Contacts of the helix formed by residues 149 - 160 (chain D) in PDB entry 2OTD
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 GLU 149 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE 5.1 0.2 - - - +
117D PRO* 3.9 24.2 - - + -
122D GLY* 5.6 0.2 - - - -
147D SER* 2.9 20.8 + - - +
148D PHE* 1.3 90.5 - - + +
150D ILE* 1.3 65.2 + - - +
151D ASP* 3.9 22.2 - - - +
152D ALA* 3.9 8.1 - - + -
153D LEU* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 150 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D PHE 3.8 6.0 + - - +
149D GLU* 1.3 69.8 - - - +
151D ASP* 1.3 60.8 + - - +
153D LEU* 3.2 8.8 + - - +
154D GLU* 2.8 47.2 + - + +
167D LEU* 4.4 18.2 - - + -
173D ARG* 4.2 25.1 - - - +
179D LEU* 4.3 19.7 - - + -
182D ARG* 3.9 24.5 - - - +
183D LEU* 4.7 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 151 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLY* 3.5 20.8 + - - -
123D PRO* 3.9 26.2 - - + +
149D GLU* 3.9 16.9 - - - +
150D ILE* 1.3 80.1 + - - +
152D ALA* 1.3 57.8 + - - +
154D GLU* 3.4 15.7 + - - +
155D ALA* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 152 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.1 21.5 - - + -
117D PRO* 4.3 4.7 - - + -
122D GLY 3.8 21.5 + - - +
126D GLY* 3.6 8.6 - - - -
147D SER* 3.7 14.8 - - - +
149D GLU* 3.5 17.6 + - + +
150D ILE 3.2 0.6 - - - -
151D ASP* 1.3 80.4 + - - +
153D LEU* 1.3 59.0 + - - +
155D ALA* 3.4 0.7 + - - -
156D ALA* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 153 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 5.6 2.0 - - + -
145D LEU* 4.3 7.4 - - + +
146D SER* 4.4 2.2 - - - -
147D SER* 3.6 24.2 - - - +
149D GLU 3.3 8.4 + - - +
150D ILE* 3.2 7.9 + - - +
152D ALA* 1.3 75.7 - - - +
154D GLU* 1.3 54.2 + - - +
156D ALA* 3.2 7.6 + - + +
157D GLN* 2.6 36.1 + - - +
165D ARG* 3.8 34.7 - - + -
166D GLY 3.7 20.4 - - - +
167D LEU* 3.3 35.7 - - + -
183D LEU* 4.2 20.1 - - + +
185D CYS* 5.2 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 154 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150D ILE* 2.8 26.2 + - - +
151D ASP* 3.6 19.3 + - - +
152D ALA 3.4 0.2 - - - -
153D LEU* 1.3 71.6 - - - +
155D ALA* 1.3 58.5 + - - +
157D GLN* 3.1 13.9 + - - +
158D GLN* 3.0 32.1 + - + +
182D ARG* 2.8 30.1 + - - +
183D LEU* 3.9 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D PRO* 3.3 33.2 - - + +
126D GLY 4.0 0.2 - - - -
127D LYS* 3.6 16.1 - - + +
151D ASP 2.9 17.4 + - - +
152D ALA 3.8 2.7 - - - +
153D LEU 3.3 0.2 - - - -
154D GLU* 1.3 73.9 - - - +
156D ALA* 1.3 60.5 + - - +
158D GLN* 3.5 6.4 + - - +
159D ALA* 3.0 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115D ILE* 4.3 12.1 - - + -
126D GLY 3.9 7.3 + - - +
130D ALA* 3.8 17.9 - - + -
145D LEU* 4.7 9.0 - - + -
152D ALA 2.9 14.6 + - - +
153D LEU* 3.2 14.3 + - + +
155D ALA* 1.3 73.4 - - - +
157D GLN* 1.3 67.3 + - - +
160D ALA* 2.9 30.5 + - - +
165D ARG* 4.1 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D LEU 2.6 17.0 + - - +
154D GLU* 3.1 15.9 + - - +
156D ALA* 1.3 76.5 - - - +
158D GLN* 1.3 83.4 + - - +
161D PRO* 3.1 28.3 - - + +
165D ARG* 3.6 31.4 - - - +
182D ARG 2.9 26.8 + - - +
183D LEU* 2.9 22.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 158 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D GLU* 3.0 20.3 + - + +
155D ALA* 3.5 6.9 + - - +
156D ALA 3.4 0.2 - - - -
157D GLN* 1.3 102.7 + - - +
159D ALA* 1.3 63.3 + - - +
161D PRO* 3.9 9.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135C GLN* 5.6 1.7 + - - -
127D LYS* 4.1 22.7 - - + +
130D ALA* 4.1 4.3 - - + -
131D LEU* 3.2 31.5 - - + +
134D ARG* 3.5 18.9 + - - -
155D ALA 3.0 17.2 + - - +
158D GLN* 1.3 79.7 - - - +
160D ALA* 1.3 59.7 + - - +
161D PRO* 3.8 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 160 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130D ALA* 3.9 22.0 - - + +
131D LEU* 4.7 0.4 - - + +
134D ARG* 3.4 15.9 - - + +
145D LEU* 5.3 1.3 - - + +
156D ALA* 2.9 15.5 + - - +
159D ALA* 1.3 78.6 - - - +
161D PRO* 1.3 67.3 - - - +
162D GLU* 3.3 4.3 + - - +
163D LEU* 3.3 43.8 + - + +
165D ARG* 4.1 1.6 + - - -
----------------------------------------------------------
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