Contacts of the helix formed by residues 160 - 167 (chain B) in PDB entry 3G33
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 PHE 160 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.3 19.7 - - + -
31B LEU* 4.0 28.3 - - + -
32B LEU* 3.9 18.4 - - + -
35B GLU* 3.8 17.0 - - + -
155B VAL* 3.8 12.8 - - + -
156B ILE 4.0 4.5 - - - -
157B ALA 2.9 16.2 + - - +
159B ASP* 1.3 83.6 - - - +
161B LEU* 1.3 68.5 + - - +
162B ALA 3.6 1.1 - - - -
163B PHE* 3.3 6.7 + + - +
164B ILE* 3.1 30.8 + - + +
200B PRO* 3.8 12.6 - - + -
201B SER* 3.5 42.4 - - - -
204B ALA* 3.5 12.6 - - + -
233B THR* 4.9 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA 4.1 0.2 + - - -
158B HIS* 3.2 37.3 + - + +
160B PHE* 1.3 80.5 - - - +
162B ALA* 1.3 67.9 + - - +
164B ILE* 3.3 7.0 - - + +
165B LEU* 2.9 30.1 + - + +
179B LYS* 4.2 23.6 - - + +
182B ALA* 4.6 7.0 - - + -
183B GLN* 4.0 13.2 - - + +
186B LEU* 3.8 33.7 - - + -
204B ALA* 5.1 5.4 - - + +
207B SER* 5.7 0.2 - - - +
208B ILE* 3.7 28.9 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
158B HIS 4.9 0.6 + - - -
159B ASP 5.3 0.6 + - - -
160B PHE 3.6 0.4 - - - -
161B LEU* 1.3 78.5 - - - +
163B PHE* 1.3 69.6 + - + +
165B LEU* 3.4 7.9 + - - +
166B HIS* 2.8 45.8 + - + +
175B GLN* 6.1 0.2 - - - -
179B LYS* 6.2 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 4.0 36.3 - - + -
27B VAL* 3.5 37.9 - - + -
28B LEU* 4.2 28.3 - - + +
31B LEU* 3.8 13.2 - - + -
159B ASP 3.5 25.8 - - - -
160B PHE* 3.8 6.5 - - - +
161B LEU 3.1 1.0 - - - -
162B ALA* 1.3 85.3 - - + +
164B ILE* 1.3 61.8 + - - +
166B HIS* 3.4 9.1 + - - +
167B ARG* 3.4 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.9 1.8 - - + -
160B PHE* 3.1 30.7 + - + +
161B LEU* 3.0 10.1 + - + +
163B PHE* 1.3 76.7 - - + +
165B LEU* 1.3 59.3 + - - +
167B ARG 3.8 3.0 + - - -
168B LEU* 2.9 29.0 - - - +
204B ALA* 4.1 5.6 - - + +
205B THR* 4.0 18.4 - - - +
208B ILE* 3.3 43.1 - - + -
229B LEU* 5.3 3.1 - - + -
232B ILE* 3.9 33.4 - - + +
233B THR* 4.0 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 2.9 27.1 + - + +
162B ALA* 3.7 7.9 - - - +
164B ILE* 1.3 75.4 - - - +
166B HIS* 1.3 65.1 + - - +
167B ARG 3.1 1.6 - - - -
168B LEU* 3.1 38.0 + - + +
170B LEU* 4.9 4.4 - - + +
175B GLN* 3.8 39.9 + - + +
178B VAL* 4.3 19.3 - - + -
179B LYS* 4.2 33.9 - - + -
208B ILE* 3.5 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 4.7 16.9 + - - +
162B ALA* 2.8 37.9 + - + +
163B PHE* 3.7 7.9 - - - +
165B LEU* 1.3 78.1 - - - +
167B ARG* 1.3 58.7 + - + +
168B LEU 3.1 10.3 + - - +
170B LEU 5.6 1.0 - - - +
172B ARG* 3.1 40.7 + - + -
175B GLN* 4.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASP* 5.4 2.8 - - - +
25B GLN* 3.3 41.0 - - - +
28B LEU* 3.8 22.0 - - + +
163B PHE 3.4 13.7 + - - +
164B ILE 4.2 0.4 - - - +
165B LEU 3.1 1.2 - - - -
166B HIS* 1.3 77.6 - - + +
168B LEU* 1.3 67.9 + - - +
228B LEU* 5.1 8.3 - - - +
231B GLY 4.7 2.6 + - - -
232B ILE* 3.5 64.0 + - + +
----------------------------------------------------------
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