Contacts of the helix formed by residues 166 - 174 (chain A) in PDB entry 1IEV
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 ASP 166 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 4.4 1.3 - - - -
152A ARG* 5.0 1.6 - - - +
164A SER* 2.8 12.8 + - - +
165A GLU* 1.3 78.8 - - + +
167A ARG* 1.3 60.3 + - - +
168A ARG* 2.8 66.7 + - - +
169A ILE* 2.7 40.8 + - + +
170A VAL 3.4 2.8 + - - -
582A VAL* 5.0 5.6 - - + -
593A LEU* 4.2 24.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A VAL* 3.9 19.8 - - + +
165A GLU 3.8 4.4 + - - -
166A ASP* 1.3 73.1 + - - +
168A ARG* 1.3 76.6 + - - +
170A VAL* 3.7 3.9 - - + +
171A GLN* 2.7 75.1 + - + +
232A ASN* 2.8 36.7 + - - +
233A ILE* 3.3 33.2 - - + +
236A PRO* 3.2 16.8 - - + +
237A ALA* 5.6 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ASP* 2.8 40.2 + - - +
167A ARG* 1.3 102.2 - - - +
169A ILE* 1.4 57.8 + - + +
171A GLN* 3.5 12.1 + - - +
172A SER* 3.2 24.6 + - - -
582A VAL* 5.7 6.3 - - - +
593A LEU* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLY* 4.3 13.2 - - - +
119A ARG* 3.2 42.4 - - - +
163A TYR* 4.6 1.3 - - + +
164A SER* 3.5 28.3 - - - +
166A ASP* 2.7 26.6 + - + +
168A ARG* 1.4 75.4 - - + +
170A VAL* 1.3 64.0 + - - +
171A GLN 3.2 1.3 - - - -
172A SER* 2.7 25.3 + - - +
173A MET* 2.9 30.4 + - + +
568A PRO* 4.6 3.1 - - + -
593A LEU* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A ILE* 3.6 42.8 - - + +
149A ALA 3.7 12.1 - - - +
150A VAL* 4.0 11.7 - - + -
163A TYR* 3.9 17.2 - - + -
164A SER 3.6 34.5 - - - +
166A ASP 3.4 6.0 + - - +
167A ARG* 3.2 8.4 + - - +
169A ILE* 1.3 76.2 - - - +
171A GLN* 1.3 64.2 + - - +
173A MET* 3.0 11.8 + - - +
174A THR* 3.4 11.1 + - - +
237A ALA* 4.0 7.9 - - + -
----------------------------------------------------------
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 ARG* 2.7 69.3 + - + +
168A ARG* 3.6 11.9 - - - +
170A VAL* 1.3 72.0 - - - +
172A SER* 1.3 60.9 + - - +
174A THR* 3.2 28.1 + - - +
236A PRO* 3.3 17.7 - - + +
237A ALA* 3.9 12.6 - - - +
240A ASN* 2.8 35.7 + - - +
244A LYS* 4.1 4.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A PRO* 3.3 37.6 - - - +
168A ARG 3.2 10.5 + - - -
169A ILE* 2.7 22.8 + - - +
171A GLN* 1.3 81.4 - - - +
173A MET* 1.3 68.3 + - - +
174A THR 3.4 0.9 + - - -
175A GLU* 3.7 10.2 + - - +
244A LYS* 4.6 1.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU 3.7 20.6 - - - +
116A GLY* 4.1 8.1 - - - +
119A ARG* 3.7 26.9 - - - +
120A ASP 3.8 6.5 - - - +
121A PRO* 4.0 11.0 - - - -
124A VAL* 3.6 30.3 - - + +
163A TYR* 3.5 50.5 + - + -
169A ILE* 2.9 15.5 + - + +
170A VAL 3.0 2.1 + - - +
172A SER* 1.3 85.6 - - - +
174A THR* 1.3 52.5 + - - +
175A GLU* 2.7 18.0 + - - -
176A LEU* 2.9 17.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PRO* 5.3 1.8 - - - -
148A ILE* 4.2 20.9 - - + -
163A TYR* 5.1 0.2 - - - -
170A VAL 3.4 10.5 + - - +
171A GLN* 3.2 19.9 + - - +
172A SER 3.3 0.8 - - - -
173A MET* 1.3 68.2 - - - +
175A GLU* 1.3 54.1 + - - +
176A LEU* 2.8 7.4 - - - +
177A ILE* 2.9 40.9 + - - +
178A PRO* 3.4 3.8 - - - +
237A ALA* 4.0 21.1 - - + +
240A ASN* 3.8 8.3 - - + +
241A ALA* 4.8 2.2 - - + -
244A LYS* 2.6 36.1 + - - +
----------------------------------------------------------
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