Contacts of the strand formed by residues 203 - 207 (chain F) in PDB entry 2Q9Q
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 GLN 203 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E LYS* 3.3 9.9 - - - +
145E LEU* 2.9 54.7 + - + +
146E ASP* 3.2 14.8 + - - +
148E LEU 2.9 28.4 + - - +
150E LEU 5.8 0.2 + - - -
153E ILE* 3.7 16.1 - - + +
173F LEU 3.2 10.8 - - - +
174F ARG* 3.1 40.4 + - + +
202F SER* 1.3 80.4 - - - +
204F HIS* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 204 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142E HIS* 2.7 35.5 + + + +
143E ALA 3.4 2.9 + - - +
144E LYS* 3.4 29.3 - - + +
145E LEU* 4.8 2.2 - - - +
171F VAL 3.6 1.0 - - - +
172F PHE* 3.1 9.7 - - - +
173F LEU* 2.8 53.5 + - + +
175F VAL* 4.1 7.6 - - + -
196F ILE* 5.1 1.3 - - + -
197F ASP 4.3 10.8 + - - -
198F LEU* 3.4 30.1 - - + +
199F GLU* 5.5 0.6 + - - -
202F SER* 3.1 26.3 + - - -
203F GLN* 1.3 78.5 - - - +
205F LEU* 1.3 61.2 + - - +
206F ILE* 4.1 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E PHE* 4.3 16.4 - - + -
142E HIS* 3.3 6.4 + - - -
143E ALA* 2.9 38.1 + - + +
145E LEU* 4.1 9.8 - - + +
160E LEU* 5.2 10.3 - - + -
161E THR* 4.1 16.8 - - + -
164E LEU* 3.7 28.9 - - + -
170F TYR* 4.3 7.6 - - + -
171F VAL 3.4 14.6 - - - +
172F PHE* 3.9 36.1 - - + -
204F HIS* 1.3 72.8 - - - +
206F ILE* 1.3 65.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ALA 3.8 13.5 - - - +
142E HIS* 4.1 16.4 - - + +
170F TYR* 3.4 13.5 - - - -
171F VAL* 2.8 31.7 + - + +
173F LEU* 4.2 15.5 - - + -
182F ILE* 4.3 15.5 - - + -
184F VAL* 4.2 22.4 - - + -
196F ILE* 5.7 1.1 - - + -
204F HIS* 5.0 3.1 - - + -
205F LEU* 1.3 81.5 - - - +
207F ARG* 1.3 81.1 + - + +
210F THR* 3.9 20.0 - - + -
211F ILE* 4.2 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 207 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E ALA 5.6 0.9 - - - +
168E TYR* 3.8 27.1 + - - -
168F ASP* 2.7 61.9 + - - +
169F SER 3.6 4.5 - - - -
170F TYR* 3.5 27.9 + - + +
185F GLU* 2.9 56.9 + - - +
206F ILE* 1.3 86.5 - - + +
208F TYR* 1.3 65.7 + - - +
209F LYS* 3.9 22.9 - - - +
210F THR* 3.2 34.4 - - + +
211F ILE* 3.7 1.6 - - - +
----------------------------------------------------------
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