Contacts of the helix formed by residues 201 - 214 (chain A) in PDB entry 2OI8
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 201 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A PHE* 1.3 77.4 - - - +
202A SER* 1.3 53.3 + - - +
203A ALA* 3.3 19.6 + - - +
204A LEU* 2.7 68.2 + - + +
205A LEU 3.3 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 4.0 1.2 + - - -
186A VAL* 4.4 2.1 - - - +
190A GLU* 2.4 33.5 + - - +
195A PHE* 3.7 34.1 - - - -
200A PHE* 3.5 20.3 + - - -
201A ASP* 1.3 72.8 + - - +
203A ALA* 1.3 57.2 + - - +
205A LEU* 3.2 5.3 + - - +
206A PHE* 2.8 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ARG* 3.4 29.1 + - - +
201A ASP* 3.1 17.3 + - - +
202A SER* 1.3 81.8 + - - +
204A LEU* 1.3 61.2 + - + +
206A PHE* 3.4 3.8 - - - +
207A GLU* 3.0 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A ASP* 2.7 46.0 + - + +
203A ALA* 1.3 77.2 - - + +
205A LEU* 1.3 53.1 + - - +
207A GLU* 3.1 14.1 + - + +
208A ALA* 2.7 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A VAL* 4.3 13.9 - - + -
195A PHE* 3.8 33.9 - - + -
200A PHE* 4.1 19.9 - - + -
201A ASP 3.3 3.2 + - - -
202A SER* 3.2 14.8 + - - +
204A LEU* 1.3 77.1 - - - +
206A PHE* 1.3 57.3 + - - +
208A ALA* 3.1 9.8 + - + +
209A GLU* 2.9 46.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ALA* 3.3 40.8 - - + -
94A HIS* 4.5 4.9 - + - -
96A LEU* 5.6 0.2 - - + -
97A ARG* 3.4 44.9 - - + +
183A LEU* 3.9 30.5 - - + +
186A VAL* 3.6 21.7 - - + +
187A LEU* 3.9 24.7 - - + -
202A SER 2.8 12.1 + - - +
203A ALA 3.4 9.6 - - - +
205A LEU* 1.3 71.2 - - - +
207A GLU* 1.3 74.2 + - - +
209A GLU* 3.3 6.7 + - - +
210A LEU* 3.0 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A HIS* 2.7 40.0 + - - -
97A ARG* 5.7 0.3 - - - -
203A ALA 3.0 17.7 + - - +
204A LEU* 3.3 19.1 - - + +
206A PHE* 1.3 80.9 - - - +
208A ALA* 1.3 58.7 + - - +
210A LEU* 3.4 13.0 + - - +
211A LYS* 2.9 47.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU 2.7 15.2 + - - +
205A LEU* 3.1 16.1 + - + +
207A GLU* 1.3 71.5 - - - +
209A GLU* 1.3 60.7 + - + +
211A LYS* 3.2 12.8 + - - +
212A ASP* 2.9 32.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 4.0 32.6 - - + +
183A LEU* 4.6 9.4 - - + -
186A VAL* 4.3 20.6 - - + -
205A LEU* 2.9 34.7 + - + +
206A PHE 3.8 4.3 - - - +
208A ALA* 1.3 78.5 - - - +
210A LEU* 1.3 61.1 + - - +
212A ASP* 3.6 15.4 - - - +
213A LEU* 3.2 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.1 4.7 - - + +
90A ALA* 3.8 25.4 - - + +
93A ALA* 3.6 31.4 - - + -
94A HIS* 4.0 22.9 - - + +
179A PHE* 4.7 6.7 - - + -
183A LEU* 4.3 8.8 - - + +
206A PHE* 3.0 19.3 + - + +
207A GLU* 3.6 18.6 - - - +
209A GLU* 1.3 72.3 - - - +
211A LYS* 1.3 66.3 + - - +
213A LEU* 2.9 23.5 + - + +
214A LEU* 2.9 27.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A GLU* 2.9 52.0 + - - +
208A ALA* 3.2 8.8 + - - +
210A LEU* 1.3 76.3 - - - +
212A ASP* 1.3 54.7 + - - +
213A LEU 2.9 10.2 + - - -
214A LEU* 3.0 28.3 + - + +
216A PRO* 5.5 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A ARG* 4.5 12.3 + - - +
208A ALA 2.9 20.2 + - - +
209A GLU* 3.6 18.3 - - - +
211A LYS* 1.3 70.9 - - - +
213A LEU* 1.3 56.9 + - - +
216A PRO* 3.0 28.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.4 4.8 - - + +
175A ARG* 4.0 19.3 + - + +
178A SER* 4.0 13.9 - - - +
179A PHE* 3.6 58.3 - - + +
182A ARG* 3.9 26.5 - - + +
183A LEU* 4.5 11.0 - - + -
209A GLU 3.2 17.0 - - - +
210A LEU* 2.9 14.3 + - + +
212A ASP* 1.3 77.9 - - - +
214A LEU* 1.3 66.7 + - - +
215A GLY 3.1 4.2 + - - -
216A PRO* 3.6 11.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASP* 4.3 12.6 - - + +
89A LEU* 4.5 20.4 - - + -
90A ALA* 3.9 33.4 - - + +
175A ARG* 4.7 2.2 - - - +
210A LEU* 2.9 21.9 + - + +
211A LYS* 3.0 21.0 + - + +
213A LEU* 1.3 73.5 - - - +
215A GLY* 1.3 67.7 + - - +
216A PRO* 3.4 2.6 - - - +
----------------------------------------------------------
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