Contacts of the helix formed by residues 205 - 210 (chain T) in PDB entry 6QX2
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 SER 205 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203T ASP 3.6 2.5 + - - -
204T ILE* 1.3 76.8 - - - +
206T ILE* 1.3 63.4 + - - +
207T ALA* 3.5 11.2 + - - +
208T GLU* 3.0 30.6 + - - +
209T LEU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 206 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204T ILE 4.3 0.2 + - - -
205T SER* 1.3 71.9 - - - +
207T ALA* 1.3 56.7 + - - +
209T LEU* 3.1 10.1 + - + +
210T MET* 2.9 37.2 + - + +
234T TYR* 3.5 43.3 - - + +
235T GLU* 3.8 33.9 - - - +
347T ASN* 3.9 9.2 - - - +
348T LEU* 4.4 5.4 - - + -
349T LYS* 3.6 37.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205T SER* 3.5 11.1 + - - +
206T ILE* 1.3 80.2 - - - +
208T GLU* 1.3 59.4 + - - +
210T MET* 3.3 21.8 + - - +
211T GLU* 3.6 12.3 + - - +
231T ARG* 6.3 3.1 - - - +
235T GLU* 4.8 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 208 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201T ASN* 4.3 14.0 + - - -
204T ILE* 3.6 25.0 - - + +
205T SER* 3.0 24.9 + - - +
207T ALA* 1.3 73.0 - - - +
209T LEU* 1.3 65.9 + - - +
210T MET 3.1 0.2 - - - -
211T GLU* 3.1 41.9 + - - +
212T ASP* 4.0 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194T GLY* 3.5 30.1 - - - +
197T SER* 4.8 1.1 - - - -
198T LEU* 4.5 5.2 - - + -
204T ILE* 4.0 31.1 - - + +
205T SER 3.0 16.4 + - - +
206T ILE* 3.3 13.7 - - - +
208T GLU* 1.3 74.9 - - - +
210T MET* 1.3 58.0 + - - +
212T ASP* 3.0 14.1 + - - +
213T ILE* 2.9 27.0 + - + +
348T LEU* 4.5 12.6 - - + -
349T LYS* 3.9 32.5 - - + +
352T LEU* 3.9 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 210 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206T ILE* 2.9 29.2 + - + +
207T ALA* 3.6 13.5 - - - +
208T GLU 3.1 0.8 - - - -
209T LEU* 1.3 73.5 - - - +
211T GLU* 1.3 62.1 + - - +
212T ASP 3.2 1.1 - - - -
213T ILE 3.4 21.0 - - - +
214T GLU* 3.7 22.0 + - - +
227T LYS* 3.9 35.6 - - + +
230T ILE* 4.1 12.8 - - + -
231T ARG* 4.2 29.6 - - + +
234T TYR* 3.8 24.5 - - + -
348T LEU* 4.6 2.7 - - + -
----------------------------------------------------------
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