Contacts of the helix formed by residues 158 - 177 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A VAL* 1.3 74.1 - - - +
159A LEU* 1.3 79.8 + - - +
160A LYS* 2.9 32.5 + - - +
161A THR* 2.9 21.2 + - - +
162A LYS 2.9 18.5 + - - -
32B PRO* 4.6 12.9 - - + +
33B THR 5.6 0.8 - - - +
185B HIS* 3.5 30.8 - - + +
187B LEU* 5.3 2.1 - - - +
225B PHE* 3.3 34.0 - - + +
228B ALA* 5.0 0.7 - - - +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A VAL 3.5 2.8 + - - -
158A ASP* 1.3 74.7 + - - +
160A LYS* 1.3 65.5 + - - +
162A LYS* 2.9 39.4 + - + +
163A GLY 3.2 4.7 + - - -
188A ILE* 4.0 27.4 - - + -
185B HIS* 4.3 3.4 + - - -
186B ASP* 3.2 28.3 - - - +
187B LEU* 3.7 32.3 - - + +
188B ILE* 4.0 8.3 - - + +
228B ALA* 3.8 13.7 - - + +
231B LEU* 3.6 8.7 - - + +
232B LEU* 4.0 18.4 - - + -
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Residues in contact with LYS 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ASP* 2.9 18.8 + - - +
159A LEU* 1.3 79.4 - - - +
161A THR* 1.3 66.9 + - - +
163A GLY 3.6 5.0 + - - -
164A VAL* 3.8 26.4 - - + +
224B GLU* 3.5 32.2 + - + +
225B PHE* 3.4 25.8 - - + +
227B SER* 3.3 26.8 + - - +
228B ALA* 3.2 14.7 - - + +
231B LEU* 3.7 7.8 - - + +
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Residues in contact with THR 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A GLN* 5.7 1.6 - - - +
157A VAL* 3.6 16.4 - - + -
158A ASP* 2.9 26.4 + - - +
160A LYS* 1.3 77.3 - - - +
162A LYS* 1.3 66.6 + - - +
164A VAL* 2.6 38.7 - - + +
165A LEU* 3.0 16.1 + - + +
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Residues in contact with LYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A LEU* 4.1 32.5 - - + +
155A SER* 6.0 0.4 - - - +
157A VAL* 3.8 14.8 + - + +
158A ASP 2.9 12.8 + - - +
159A LEU* 2.9 34.4 + - + +
161A THR* 1.3 74.0 - - - +
163A GLY* 1.3 65.0 + - - +
165A LEU* 2.8 10.0 + - - +
166A MET* 2.7 32.9 + - - +
186A ASP* 2.8 33.1 + - - +
188A ILE* 4.7 6.1 - - + +
189A GLU* 3.4 26.6 + - + -
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Residues in contact with GLY 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A LEU 3.2 7.7 + - - -
161A THR 3.3 0.2 - - - -
162A LYS* 1.3 78.6 - - - +
164A VAL* 1.3 63.7 + - - +
166A MET* 3.1 20.7 + - - +
167A GLU* 3.1 23.4 + - - +
170A ARG* 5.5 0.3 + - - -
231B LEU* 3.1 30.8 - - - +
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Residues in contact with VAL 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LYS* 3.8 32.9 + - - +
161A THR* 2.6 33.4 - - + +
163A GLY* 1.3 75.7 - - - +
165A LEU* 1.3 76.0 + - + +
167A GLU* 3.3 14.1 + - - +
168A GLU* 3.2 31.1 + - - +
231B LEU* 4.5 1.1 - - + +
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Residues in contact with LEU 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A GLY* 5.4 0.7 - - - -
133A GLN* 3.3 44.4 - - + +
134A ARG* 6.2 1.1 - - - +
154A LEU* 3.9 24.5 - - + -
157A VAL* 4.1 12.8 - - + -
161A THR* 3.5 24.9 - - + +
162A LYS* 2.8 13.7 + - - +
164A VAL* 1.3 78.7 - - + +
166A MET* 1.3 65.8 + - - +
168A GLU* 2.9 37.4 + - + +
169A LEU* 3.0 17.1 + - + +
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Residues in contact with MET 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A LEU* 3.8 10.3 - - + -
162A LYS* 2.7 39.7 + - - +
163A GLY* 3.1 12.8 + - - +
165A LEU* 1.3 70.7 - - - +
167A GLU* 1.3 59.1 + - - +
169A LEU* 2.8 23.6 + - - +
170A ARG* 3.0 15.8 + - - +
188A ILE* 4.3 5.4 - - - +
189A GLU* 3.0 47.6 - - + -
192A MET* 3.6 30.7 - - + -
193A LEU* 3.2 33.6 - - + +
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Residues in contact with GLU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLY 3.1 23.1 + - - +
164A VAL* 3.4 13.0 + - - +
165A LEU 3.2 0.2 - - - -
166A MET* 1.3 76.2 - - - +
168A GLU* 1.3 57.2 + - + +
170A ARG* 3.2 40.6 + - - +
171A PHE* 3.0 27.9 + - - +
231B LEU* 4.3 13.7 - - - +
234B LYS* 4.6 11.5 + - - -
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Residues in contact with GLU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 6.1 0.7 - - - +
134A ARG* 3.5 34.6 + - - +
137A LEU* 6.2 0.7 - - + -
164A VAL* 3.2 22.0 + - - +
165A LEU* 2.9 35.3 + - + +
167A GLU* 1.3 74.6 - - + +
169A LEU* 1.3 59.7 + - + +
171A PHE* 3.4 8.5 + - + +
172A VAL* 2.8 39.2 + - + +
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Residues in contact with LEU 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A TYR* 3.3 32.2 - - + +
137A LEU* 4.5 23.3 - - + -
150A LEU* 4.4 16.8 - - + -
153A PRO* 5.2 2.2 - - + -
154A LEU* 4.2 19.7 - - + -
165A LEU* 3.0 13.8 + - + +
166A MET* 2.8 8.5 + - - +
168A GLU* 1.3 74.5 - - - +
170A ARG* 1.3 67.4 + - - +
172A VAL* 3.0 6.1 + - + +
173A GLN* 2.8 24.3 + - - +
180A ILE* 4.7 6.4 - - + +
182A HIS* 3.8 19.1 - - + -
193A LEU* 3.9 10.8 - - + -
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Residues in contact with ARG 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A TYR* 4.8 5.2 - - + -
163A GLY 5.5 0.4 + - - -
166A MET* 3.0 17.7 + - - +
167A GLU* 3.2 42.8 + - - +
169A LEU* 1.3 75.7 - - - +
171A PHE* 1.3 66.0 + - - +
173A GLN* 3.0 8.7 + - - +
174A ARG* 2.9 47.2 + - - +
192A MET* 3.3 51.4 + - - +
193A LEU* 3.7 16.3 - - + +
231B LEU* 6.4 0.2 - - - +
234B LYS* 6.1 2.2 - - - +
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Residues in contact with PHE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS 5.7 4.9 - - - -
167A GLU 3.0 14.4 + - - +
168A GLU* 3.5 10.3 - - + +
170A ARG* 1.3 80.6 - - - +
172A VAL* 1.3 61.0 + - + +
174A ARG* 3.0 12.0 + - + +
175A GLU* 2.6 73.1 + - + +
176A PHE* 6.0 1.3 - + - -
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Residues in contact with VAL 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A LEU* 4.7 14.4 - - + -
137A LEU* 4.1 27.6 - - + -
141A LEU* 3.9 20.9 - - + -
148A LEU* 5.6 0.7 - - + -
168A GLU* 2.8 36.3 + - + +
169A LEU* 3.5 7.4 - - + +
171A PHE* 1.3 78.6 - - + +
173A GLN* 1.3 57.6 + - - +
175A GLU* 4.2 2.0 - - - -
176A PHE* 2.9 58.4 + - + +
178A VAL* 5.5 1.0 - - + +
180A ILE* 5.5 6.5 - - + -
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Residues in contact with GLN 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG 5.6 0.2 - - - -
25A ASP* 2.9 12.0 - - - +
26A TYR* 2.8 49.4 + - + +
169A LEU 2.8 12.6 + - - +
170A ARG* 3.4 9.4 + - - +
172A VAL* 1.3 76.3 - - - +
174A ARG* 1.3 70.6 + - - +
177A ASP* 2.8 30.0 + - - +
178A VAL* 3.2 26.7 + - - +
180A ILE* 3.9 16.3 + - + +
195A ASP* 4.5 5.5 + - - -
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Residues in contact with ARG 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ARG* 2.9 37.9 + - - +
171A PHE* 3.6 13.0 - - + +
173A GLN* 1.3 86.4 - - - +
175A GLU* 1.3 60.5 + - - +
177A ASP* 3.2 21.4 - - - +
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Residues in contact with GLU 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LYS* 5.4 7.3 + - + +
171A PHE* 2.6 54.7 + - + +
172A VAL* 3.8 4.0 - - - +
174A ARG* 1.3 76.2 - - - +
176A PHE* 1.3 81.2 + - + +
177A ASP* 5.2 1.0 - - - -
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Residues in contact with PHE 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A MET* 3.9 32.8 - - + -
113A LYS* 4.0 37.5 - - + -
114A LEU* 5.2 4.0 - - + -
141A LEU* 4.1 15.3 - - + -
171A PHE* 6.0 1.3 - + - -
172A VAL* 2.9 53.6 + - + +
175A GLU* 1.3 97.8 - - + +
177A ASP* 1.3 72.2 + - - +
178A VAL* 3.0 24.0 + - + +
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Residues in contact with ASP 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG 5.6 1.3 - - - -
173A GLN* 2.8 12.2 + - - +
174A ARG* 3.2 20.1 - - - +
175A GLU 3.5 1.5 - - - -
176A PHE* 1.3 79.0 - - - +
178A VAL* 1.3 60.3 + - - +
179A PRO* 3.7 8.6 - - - +
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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
------------------------------------------------------------
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