Contacts of the helix formed by residues 169 - 184 (chain A) in PDB entry 2Y4U
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 169 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 2.6 34.0 + - + +
165A PHE* 3.7 0.9 + - - -
167A SER* 3.6 4.7 + - - +
168A GLY* 1.3 70.8 - - - +
170A TYR* 1.3 62.2 + - - +
171A THR* 2.9 26.2 + - - -
172A ALA* 3.0 23.8 + - + +
173A ALA* 3.5 10.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PHE* 4.0 39.3 - + - -
168A GLY* 3.3 22.6 + - - -
169A ASP* 1.3 73.5 + - - +
171A THR* 1.3 57.2 + - - +
172A ALA 3.1 1.6 - - - -
173A ALA* 3.0 5.8 + - - +
174A ILE* 2.8 40.8 + - + +
197A CYS* 4.5 17.9 - - + +
200A LYS* 3.5 53.6 - - + +
201A GLU* 3.3 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A ASP* 2.9 16.5 + - - -
170A TYR* 1.3 75.0 - - - +
172A ALA* 1.3 65.1 + - - +
174A ILE* 3.3 20.6 + - + +
175A ALA* 3.4 12.8 + - - +
201A GLU* 3.6 27.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
164A ALA* 3.8 10.5 - - + -
169A ASP* 3.0 37.1 + - + +
171A THR* 1.3 81.5 + - - +
173A ALA* 1.3 57.8 + - - +
174A ILE 3.0 0.3 + - - -
175A ALA* 3.1 11.3 + - - +
176A PHE* 2.8 33.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ALA 3.5 24.5 - - - +
164A ALA* 3.6 9.4 - - + -
165A PHE* 3.9 11.4 - - + +
169A ASP 3.5 9.5 + - - +
170A TYR 3.0 6.0 + - - +
172A ALA* 1.3 79.1 - - - +
174A ILE* 1.3 62.6 + - - +
176A PHE* 3.5 12.6 + - - +
177A LEU* 3.0 32.4 + - + +
197A CYS* 4.6 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A TYR* 2.8 26.1 + - + +
171A THR* 3.5 24.7 - - + +
172A ALA 3.0 0.4 + - - -
173A ALA* 1.3 71.7 - - - +
175A ALA* 1.3 53.7 + - - +
177A LEU* 2.9 11.7 + - - +
178A ASP* 2.8 53.2 + - - +
194A ARG* 4.5 5.3 - - + -
197A CYS* 3.8 22.2 - - + -
198A PHE* 3.9 39.5 - - + +
201A GLU* 5.0 8.5 - - + -
203A GLU* 5.2 2.2 - - - +
----------------------------------------------------------
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 THR 3.4 6.2 + - - +
172A ALA* 3.1 10.2 + - - +
174A ILE* 1.3 79.3 - - - +
176A PHE* 1.3 64.0 + - + +
178A ASP* 3.3 21.7 - - - +
179A LYS* 3.7 19.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.1 15.6 - - + +
160A GLN* 3.5 48.7 - - + -
161A ALA* 3.9 17.7 - - + +
164A ALA* 4.6 3.4 - - + -
172A ALA* 2.8 44.9 - - + -
173A ALA* 3.6 9.4 - - - +
174A ILE 3.2 0.6 - - - -
175A ALA* 1.3 78.3 - - + +
177A LEU* 1.3 63.2 + - - +
179A LYS* 3.1 15.9 + - - +
180A ILE* 3.0 22.1 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
161A ALA* 3.9 19.5 - - + -
162A LEU* 5.5 0.2 - - + -
173A ALA* 3.0 26.2 + - + +
174A ILE* 2.9 5.2 + - - +
176A PHE* 1.3 73.3 - - - +
178A ASP* 1.3 68.1 + - - +
180A ILE* 3.2 13.8 + - + +
181A LEU* 2.9 31.5 + - + +
190A LEU* 4.2 31.0 - - + +
193A LEU* 4.3 20.9 - - + -
194A ARG* 3.9 41.1 - - + +
197A CYS* 4.5 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A ILE* 2.8 42.6 + - - +
175A ALA* 3.3 14.1 - - - +
177A LEU* 1.3 77.0 - - - +
179A LYS* 1.3 66.3 + - + +
181A LEU* 3.4 8.1 + - - +
182A GLU* 3.4 16.2 + - - +
194A ARG* 2.8 31.6 + - - +
198A PHE* 5.2 3.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A MSE 5.2 1.3 - - + -
157A LEU* 4.4 19.3 - - + -
175A ALA* 3.7 17.3 + - - +
176A PHE* 3.1 10.3 + - - +
178A ASP* 1.3 76.0 - - + +
180A ILE* 1.3 54.2 + - - +
181A LEU 2.7 15.2 + - - -
182A GLU* 2.7 29.7 + - + +
183A VAL* 3.8 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 6.3 0.7 - - + -
154A MSE 4.0 23.6 - - + -
157A LEU* 3.4 46.8 - - + +
158A ARG* 3.8 11.0 - - + +
161A ALA* 3.8 17.9 - - + -
176A PHE* 3.0 18.6 + - + +
177A LEU* 3.2 16.4 + - + +
179A LYS* 1.3 74.4 - - - +
181A LEU* 1.3 59.6 + - + +
182A GLU 3.3 0.2 - - - -
183A VAL* 3.6 2.9 + - - +
184A CYS* 3.1 32.4 + - - +
190A LEU* 4.3 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LEU* 2.9 21.3 + - + +
178A ASP 3.7 6.1 - - - +
179A LYS 2.7 1.6 + - - -
180A ILE* 1.3 79.9 - - + +
182A GLU* 1.3 63.6 + - - +
183A VAL 3.3 0.7 - - - -
184A CYS 3.6 18.2 - - - +
185A VAL* 3.4 25.1 - - - +
187A ASP 4.5 1.3 - - - +
190A LEU* 4.2 29.2 - - + -
191A ARG* 4.1 30.9 + - + +
194A ARG* 3.4 44.9 - - + +
210A ASP* 4.0 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A ASP* 3.4 13.5 - - - +
179A LYS* 2.7 19.4 + - - +
181A LEU* 1.3 79.6 - - - +
183A VAL* 1.3 66.8 + - + +
185A VAL* 3.8 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU* 3.6 30.5 - - + +
117A LYS* 3.9 14.7 + - - +
150A LYS* 4.1 23.8 - - + +
154A MSE 3.5 48.0 - - + -
179A LYS 4.5 5.2 - - - +
180A ILE 3.6 1.2 + - - -
182A GLU* 1.3 84.7 - - + +
184A CYS* 1.3 59.3 + - - +
185A VAL* 3.5 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A LEU 3.3 19.3 - - - +
117A LYS 3.2 10.5 - - - +
119A GLY* 3.6 20.2 - - - +
121A LEU* 4.3 14.1 - - - -
154A MSE 4.4 13.0 - - - -
180A ILE* 3.1 24.6 + - + +
181A LEU* 3.6 23.6 - - + +
183A VAL* 1.3 78.5 - - - +
185A VAL* 1.3 58.4 + - - +
186A TRP 3.1 6.3 + - - -
187A ASP* 3.6 14.4 + - + -
190A LEU* 5.3 0.9 - - + -
----------------------------------------------------------
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