Contacts of the helix formed by residues 186 - 194 (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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A VAL* 5.9 0.2 - - - +
30A LEU* 3.6 7.6 - - - +
162A LYS* 2.8 29.5 + - - +
184A THR* 3.1 17.6 - - + +
185A HIS* 1.3 87.9 - - + +
187A LEU* 1.3 65.6 + - - +
188A ILE* 3.0 23.6 + - - +
189A GLU* 3.1 25.9 + - - +
190A ALA 3.3 6.9 + - - -
159B LEU* 3.2 30.5 - - - +
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Residues in contact with LEU 187 (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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30A LEU* 3.5 26.2 - - + +
185A HIS 3.9 1.7 + - - +
186A ASP* 1.3 72.9 + - - +
188A ILE* 1.3 56.3 + - - +
190A ALA* 2.6 25.4 + - - +
191A ALA* 2.7 13.0 + - - +
225A PHE* 4.2 8.7 - - + +
226A LEU* 3.7 16.4 - - + +
228A ALA* 3.3 34.5 - - + +
229A ARG* 2.5 60.3 + - - +
232A LEU* 4.3 1.3 - - + -
158B ASP* 5.4 1.6 - - - +
159B LEU* 3.8 16.2 - - + +
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Residues in contact with ILE 188 (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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159A LEU* 4.0 18.8 - - + -
162A LYS* 4.7 8.5 - - + +
166A MET* 4.6 9.0 - - - -
186A ASP* 3.0 23.3 + - - +
187A LEU* 1.3 78.6 - - - +
189A GLU* 1.3 56.0 + - - +
191A ALA* 4.0 6.3 - - - +
192A MET* 3.0 33.5 + - + +
232A LEU* 3.8 34.3 - - + -
159B LEU* 4.1 1.8 - - + -
188B ILE* 4.1 7.4 - - + -
231B LEU* 5.5 5.8 - - + +
232B LEU* 3.9 19.3 - - + -
235B VAL* 3.9 22.7 - - + -
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Residues in contact with GLU 189 (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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28A VAL* 4.9 2.5 - - + +
152A GLU* 5.8 0.2 - - - -
153A PRO* 5.1 0.2 - - - +
154A LEU* 3.1 30.4 + - - +
155A SER* 4.9 0.9 + - - -
162A LYS* 3.4 21.3 - - + -
166A MET* 3.0 21.5 - - + -
182A HIS* 3.0 27.3 + - + +
184A THR* 3.2 32.0 + - - +
185A HIS* 5.7 0.2 - - - -
186A ASP* 3.1 20.6 + - - +
187A LEU 2.7 4.6 + - - -
188A ILE* 1.3 72.3 - - - +
190A ALA* 1.3 65.6 + - - +
192A MET 3.3 0.2 + - - -
193A LEU* 3.0 32.8 + - + +
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Residues in contact with ALA 190 (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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28A VAL* 3.7 21.5 - - + +
30A LEU* 3.8 37.2 - - + -
186A ASP 3.3 2.2 + - - -
187A LEU* 2.6 12.9 + - - +
189A GLU* 1.3 73.8 - - - +
191A ALA* 1.3 62.2 + - - +
194A ALA* 3.0 30.1 + - - +
197A VAL* 4.2 10.6 - - + +
211A LEU* 4.2 7.8 - - + +
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Residues in contact with ALA 191 (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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187A LEU 2.7 18.2 + - - +
188A ILE 4.0 4.7 - - - +
190A ALA* 1.3 74.8 - - - +
192A MET* 1.3 67.5 + - + +
193A LEU 3.8 0.2 + - - -
194A ALA 5.2 1.9 + - - +
211A LEU* 3.5 19.2 - - + +
229A ARG* 4.3 0.9 - - - +
235B VAL* 4.5 5.8 - - + -
238B ILE* 4.2 15.3 - - + +
239B LEU* 3.6 34.5 - - + -
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Residues in contact with MET 192 (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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166A MET* 3.6 28.0 - - + -
170A ARG* 3.3 45.1 + - - +
188A ILE* 3.0 26.1 + - + +
190A ALA 3.2 0.4 - - - -
191A ALA* 1.3 81.7 - - - +
193A LEU* 1.3 58.8 + - + +
231B LEU* 5.1 8.1 - - + +
234B LYS* 4.2 12.3 - - + -
235B VAL* 3.2 41.7 - - + +
238B ILE* 3.6 32.8 - - + -
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Residues in contact with LEU 193 (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* 3.4 44.1 - - + +
28A VAL* 4.6 1.1 - - + -
166A MET* 3.2 59.2 - - + +
169A LEU* 3.9 14.1 - - + -
170A ARG* 3.7 19.1 - - + +
182A HIS* 4.1 20.4 - - + +
189A GLU* 3.0 14.1 + - + +
190A ALA 3.3 0.2 + - - -
192A MET* 1.3 81.1 - - - +
194A ALA* 1.3 68.9 + - - +
195A ASP* 3.6 9.9 + - - +
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Residues in contact with ALA 194 (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 3.4 6.1 - - - -
28A VAL* 3.5 18.3 - - + +
190A ALA 3.0 13.7 + - - +
191A ALA 5.4 1.7 - - - +
193A LEU* 1.3 81.7 + - - +
195A ASP* 1.3 60.9 + - - +
196A GLU 2.9 23.3 - - - +
197A VAL* 3.3 22.2 - - + -
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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
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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