Contacts of the helix formed by residues 172 - 185 (chain A) in PDB entry 2OZL
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 GLN 172 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 3.3 29.0 + - + +
139A GLY* 4.0 3.8 - - - -
169A ALA 2.9 16.8 + - - +
170A ALA 3.3 0.6 - - - -
171A ASN* 1.3 76.4 - - - +
173A GLY* 1.3 66.4 + - - +
174A GLN* 3.0 29.7 + - + +
175A ILE* 3.1 23.2 + - + +
176A PHE* 3.4 12.5 - - - -
2330A TPP 4.1 3.2 - - - +
177C GLU* 3.9 4.5 + - - +
57D ILE* 3.2 24.1 + - - +
58D SER* 4.3 3.4 - - - +
59D GLU* 3.2 10.1 + - - -
88D GLN* 3.0 29.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLN* 1.3 72.4 + - - +
174A GLN* 1.3 62.7 + - - +
176A PHE* 3.0 18.7 + - - +
177A GLU 3.2 8.5 + - - -
173C GLY* 3.3 40.7 - - - -
177C GLU* 2.8 24.5 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
139A GLY* 3.4 19.5 - - - +
140A ALA* 3.5 16.7 - - - +
143A PRO* 3.4 14.8 - - + +
172A GLN* 3.0 27.9 + - + +
173A GLY* 1.3 74.8 - - - +
175A ILE* 1.3 60.8 + - - +
176A PHE 3.3 0.2 - - - -
177A GLU* 3.3 14.5 + - - +
178A ALA* 3.0 27.9 + - - +
60B MET* 3.3 34.1 - - + +
61B GLY* 4.8 0.6 - - - +
91B ASP* 5.5 0.4 + - - -
92B GLN* 3.1 28.6 + - - -
88D GLN* 3.4 15.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A GLY* 4.6 4.0 - - - +
142A VAL* 3.6 36.3 - - + -
165A TYR* 3.6 29.6 - - + -
169A ALA* 3.0 29.8 - - + +
170A ALA* 3.9 6.3 - - - +
172A GLN* 3.1 16.1 + - + +
173A GLY 3.1 0.8 + - - -
174A GLN* 1.3 78.3 - - - +
176A PHE* 1.3 61.4 + - + +
178A ALA* 3.2 4.2 + - - +
179A TYR* 2.9 61.8 + - + +
----------------------------------------------------------
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
----------------------------------------------------------
170A ALA 3.3 23.3 - - - -
171A ASN* 4.6 5.2 - - - -
172A GLN 3.4 17.0 - - - -
173A GLY 3.0 7.2 + - - +
175A ILE* 1.3 77.2 - - + +
177A GLU* 1.3 64.4 + - - +
179A TYR* 3.3 24.7 + + - +
180A ASN* 3.2 22.2 + - - +
216A ARG* 3.5 55.2 - - + -
219A PHE* 5.2 0.9 - - - -
176C PHE* 3.7 61.0 - + + -
216C ARG* 5.4 2.8 + - - -
219C PHE* 6.4 0.2 - + - -
----------------------------------------------------------
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
----------------------------------------------------------
173A GLY 3.2 4.6 + - - +
174A GLN* 3.6 10.6 - - - +
175A ILE 3.3 0.2 - - - -
176A PHE* 1.3 76.9 - - - +
178A ALA* 1.3 62.1 + - - +
180A ASN* 3.5 5.7 + - - +
181A MET* 3.3 28.9 + - - +
58B SER* 3.4 34.8 + - - +
59B GLU 4.4 0.3 + - - -
60B MET* 3.7 10.4 + - - +
61B GLY* 2.7 37.2 + - - -
88B GLN* 5.1 1.9 + - - -
171C ASN 3.6 12.3 - - - +
172C GLN* 3.7 8.8 + - - +
173C GLY* 2.8 39.9 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
142A VAL* 3.9 21.3 - - + +
143A PRO* 4.4 17.0 - - + -
146A ALA* 4.7 6.7 - - + +
174A GLN 3.0 14.1 + - - +
175A ILE 3.4 8.7 - - - +
177A GLU* 1.3 75.0 - - - +
179A TYR* 1.3 66.3 + - - +
181A MET* 3.4 9.1 + - - +
182A ALA* 2.9 27.0 + - - +
191A PHE* 4.1 8.5 - - + -
61B GLY* 5.2 0.6 - - - -
65B ILE* 5.2 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A TYR* 2.7 25.2 + - - -
170A ALA* 5.3 2.3 + - - +
175A ILE* 2.9 43.1 + - + +
176A PHE* 3.3 34.1 + + - +
178A ALA* 1.3 75.0 - - - +
180A ASN* 1.3 64.3 + - - +
182A ALA* 3.7 0.3 - - - +
183A ALA* 3.0 20.6 + - - +
191A PHE* 4.0 29.6 - + - -
216A ARG* 3.8 14.6 - - - +
217A GLY* 3.8 18.8 - - - +
219A PHE* 3.9 11.4 - + + -
220A ILE* 3.4 26.7 - - + +
252A LEU* 3.7 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A PHE 3.2 8.9 + - - +
177A GLU* 3.6 10.3 + - - +
178A ALA 3.2 0.2 - - - -
179A TYR* 1.3 80.8 - - - +
181A MET* 1.3 58.2 + - - +
183A ALA* 3.8 2.1 - - - +
184A LEU* 2.9 30.2 + - - +
219A PHE* 3.6 14.6 - - + -
56B PRO* 3.5 18.4 - - - +
58B SER* 5.2 1.0 + - - -
171C ASN* 3.5 22.5 + - + +
207C ALA 2.9 23.4 + - - -
208C ALA* 3.6 2.8 - - - -
209C ALA* 3.0 29.7 + - - +
216C ARG* 4.2 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A GLU 3.3 21.6 + - - +
178A ALA 4.1 1.1 - - - +
180A ASN* 1.3 79.7 - - - +
182A ALA* 1.3 57.7 + - - +
184A LEU* 3.2 7.7 + - - +
185A TRP* 2.9 68.2 + - + +
187A LEU* 4.8 0.2 - - - -
56B PRO* 3.7 32.5 - - + -
58B SER* 4.2 9.6 - - - +
61B GLY* 3.4 14.1 - - - -
62B PHE* 3.4 40.4 - - - +
65B ILE* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ALA* 5.1 2.5 - - + -
178A ALA 2.9 18.9 + - - +
179A TYR 3.7 2.7 - - - +
181A MET* 1.3 76.9 - - - +
183A ALA* 1.3 58.2 + - - +
186A LYS 2.9 22.3 + - - -
187A LEU* 3.0 34.4 + - + +
189A CYS* 4.9 2.9 - - + -
191A PHE* 3.7 27.8 - - + -
250A PRO* 3.2 12.9 - - + +
65B ILE* 5.5 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A TYR 3.0 17.3 + - - +
182A ALA* 1.3 74.9 - - - +
184A LEU* 1.3 67.4 + - - +
186A LYS* 3.4 20.3 + - - +
219A PHE* 3.7 25.4 - - + +
220A ILE* 4.1 8.5 - - + -
250A PRO* 3.7 11.4 - - + +
209C ALA* 3.7 12.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN 2.9 17.6 + - - +
181A MET* 3.4 6.5 - - - +
183A ALA* 1.3 79.5 - - - +
185A TRP* 1.3 80.9 + - + +
186A LYS* 3.8 2.9 + - - +
54B ASP 5.6 1.1 - - - +
56B PRO* 3.9 27.6 - - + -
205C GLU 4.1 15.5 - - - +
206C ARG* 3.4 28.9 - - - +
207C ALA 3.9 4.9 - - - +
208C ALA 4.2 0.9 - - - -
209C ALA* 4.1 23.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A LEU* 5.0 13.2 - - + -
153A LYS* 3.0 28.5 + - - +
181A MET* 2.9 55.1 + - + +
184A LEU* 1.3 98.7 - - + +
186A LYS* 1.3 70.1 + - - +
187A LEU* 3.2 27.6 + - + +
26B LEU* 5.1 5.4 - - + -
53B ILE* 3.4 35.3 - - + +
54B ASP 3.7 14.2 + - - -
55B THR* 4.0 15.3 - - + -
56B PRO* 4.5 2.2 - - + -
65B ILE* 4.2 17.9 - - + -
----------------------------------------------------------
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