Contacts of the strand formed by residues 244 - 249 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A ASN* 3.4 32.3 + - - +
186A THR* 3.7 1.2 + - - +
187A ARG* 3.5 2.8 - - - -
188A ASN* 2.9 46.0 + - - +
189A ASN* 4.7 10.7 + - - +
242A GLY 4.7 1.1 - - - +
243A ASP* 1.3 74.7 - - - +
245A PHE* 1.3 64.6 + - - +
246A GLU* 2.8 39.3 + - - +
256A ALA* 3.9 8.6 - - - +
257A ALA 3.5 3.8 - - - +
258A THR* 3.6 23.4 + - + +
179D LYS* 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ILE* 3.1 40.6 - - + -
137A LEU* 4.7 12.6 - - + -
185A MET* 4.3 13.0 - - + -
186A THR 3.4 12.8 - - - -
187A ARG* 3.5 31.0 - - + -
192A VAL* 4.4 2.0 - - + -
237A VAL* 3.5 12.3 - - + -
238A ALA 3.8 13.5 - - - -
239A VAL* 4.0 10.5 - - + -
243A ASP* 3.5 24.2 - - + -
244A ARG* 1.3 79.3 - - - +
246A GLU* 1.3 62.8 + - - +
256A ALA* 3.2 5.2 - - - +
257A ALA* 2.8 35.6 + - + +
259A PHE* 3.9 20.4 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 5.3 0.7 - - - -
184A LYS 4.0 0.9 - - - +
185A MET* 3.3 3.3 - - - -
186A THR* 2.8 47.5 + - - +
244A ARG* 2.8 33.8 + - - +
245A PHE* 1.3 77.0 - - - +
247A ALA* 1.3 62.7 + - - +
248A HIS* 3.6 32.4 + - + +
254A SER* 3.9 13.0 + - - -
255A VAL 3.2 9.9 - - - +
256A ALA* 4.3 2.6 - - + +
179D LYS* 3.3 19.7 + - - -
180D ASN* 5.1 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 3.8 28.3 - - + -
137A LEU* 3.9 16.7 - - + +
183A MET* 4.8 2.2 - - + -
184A LYS 3.3 8.7 - - - +
185A MET* 4.1 7.4 - - + -
246A GLU* 1.3 75.4 - - - +
248A HIS* 1.3 62.8 + - - +
249A ILE* 4.2 2.2 - - + -
254A SER* 3.2 8.7 - - - -
255A VAL* 2.9 37.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ALA 3.5 1.4 - - - +
183A MET* 3.2 6.8 - - - +
184A LYS* 2.8 44.5 + - + +
186A THR* 5.9 6.3 - - + -
246A GLU* 3.6 33.7 - - + +
247A ALA* 1.3 79.0 - - - +
249A ILE* 1.3 63.4 + - - +
250A GLU 4.0 0.4 - - - +
253A GLY 3.7 4.4 + - - +
254A SER* 3.9 13.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ALA* 4.7 5.4 - - + -
107A GLU 3.7 26.7 - - - +
108A ILE* 4.6 3.4 - - + -
135A PRO* 3.8 22.7 - - + -
136A ALA 4.5 2.0 - - - +
181A CYS* 3.9 18.2 - - + +
182A ALA 3.5 4.5 - - - +
183A MET* 4.0 8.3 - - + -
233A LEU* 3.7 25.1 - - + -
247A ALA* 5.3 1.1 - - + -
248A HIS* 1.3 78.4 - - - +
250A GLU* 1.3 65.8 + - - +
251A GLY 3.3 0.3 + - - -
252A ILE* 3.0 31.7 + - + -
253A GLY 2.8 36.4 + - - +
255A VAL* 5.0 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