Contacts of the strand formed by residues 231 - 234 (chain B) in PDB entry 1QAP
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 ILE 231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B PRO* 4.4 15.0 - - + -
211B VAL 3.7 10.5 - - - +
212B GLU* 2.9 56.7 - - + +
213B VAL 3.3 2.4 + - - -
229B ALA* 4.4 1.2 - - - +
230B ASP* 1.3 90.5 - - + +
232B ILE* 1.3 65.3 + - - +
254B ARG* 2.9 32.3 - - + +
256B GLU* 4.0 24.9 - - + +
276B PHE* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B GLU* 4.4 1.3 - - - -
213B VAL* 3.4 25.1 - - + +
215B VAL* 4.4 8.3 - - + -
221B LEU* 3.4 37.0 - - + +
224B ALA* 4.3 15.0 - - + -
225B LEU* 4.0 28.5 - - + -
229B ALA* 4.5 9.0 - - + -
230B ASP 5.6 1.1 - - - -
231B ILE* 1.3 77.4 - - - +
233B MET* 1.3 61.7 + - - +
234B LEU* 3.6 3.6 + - + +
249B VAL* 5.0 0.7 - - + -
252B GLN 5.7 1.3 - - - +
254B ARG 2.9 6.5 + - - +
255B LEU* 3.5 28.7 - - + +
256B GLU 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LEU* 3.4 32.8 - - + -
185B LYS* 4.1 6.7 - - - -
212B GLU* 3.2 16.3 + - - +
213B VAL 2.9 7.9 + - - +
214B GLU* 3.3 42.6 - - + +
215B VAL* 2.9 29.8 + - - +
232B ILE* 1.3 70.1 - - - +
234B LEU* 1.3 64.3 + - - +
235B ASP* 3.4 3.0 + - - +
256B GLU* 3.2 33.0 - - - +
258B SER* 4.3 24.5 - - - +
301B NTM 4.6 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B VAL* 3.9 7.4 - - + -
221B LEU* 4.1 18.2 - - + -
232B ILE* 3.9 6.7 - - + +
233B MET* 1.3 72.9 - - - +
235B ASP* 1.3 63.0 + - - +
236B ASN 3.6 2.9 + - - -
237B PHE* 3.8 42.4 + - + -
242B MET* 4.4 15.9 - - + +
245B ALA* 4.1 8.1 - - + -
255B LEU* 3.7 44.0 - - + -
256B GLU 3.1 13.8 + - - +
257B VAL* 3.9 21.7 - - + +
258B SER 5.0 3.1 + - - +
274B VAL* 5.0 7.4 - - + -
----------------------------------------------------------
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