Contacts of the helix formed by residues 158 - 177 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F VAL* 1.3 73.7 - - - +
159F LEU* 1.3 79.3 + - - +
160F LYS* 2.9 32.0 + - - +
161F THR* 2.9 20.9 + - - +
162F LYS 2.9 18.7 + - - -
32G PRO* 4.8 11.8 - - + +
33G THR 5.5 1.1 - - - +
185G HIS* 3.5 35.6 - - + +
187G LEU* 5.6 2.1 - - - +
225G PHE* 3.5 26.4 - - + +
228G ALA* 5.2 0.3 - - - +
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Residues in contact with LEU 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157F VAL 3.5 3.0 + - - +
158F ASP* 1.3 74.5 + - - +
160F LYS* 1.3 66.8 + - - +
162F LYS* 2.9 39.6 + - + +
163F GLY 3.2 4.5 + - - -
188F ILE* 4.0 26.9 - - + -
185G HIS* 4.5 3.6 + - - +
186G ASP* 3.1 29.4 - - - +
187G LEU* 3.9 27.8 - - + +
188G ILE* 4.2 13.2 - - + -
228G ALA* 3.9 12.6 - - + +
231G LEU* 3.6 11.0 - - + +
232G LEU* 4.3 12.8 - - + -
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Residues in contact with LYS 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F ASP* 2.9 20.0 + - - +
159F LEU* 1.3 80.4 - - - +
161F THR* 1.3 66.2 + - - +
163F GLY 3.6 5.5 + - - -
164F VAL* 3.8 28.5 + - - +
224G GLU* 3.6 34.5 + - + +
225G PHE* 3.6 25.4 - - + +
227G SER* 3.5 25.9 + - - +
228G ALA* 3.4 13.0 - - + +
231G LEU* 3.9 5.5 - - + +
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Residues in contact with THR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLN* 5.7 1.6 - - - +
157F VAL* 3.6 16.8 - - + -
158F ASP* 2.9 25.7 + - - +
160F LYS* 1.3 75.4 - - - +
162F LYS* 1.3 66.2 + - - +
164F VAL* 2.6 38.7 - - + +
165F LEU* 3.0 15.7 + - + +
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Residues in contact with LYS 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LEU* 4.1 33.2 - - + +
155F SER* 6.0 0.2 - - - +
157F VAL* 3.8 14.4 + - + +
158F ASP 2.9 11.4 + - - +
159F LEU* 2.9 33.5 + - + +
161F THR* 1.3 74.2 - - - +
163F GLY* 1.3 66.0 + - - +
165F LEU* 2.8 10.2 + - - +
166F MET* 2.7 32.8 + - - +
186F ASP* 2.8 33.4 + - - +
188F ILE* 4.7 6.2 - - + +
189F GLU* 3.4 27.5 + - + -
231G LEU* 5.4 0.2 - - + -
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Residues in contact with GLY 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F LEU 3.2 7.5 + - - -
161F THR 3.3 0.4 - - - -
162F LYS* 1.3 79.7 - - - +
164F VAL* 1.3 63.5 + - - +
166F MET* 3.1 20.8 + - - +
167F GLU* 3.1 23.8 + - - +
170F ARG* 5.5 0.2 + - - -
231G LEU* 3.2 30.8 - - - +
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Residues in contact with VAL 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160F LYS* 3.8 33.4 + - - +
161F THR* 2.6 33.0 + - + +
163F GLY* 1.3 75.2 - - - +
165F LEU* 1.3 75.3 + - + +
167F GLU* 3.3 15.5 + - - +
168F GLU* 3.2 31.4 + - - +
231G LEU* 4.7 0.8 - - + +
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Residues in contact with LEU 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F GLY* 5.4 0.4 - - - -
133F GLN* 3.3 44.4 - - + +
134F ARG* 6.2 1.1 - - - +
154F LEU* 3.9 25.6 - - + -
157F VAL* 4.1 18.6 - - + -
161F THR* 3.5 19.1 - - + +
162F LYS* 2.8 13.2 + - - +
164F VAL* 1.3 79.4 - - + +
166F MET* 1.3 66.9 + - - +
168F GLU* 2.9 36.5 + - + +
169F LEU* 3.0 17.1 + - + +
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Residues in contact with MET 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F LEU* 3.8 11.0 - - + -
162F LYS* 2.7 38.3 + - - +
163F GLY* 3.5 12.8 - - - +
165F LEU* 1.3 70.9 - - - +
167F GLU* 1.3 64.4 + - - +
169F LEU* 2.8 18.3 + - - +
170F ARG* 3.0 16.3 + - - +
188F ILE* 4.3 5.6 - - - +
189F GLU* 3.0 48.0 - - + -
192F MET* 3.6 31.9 - - + -
193F LEU* 3.2 32.0 - - + +
231G LEU* 6.6 0.2 - - - -
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163F GLY 3.1 23.4 + - - +
164F VAL* 3.5 12.3 + - - +
166F MET* 1.3 77.3 - - - +
168F GLU* 1.3 57.7 + - + +
170F ARG* 3.2 39.4 + - - +
171F PHE* 3.0 28.1 + - - +
231G LEU* 4.5 13.0 - - - +
234G LYS* 4.6 10.6 + - - -
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Residues in contact with GLU 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F LEU* 6.1 0.5 - - - +
134F ARG* 3.5 35.2 + - - +
137F LEU* 6.5 0.7 - - + -
164F VAL* 3.2 20.7 + - - +
165F LEU* 2.9 34.8 + - + +
167F GLU* 1.3 75.6 - - + +
169F LEU* 1.3 58.5 + - + +
171F PHE* 3.4 9.4 + - + +
172F VAL* 2.8 38.9 + - + +
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Residues in contact with LEU 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F TYR* 3.3 32.4 - - + +
137F LEU* 4.5 23.6 - - + -
150F LEU* 4.4 16.8 - - + -
153F PRO* 5.2 2.7 - - + -
154F LEU* 4.2 20.4 - - + -
165F LEU 3.0 14.7 + - - +
166F MET* 2.8 8.8 + - - +
168F GLU* 1.3 74.5 - - + +
170F ARG* 1.3 67.3 + - - +
172F VAL* 3.1 5.9 + - + +
173F GLN* 2.8 24.3 + - - +
180F ILE* 4.7 5.8 - - + +
182F HIS* 3.8 19.1 - - + -
193F LEU* 3.9 11.0 - - + -
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Residues in contact with ARG 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F TYR* 4.8 5.6 - - + -
163F GLY 5.5 0.2 + - - -
166F MET* 3.0 19.3 + - - +
167F GLU* 3.2 42.6 + - - +
169F LEU* 1.3 76.7 - - - +
171F PHE* 1.3 65.9 + - - +
173F GLN* 3.0 8.1 + - - +
174F ARG* 2.9 47.7 + - - +
192F MET* 3.2 52.2 + - - +
193F LEU* 3.7 15.6 - - + +
231G LEU* 6.2 1.2 - - - +
234G LYS* 5.8 6.5 - - - +
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Residues in contact with PHE 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LYS 5.6 5.4 - - - -
167F GLU 3.0 14.7 + - - +
168F GLU* 3.5 10.3 - - + +
170F ARG* 1.3 79.5 - - - +
172F VAL* 1.3 60.5 + - + +
174F ARG* 3.0 11.9 + - + +
175F GLU* 2.6 71.9 + - + +
176F PHE* 6.0 1.1 - + - -
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Residues in contact with VAL 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F LEU* 4.7 13.9 - - + -
137F LEU* 4.1 28.0 - - + -
141F LEU* 3.9 20.4 - - + -
148F LEU* 5.7 0.9 - - + -
168F GLU* 2.8 36.4 + - + +
169F LEU* 3.5 7.4 - - + +
171F PHE* 1.3 79.2 - - + +
173F GLN* 1.3 57.3 + - - +
175F GLU* 4.1 1.1 - - - -
176F PHE* 2.8 61.1 + - + +
178F VAL* 5.5 0.6 - - + +
180F ILE* 5.5 6.5 - - + -
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Residues in contact with GLN 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ARG 5.6 0.2 - - - -
25F ASP* 2.9 11.8 - - - +
26F TYR* 2.7 49.6 + - + +
169F LEU 2.8 12.6 + - - +
170F ARG* 3.4 9.4 + - - +
172F VAL* 1.3 76.5 - - - +
174F ARG* 1.3 72.0 + - - +
177F ASP* 2.8 29.4 + - - +
178F VAL* 3.2 27.1 - - - +
180F ILE* 3.9 15.5 - - + +
195F ASP* 4.5 5.9 + - - -
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Residues in contact with ARG 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F ARG* 2.9 37.1 + - - +
171F PHE* 3.6 11.7 - - + +
173F GLN* 1.3 85.6 - - - +
175F GLU* 1.3 61.4 + - - +
177F ASP* 3.2 21.0 - - - +
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Residues in contact with GLU 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113F LYS* 5.4 7.4 + - + +
171F PHE* 2.6 55.2 + - + +
172F VAL* 3.8 4.0 - - - +
174F ARG* 1.3 75.9 - - - +
176F PHE* 1.3 82.0 + - + +
177F ASP* 5.2 1.6 - - - +
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Residues in contact with PHE 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F MET* 3.9 33.7 - - + -
113F LYS* 4.0 38.8 - - + -
114F LEU* 5.2 3.8 - - + -
141F LEU* 4.1 15.3 - - + -
171F PHE* 6.0 1.1 - + - -
172F VAL* 2.8 52.7 + - + +
175F GLU* 1.3 97.3 - - + +
177F ASP* 1.3 73.0 + - - +
178F VAL* 3.0 24.2 + - + +
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Residues in contact with ASP 177 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F ARG 5.7 1.8 - - - -
173F GLN* 2.8 13.2 + - - +
174F ARG* 3.2 19.9 - - - +
175F GLU 5.2 1.5 - - - +
176F PHE* 1.3 79.2 - - - +
178F VAL* 1.3 58.2 + - - +
179F PRO* 3.7 9.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
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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