Contacts of the helix formed by residues 166 - 179 (chain A) in PDB entry 4JU5
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 SER 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 4.6 4.3 - - - +
163A ASP* 3.3 34.0 + - - -
164A VAL 3.5 0.4 - - - -
165A GLU* 1.3 80.6 - - - +
167A ASP* 1.3 54.5 + - - +
168A SER* 3.7 7.7 + - - -
169A ALA* 3.2 14.0 + - - +
170A LYS* 2.8 34.2 + - - +
201A ASP* 5.0 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLU 5.2 0.5 - - - +
166A SER* 1.3 73.8 - - - +
168A SER* 1.3 59.2 + - - +
170A LYS* 3.3 13.1 + - - +
171A GLN* 2.9 37.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.5 23.6 - - - -
166A SER* 3.3 5.5 + - - -
167A ASP* 1.3 74.0 - - - +
169A ALA* 1.3 66.6 + - - +
171A GLN 3.2 1.2 + - - -
172A PHE* 3.0 20.1 + - - +
201A ASP* 5.7 1.3 - - - -
220A VAL* 3.4 38.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.8 27.3 - - + -
163A ASP 3.4 19.7 - - - +
164A VAL* 3.1 26.7 - - - +
166A SER* 3.2 8.8 + - - +
168A SER* 1.3 77.9 - - - +
170A LYS* 1.3 55.9 + - - +
172A PHE* 3.4 2.6 + - - +
173A LEU* 3.1 33.6 + - - +
186A ILE* 4.5 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL 5.1 1.1 - - - +
165A GLU* 3.4 40.4 + - - +
166A SER 2.8 17.0 + - - +
167A ASP* 3.5 12.6 - - - +
169A ALA* 1.3 73.4 - - - +
171A GLN* 1.3 68.5 + - - +
173A LEU* 3.4 10.5 + - + +
174A GLN* 3.2 31.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A ASP* 2.9 21.0 + - + +
168A SER 3.2 6.0 + - - +
170A LYS* 1.3 77.6 - - - +
172A PHE* 1.3 57.7 + - - +
174A GLN* 3.2 23.8 + - - +
175A ALA* 3.0 26.5 + - - +
220A VAL* 3.4 27.4 - - + +
221A THR* 4.1 7.2 - - - +
222A LYS* 3.2 37.3 + - - +
225A LEU* 4.3 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA* 4.3 4.0 - - + -
157A VAL* 3.9 11.2 - - + -
158A ILE 4.2 0.2 - - - -
159A GLY* 3.3 19.5 - - - -
161A PHE* 3.7 16.2 - + + -
168A SER 3.0 15.7 + - - +
169A ALA 3.6 3.6 - - - +
171A GLN* 1.3 73.8 - - - +
173A LEU* 1.3 70.0 + - + +
175A ALA* 3.0 5.5 + - + +
176A ALA* 2.8 27.6 + - + +
184A PHE* 3.8 32.1 - + + -
185A GLY 3.3 27.1 - - - -
186A ILE* 4.0 29.8 - - + -
203A VAL* 4.0 17.5 - - + -
225A LEU* 3.6 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 4.4 8.3 - - + +
137A ALA* 3.8 34.8 - - + +
164A VAL* 4.2 22.2 - - + +
169A ALA 3.1 21.7 + - - +
170A LYS* 3.8 9.6 - - + +
171A GLN 3.4 0.2 - - - -
172A PHE* 1.3 84.4 - - + +
174A GLN* 1.3 56.6 + - + +
176A ALA* 3.3 6.4 + - - +
177A GLU* 2.9 38.6 + - - +
186A ILE* 4.2 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS* 3.2 19.2 + - - +
171A GLN* 3.4 27.5 + - - +
172A PHE 3.2 0.2 - - - -
173A LEU* 1.3 75.9 - - + +
175A ALA* 1.3 63.9 + - - +
177A GLU* 3.4 15.0 + - - +
178A ALA* 3.3 21.0 + - - +
222A LYS* 3.7 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A GLN 3.0 12.6 + - - +
172A PHE* 3.4 8.3 - - + +
174A GLN* 1.3 75.9 - - - +
176A ALA* 1.3 62.6 + - - +
178A ALA* 3.2 12.1 + - - +
179A ILE* 3.5 8.7 + - - +
184A PHE* 4.2 12.3 - - + -
222A LYS* 4.1 11.1 - - + +
225A LEU* 3.9 30.5 - - + -
226A LEU* 3.8 22.9 - - + +
229A ILE* 5.4 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA 3.5 25.6 - - - +
137A ALA* 4.4 2.9 - - + -
172A PHE* 2.8 13.9 + - + +
173A LEU* 3.3 15.5 - - - +
175A ALA* 1.3 78.2 - - - +
177A GLU* 1.3 60.5 + - - +
179A ILE 3.5 17.7 - - - +
184A PHE* 3.5 37.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A ALA* 3.8 27.0 - - + +
173A LEU* 2.9 30.5 + - - +
174A GLN* 3.6 16.5 + - - +
175A ALA 3.2 0.2 - - - -
176A ALA* 1.3 76.7 - - - +
178A ALA* 1.3 59.4 + - - +
179A ILE 3.4 1.4 + - - -
180A ASP* 4.7 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLN 3.3 11.4 + - - +
175A ALA* 3.2 11.2 + - - +
177A GLU* 1.3 79.1 - - - +
179A ILE* 1.3 62.2 + - - +
180A ASP* 4.2 5.4 + - - +
222A LYS* 4.5 13.0 - - - -
226A LEU* 3.8 18.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A ALA 3.5 8.1 + - - +
176A ALA 3.5 12.5 - - - +
177A GLU 3.4 1.7 - - - -
178A ALA* 1.3 83.0 - - - +
180A ASP* 1.3 64.2 + - - +
181A ASP* 3.8 18.6 - - + +
182A ILE* 3.8 35.8 - - + +
184A PHE* 4.0 4.4 - - + -
226A LEU* 3.9 24.2 - - + +
229A ILE* 3.7 40.4 - - + -
230A LYS* 5.4 1.6 - - + +
233A GLN* 4.6 7.6 - - - +
----------------------------------------------------------
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