Contacts of the strand formed by residues 227 - 231 (chain D) in PDB entry 3QEL
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 227 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D MET* 4.4 7.6 - - + -
166D TRP* 3.7 48.5 - - + +
168D ILE 3.7 7.1 + - - +
169D PHE* 3.1 20.1 - - + +
170D SER 3.0 24.3 + - - -
225D SER* 3.9 1.4 - - - -
226D PRO* 1.3 101.7 - - + +
228D ILE* 1.3 68.0 + - - +
229D LEU* 4.1 21.1 - - + -
255D THR* 3.4 14.1 - - - +
257D ILE* 4.2 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D SER* 3.6 13.7 - - - +
172D VAL* 4.0 21.3 - - + -
223D LEU* 4.1 21.3 - - + -
225D SER 4.2 15.5 - - - +
226D PRO 5.0 0.2 - - - -
227D ILE* 1.3 79.0 - - - +
229D LEU* 1.3 67.7 + - - +
230D LEU 3.7 1.2 + - - -
249D LEU* 4.9 3.6 - - + +
254D TYR* 4.4 14.6 - - + -
255D THR 2.8 8.9 + - - +
256D TRP* 3.2 63.8 - - + +
257D ILE 2.9 22.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157D MET* 3.3 33.0 - - + -
158D LEU* 5.2 0.2 - - + -
161D MET* 3.3 33.7 - - + -
169D PHE* 3.7 27.6 - - + -
170D SER 3.0 13.3 + - - +
171D ILE* 3.3 9.0 - - + +
172D VAL 2.7 31.2 + - - +
182D PHE* 4.2 8.5 - - + -
186D ILE* 4.3 15.7 - - + -
227D ILE* 4.1 3.8 - - + -
228D ILE* 1.3 72.8 - - - +
230D LEU* 1.3 54.9 + - - +
257D ILE* 3.4 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D VAL* 3.2 41.1 - - + +
173D THR* 5.3 0.4 - - - -
182D PHE* 5.1 2.9 - - - -
228D ILE 3.7 0.8 + - - -
229D LEU* 1.3 73.0 - - - +
231D TYR* 1.3 59.9 + - - +
232D CYS* 3.7 30.1 - - + -
237D ALA* 4.0 9.2 - - + -
240D ILE* 4.2 18.4 - - + -
241D PHE* 3.8 23.6 - - + -
256D TRP* 4.0 17.7 - - + -
257D ILE 2.9 11.9 + - - +
258D VAL* 3.6 26.2 - - + +
259D PRO* 2.9 26.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133D ILE 5.2 1.9 + - - -
150D ILE* 3.4 28.4 - - + +
153D GLN* 6.2 0.9 - - - -
172D VAL 2.8 9.3 + - - -
173D THR* 3.0 37.7 - - + -
174D THR 3.1 5.6 + - - -
176D PHE* 3.4 30.9 - + + -
177D PRO 2.7 20.7 + - - -
178D GLY 4.0 4.7 - - - -
179D TYR* 3.3 37.5 - - + -
182D PHE* 3.8 27.8 - + + -
229D LEU 4.1 1.0 + - - -
230D LEU* 1.3 72.6 - - - +
232D CYS* 1.3 62.2 + - - +
259D PRO* 3.6 24.5 - - + -
261D LEU* 4.4 10.8 - - + +
----------------------------------------------------------
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