Contacts of the helix formed by residues 159 - 173 (chain B) in PDB entry 2O1X
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 GLY 159 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 3.8 13.2 - - - -
155B GLY 4.3 0.4 + - - -
156B SER 3.2 7.5 + - - -
157B LEU 3.7 1.0 - - - +
158B THR* 1.3 80.0 - - - +
160B GLY* 1.3 66.9 + - - -
161B MET* 3.0 5.5 + - - -
162B ALA* 3.1 13.3 + - - +
163B LEU* 3.1 12.0 + - - +
371B ILE 3.5 22.7 + - - -
372B ALA* 4.9 0.7 - - - -
401B ARG* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A GLY* 3.2 34.5 - - - -
164A ALA* 4.0 9.1 - - - +
374A GLU* 5.8 1.6 - - - -
158B THR 3.7 2.2 + - - -
159B GLY* 1.3 70.7 - - - -
161B MET* 1.3 52.7 + - - +
163B LEU* 4.6 3.1 - - - -
164B ALA* 2.8 38.5 + - - +
372B ALA* 5.1 0.6 - - - +
374B GLU* 4.5 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A GLU* 4.3 17.4 - - + +
375A VAL* 4.0 4.4 - - + +
378A THR* 3.2 36.6 - - - +
405A GLN* 3.3 26.0 - - + +
409A ASP* 3.4 11.9 - - - +
126B SER* 3.4 21.3 - - - +
127B THR* 3.7 11.9 - - + -
130B THR* 3.7 18.1 - - + +
159B GLY* 3.0 0.4 - - - -
160B GLY* 1.3 75.3 - - - +
162B ALA* 1.3 63.4 + - - +
164B ALA* 4.9 2.2 - - - -
165B ALA* 3.1 24.9 + - - +
374B GLU* 5.5 4.9 + - - +
401B ARG* 3.8 24.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 162 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B SER* 3.7 10.5 + - - +
129B LEU* 3.8 11.5 - - + +
152B ILE* 3.9 21.5 - - + -
156B SER 3.5 24.0 - - - +
157B LEU* 3.8 10.5 - - + +
159B GLY 3.1 4.8 + - - +
161B MET* 1.3 77.6 - - - +
163B LEU* 1.3 65.9 + - - +
165B ALA* 3.2 4.3 + - - +
166B LEU* 3.1 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 3.7 46.5 - - + +
164A ALA* 4.0 9.4 - - - +
167A ASN* 4.6 9.0 - - + +
251A MET* 4.4 8.5 - - + -
157B LEU* 3.4 31.4 - - + +
158B THR* 4.2 8.7 - - - +
159B GLY 3.1 8.5 + - - +
160B GLY* 3.9 3.6 - - - +
162B ALA* 1.3 79.5 - - - +
164B ALA* 1.3 65.4 + - - +
166B LEU* 3.8 6.0 + - + -
167B ASN 3.6 4.9 + - - -
195B ASN 4.1 17.3 - - - +
196B LYS* 4.6 5.6 - - + +
248B PHE* 5.6 0.4 - - + -
251B MET* 3.6 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR 3.9 10.0 - - - +
160A GLY* 3.8 20.6 - - - +
163A LEU* 3.9 9.8 - - - +
372A ALA* 4.2 8.1 - - + -
374A GLU* 5.2 1.1 - - - +
375A VAL* 3.8 18.8 - - + -
160B GLY 2.8 21.6 + - - +
161B MET* 4.9 0.4 - - - -
163B LEU* 1.3 68.9 - - - +
165B ALA* 1.3 67.4 + - - +
167B ASN* 3.1 15.0 + - - +
168B THR* 3.1 13.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375A VAL* 3.9 8.2 - - + +
129B LEU* 3.9 20.2 - - + -
130B THR* 3.6 23.3 - - + +
133B LEU* 5.3 1.5 - - + +
161B MET 3.1 22.4 + - - +
162B ALA 3.2 5.4 + - - +
164B ALA* 1.3 75.4 - - - +
166B LEU* 1.3 50.4 + - - +
168B THR* 2.8 11.0 + - - +
169B ILE* 2.6 39.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 4.0 12.3 - - + -
157B LEU* 4.2 15.3 - - + -
162B ALA 3.1 18.0 + - - +
163B LEU* 3.9 6.1 - - + +
165B ALA* 1.3 73.6 - - - +
167B ASN* 1.3 54.0 + - - +
169B ILE* 3.5 7.6 - - + +
170B GLY* 2.7 33.4 + - - -
178B ILE* 3.9 30.3 - - + -
248B PHE* 3.6 35.4 - - + -
251B MET* 3.8 30.3 - - + +
253B VAL* 4.3 7.9 - - + +
282B ILE* 4.1 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 3.6 32.1 + - - +
163A LEU* 4.8 3.8 - - + -
191A VAL 4.5 1.0 + - - -
192A GLY 2.8 19.0 + - - +
193A ALA* 2.8 28.7 - - - +
194A MET* 2.8 50.7 + - - +
163B LEU 3.6 6.4 + - - +
164B ALA* 3.1 12.4 + - - +
166B LEU* 1.3 79.6 - - - +
168B THR* 1.3 63.1 + - - +
171B ASP* 3.4 2.9 + - - +
251B MET* 3.9 14.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A THR* 5.7 0.5 - - - +
192A GLY 5.1 0.2 - - - -
367A LEU* 4.6 4.5 - - + -
368A ASP 5.5 0.9 - - - +
369A VAL* 3.6 44.0 + - + +
372A ALA* 5.9 0.2 - - - +
375A VAL* 4.3 6.4 - - + +
133B LEU* 3.6 26.0 - - + -
164B ALA 3.1 9.2 + - - -
165B ALA* 2.8 11.8 + - - -
167B ASN* 1.3 79.0 + - - +
169B ILE* 1.3 64.0 + - - -
171B ASP* 3.2 7.9 + - + +
172B MET* 3.0 31.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B LEU* 3.7 34.5 - - + +
133B LEU* 4.0 20.9 - - + -
165B ALA* 2.6 28.8 + - + +
166B LEU* 3.5 11.4 - - + +
168B THR* 1.3 72.9 - - - +
170B GLY* 1.3 57.9 + - - +
172B MET* 3.3 2.4 + - - +
173B GLY* 2.9 27.2 + - - -
174B ARG 4.2 2.2 + - - +
176B MET* 3.9 30.3 - - + -
178B ILE* 4.2 15.5 - - + -
253B VAL* 4.8 4.3 - - + -
280B PRO* 3.5 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 4.1 3.1 - - - -
196A LYS* 5.2 0.9 + - - -
166B LEU 2.7 15.0 + - - -
169B ILE* 1.3 74.0 - - - +
171B ASP* 1.3 62.8 + - - +
173B GLY* 3.4 9.9 + - - -
251B MET 3.0 27.8 - - - -
252B GLY* 4.1 11.9 - - - +
253B VAL* 4.0 8.9 - - - +
280B PRO* 4.5 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.8 13.0 - - - +
192A GLY* 2.8 31.6 + - - -
193A ALA* 3.5 14.4 - - - +
196A LYS* 2.7 47.5 + - - +
368A ASP 5.2 1.4 - - - +
167B ASN 3.4 11.1 + - - +
168B THR* 3.2 11.8 + - + +
170B GLY* 1.3 77.7 - - - +
172B MET* 1.3 70.9 + - - +
173B GLY* 4.3 0.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 6.2 1.8 - - + -
366A TYR 5.5 3.8 - - - +
367A LEU* 3.6 31.6 - - + -
133B LEU* 4.2 18.6 - - + -
137B LEU* 4.1 9.2 - - + -
168B THR* 3.0 23.9 + - + +
169B ILE 3.8 3.4 - - - +
171B ASP* 1.3 83.5 - - - +
173B GLY* 1.3 64.7 + - - +
174B ARG* 3.3 52.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169B ILE 2.9 14.8 + - - -
170B GLY 3.4 7.4 + - - -
171B ASP 3.2 4.4 - - - -
172B MET* 1.3 76.9 - - - +
174B ARG* 1.3 62.6 + - - -
252B GLY 5.9 0.2 - - - -
279B GLY* 3.8 9.6 + - - -
280B PRO* 3.7 16.2 - - - -
----------------------------------------------------------
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