Contacts of the strand formed by residues 244 - 249 (chain T) in PDB entry 2WQT
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 ARG 244 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Q LYS* 3.8 12.3 - - - +
91T ASN* 3.4 31.3 + - - +
186T THR* 3.8 1.0 + - - +
187T ARG* 3.5 1.6 - - - -
188T ASN* 2.8 46.4 + - - +
189T ASN* 4.6 13.0 + - - +
242T GLY 4.7 1.3 - - - +
243T ASP* 1.3 74.6 - - - +
245T PHE* 1.3 63.9 + - - +
246T GLU* 2.8 39.1 + - - +
256T ALA* 4.0 8.4 - - - +
257T ALA 3.5 4.5 - - - +
258T THR* 3.7 24.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104T ILE* 3.2 40.8 - - + -
137T LEU* 4.7 13.5 - - + -
185T MET* 4.4 12.1 - - + -
186T THR 3.3 15.3 - - - -
187T ARG* 3.4 33.9 - - + -
192T VAL* 4.3 1.8 - - + -
237T VAL* 3.5 11.2 - - + -
238T ALA 3.8 12.6 - - - -
239T VAL* 4.0 10.5 - - + -
243T ASP* 3.5 23.8 - - + -
244T ARG* 1.3 78.6 - - - +
246T GLU* 1.3 62.0 + - - +
256T ALA* 3.2 5.0 - - - +
257T ALA* 2.8 35.1 + - + +
259T PHE* 3.9 20.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Q LYS* 3.4 18.0 + - - -
180Q ASN* 5.3 1.6 - - - +
137T LEU* 5.3 0.4 - - - -
184T LYS 4.0 0.9 - - - +
185T MET* 3.3 3.4 - - - -
186T THR* 2.8 47.7 + - - +
244T ARG* 2.8 33.9 + - - +
245T PHE* 1.3 76.6 - - - +
247T ALA* 1.3 62.7 + - - +
248T HIS* 3.6 32.0 + - + +
254T SER* 4.0 12.6 + - - -
255T VAL 3.3 10.1 - - - +
256T ALA* 4.4 3.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T ALA* 3.8 29.2 - - + -
137T LEU* 3.8 16.3 - - + +
183T MET* 4.8 2.5 - - + -
184T LYS 3.3 8.7 - - - +
185T MET* 4.0 7.0 - - + -
246T GLU* 1.3 74.8 - - - +
248T HIS* 1.3 63.6 + - - +
249T ILE* 4.2 1.8 - - + -
254T SER* 3.2 8.5 - - - -
255T VAL* 2.9 38.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182T ALA 3.5 1.4 - - - +
183T MET* 3.2 6.9 - - - +
184T LYS* 2.8 46.7 + - + +
186T THR* 5.9 5.8 - - + -
246T GLU* 3.6 35.4 - - + +
247T ALA* 1.3 79.4 - - - +
249T ILE* 1.3 63.3 + - - +
250T GLU 4.0 0.4 - - - +
253T GLY 3.7 5.1 + - - +
254T SER* 3.9 12.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106T ALA* 4.7 5.6 - - + -
107T GLU 3.6 27.4 - - - +
108T ILE* 4.5 3.1 - - + -
135T PRO* 3.8 22.9 - - + -
136T ALA 4.5 2.9 - - - +
181T CYS* 3.9 17.5 - - + +
182T ALA 3.5 4.5 - - - +
183T MET* 4.0 8.3 - - + -
233T LEU* 3.8 25.1 - - + -
247T ALA* 5.2 1.1 - - + +
248T HIS* 1.3 78.1 - - - +
250T GLU* 1.3 66.3 + - - +
251T GLY 3.3 0.7 + - - -
252T ILE* 3.0 31.5 + - + -
253T GLY 2.9 35.6 + - - +
255T VAL* 4.9 4.3 - - + -
----------------------------------------------------------
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