Contacts of the helix formed by residues 168 - 180 (chain O) in PDB entry 1NJI
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 LEU 168 (chain O).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O TRP* 5.5 2.1 - - - -
143O ARG 4.9 0.2 - - - +
163O PHE* 4.2 16.1 - - + -
164O ASP* 3.4 22.0 + - + +
167O ASP* 1.3 94.4 - - - +
169O PRO* 1.3 65.4 - - - +
170O GLU* 2.9 23.7 + - + +
171O HIS* 3.2 36.4 + - + +
172O PHE* 3.7 3.1 + - - +
174O GLU* 5.8 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 169 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O ARG* 3.4 50.3 + - + +
144O GLY 3.8 22.7 - - - +
145O ALA* 4.2 5.6 - - + +
147O ILE* 5.5 0.7 - - + -
148O ALA* 3.9 18.2 - - + -
167O ASP* 4.1 5.2 - - + +
168O LEU* 1.3 86.0 - - - +
170O GLU* 1.3 70.1 + - - +
171O HIS 3.3 0.2 - - - -
172O PHE* 3.0 21.9 - - + +
173O ASP* 3.0 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 170 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143O ARG* 3.7 15.4 + - - +
167O ASP 4.5 0.2 - - - +
168O LEU* 3.3 29.8 - - + +
169O PRO* 1.3 89.5 - - - +
171O HIS* 1.3 64.3 + - - +
172O PHE 2.9 2.0 - - - -
173O ASP* 3.0 15.4 + - - +
174O GLU* 3.0 33.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 171 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70O GLY 2.8 23.1 + - - -
71O TRP* 3.8 17.9 - + + -
72O GLU* 3.2 44.6 + - + -
73O ALA* 4.3 1.1 - - - +
163O PHE* 3.0 25.0 - + + -
168O LEU* 3.2 27.7 + - + +
170O GLU* 1.3 78.3 - - - +
172O PHE* 1.3 62.1 + - - +
174O GLU* 3.2 23.3 + - + +
175O LEU* 3.2 20.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 172 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71O TRP* 4.0 9.8 - - + -
79O PRO* 3.6 26.0 - - + -
82O TYR* 3.8 21.1 - + - -
83O LEU* 3.6 33.4 - - + -
139O TRP* 3.8 24.0 - + - -
142O THR* 3.9 15.9 - - + -
143O ARG* 3.4 48.2 - - + +
168O LEU 3.7 1.7 + - - +
169O PRO* 3.0 14.9 + - + +
171O HIS* 1.3 79.4 - - - +
173O ASP* 1.3 68.7 + - - +
175O LEU* 3.1 5.4 + - - +
176O ARG* 2.9 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 173 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139O TRP* 5.2 5.2 + - - -
143O ARG* 2.4 37.1 + - - +
169O PRO 3.0 10.4 - - - +
170O GLU* 3.0 15.4 + - - +
172O PHE* 1.3 85.3 - - - +
174O GLU* 1.3 54.8 - - + +
176O ARG* 3.8 6.5 - - - +
177O GLU* 2.7 38.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 174 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168O LEU* 5.8 1.7 - - - +
170O GLU* 3.0 19.2 + - + +
171O HIS* 3.2 31.5 - - + +
173O ASP* 1.3 75.8 - - + +
175O LEU* 1.3 53.0 + - - +
177O GLU* 3.3 8.8 - - - +
178O THR* 2.7 36.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O LEU* 3.9 19.3 - - + -
69O TYR* 3.5 40.4 - - + +
70O GLY 4.6 5.2 - - - +
71O TRP* 3.1 36.6 - - + -
83O LEU* 3.4 20.4 - - + -
171O HIS* 3.2 10.8 + - + +
172O PHE 3.1 9.0 + - - +
174O GLU* 1.3 75.9 - - - +
176O ARG* 1.3 69.0 + - - +
177O GLU 3.1 0.9 - - - -
178O THR* 2.8 20.1 + - - +
179O LEU* 2.9 20.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 176 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82O TYR* 2.5 36.5 + - + -
83O LEU* 3.9 18.7 - - + +
86O LEU* 4.4 9.9 - - + -
124O ASP* 3.9 13.8 + - - +
139O TRP* 3.0 36.9 - - - -
172O PHE* 2.9 23.2 + - + +
173O ASP* 3.8 7.2 - - - +
175O LEU* 1.3 74.1 - - - +
177O GLU* 1.3 66.7 + - - +
179O LEU* 3.1 11.6 + - - +
180O LEU* 3.2 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 177 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173O ASP 2.7 23.2 + - - +
174O GLU* 3.3 9.6 - - - +
176O ARG* 1.3 77.4 - - - +
178O THR* 1.3 60.4 + - - +
180O LEU* 3.2 15.0 + - - +
181O ASP* 2.9 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 178 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69O TYR* 4.5 25.9 + - + +
174O GLU 2.7 21.4 + - - -
175O LEU* 2.8 19.4 + - + +
177O GLU* 1.3 78.2 - - - +
179O LEU* 1.3 63.0 + - + +
180O LEU 3.0 1.7 + - - -
181O ASP* 3.2 25.1 + - - +
183O ASP* 4.1 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 179 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66O LEU* 5.0 4.3 - - + -
69O TYR* 4.0 29.6 - - + -
83O LEU* 4.3 29.2 - - + +
86O LEU* 4.0 28.5 - - + -
87O LEU* 4.3 14.4 - - + +
90O LEU* 3.3 23.6 - - + +
175O LEU* 2.9 24.5 + - + +
176O ARG 3.5 6.3 - - - +
178O THR* 1.3 76.2 - - + +
180O LEU* 1.3 57.7 + - - +
181O ASP 3.1 6.4 + - - -
183O ASP* 4.1 2.7 - - - +
186O LEU* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 180 (chain O).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86O LEU* 4.1 28.7 - - + -
90O LEU* 5.1 6.7 - - + -
124O ASP* 5.1 7.0 - - + +
176O ARG* 3.2 46.4 + - + +
177O GLU* 3.7 15.9 - - - +
178O THR 3.0 3.0 + - - -
179O LEU* 1.3 77.8 - - - +
181O ASP* 1.3 65.8 + - - +
----------------------------------------------------------
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