYR* 3.8 26.5 + - - +
240F THR* 3.0 45.0 + - + +
241F TRP* 3.7 5.6 - - - +
243F ILE* 1.3 76.4 - - - +
245F GLN* 1.3 63.4 + - - +
247F ILE* 4.8 2.7 - - - -
248F ASN* 2.9 33.8 + - - +
5H T 4.2 18.8 + - - +
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Residues in contact with GLN 245 (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 TRP* 2.8 57.4 + - + +
242F TRP* 3.5 16.2 - - + +
243F ILE 3.2 0.2 - - - -
244F ARG* 1.3 77.7 - - - +
246F ALA* 1.3 55.9 + - - +
248F ASN* 4.0 3.4 - - - +
249F ARG* 3.1 28.9 + - + +
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Residues in contact with ALA 246 (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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215F GLU* 3.3 29.7 - - + +
218F GLN* 5.0 2.2 - - + -
219F GLY* 3.6 15.0 - - - +
242F TRP 2.9 18.3 + - - +
243F ILE* 3.1 4.9 + - - +
245F GLN* 1.3 73.3 - - - +
247F ILE* 1.3 65.1 + - - +
249F ARG* 3.4 10.9 + - - +
250F ALA* 3.1 23.0 + - - +
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Residues in contact with ILE 247 (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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195F VAL 5.1 0.2 - - - +
198F ILE* 4.2 15.0 - - + +
199F ALA* 3.7 38.1 - - + +
202F TYR* 3.5 38.6 - - + -
212F LEU* 3.8 18.4 - - + +
215F GLU* 4.6 2.7 - - - -
216F GLY* 3.7 20.0 - - - -
243F ILE* 3.0 21.8 + - + +
244F ARG* 4.1 2.7 - - - +
246F ALA* 1.3 71.4 - - - +
248F ASN* 1.3 68.4 + - - +
250F ALA* 3.0 17.9 + - - +
251F ILE* 3.0 23.3 + - + +
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Residues in contact with ASN 248 (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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202F TYR* 2.9 36.6 + - - -
205F ARG* 3.5 20.7 + - - -
244F ARG* 2.9 27.1 + - - +
245F GLN* 4.1 3.8 - - - +
247F ILE* 1.3 80.1 - - - +
249F ARG* 1.3 63.4 + - - +
251F ILE* 3.5 6.4 + - - +
252F ALA* 3.0 24.6 + - - +
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Residues in contact with ARG 249 (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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215F GLU* 3.3 31.7 + - - -
218F GLN* 5.0 2.4 + - - -
245F GLN* 3.1 18.0 + - + +
246F ALA* 3.9 7.6 + - - +
247F ILE 3.2 0.4 - - - -
248F ASN* 1.3 78.2 - - - +
250F ALA* 1.3 61.9 + - - +
252F ALA* 3.3 6.4 + - - +
253F ASP* 2.7 58.1 + - + +
254F GLN* 4.3 5.9 - - - +
262F VAL* 5.3 12.6 - - + -
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Residues in contact with ALA 250 (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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207F LEU* 3.7 13.6 - - + +
212F LEU* 5.7 0.9 - - + -
215F GLU* 3.3 42.0 - - + +
246F ALA 3.1 9.4 + - - +
247F ILE* 3.0 10.1 + - - +
249F ARG* 1.3 81.1 - - - +
251F ILE* 1.3 61.7 + - + +
253F ASP* 4.5 0.7 - - - -
254F GLN* 2.8 38.9 + - - +
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Residues in contact with ILE 251 (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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202F TYR* 4.1 5.8 - - + +
205F ARG* 3.8 68.2 - - + +
207F LEU* 4.3 11.7 - - + -
212F LEU* 3.7 23.8 - - + -
247F ILE* 3.0 35.0 + - + +
248F ASN* 3.8 6.5 - - - +
250F ALA* 1.3 75.6 - - - +
252F ALA* 1.3 62.7 + - - +
253F ASP 3.3 0.3 + - - -
255F ALA* 3.3 25.7 + - + +
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Residues in contact with ALA 252 (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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248F ASN 3.0 18.6 + - - +
249F ARG* 3.6 4.5 - - - +
251F ILE* 1.3 79.9 - - - +
253F ASP* 1.3 59.7 + - - +
255F ALA 4.9 0.6 + - - -
256F ARG* 6.1 0.9 - - - -
260F ILE 4.0 9.7 + - - +
262F VAL* 4.1 28.5 - - + +
265F VAL* 3.9 36.7 - - + +
266F GLU* 6.0 1.8 - - + +
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Residues in contact with ASP 253 (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 ARG* 2.7 44.0 + - + +
250F ALA* 3.2 2.7 + - - +
252F ALA* 1.3 76.4 - - - +
254F GLN* 1.3 72.0 + - + +
255F ALA 3.7 0.7 - - - -
256F ARG 5.1 2.3 + - - +
259F ARG* 2.9 49.6 + - - +
260F ILE 5.0 1.1 + - - +
262F VAL* 6.2 1.1 - - - -
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Residues in contact with GLN 254 (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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29D PRO* 5.7 2.0 - - + -
545D ARG* 3.0 27.9 + - - +
549D ASN* 3.6 43.7 + - - +
553D ARG* 4.5 6.3 + - - +
207F LEU* 3.6 28.5 - - + +
211F ASP* 5.4 1.7 - - - +
215F GLU* 3.0 29.5 + - - +
249F ARG* 4.3 10.7 - - - +
250F ALA* 2.8 21.5 + - - +
253F ASP* 1.3 84.1 + - + +
255F ALA* 1.3 58.0 + - - +
256F ARG 3.2 3.6 - - - -
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Residues in contact with ALA 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545D ARG* 4.3 6.3 + - - -
594D PRO* 6.1 1.0 - - - +
205F ARG 3.7 22.7 - - - +
206F GLY* 4.2 22.7 - - - +
207F LEU* 4.6 2.2 - - + +
250F ALA 4.2 0.2 + - - -
251F ILE* 3.3 22.3 + - + +
252F ALA 4.9 0.4 + - - -
253F ASP 3.7 1.6 - - - -
254F GLN* 1.3 77.3 - - - +
256F ARG* 1.3 62.5 + - + +
257F THR 4.2 0.9 + - - -
313F GLU* 4.0 8.3 - - - +
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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