Contacts of the helix formed by residues 282 - 292 (chain X) in PDB entry 5LIK
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 282 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241X HIS* 4.9 0.8 - - - -
280X LYS* 3.6 7.2 + - - +
281X LEU* 1.3 77.2 - - - +
283X ASP* 1.3 59.9 + - - +
284X GLU* 3.4 10.3 + - - +
285X GLU* 2.9 40.0 + - - +
286X MET* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 283 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255X GLN* 5.8 0.3 + - - -
280X LYS* 4.7 11.4 + - - -
281X LEU 4.7 0.2 - - - +
282X SER* 1.3 72.8 - - - +
284X GLU* 1.3 61.3 + - - +
286X MET* 3.8 8.1 - - - +
287X ALA* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 284 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282X SER* 3.2 8.7 + - - +
283X ASP* 1.3 78.8 - - - +
285X GLU* 1.3 60.0 + - + +
287X ALA* 3.3 6.6 + - - +
288X THR* 2.8 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 285 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237X ILE* 4.0 29.9 - - + +
240X LYS* 3.5 21.5 - - - +
241X HIS* 2.9 34.3 + - - -
281X LEU* 3.4 9.3 - - + +
282X SER* 2.9 38.4 + - - +
284X GLU* 1.3 79.3 - - + +
286X MET* 1.3 60.5 + - - +
288X THR* 3.2 6.7 + - - -
289X ILE* 2.8 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 286 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252X PHE* 3.5 41.4 - - + +
255X GLN* 3.7 36.3 - - + +
256X ARG* 3.9 15.7 - - + -
281X LEU* 3.7 28.5 - - + +
282X SER 2.9 20.3 + - - +
283X ASP* 3.8 8.3 - - - +
284X GLU 3.4 0.2 - - - -
285X GLU* 1.3 75.5 - - - +
287X ALA* 1.3 56.8 + - - +
289X ILE* 3.5 4.3 + - - +
290X LEU* 3.0 40.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 287 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283X ASP 2.9 18.8 + - - +
284X GLU* 3.6 5.8 - - - +
286X MET* 1.3 75.4 - - - +
288X THR* 1.3 65.9 + - - +
290X LEU* 3.5 10.4 + - - +
291X SER* 3.1 22.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 288 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237X ILE* 4.5 9.9 - - + -
284X GLU* 2.8 28.0 + - - +
285X GLU* 3.2 7.7 + - - -
287X ALA* 1.3 77.0 - - - +
289X ILE* 1.3 62.7 + - - +
291X SER* 2.2 29.3 + - - +
292X PHE* 3.3 32.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 289 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X PRO* 3.5 36.2 - - + +
234X ILE* 4.7 2.2 - - + -
237X ILE* 3.6 24.9 - - + -
248X VAL* 4.1 16.4 - - + -
252X PHE* 3.5 26.5 - - + -
281X LEU* 3.9 27.8 - - + -
285X GLU 2.8 25.8 + - - +
286X MET* 3.7 5.4 - - - +
288X THR* 1.3 72.9 - - - +
290X LEU* 1.3 56.8 + - - +
292X PHE* 2.9 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 290 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192X THR* 3.9 15.8 - - + +
194X GLU* 3.4 33.1 - - + +
252X PHE* 4.1 11.0 - - + -
256X ARG* 3.6 35.2 - - + +
286X MET* 3.0 30.6 + - + +
287X ALA* 3.8 8.7 - - - +
289X ILE* 1.3 76.4 - - - +
291X SER* 1.3 61.1 + - - +
292X PHE 3.2 1.0 + - - -
293X ASN* 3.2 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 291 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287X ALA 3.1 11.1 + - - -
288X THR* 2.2 34.9 + - - +
290X LEU* 1.3 71.5 - - - +
292X PHE* 1.3 66.3 + - - +
293X ASN* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 292 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189X PRO* 3.2 15.9 - - + +
190X TYR* 3.9 3.7 - + + -
231X ASP* 5.1 3.8 - - - -
233X MLZ 3.4 52.0 - - + -
234X ILE* 3.7 32.3 - - + -
288X THR* 3.3 35.0 - - + -
289X ILE* 2.9 28.8 + - + +
291X SER* 1.3 82.6 - - - +
293X ASN* 1.3 65.8 + - - +
294X ARG* 3.3 33.6 + - - +
----------------------------------------------------------
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