Contacts of the helix formed by residues 166 - 178 (chain A) in PDB entry 1EEJ
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
----------------------------------------------------------
77A GLU* 4.6 5.7 + - - +
137A LYS* 5.5 0.7 - - - +
164A ASP 3.4 6.7 + - - +
165A VAL* 1.3 75.5 - - - +
167A ILE* 1.3 63.7 + - - +
168A ALA* 2.9 36.5 + - - +
169A ASP* 2.8 40.9 + - - +
170A HIS* 3.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA* 3.5 35.0 - - + +
124A PRO* 3.9 21.3 - - + -
128A LEU* 4.6 1.1 - - + -
133A GLU* 4.0 27.8 - - + +
136A MET* 4.0 19.7 - - + +
137A LYS* 3.8 31.5 - - + +
140A TRP* 4.4 5.4 - - + -
165A VAL* 3.8 15.3 + - + -
166A ASP* 1.3 71.3 + - - +
168A ALA* 1.3 63.1 + - - +
170A HIS* 3.0 9.7 + - - +
171A TYR* 3.0 19.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LEU* 3.5 36.7 - - + +
133A GLU* 5.8 0.4 - - - -
166A ASP* 2.8 21.9 + - - +
167A ILE* 1.3 78.9 - - - +
169A ASP* 1.3 56.6 + - - +
171A TYR* 3.4 2.8 + - - +
172A ALA* 2.8 30.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.5 16.9 - - + +
77A GLU* 5.3 2.2 - - - +
166A ASP* 2.8 34.1 + - - +
168A ALA* 1.3 76.9 - - - +
170A HIS* 1.3 64.8 + - + +
172A ALA* 3.8 6.5 - - - +
173A LEU* 3.0 30.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LEU* 4.0 17.5 - - + +
77A GLU* 2.8 32.8 + - - +
93A PHE* 3.3 13.0 - - - -
121A LEU* 3.7 21.2 - - + +
122A ALA* 2.9 45.5 + - + +
140A TRP* 3.6 33.9 - + - -
165A VAL* 4.5 7.5 - - + +
166A ASP 4.0 9.4 - - - -
167A ILE* 3.0 9.2 + - + +
169A ASP* 1.3 78.9 - - + +
171A TYR* 1.3 57.0 + - - +
173A LEU* 3.5 1.6 + - - +
174A GLY* 3.0 23.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ALA 3.7 1.3 + - - -
123A PHE* 3.6 36.7 - + - -
124A PRO* 3.3 38.8 - - + -
125A ARG 4.7 4.6 + - - -
127A GLY* 4.1 19.0 + - - -
128A LEU* 3.9 30.7 - - + -
167A ILE 3.0 11.8 + - - +
168A ALA 3.6 7.4 - - - +
170A HIS* 1.3 75.0 - - - +
172A ALA* 1.3 68.5 + - - +
174A GLY 3.3 0.5 + - - -
175A VAL* 2.9 43.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ALA 2.8 21.6 + - - +
169A ASP* 3.8 8.3 - - - +
171A TYR* 1.3 78.9 - - + +
173A LEU* 1.3 61.2 + - - +
175A VAL* 3.4 7.1 + - - +
176A GLN* 3.1 37.8 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
67A LEU* 4.4 11.4 - - + +
70A GLN* 4.1 21.5 - - + -
71A LEU* 3.8 42.2 - - + +
74A LEU* 3.9 18.8 - - + -
93A PHE* 4.3 0.9 - - + -
121A LEU* 4.3 5.6 - - + -
169A ASP 3.0 18.5 + - - +
170A HIS 3.8 3.8 - - - +
172A ALA* 1.3 72.9 - - - +
174A GLY* 1.3 66.8 + - - +
176A GLN* 3.2 21.5 + - - +
177A LEU* 2.9 47.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.5 24.4 - - - -
123A PHE* 4.0 2.7 - - - -
170A HIS 3.0 12.4 + - - -
171A TYR 3.7 2.9 - - - -
173A LEU* 1.3 75.6 - - - +
175A VAL* 1.3 61.9 + - - +
177A LEU* 3.1 3.8 + - - +
178A GLY 3.0 6.4 + - - -
179A VAL* 2.9 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A PHE* 3.8 15.6 - - + -
171A TYR* 2.9 46.5 + - + +
172A ALA* 3.6 6.1 - - - +
174A GLY* 1.3 73.4 - - - +
176A GLN* 1.3 61.7 + - + +
178A GLY* 2.9 20.1 + - - -
179A VAL 4.4 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A LEU* 4.3 13.2 - - - +
32A THR 4.5 2.9 - - - +
33A ASN 5.9 0.5 - - - -
35A GLY* 4.0 28.7 + - - -
36A VAL* 5.2 3.8 - - + +
50A PRO* 6.1 0.9 - - - +
63A THR* 5.5 2.8 - - - +
64A ASN* 4.2 4.9 - - - +
67A LEU* 3.7 35.7 - - + +
70A GLN* 5.5 1.6 - - - +
172A ALA* 3.1 22.8 + - - +
173A LEU* 3.2 19.3 + - - +
175A VAL* 1.3 78.2 - - + +
177A LEU* 1.3 61.4 + - - +
178A GLY* 3.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A ASN* 5.2 1.4 + - - -
64A ASN* 3.3 47.3 + - + +
67A LEU* 3.6 27.4 - - + -
68A LEU* 6.3 1.3 - - + -
71A LEU* 4.9 6.3 - - + -
93A PHE* 3.7 30.3 - - + -
173A LEU* 2.9 35.0 + - + +
174A GLY* 3.1 5.6 + - - +
176A GLN* 1.3 74.6 - - - +
178A GLY* 1.3 58.9 + - - +
179A VAL* 3.7 2.5 - - + -
186A VAL* 4.1 16.2 - - + -
190A GLY* 4.9 2.7 - - - +
192A LEU* 3.1 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A VAL 2.9 13.8 + - - -
176A GLN 3.0 2.3 - - - -
177A LEU* 1.3 78.4 - - - +
179A VAL* 1.3 65.6 + - - +
180A SER* 3.1 11.8 + - - -
192A LEU* 3.0 15.0 - - - +
194A PRO* 5.0 1.0 - - - +
----------------------------------------------------------
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