Contacts of the helix formed by residues 176 - 190 (chain A) in PDB entry 2CWE
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 176 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 2.5 32.3 + - + +
172A GLU 3.9 4.4 + - - +
173A LEU* 3.0 15.0 + - + +
174A ALA 3.4 0.2 - - - -
175A ARG* 1.3 77.5 - - - +
177A GLU* 1.3 62.2 + - - +
178A GLU* 2.5 36.6 + - - +
179A TYR* 2.6 25.6 + - + +
180A LEU* 3.1 17.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ARG 3.8 4.7 + - - +
176A ASP* 1.3 68.7 + - - +
178A GLU* 1.3 65.1 + - - +
180A LEU* 3.4 14.8 + - + +
181A GLU* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A ARG* 5.0 12.0 + - - +
134A LYS* 2.3 36.3 + - - +
176A ASP* 2.5 15.8 + - - +
177A GLU* 1.3 74.6 - - - +
179A TYR* 1.3 55.5 + - - +
181A GLU* 2.9 13.5 + - + +
182A LEU* 2.8 48.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET* 3.7 48.4 - - + +
134A LYS* 4.3 14.3 - - + +
135A GLU* 3.5 16.4 + - + -
173A LEU* 3.6 52.7 - - + +
174A ALA* 5.2 0.2 - - - -
176A ASP* 2.6 35.2 + - + +
178A GLU* 1.3 72.9 - - - +
180A LEU* 1.3 59.3 + - + +
182A LEU* 3.1 8.0 + - + +
183A LEU* 2.7 55.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A LEU 4.0 8.7 - - - +
174A ALA* 3.9 29.6 - - + +
176A ASP 3.1 16.5 + - - +
177A GLU* 3.7 14.4 - - + +
178A GLU 3.3 0.2 - - - -
179A TYR* 1.3 82.6 - - + +
181A GLU* 1.3 57.0 + - - +
183A LEU* 3.4 14.4 + - + +
184A LYS* 3.0 49.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU 3.1 12.2 + - - +
178A GLU* 2.9 15.5 + - + +
180A LEU* 1.3 74.3 - - - +
182A LEU* 1.3 70.3 - - + +
184A LYS* 3.2 11.6 + - - +
185A ARG* 3.0 32.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 3.8 18.1 - - + +
130A ARG* 3.5 56.5 - - + +
131A MET* 3.5 20.0 - - + +
134A LYS* 4.8 3.6 - - + -
178A GLU* 2.8 37.0 + - + +
179A TYR* 3.5 13.0 - - + +
181A GLU* 1.3 80.6 - - + +
183A LEU* 1.3 63.4 + - - +
185A ARG* 3.4 7.9 + - + +
186A LEU* 3.0 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET* 3.7 24.6 - - + +
179A TYR* 2.7 37.5 + - + +
180A LEU* 3.4 15.3 - - + +
181A GLU 3.2 0.2 - - - -
182A LEU* 1.3 76.7 - - - +
184A LYS* 1.3 64.2 + - + +
186A LEU* 3.2 12.5 + - + +
187A GLY* 3.0 17.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A LEU* 3.0 38.7 + - - +
181A GLU* 3.2 11.0 + - - +
183A LEU* 1.3 75.1 - - + +
185A ARG* 1.3 58.2 + - - +
187A GLY* 2.7 23.2 + - - -
188A SER* 2.9 15.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A GLU* 2.7 33.2 + - - +
127A ILE* 3.4 20.0 - - + -
181A GLU* 3.0 24.7 + - + +
182A LEU* 3.7 10.1 - - + +
184A LYS* 1.3 75.7 - - + +
186A LEU* 1.3 54.2 + - - +
188A SER* 2.8 22.1 + - - +
189A ILE* 2.6 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A LEU* 4.3 13.7 - - + -
127A ILE* 4.1 16.5 - - + +
128A MET* 5.1 6.5 - - - -
131A MET* 3.6 28.9 - - + -
182A LEU 3.0 13.0 + - - +
183A LEU* 3.2 15.9 - - + +
185A ARG* 1.3 74.8 - - - +
187A GLY* 1.3 63.6 + - - +
189A ILE* 4.3 4.5 - - + -
190A LEU* 3.0 57.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LEU 3.0 9.6 + - - -
184A LYS* 2.7 17.0 + - - -
186A LEU* 1.3 74.2 - - - +
188A SER* 1.3 60.2 + - - +
190A LEU 4.1 10.0 + - - +
191A LYS* 5.2 1.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LYS* 2.9 11.0 + - - +
185A ARG* 2.8 32.4 + - - -
187A GLY* 1.3 78.0 - - - +
189A ILE* 1.3 63.3 + - - +
191A LYS* 4.2 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A PHE* 4.2 22.6 - - + +
120A GLU 5.6 0.9 - - - +
123A GLU* 3.5 16.6 - - + +
124A LEU* 3.8 36.3 - - + +
127A ILE* 3.9 15.5 - - + -
185A ARG* 2.6 57.0 + - - +
186A LEU* 3.8 5.6 - - - +
188A SER* 1.3 73.4 - - - +
190A LEU* 1.3 54.9 + - - +
191A LYS* 2.6 29.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A PHE* 3.7 45.8 - - + -
117A TYR* 3.5 28.9 - - + -
119A PHE* 4.1 10.5 - - + -
124A LEU* 4.6 6.7 - - + -
128A MET* 5.3 1.1 - - - -
186A LEU* 3.0 44.1 + - + +
187A GLY 4.4 8.1 - - - +
188A SER 3.8 0.2 - - - -
189A ILE* 1.3 70.4 - - - +
191A LYS* 1.3 69.1 + - - +
----------------------------------------------------------
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