Contacts of the helix formed by residues 154 - 165 (chain B) in PDB entry 4OE5
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 THR 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B MET* 4.1 0.9 - - - -
152B GLY 3.7 1.0 + - - -
153B LYS* 1.3 75.6 - - - +
155B VAL* 1.3 67.4 + - - +
156B ILE* 3.9 5.3 + - - +
157B GLN* 3.2 24.0 + - - +
158B ALA* 2.9 21.1 + - - +
343B TYR* 5.6 2.3 + - - +
380B PRO* 3.9 12.1 - - + -
384B PHE 6.2 0.4 - - - -
386B THR* 3.4 35.4 - - + +
387B PHE 3.5 21.3 + - - +
388B PHE* 3.9 11.0 - - + -
389B SER 4.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B PHE* 3.9 32.8 - - + -
50B LEU* 3.7 25.6 - - + -
144B LEU* 5.2 1.2 - - + +
148B MET* 3.6 25.6 - - + +
154B THR* 1.3 74.7 - - - +
156B ILE* 1.3 67.0 + - + +
158B ALA* 3.7 1.4 - - - +
159B GLU* 2.9 29.3 + - + +
380B PRO* 5.1 0.8 + - - +
384B PHE* 3.9 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 6.1 2.0 - - + -
38B LEU 4.6 11.0 - - - +
39B ALA* 4.4 18.4 - - - +
40B PHE* 5.1 2.7 - - + -
154B THR* 3.3 4.8 + - - +
155B VAL* 1.3 91.3 - - + +
157B GLN* 1.3 57.2 + - - +
159B GLU* 3.9 3.6 - - + +
160B ILE* 3.0 49.3 + - + +
342B GLU* 6.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 157 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 4.1 14.8 - - + -
154B THR* 3.2 27.0 + - - +
156B ILE* 1.3 80.9 - - - +
158B ALA* 1.3 61.9 + - - +
160B ILE* 3.4 10.6 + - - +
161B ASP* 2.7 65.0 + - - +
342B GLU* 4.6 7.3 - - - +
343B TYR* 4.3 21.6 - - + +
347B LYS* 3.1 39.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 3.3 14.4 - - + +
147B THR* 3.4 23.0 + - - +
148B MET* 3.8 16.6 - - + -
153B LYS* 3.8 15.5 + - + +
154B THR 2.9 16.6 + - - +
155B VAL* 3.7 3.6 - - - +
157B GLN* 1.3 77.5 - - - +
159B GLU* 1.3 58.7 + - - +
161B ASP* 3.6 1.6 + - - +
162B ALA* 2.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 3.5 21.7 - - + -
38B LEU* 2.7 23.6 + - - +
40B PHE* 3.7 24.4 - - + -
140B ARG* 2.4 47.8 + - - -
144B LEU* 3.5 19.1 - - + +
155B VAL 2.9 17.4 + - - +
156B ILE* 3.9 6.1 - - + +
158B ALA* 1.3 73.9 - - - +
160B ILE* 1.3 65.9 + - - +
162B ALA* 3.2 1.4 + - - +
163B ALA* 3.0 21.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B VAL* 4.3 24.2 - - + -
156B ILE* 3.0 40.2 + - + +
157B GLN* 3.8 11.7 - - - +
159B GLU* 1.3 74.7 - - - +
161B ASP* 1.3 68.6 + - - +
163B ALA* 4.0 0.5 - - - +
164B ALA* 2.9 39.6 + - + +
347B LYS* 6.2 1.1 - - - +
514B ILE* 5.3 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LYS* 2.8 37.5 + - - +
157B GLN* 2.7 40.0 + - - +
158B ALA 3.9 1.3 - - - +
160B ILE* 1.3 80.1 - - - +
162B ALA* 1.3 64.9 + - - +
165B GLU* 3.1 35.4 + - + +
166B LEU* 3.2 4.2 + - - +
343B TYR* 5.4 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ARG* 5.4 2.9 - - + +
143B ILE* 4.4 17.3 - - + -
144B LEU* 3.6 19.7 - - + -
158B ALA 2.9 21.2 + - - +
159B GLU* 3.2 5.3 + - - +
161B ASP* 1.3 73.5 - - - +
163B ALA* 1.3 58.4 + - - +
166B LEU* 3.5 12.7 - - + +
167B ILE* 2.9 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU* 3.7 39.8 - - + +
36B PRO 3.9 2.7 - - - +
37B VAL* 4.0 12.1 - - + -
140B ARG* 3.9 11.4 - - - +
159B GLU 3.0 14.9 + - - +
162B ALA* 1.3 77.0 - - - +
164B ALA* 1.3 60.0 + - - +
167B ILE* 3.7 3.4 - - - +
168B ASP* 3.0 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B GLU 5.9 0.2 - - - -
37B VAL* 5.5 5.2 - - + -
160B ILE* 2.9 26.8 + - + +
161B ASP* 5.3 0.2 - - - -
163B ALA* 1.3 76.6 - - + +
165B GLU* 1.3 59.4 + - + +
168B ASP* 3.3 22.0 - - - +
169B PHE* 4.0 3.8 - - - -
524B ARG* 3.6 21.5 + - + -
525B ALA* 3.1 32.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 3.1 23.7 + - + +
164B ALA* 1.3 79.4 - - - +
166B LEU* 1.3 71.4 + - + +
169B PHE* 3.0 49.6 + - - +
216B GLY* 5.6 4.7 - - - +
217B GLY 5.6 2.4 + - - +
218B ASN* 4.1 19.6 + - - +
525B ALA* 3.8 19.0 - - + +
----------------------------------------------------------
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