Contacts of the helix formed by residues 165 - 181 (chain A) in PDB entry 2O0K
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 165 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 5.8 0.7 - - - -
142A TYR* 3.6 4.1 + - - -
143A GLN* 3.7 13.5 + - - -
163A GLN* 3.5 3.4 - - - +
164A LEU* 1.3 79.6 - - - +
166A LYS* 1.3 63.3 + - - +
167A THR* 3.4 4.1 + - - -
168A THR* 3.6 15.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A TYR* 4.1 9.0 - - + +
146A MET* 5.0 1.8 - - + -
160A LEU* 3.5 33.9 - - + -
161A SER 5.9 1.6 - - - +
164A LEU* 3.6 2.9 - - + -
165A GLY* 1.3 72.8 - - - +
167A THR* 1.3 76.9 + - - +
168A THR 3.1 3.1 - - - -
169A VAL* 2.9 31.3 - - + +
170A VAL* 3.2 15.4 + - + +
199A VAL* 5.3 0.2 - - - +
253A TYR* 3.0 12.3 + - - -
255A GLU* 2.4 45.7 + - - +
256A ASP* 5.8 0.2 - - - -
285A THR* 3.9 14.1 - - - +
286A THR* 5.9 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 167 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY 3.4 1.8 - - - -
166A LYS* 1.3 99.4 + - - +
168A THR* 1.3 57.4 - - - +
170A VAL* 4.2 4.7 - - + -
171A ALA* 2.8 28.1 + - - +
198A GLU* 5.4 6.9 + - + +
199A VAL* 4.5 23.6 - - + -
202A ARG* 2.9 37.9 - - + -
255A GLU* 4.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 168 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A ILE* 4.8 12.1 - - + +
137A VAL* 4.2 27.1 - - + -
143A GLN* 4.1 9.9 - - - +
165A GLY* 3.6 14.3 + - - -
166A LYS 3.1 0.8 - - - -
167A THR* 1.3 79.4 - - - +
169A VAL* 1.3 62.2 + - - +
171A ALA* 3.6 4.4 - - - +
172A ILE* 3.0 35.8 + - + +
202A ARG* 2.8 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A LEU* 5.0 1.1 - - + -
143A GLN* 3.6 36.4 - - + +
146A MET* 4.1 28.0 - - + -
147A LEU* 3.4 34.5 - - + -
150A MET* 4.2 7.9 - - + -
166A LYS* 2.9 29.5 - - - +
168A THR* 1.3 77.7 - - - +
170A VAL* 1.3 66.3 + - + +
172A ILE* 3.3 9.8 + - - +
173A PHE* 3.0 22.7 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
146A MET* 5.2 2.0 - - + -
150A MET* 5.1 7.2 - - + -
166A LYS* 3.2 23.7 + - + +
167A THR* 3.3 10.3 + - - +
169A VAL* 1.3 81.9 - - + +
171A ALA* 1.3 62.5 + - - +
173A PHE* 3.2 8.1 + - + +
174A LEU* 3.2 33.6 + - + +
199A VAL* 4.1 14.6 - - + -
253A TYR* 3.8 48.7 - - + +
285A THR* 4.4 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 171 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A THR* 2.8 18.8 + - + +
168A THR* 3.6 7.2 - - - +
170A VAL* 1.3 76.8 - - - +
172A ILE* 1.3 63.2 + - + +
175A ALA* 3.2 24.3 + - - +
199A VAL* 4.8 1.3 - - - +
202A ARG* 3.8 40.6 - - + +
203A THR* 3.5 18.5 - - - +
206A ALA* 4.9 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 172 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 5.3 2.5 - - + -
120A PHE* 4.1 6.0 - - + -
121A ALA* 4.0 19.5 - - + +
125A CYS* 3.7 40.6 - - + -
137A VAL* 4.7 9.0 - - + -
139A LEU* 4.4 18.6 - - + -
147A LEU* 4.4 10.3 - - + -
168A THR* 3.0 31.6 + - + +
169A VAL* 3.5 12.6 - - - +
171A ALA* 1.3 77.5 - - + +
173A PHE* 1.3 61.8 + - - +
175A ALA* 3.3 7.8 + - - +
176A HIS* 3.1 20.3 + - - +
206A ALA* 5.1 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ILE* 3.5 24.2 - - + -
147A LEU* 4.1 12.6 - - + -
150A MET* 3.7 33.7 - - + -
151A SER* 3.9 25.1 - - - -
169A VAL 3.0 13.4 + - - +
170A VAL* 3.2 9.8 + - + +
172A ILE* 1.3 78.4 - - - +
174A LEU* 1.3 64.5 + - + +
176A HIS* 3.1 9.2 + + - +
177A PHE* 2.9 30.3 + + + +
251A MET* 3.3 25.4 - - + -
281A LYS* 4.3 8.1 - - - -
283A ILE* 3.2 30.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 3.2 29.0 + - + +
173A PHE* 1.3 79.0 - - + +
175A ALA* 1.3 65.8 + - - +
176A HIS 3.1 1.6 - - - -
177A PHE* 3.7 3.4 - - - +
178A VAL* 3.1 29.5 + - - +
186A VAL* 3.9 21.3 - - + -
188A ILE* 4.2 29.2 - - + -
199A VAL* 4.5 2.5 - - + -
203A THR* 3.9 24.0 - - + +
234A ILE* 4.3 8.3 - - + -
251A MET* 3.8 30.5 - - + -
253A TYR* 4.8 9.6 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
120A PHE* 4.6 9.6 - - + -
125A CYS* 6.0 0.9 - - - -
171A ALA 3.2 18.3 + - - +
172A ILE* 3.5 8.3 - - - +
174A LEU* 1.3 77.7 - - - +
176A HIS* 1.3 56.0 + - - +
178A VAL* 4.0 0.4 - - - +
179A CYS* 2.7 37.0 + - - +
203A THR* 3.8 9.8 - - + +
206A ALA* 4.5 9.4 - - + +
207A ILE* 3.8 28.9 - - + +
210A LEU* 5.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 176 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A CYS 2.8 29.4 - - - -
114A ARG 3.6 14.1 + - - -
117A ILE* 3.8 39.2 + - + +
120A PHE* 3.4 29.7 - - + -
151A SER* 5.7 2.4 + - - -
172A ILE 3.1 11.7 + - - +
173A PHE* 3.3 12.3 - + - +
174A LEU 3.1 0.2 - - - -
175A ALA* 1.3 77.3 - - - +
177A PHE* 1.3 68.4 + + - +
179A CYS 3.3 0.2 + - - -
180A PHE* 3.0 51.6 + + + +
181A ASN* 5.6 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 2.9 23.1 + + + +
174A LEU* 3.7 7.2 - - + +
176A HIS* 1.3 79.5 - - - +
178A VAL* 1.3 63.0 + - + +
181A ASN* 2.6 51.5 + - - +
184A LYS* 3.7 36.1 - - + -
186A VAL* 3.5 27.8 - - + -
250A ALA* 4.8 5.8 - - + -
251A MET* 3.4 40.8 - - + -
281A LYS* 3.8 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU 3.1 15.4 + - - +
175A ALA* 4.0 8.1 - - - +
177A PHE* 1.3 79.0 - - + +
179A CYS* 1.3 56.3 + - - +
180A PHE 3.4 0.2 - - - -
181A ASN 3.4 4.0 - - - +
186A VAL* 4.0 14.4 - - + -
207A ILE* 4.4 9.0 - - + -
226A ILE* 5.0 0.9 - - + -
228A LEU* 3.7 25.7 - - + +
230A ASN* 2.7 30.0 - - - +
232A SER* 3.7 17.6 + - - -
233A SER 4.0 10.5 - - - +
234A ILE* 3.6 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 4.8 7.1 + - - -
120A PHE* 5.3 0.9 - - + -
175A ALA* 2.7 29.6 + - - +
176A HIS* 3.3 3.5 + - - +
177A PHE 3.2 1.0 - - - -
178A VAL* 1.3 84.5 - - - +
180A PHE* 1.3 77.9 + - + +
181A ASN 3.6 0.8 + - - -
207A ILE* 4.9 7.4 - - - -
210A LEU* 3.9 23.3 - - - -
214A LEU 4.2 6.8 - - - +
216A PRO* 3.7 35.9 - - + +
228A LEU* 5.2 0.2 - - - -
230A ASN* 4.1 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 180 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A TRP* 3.6 55.3 - + - -
113A CYS* 3.4 19.7 - - + -
114A ARG* 3.4 38.1 - - + +
120A PHE* 3.9 17.3 - + - -
176A HIS* 3.0 57.1 + + - +
179A CYS* 1.3 86.7 - - + +
181A ASN* 1.3 68.9 + - - +
214A LEU* 3.8 15.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A HIS* 4.3 4.2 + - - -
177A PHE* 2.6 53.4 + - + +
178A VAL 3.4 1.7 - - - +
179A CYS 3.6 0.6 - - - -
180A PHE* 1.3 88.6 - - - +
182A LYS* 1.3 56.4 + - - +
184A LYS* 3.7 27.3 - - + +
230A ASN* 3.2 11.9 - - - +
232A SER* 2.5 25.0 + - - +
----------------------------------------------------------
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