Contacts of the helix formed by residues 235 - 247 (chain F) in PDB entry 3KQG
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 235 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F VAL* 3.8 2.1 - - - +
234F THR* 1.3 83.4 + - - +
236F GLU* 1.3 65.9 + - - +
237F SER* 3.3 11.3 + - - -
238F GLU* 3.2 24.7 + - - +
239F GLN* 2.9 23.4 + - - +
276F GLN* 3.7 8.6 - - - +
280F PHE* 3.9 7.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 236 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235F SER* 1.3 72.4 - - - +
237F SER* 1.3 52.7 + - - +
239F GLN* 3.2 3.9 + - - +
240F GLU* 2.8 36.0 + - - +
276F GLN* 5.1 0.4 - - - +
279F ARG* 3.2 42.6 + - - +
280F PHE* 3.8 15.5 - - + -
303F LEU* 3.6 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F PHE* 3.5 14.6 - - - -
203F LYS* 3.5 34.5 + - - +
235F SER* 3.3 11.7 + - - -
236F GLU* 1.3 80.6 - - - +
238F GLU* 1.3 59.3 + - - +
240F GLU* 3.3 16.5 + - - +
241F PHE 2.8 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202F PHE* 3.7 15.3 - - + -
205F ASN* 5.6 1.6 - - - -
207F TYR* 2.7 33.4 + - + +
231F THR* 4.0 0.2 + - - -
232F SER 3.1 14.7 - - - +
233F VAL* 3.7 1.5 - - + -
234F THR* 2.7 39.9 + - - +
235F SER* 3.2 16.6 + - - +
237F SER* 1.3 78.4 + - - +
239F GLN* 1.3 66.6 + - - +
241F PHE* 3.2 2.5 + - + +
242F LEU* 3.0 38.8 + - + +
320F LYS* 2.9 20.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 239 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F VAL* 3.1 28.7 - - + +
235F SER 2.9 14.1 + - - +
236F GLU 3.4 8.5 - - - +
238F GLU* 1.3 76.3 - - - +
240F GLU* 1.3 59.7 + - - +
242F LEU* 3.5 3.1 + - - +
243F TYR* 3.1 28.1 + - + -
280F PHE* 3.6 27.4 + - + -
298F ILE* 4.6 6.1 - - - +
303F LEU* 3.0 43.2 + - + +
305F ALA* 3.9 11.0 - - - +
306F TRP* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236F GLU 2.8 17.0 + - - +
237F SER* 3.5 13.8 - - - +
238F GLU 3.1 0.2 - - - -
239F GLN* 1.3 76.2 - - - +
241F PHE* 1.3 63.0 + - - +
243F TYR* 3.5 25.9 + - + +
244F LYS* 2.9 46.7 + - + +
303F LEU* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 241 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLN* 4.0 28.9 - - + -
200F LYS* 4.5 11.0 - - + -
201F TYR 4.3 4.9 - - - -
202F PHE* 3.4 50.7 - + + -
207F TYR* 3.5 36.3 - + + -
209F PHE* 4.4 10.1 - + - -
237F SER 2.8 14.6 + - - +
238F GLU* 3.5 6.3 - - + +
240F GLU* 1.3 77.0 - - - +
242F LEU* 1.3 75.5 + - + +
244F LYS* 3.7 4.1 - - + +
245F THR* 2.6 53.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F TYR* 3.8 18.6 - - + -
209F PHE* 3.9 17.8 - - + -
231F THR* 4.1 19.1 - - + +
233F VAL* 4.0 27.8 - - + -
238F GLU* 3.0 30.4 + - + +
239F GLN* 3.9 3.1 - - - +
240F GLU 3.2 0.4 - - - -
241F PHE* 1.3 99.3 - - + +
243F TYR* 1.3 63.1 + - - +
245F THR* 3.4 1.6 + - - -
246F ALA* 2.9 28.3 + - - +
298F ILE* 3.7 21.3 - - + -
318F ILE* 4.4 10.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226E ARG* 4.2 5.0 + - - -
239F GLN* 3.1 25.9 + - + +
240F GLU* 3.5 30.0 + - + +
242F LEU* 1.3 75.2 - - - +
244F LYS* 1.3 98.1 + - + +
246F ALA* 3.5 13.6 + - - +
247F GLY* 3.6 6.9 + - - -
248F GLY 4.6 2.6 + - - -
298F ILE* 4.1 19.7 - - + +
300F ALA 4.2 5.4 - - - +
301F PRO* 3.4 38.8 + - + +
302F SER* 3.7 31.2 - - - +
303F LEU* 4.0 11.5 + - + +
305F ALA* 4.3 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 244 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TYR* 4.9 1.9 + - - -
225E SER* 3.4 24.7 + - - -
226E ARG* 2.6 57.0 + - - +
240F GLU* 2.9 38.3 + - + +
241F PHE* 3.7 5.6 - - - +
242F LEU 3.2 0.2 - - - -
243F TYR* 1.3 106.5 + - + +
245F THR* 1.3 57.9 + - - +
247F GLY* 2.9 12.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 245 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197E GLN* 3.8 18.1 + - - +
198E GLY* 5.4 0.7 - - - -
208E TYR* 4.3 11.4 + - + -
211E LEU* 5.6 4.9 - - - +
200F LYS* 3.7 28.5 - - + -
209F PHE* 3.5 30.3 - - + -
241F PHE* 2.6 41.1 + - + -
244F LYS* 1.3 77.5 - - - +
246F ALA* 1.3 61.1 + - - +
247F GLY* 3.3 2.0 + - - -
251F TYR* 5.0 2.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211E LEU* 6.0 1.5 - - - +
209F PHE* 4.1 3.8 - - + -
242F LEU 2.9 18.0 + - - +
243F TYR* 3.6 12.1 - - - +
244F LYS 3.1 0.4 - - - -
245F THR* 1.3 77.5 - - - +
247F GLY* 1.3 64.8 + - - +
248F GLY 3.2 1.3 - - - +
249F LEU* 2.9 42.1 + - - +
251F TYR* 3.7 22.9 + - + -
298F ILE* 4.8 9.2 - - + -
318F ILE* 5.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208E TYR* 4.3 10.8 - - - -
212E ILE* 3.3 29.5 + - - +
214E LYS* 5.4 0.4 - - - -
222E PHE* 4.0 14.1 - - - -
226E ARG* 3.8 11.2 - - - -
243F TYR 3.6 2.2 + - - -
244F LYS 2.9 16.5 + - - -
245F THR 3.1 2.2 - - - -
246F ALA* 1.3 79.1 - - - +
248F GLY* 1.3 56.4 + - - +
249F LEU* 3.4 3.3 + - - +
----------------------------------------------------------
Back to top of page
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