Contacts of the strand formed by residues 189 - 195 (chain F) in PDB entry 2HU4
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 TRP 189 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123F SER* 3.3 46.2 - - - -
124F CYS* 3.8 7.2 - - - -
125F SER* 4.0 20.9 + - - -
128F GLU* 4.7 5.9 + - + -
130F ARG* 4.0 28.3 - - + +
132F PHE* 3.6 25.8 - + - -
172F ARG* 4.1 19.8 - - - +
174F GLU* 5.8 2.0 - - - +
183F CYS* 3.3 36.8 - - - -
184F HIS* 3.3 22.1 + + + -
188F SER* 1.3 76.0 - - - +
190F LEU* 1.3 61.4 + - - +
191F THR* 4.1 8.7 - - + +
206F LYS 3.4 1.0 - - - +
207F TYR* 3.4 6.0 - - - -
208F ASN* 2.8 35.2 + - - +
209F GLY 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182F ALA* 3.1 6.8 - - - +
183F CYS* 2.8 48.8 + - - +
185F ASP* 6.2 0.9 - - + +
188F SER 3.9 0.4 + - - +
189F TRP* 1.3 73.3 - - - +
191F THR* 1.3 78.1 + - - +
192F ILE* 4.2 11.4 - - + -
205F LEU* 4.5 6.5 - - + -
206F LYS 3.2 14.8 - - - +
207F TYR* 4.5 11.4 - - + -
230F CYS* 4.3 1.8 - - - -
237F CYS* 3.8 32.3 - - + -
257F MET* 4.1 25.4 - - + -
260F GLY* 4.0 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 191 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132F PHE* 4.3 5.8 - - + -
158F LEU* 4.1 15.9 - - + -
174F GLU* 3.8 31.6 + - - +
175F SER* 4.8 3.1 - - - -
181F SER 3.5 3.4 - - - -
182F ALA* 3.9 12.8 - - + -
189F TRP* 4.9 8.5 - - + -
190F LEU* 1.3 82.2 - - - +
192F ILE* 1.3 65.0 + - - +
193F GLY 4.0 0.7 - - - -
204F VAL 3.5 1.4 - - - +
205F LEU* 3.5 5.2 - - - -
206F LYS* 3.1 50.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 192 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F LEU* 4.8 1.3 - - - -
179F SER 3.8 0.2 - - - +
180F ALA* 2.9 31.7 - - - +
181F SER* 2.6 26.3 + - - +
190F LEU* 4.2 12.1 - - + -
191F THR* 1.3 79.7 - - - +
193F GLY* 1.3 58.0 + - - +
194F ILE* 4.9 2.7 - - + -
203F ALA* 4.1 7.9 - - + -
204F VAL 3.5 2.2 - - - -
205F LEU* 3.4 28.0 - - + -
225F THR* 5.1 2.2 - - + -
230F CYS* 4.8 2.2 - - - -
239F THR* 4.0 18.4 - - + +
241F MET* 3.5 25.8 - - + -
257F MET* 3.4 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F LEU* 5.0 0.2 - - - -
175F SER* 4.1 15.7 + - - -
176F VAL 4.1 3.9 - - - +
177F ALA* 3.3 20.4 - - - -
179F SER 3.6 1.3 - - - -
180F ALA* 4.2 2.5 - - - -
191F THR 4.0 0.8 - - - -
192F ILE* 1.3 73.9 - - - +
194F ILE* 1.3 60.8 + - - -
195F SER 4.1 0.3 + - - -
202F VAL 3.9 0.7 - - - +
204F VAL* 2.8 43.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177F ALA* 3.1 2.1 - - - +
178F TRP* 2.8 44.4 + - + -
179F SER* 2.9 20.1 + - - +
192F ILE* 4.9 1.1 - - + -
193F GLY* 1.3 72.6 - - - -
195F SER* 1.3 63.2 + - - +
201F ALA* 3.8 13.7 - - + -
202F VAL 3.6 9.9 - - - +
203F ALA* 3.4 22.4 - - + -
223F LEU* 3.5 43.1 - - + +
224F ARG* 3.7 21.5 - - - -
225F THR* 4.1 8.3 - - + +
241F MET* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 195 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F SER 5.1 1.2 + - - -
176F VAL* 3.7 24.2 - - - +
177F ALA* 4.2 3.3 - - - -
178F TRP* 3.7 13.2 + - - +
193F GLY 4.1 0.6 + - - -
194F ILE* 1.3 75.5 - - - +
196F GLY* 1.3 66.4 + - - +
201F ALA* 3.6 2.1 - - - -
202F VAL* 3.1 36.1 + - - +
204F VAL* 6.5 0.4 - - - -
99G VAL* 4.6 7.6 - - - -
456G TRP* 3.7 5.4 - - - -
458G TRP* 3.1 32.8 + - - -
----------------------------------------------------------
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