Contacts of the strand formed by residues 165 - 169 (chain F) in PDB entry 2PGW
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 VAL 165 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139F TYR 4.5 2.9 + - - +
140F PHE* 3.3 17.3 - - + -
141F TYR* 2.8 28.4 + - - +
163F GLU* 4.8 0.4 + - - +
164F ARG* 1.3 90.6 - - + +
166F PHE* 1.3 61.8 + - - +
192F ARG* 3.5 36.8 - - + +
194F ARG* 3.4 45.5 - - + +
219F GLU* 4.3 3.4 - - - +
322F ASP 4.3 14.8 - - - +
323F GLY* 4.3 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 166 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141F TYR* 3.7 30.7 - + + -
143F LEU* 4.3 15.3 - - + -
155F ALA* 3.6 19.5 - - - -
158F GLY 3.9 0.2 - - - -
159F HIS* 3.5 28.0 - + - -
163F GLU* 3.8 24.0 - - + -
164F ARG 4.7 0.2 - - - -
165F VAL* 1.3 77.1 - - - +
167F TYR* 1.3 59.2 + - - +
168F LEU 4.1 0.4 - - - -
188F ILE* 3.5 31.2 - - + -
191F ALA* 3.7 21.1 - - + -
192F ARG 3.0 19.5 + - - +
193F LEU* 3.6 15.9 - - + +
194F ARG* 2.8 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140F PHE* 3.4 40.2 - + + -
141F TYR 3.0 13.7 + - - +
142F PHE* 3.9 22.8 - + - -
143F LEU* 3.1 29.5 + - - +
165F VAL 3.8 0.2 + - - -
166F PHE* 1.3 73.5 - - - +
168F LEU* 1.3 63.4 + - - +
169F LYS* 4.5 2.8 + - + -
194F ARG* 3.6 27.8 - - + -
196F ASP* 3.2 39.7 + - + +
220F PHE* 5.1 1.6 - + - -
222F GLU* 2.9 45.0 + - + -
247F ASP* 4.6 0.2 + - - -
325F GLN* 3.4 14.6 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 168 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143F LEU* 4.0 15.9 - - + -
151F LEU* 3.9 38.4 - - + -
167F TYR* 1.3 75.6 - - - +
169F LYS* 1.3 72.9 + - - +
170F VAL* 3.7 0.6 + - + -
172F ARG* 4.2 1.6 - - - +
180F ILE* 4.0 6.5 - - + +
181F THR* 3.8 31.9 - - + +
184F VAL* 4.0 16.6 - - + -
193F LEU* 4.4 5.4 - - + -
194F ARG 3.0 7.6 + - - +
195F LEU* 3.2 30.2 - - + +
196F ASP* 2.8 25.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 169 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F TYR* 5.3 7.0 + - - +
23F HIS 4.0 18.8 + - - -
24F TRP* 5.3 3.4 - - - +
142F PHE* 6.3 2.7 - - + -
143F LEU 5.9 0.6 + - - -
146F GLU* 6.0 0.2 + - - -
167F TYR* 4.5 3.0 + - + -
168F LEU* 1.3 77.2 - - - +
170F VAL* 1.3 71.5 + - - +
172F ARG* 3.0 46.1 + - - +
180F ILE* 3.6 8.0 - - - +
196F ASP* 3.4 24.7 - - + +
198F ASN* 4.2 28.7 - - + +
----------------------------------------------------------
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