Contacts of the helix formed by residues 207 - 216 (chain F) in PDB entry 4Q44
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 ASP 207 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F CYS* 1.3 75.1 - - - +
208F LEU* 1.3 70.1 + - - +
209F VAL* 3.3 34.5 + - - +
210F MET* 3.4 19.1 + - + +
211F LEU* 3.2 22.7 + - - +
213F LYS* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 208 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F CYS 3.7 3.6 + - - -
207F ASP* 1.3 77.4 + - - +
209F VAL* 1.3 60.2 + - + +
211F LEU* 3.2 6.3 + - + +
212F LEU* 2.9 45.2 + - + +
219F GLY 4.6 1.3 - - - +
220F ARG* 4.0 46.9 - - + +
223F TRP* 3.7 57.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 209 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ASP* 3.2 23.1 - - - +
208F LEU* 1.3 80.6 - - + +
210F MET* 1.3 57.6 + - - +
212F LEU* 3.4 11.0 + - + +
213F LYS* 2.9 52.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195F MET* 5.0 9.9 - - - -
197F LEU* 5.1 2.7 - - + -
206F CYS* 5.0 14.8 - - + -
207F ASP* 3.4 22.7 + - + +
208F LEU 3.3 0.4 - - - -
209F VAL* 1.3 75.7 - - - +
211F LEU* 1.3 89.3 + - + +
213F LYS* 3.2 19.0 + - + +
214F ARG* 2.9 68.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192F LEU* 5.2 0.2 - - + -
197F LEU* 5.1 8.5 - - + -
203F VAL* 3.7 29.8 - - + -
206F CYS* 4.4 8.5 - - + -
207F ASP 3.2 11.3 + - - +
208F LEU* 3.4 10.3 - - - +
210F MET* 1.3 98.9 - - + +
212F LEU* 1.3 57.4 + - - +
214F ARG* 4.6 1.1 - - + -
215F PHE* 2.9 48.1 + - + +
219F GLY* 3.5 39.4 - - - +
222F LEU* 4.9 6.5 - - + -
223F TRP* 4.0 16.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208F LEU* 2.9 38.4 + - + +
209F VAL* 3.7 10.3 - - + +
210F MET 3.2 0.2 - - - -
211F LEU* 1.3 73.2 - - - +
213F LYS* 1.3 58.9 + - + +
214F ARG 3.1 4.7 - - - -
216F GLY* 2.9 46.8 + - - +
217F LYS* 4.8 1.6 - - - +
220F ARG* 3.6 46.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207F ASP* 5.5 1.2 + - - -
209F VAL* 2.9 40.9 + - + +
210F MET* 3.2 19.9 + - + +
212F LEU* 1.3 76.3 - - + +
214F ARG* 1.3 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191F LYS* 4.0 15.1 + - - +
195F MET* 3.4 38.5 - - + +
210F MET* 2.9 51.1 + - + +
211F LEU* 4.0 2.5 - - - +
213F LYS* 1.3 85.2 - - - +
215F PHE* 1.3 78.7 + - + +
216F GLY 3.8 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188F SER* 5.8 1.6 - - - -
191F LYS* 3.6 42.0 - - + -
192F LEU* 3.5 30.3 - - + -
195F MET* 3.8 26.5 - - + -
211F LEU* 2.9 32.4 + - + +
214F ARG* 1.3 88.4 - - + +
216F GLY* 1.3 63.9 + - - +
217F LYS 3.6 0.3 + - - -
218F PHE* 3.3 38.0 + + + +
219F GLY* 3.5 15.3 - - - +
222F LEU* 4.5 1.6 - - + -
847G T 4.8 4.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212F LEU* 2.9 39.1 + - - +
214F ARG 3.8 0.6 - - - -
215F PHE* 1.3 76.5 - - - +
217F LYS* 1.3 61.3 + - - -
219F GLY* 2.9 15.6 + - - -
847G T 4.4 5.4 - - - -
----------------------------------------------------------
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