Contacts of the helix formed by residues 158 - 177 (chain B) in PDB entry 2ONK
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 158 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A PRO* 4.8 11.9 - - + +
33A THR 5.7 1.3 - - - +
185A HIS* 3.7 27.4 - - + +
187A LEU* 5.4 1.9 - - - +
225A PHE* 3.5 34.8 - - + +
228A ALA* 4.9 0.5 - - - +
157B VAL* 1.3 74.0 - - - +
159B LEU* 1.3 80.2 + - - +
160B LYS* 2.9 34.1 + - - +
161B THR* 2.9 21.4 + - - +
162B LYS 2.9 18.5 + - - -
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Residues in contact with LEU 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A HIS* 4.4 2.6 + - - -
186A ASP* 3.2 28.0 - - - +
187A LEU* 3.8 30.7 - - + +
188A ILE* 4.1 6.1 - - + +
228A ALA* 3.7 13.0 - - + +
231A LEU* 3.5 10.4 - - + +
232A LEU* 4.0 21.3 - - + -
157B VAL 3.5 3.4 + - - -
158B ASP* 1.3 75.1 + - - +
160B LYS* 1.3 66.8 + - - +
162B LYS* 2.9 40.7 + - + +
163B GLY 3.2 4.3 + - - -
188B ILE* 4.0 27.1 - - + -
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A GLU* 3.8 29.0 + - + +
225A PHE* 3.6 23.3 - - + +
227A SER* 3.3 25.8 + - - +
228A ALA* 3.2 14.5 - - + +
231A LEU* 3.6 8.2 - - + +
158B ASP* 2.9 21.0 + - - +
159B LEU* 1.3 79.8 - - - +
161B THR* 1.3 66.9 + - - +
163B GLY 3.6 5.4 + - - -
164B VAL* 3.8 27.3 - - - +
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Residues in contact with THR 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B GLN* 5.7 1.6 - - - +
157B VAL* 3.6 17.0 - - + -
158B ASP* 2.9 25.8 + - - +
160B LYS* 1.3 76.5 - - - +
162B LYS* 1.3 66.0 + - - +
164B VAL* 2.6 39.1 - - + +
165B LEU* 3.0 15.1 + - + +
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Residues in contact with LYS 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 4.1 33.7 - - + +
157B VAL* 3.8 14.8 + - + +
158B ASP 2.9 12.0 + - - +
159B LEU* 2.9 33.7 + - + +
161B THR* 1.3 73.6 - - - +
163B GLY* 1.3 64.5 - - - +
165B LEU* 2.8 10.3 + - - +
166B MET* 2.7 32.7 + - - +
186B ASP* 2.9 33.7 + - - +
188B ILE* 4.7 6.3 - - + +
189B GLU* 3.4 28.0 + - + -
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Residues in contact with GLY 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.2 29.0 - - - +
159B LEU 3.2 7.5 + - - -
161B THR 3.3 0.2 - - - -
162B LYS* 1.3 77.9 - - - +
164B VAL* 1.3 64.5 + - - +
166B MET* 3.1 15.5 + - - +
167B GLU* 3.1 30.8 + - - +
170B ARG* 5.5 0.2 + - - -
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Residues in contact with VAL 164 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.6 1.5 - - + +
160B LYS* 3.8 33.8 + - - +
161B THR* 2.6 33.7 - - + +
163B GLY* 1.3 74.7 - - - +
165B LEU* 1.3 75.8 + - + +
167B GLU* 3.3 14.4 + - - +
168B GLU* 3.2 32.0 + - - +
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Residues in contact with LEU 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B GLY* 5.4 0.2 - - - -
133B GLN* 3.3 44.9 - - + +
134B ARG* 6.2 1.1 - - - +
154B LEU* 3.9 24.2 - - + -
157B VAL* 4.1 19.5 - - + -
161B THR* 3.5 19.5 - - + +
162B LYS* 2.8 13.5 + - - +
164B VAL* 1.3 78.9 - - + +
166B MET* 1.3 64.8 + - - +
168B GLU* 2.9 37.3 + - + +
169B LEU* 3.0 17.0 + - - +
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Residues in contact with MET 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B LEU* 3.8 11.2 - - + -
162B LYS* 2.7 39.7 + - - +
163B GLY* 3.5 11.9 - - - +
165B LEU* 1.3 70.9 - - - +
167B GLU* 1.3 65.1 + - - +
169B LEU* 2.8 17.9 + - - +
170B ARG* 3.0 16.1 + - - +
188B ILE* 4.3 4.9 - - - +
189B GLU* 3.0 48.0 - - + -
192B MET* 3.6 28.9 - - + -
193B LEU* 3.2 35.4 - - + +
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Residues in contact with GLU 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 4.4 12.5 - - - +
234A LYS* 4.6 11.1 + - - -
163B GLY 3.1 23.3 + - - +
164B VAL* 3.4 12.9 + - - +
165B LEU 3.2 0.2 - - - -
166B MET* 1.3 76.4 - - - +
168B GLU* 1.3 58.3 + - + +
170B ARG* 3.2 40.1 + - - +
171B PHE* 3.0 28.6 + - - +
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 6.1 0.7 - - - +
134B ARG* 3.5 35.0 + - - +
137B LEU* 6.5 0.4 - - + -
164B VAL* 3.2 21.2 + - + +
165B LEU* 2.9 35.8 + - + +
167B GLU* 1.3 75.2 - - + +
169B LEU* 1.3 59.0 + - + +
171B PHE* 3.5 9.4 - - + +
172B VAL* 2.8 39.6 + - + +
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.3 32.2 - - + +
137B LEU* 4.5 24.0 - - + -
150B LEU* 4.4 15.5 - - + -
153B PRO* 5.2 2.7 - - + -
154B LEU* 4.2 19.5 - - + -
165B LEU 3.0 15.3 + - - +
166B MET* 2.8 7.9 + - - +
168B GLU* 1.3 74.8 - - + +
170B ARG* 1.3 66.7 + - - +
172B VAL* 3.1 5.9 + - + +
173B GLN* 2.8 24.3 + - - +
180B ILE* 4.7 6.2 - - + +
182B HIS* 3.8 18.2 - - + -
193B LEU* 3.9 11.2 - - + -
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Residues in contact with ARG 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A LYS* 6.2 1.4 - - - +
26B TYR* 4.8 5.2 - - - -
163B GLY 5.5 0.4 + - - -
166B MET* 3.0 18.6 + - - +
167B GLU* 3.2 43.7 + - - +
169B LEU* 1.3 75.5 - - - +
171B PHE* 1.3 64.9 + - - +
173B GLN* 3.0 7.7 + - - +
174B ARG* 2.9 48.5 + - - +
192B MET* 3.2 51.4 + - - +
193B LEU* 3.7 15.4 - - + +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS 5.7 4.9 - - - -
167B GLU 3.0 13.9 + - - +
168B GLU* 3.5 10.1 - - + +
170B ARG* 1.3 80.2 - - - +
172B VAL* 1.3 60.9 + - + +
174B ARG* 2.9 11.5 + - + +
175B GLU* 2.6 72.4 + - + +
176B PHE* 6.0 1.6 - + - -
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Residues in contact with VAL 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 4.6 13.9 - - + -
137B LEU* 4.1 27.8 - - + -
141B LEU* 3.9 20.6 - - + -
148B LEU* 5.7 0.9 - - + -
168B GLU* 2.8 35.8 + - + +
169B LEU* 3.5 7.9 - - + +
171B PHE* 1.3 78.6 - - + +
173B GLN* 1.3 58.8 + - - +
175B GLU* 4.1 1.1 - - - -
176B PHE* 2.8 60.2 + - + +
178B VAL* 5.5 0.6 - - + +
180B ILE* 5.5 6.1 - - + -
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Residues in contact with GLN 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG 5.5 0.4 - - - -
25B ASP* 2.9 13.7 - - - +
26B TYR* 2.7 47.4 + - + +
169B LEU 2.8 13.0 + - - +
170B ARG* 3.4 9.6 + - - +
172B VAL* 1.3 75.8 - - - +
174B ARG* 1.3 69.2 + - - +
177B ASP* 2.8 29.4 + - - -
178B VAL* 3.2 27.4 + - - +
180B ILE* 3.9 16.6 - - + +
195B ASP* 4.5 5.7 + - - -
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Residues in contact with ARG 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ARG* 2.9 37.7 + - - +
171B PHE* 3.6 11.7 - - + +
173B GLN* 1.3 87.5 - - - +
175B GLU* 1.3 60.2 - - - +
177B ASP* 3.2 21.5 - - - +
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Residues in contact with GLU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LYS* 5.4 7.9 + - + +
171B PHE* 2.6 57.4 + - + +
172B VAL* 3.8 4.0 - - - +
174B ARG* 1.3 76.0 - - - +
176B PHE* 1.3 82.9 + - + +
177B ASP* 3.5 1.6 - - - -
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Residues in contact with PHE 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B MET* 3.9 33.9 - - + -
113B LYS* 4.0 37.5 - - + -
114B LEU* 5.2 4.0 - - + -
141B LEU* 4.1 14.8 - - + -
171B PHE* 6.0 1.6 - + - -
172B VAL* 2.8 52.9 + - + +
175B GLU* 1.3 96.2 - - + +
177B ASP* 1.3 72.9 + - - +
178B VAL* 3.0 23.7 + - + +
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Residues in contact with ASP 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ARG 5.7 1.1 - - - -
173B GLN* 2.8 12.8 + - - +
174B ARG* 3.2 20.5 - - - +
175B GLU 5.2 1.6 - - - -
176B PHE* 1.3 79.7 - - - +
178B VAL* 1.3 59.5 + - - +
179B PRO* 3.7 9.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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