Contacts of the helix formed by residues 184 - 198 (chain A) in PDB entry 2OZ6
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 184 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A CYS* 1.3 80.7 - - - +
185A ARG* 1.3 65.0 + - - +
186A GLU* 3.4 18.4 + - - +
187A MET* 3.1 28.8 + - - +
188A VAL* 3.2 19.1 + - - +
190A ARG* 4.9 1.2 + - - -
302A CMP 3.3 25.2 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
174A ARG* 3.7 49.9 + - + +
175A GLN* 3.9 21.2 - - - +
184A SER* 1.3 72.4 - - - +
186A GLU* 1.3 82.6 + - - +
188A VAL* 3.1 9.6 + - - +
189A GLY 2.9 24.8 + - - -
302A CMP 2.5 61.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 4.6 7.9 - - - +
184A SER* 3.5 19.3 - - - +
185A ARG* 1.3 112.3 + - - +
187A MET* 1.3 62.2 + - - +
189A GLY* 3.2 3.5 + - - -
190A ARG* 3.0 37.2 + - - +
302A CMP 4.3 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 3.7 34.8 - - + -
183A CYS* 3.9 20.9 - - + -
184A SER* 3.1 21.4 + - - +
186A GLU* 1.3 75.9 - - - +
188A VAL* 1.3 66.0 + - - +
190A ARG* 3.1 34.0 + - + +
191A VAL* 2.9 31.2 + - + +
302A CMP 6.0 1.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.9 3.6 - - + -
174A ARG* 3.7 27.8 - - + +
177A ILE* 3.8 23.8 - - + -
178A GLY* 3.7 22.9 - - - +
181A VAL* 4.6 0.2 - - + -
183A CYS* 3.5 18.2 - - - -
184A SER 3.2 13.6 + - - +
185A ARG 3.1 8.0 + - - +
187A MET* 1.3 77.3 - - - +
189A GLY* 1.3 57.2 + - - +
191A VAL* 3.1 9.0 + - - +
192A LEU* 2.8 49.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ARG* 4.0 20.4 - - - -
185A ARG 2.9 13.4 + - - -
186A GLU 3.2 4.9 + - - -
188A VAL* 1.3 77.0 - - - +
190A ARG* 1.3 61.6 + - - +
192A LEU* 3.4 6.4 + - - +
193A LYS* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A SER* 4.9 1.6 + - - -
186A GLU* 3.0 20.6 + - - +
187A MET* 3.4 55.7 - - - +
189A GLY* 1.3 74.1 - - - +
191A VAL* 1.3 65.7 + - + +
193A LYS* 3.2 11.8 + - + +
194A SER* 3.2 21.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A VAL* 3.9 26.0 - - + -
145A THR* 3.7 42.4 - - + +
148A VAL* 3.9 25.4 - - + -
187A MET* 2.9 24.5 + - + +
188A VAL 3.6 4.9 - - - +
190A ARG* 1.3 76.0 - - + +
192A LEU* 1.3 58.5 + - - +
194A SER* 3.2 8.1 + - - -
195A LEU* 2.9 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL* 4.4 8.5 - - + -
152A LEU* 4.2 18.8 - - + -
174A ARG* 4.1 16.8 - - + -
177A ILE* 4.5 4.7 - - + -
188A VAL* 2.8 36.6 + - + +
189A GLY* 3.7 5.4 - - - +
191A VAL* 1.3 75.6 - - - +
193A LYS* 1.3 55.1 + - - +
195A LEU* 3.0 12.2 + - + +
196A GLU* 2.7 39.9 + - - +
201A VAL* 4.8 4.2 - - + +
203A VAL* 4.5 19.5 - - + -
208A MET* 4.1 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A GLY 3.0 15.1 + - - +
190A ARG* 3.2 15.5 + - + +
192A LEU* 1.3 74.6 - - - +
194A SER* 1.3 57.6 + - - +
196A GLU* 3.8 6.4 - - - +
197A GLU* 2.9 57.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 5.7 4.8 - - - +
190A ARG 3.2 9.8 + - - -
191A VAL* 3.5 10.3 - - - -
192A LEU 3.1 0.6 - - - -
193A LYS* 1.3 80.2 - - - +
195A LEU* 1.3 63.5 + - - +
197A GLU* 3.2 13.8 + - - +
198A GLN* 3.0 45.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 4.5 18.6 - - + -
148A VAL* 4.3 5.2 - - + -
149A ALA* 4.9 16.2 - - + -
152A LEU* 4.1 26.9 - - + -
191A VAL* 2.9 33.1 + - + +
192A LEU* 3.0 12.5 + - + +
194A SER* 1.3 76.8 - - - +
196A GLU* 1.3 54.3 + - - +
198A GLN* 3.5 9.6 + - - +
199A GLY 3.2 2.9 + - - -
200A LEU* 2.8 56.3 + - + +
201A VAL* 3.9 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 2.7 17.2 + - - +
193A LYS* 3.8 6.0 - - - +
195A LEU* 1.3 75.2 - - - +
197A GLU* 1.3 57.4 + - - +
198A GLN 3.0 1.6 - - - -
199A GLY* 2.6 24.8 + - - -
201A VAL* 3.5 21.1 - - + +
202A HIS* 3.1 16.6 + - + +
203A VAL* 3.0 49.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LYS* 2.9 56.7 + - + +
194A SER* 3.6 14.0 + - - +
196A GLU* 1.3 75.9 - - - +
198A GLN* 1.3 62.6 + - + +
199A GLY 3.3 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A THR* 6.1 1.2 - - - +
194A SER* 3.0 34.9 + - - +
195A LEU* 3.6 11.0 + - - +
196A GLU 3.0 0.4 - - - -
197A GLU* 1.3 78.3 - - + +
199A GLY* 1.3 63.9 + - - +
200A LEU* 3.3 29.3 + - + +
----------------------------------------------------------
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