Contacts of the strand formed by residues 182 - 186 (chain A) in PDB entry 2P2Q
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 LEU 182 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 3.5 31.9 - - + -
127A LEU* 4.8 8.1 - - + -
129A ILE* 4.1 20.2 - - + -
134A VAL 4.2 1.4 + - - -
135A VAL* 3.9 11.4 - - + -
136A ALA* 2.9 30.6 + - - +
180A SER* 3.3 3.3 + - - -
181A ARG* 1.3 80.7 - - - +
183A VAL* 1.3 69.2 + - - +
184A ILE* 3.9 11.9 - - + -
214A VAL* 4.6 0.8 - - - +
216A HIS* 3.3 39.7 - - + +
218A ILE* 3.7 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.3 14.8 - - + +
138A TYR* 4.6 8.7 - - + -
162A ILE* 6.4 0.4 - - + -
171A VAL* 5.8 1.1 - - + -
175A ILE* 3.7 30.3 - - + -
182A LEU* 1.3 78.7 - - - +
184A ILE* 1.3 72.8 + - - +
202A VAL* 4.0 29.8 - - + -
206A LEU* 4.7 4.3 - - + -
214A VAL* 3.9 19.1 - - + -
216A HIS 3.2 5.7 + - - -
217A VAL* 3.2 18.1 - - + +
218A ILE 2.9 24.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PHE* 3.7 27.1 - - + -
124A LEU* 4.4 1.3 - - + -
135A VAL* 3.6 24.7 - - + -
136A ALA 2.8 12.6 + - - +
137A ILE* 3.5 7.6 - - + -
138A TYR 2.8 32.4 + - - +
139A MET* 3.7 14.4 - - + +
148A ALA* 4.2 14.8 - - + -
152A CYS* 5.2 1.6 - - - -
182A LEU* 3.9 17.3 - - + -
183A VAL* 1.3 74.9 - - - +
185A THR* 1.3 60.3 + - - +
218A ILE* 3.4 14.1 - - + +
237A TRP* 3.7 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR* 2.7 27.5 + - - -
139A MET* 3.5 15.4 - - - +
183A VAL* 4.6 0.7 - - - -
184A ILE* 1.3 77.2 - - - +
186A ALA* 1.3 74.8 + - - +
198A LEU* 3.6 10.2 - - - +
199A LYS* 4.3 14.4 - - + -
202A VAL* 4.0 20.3 - - + +
217A VAL* 3.8 25.6 - - + -
218A ILE 3.0 10.7 + - - +
219A VAL* 4.3 2.7 - - + -
220A LEU* 2.8 21.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A TYR 4.1 2.0 + - - -
139A MET* 4.1 1.5 - - - -
140A PRO* 3.9 22.0 - - + -
185A THR* 1.3 79.2 + - - +
187A ASP* 1.3 67.6 + - - +
188A GLU 3.4 16.2 - - - +
198A LEU* 3.4 6.5 - - + +
199A LYS* 3.1 19.6 + - - +
219A VAL* 3.8 5.8 - - - -
220A LEU* 3.2 22.7 - - + +
222A ARG* 4.3 7.6 - - + -
----------------------------------------------------------
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