Contacts of the helix formed by residues 247 - 257 (chain F) in PDB entry 3KHU
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 ASP 247 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212E ASN* 4.8 4.3 - - - +
215E SER* 3.0 7.2 + - - +
241F CYS* 3.7 2.5 - - - -
245F GLY 3.9 0.4 + - - +
246F ALA* 1.3 74.1 - - - +
248F VAL* 1.3 65.3 + - - +
249F GLU* 3.0 29.1 + - - +
250F GLU* 3.0 35.4 + - + +
251F VAL* 3.0 21.7 + - - +
443F ARG* 3.0 25.2 + - - -
463F GLY 3.5 4.6 - - - +
464F LYS* 4.3 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ILE* 3.9 39.3 - - + +
237F ILE* 4.2 6.3 - - + -
238F SER* 3.9 11.9 - - - +
241F CYS* 3.5 10.3 - - - -
247F ASP* 1.3 70.8 - - - +
249F GLU* 1.3 66.0 + - + +
251F VAL* 4.4 1.6 - - - +
252F ALA* 2.8 29.7 + - - +
268F ALA* 4.0 19.5 - - + -
443F ARG* 3.7 21.3 - - - +
462F ILE 4.1 2.0 - - - +
463F GLY* 3.0 27.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 249 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247F ASP* 3.0 10.9 + - - +
248F VAL* 1.3 79.0 - - + +
250F GLU* 1.3 64.6 + - - +
252F ALA* 3.8 5.1 - - - +
253F THR* 2.8 33.1 + - - +
266F LEU 4.6 3.6 - - - +
267F LYS* 4.6 13.3 - - - +
268F ALA 4.5 14.2 + - - +
443F ARG* 3.7 26.4 - - - +
446F ASP* 3.6 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E LEU* 4.3 4.1 - - - +
210E THR 5.1 2.1 - - - +
211E THR* 3.5 18.5 - - + +
212E ASN* 3.1 31.1 + - - +
215E SER* 2.9 26.1 + - - +
219E SER* 4.9 0.2 - - - -
247F ASP* 3.0 26.8 + - - +
249F GLU* 1.3 77.2 - - + +
251F VAL* 1.3 57.9 + - - +
253F THR* 3.3 6.4 + - - -
254F ALA* 3.0 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 251 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E SER* 3.7 30.7 - - - +
218E LEU* 4.4 5.6 - - + -
219E SER* 3.5 22.4 - - - +
222E ALA* 4.4 3.4 - - + -
234F ILE* 5.1 0.2 - - + -
237F ILE* 3.9 21.5 - - + -
241F CYS* 4.2 14.1 - - - -
246F ALA* 4.3 2.9 - - + -
247F ASP 3.0 15.3 + - - +
248F VAL 3.8 3.6 - - - +
250F GLU* 1.3 77.5 - - - +
252F ALA* 1.3 55.4 + - - +
254F ALA* 3.2 1.9 + - - +
255F ILE* 2.9 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234F ILE* 3.9 18.7 - - + +
248F VAL 2.8 19.3 + - - +
249F GLU* 3.8 11.4 - - - +
251F VAL* 1.3 74.3 - - - +
253F THR* 1.3 59.0 + - - +
255F ILE* 3.8 3.9 - - - +
256F GLY* 2.9 27.2 + - - -
266F LEU* 3.4 35.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 253 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209E LEU* 3.9 26.5 - - + -
249F GLU* 2.8 24.1 + - - +
250F GLU* 3.6 6.2 - - - -
251F VAL 3.3 0.2 - - - -
252F ALA* 1.3 76.1 - - - +
254F ALA* 1.3 63.4 + - - +
256F GLY* 3.3 1.7 + - - -
257F MET* 3.1 39.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162E PHE* 6.3 0.2 - - + -
177E ARG* 3.0 31.8 + - + +
179E LEU* 4.1 14.4 - - + -
209E LEU* 3.4 23.7 - - + +
211E THR* 5.2 0.4 - - + -
219E SER* 3.5 31.6 - - - +
250F GLU 3.0 12.4 + - - +
251F VAL 3.2 0.4 + - - +
253F THR* 1.3 76.6 - - - +
255F ILE* 1.3 61.3 + - - +
257F MET* 3.6 4.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E ARG* 4.3 5.8 - - - +
219E SER* 4.4 5.4 - - - +
222E ALA* 3.9 16.2 - - + -
223E ALA* 4.2 16.2 - - - +
226E PHE* 3.9 25.8 - - + -
234F ILE* 4.2 12.3 - - + -
237F ILE* 5.2 0.4 - - + -
251F VAL* 2.9 39.9 + - + +
252F ALA* 3.8 3.1 - - - +
254F ALA* 1.3 78.8 - - - +
256F GLY* 1.3 63.3 + - - +
258F ASP* 3.1 23.0 + - - +
261F ILE* 3.7 36.0 - - + +
266F LEU* 4.2 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 256 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252F ALA 2.9 17.9 + - - -
253F THR* 3.3 2.7 + - - -
255F ILE* 1.3 77.1 - - - +
257F MET* 1.3 60.2 + - - +
258F ASP 3.2 4.2 + - - +
259F GLN* 5.2 0.5 - - - +
262F GLY* 3.3 36.6 - - - -
263F ASN* 3.5 18.7 + - - +
266F LEU* 3.7 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176E ASP* 3.3 25.8 - - - +
177E ARG* 3.9 33.2 - - + -
206E GLU 3.6 24.5 - - - +
207E LYS* 4.0 11.2 - - + +
209E LEU* 4.3 23.6 - - + -
253F THR* 3.1 29.3 + - + +
254F ALA 4.0 5.8 - - - +
255F ILE 3.1 0.8 + - - -
256F GLY* 1.3 75.0 - - - +
258F ASP* 1.3 63.2 + - - +
259F GLN* 3.3 7.8 + - - +
263F ASN* 5.5 0.7 - - + -
----------------------------------------------------------
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