Contacts of the helix formed by residues 159 - 167 (chain B) in PDB entry 1U5U
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 GLY 159 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B GLU 3.5 0.2 + - - -
158B GLU* 1.3 75.1 - - - +
160B ASP* 1.3 61.3 + - - -
161B ALA 3.3 2.9 - - - -
162B ALA 3.3 1.9 + - - -
163B GLU* 3.0 26.7 + - - +
239B TRP* 2.9 32.0 + - - +
240B ILE* 4.7 6.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B GLU 4.1 0.8 + - - -
159B GLY* 1.3 71.6 - - - -
161B ALA* 1.3 56.5 + - - +
163B GLU* 3.7 18.7 - - - +
164B GLU* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155B PRO* 4.0 12.8 - - + +
156B VAL* 4.5 2.3 - - - +
157B GLU* 3.6 29.4 - - + +
158B GLU 4.7 1.4 + - - +
159B GLY 3.3 1.0 - - - -
160B ASP* 1.3 76.9 - - - +
162B ALA* 1.3 58.4 + - - +
164B GLU* 3.4 9.5 + - - +
165B TYR* 3.0 27.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
156B VAL* 4.0 13.0 - - + -
157B GLU 3.1 21.6 + - - +
159B GLY 3.3 1.5 + - - +
161B ALA* 1.3 72.4 - - - +
163B GLU* 1.3 65.9 + - - +
165B TYR* 3.4 8.1 - - + +
166B VAL* 3.1 30.4 + - + +
176B LEU* 6.1 1.1 - - + -
239B TRP* 3.6 21.1 - - + +
241B PHE* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLY 3.0 15.3 + - - +
160B ASP* 3.7 22.4 + - - +
162B ALA* 1.3 77.8 - - - +
164B GLU* 1.3 63.3 + - - +
166B VAL* 3.2 17.0 - - - +
167B TYR* 3.4 22.3 - - + -
239B TRP* 3.4 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B ASP 2.9 18.5 + - - +
161B ALA* 3.7 7.3 - - - +
163B GLU* 1.3 76.1 - - - +
165B TYR* 1.3 63.6 + - - +
167B TYR* 3.5 12.0 + - - +
168B LYS* 3.3 42.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143B ILE* 3.4 36.6 + - + +
149B SER 5.2 0.2 + - - -
152B ASP* 3.3 29.4 - - + +
153B PHE* 3.7 26.4 - + + +
156B VAL* 3.4 20.6 - - + -
161B ALA 3.0 17.3 + - - +
162B ALA* 3.4 5.6 - - + +
163B GLU 3.2 0.2 - - - -
164B GLU* 1.3 75.3 - - - +
166B VAL* 1.3 75.2 + - + +
168B LYS* 3.0 23.3 + - + +
172B TYR* 3.4 57.4 - + + -
176B LEU* 4.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 4.3 1.2 - - - -
162B ALA* 3.1 12.1 + - + +
163B GLU 3.2 18.8 - - - +
165B TYR* 1.3 83.1 - - + +
167B TYR* 1.3 59.6 + - + +
169B ASN 3.2 20.0 - - - +
172B TYR* 4.3 5.6 - - - -
173B TYR* 3.5 52.4 - - + +
176B LEU* 3.7 29.4 - - + -
238B ILE* 3.9 13.0 - - + -
239B TRP* 4.1 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B ILE* 3.3 27.5 + - - +
11B PHE* 3.4 10.8 - + - -
14B LYS* 3.6 50.2 - - + +
15B TYR* 3.1 40.9 + + - +
23B ARG* 5.1 0.5 + - - -
163B GLU* 3.4 24.0 - - + +
164B GLU* 3.5 10.4 + - - +
165B TYR 3.1 1.4 + - - -
166B VAL* 1.3 77.4 - - + +
168B LYS* 1.3 61.8 + - - +
169B ASN 3.3 2.2 - - - -
173B TYR* 3.8 25.0 + + - -
239B TRP* 4.2 25.3 - + - -
----------------------------------------------------------
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