Contacts of the helix formed by residues 154 - 166 (chain B) in PDB entry 2OUX
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 THR 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B GLN* 1.3 79.2 - - - +
155B VAL* 1.3 65.7 + - - +
156B ARG* 3.5 22.9 + - - +
157B SER* 3.0 29.1 + - - +
158B ALA* 3.0 20.3 + - - +
198B ASP 3.3 13.2 - - - +
199B ASP* 3.7 21.3 - - - +
200B THR 3.4 6.5 - - - -
201B LEU* 4.0 10.1 - - + -
202B ILE* 3.8 3.1 - - - +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B THR* 1.3 73.5 - - - +
156B ARG* 1.3 54.5 + - - +
158B ALA* 2.8 10.5 + - - +
159B MSE 2.7 45.2 + - + +
193B LEU* 3.7 35.0 - - + +
196B ASN* 4.2 7.2 - - + +
197B ASP 3.5 23.3 - - - +
198B ASP* 3.5 4.2 + - - -
200B THR* 3.0 24.6 + - - +
202B ILE* 4.7 4.0 - - + +
205B ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 156 (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 THR* 3.1 23.5 + - - +
155B VAL* 1.3 80.6 - - - +
157B SER* 1.3 67.5 + - - +
159B MSE 3.4 8.6 + - - +
160B TYR* 3.0 23.1 + - + +
198B ASP* 3.2 43.7 + - + +
199B ASP* 5.3 5.3 + - - -
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Residues in contact with SER 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B GLN* 3.0 26.2 - - - +
154B THR* 3.0 32.5 + - - +
156B ARG* 1.3 84.3 + - - +
158B ALA* 1.3 63.3 + - - +
160B TYR* 3.2 10.2 + - - +
161B VAL* 3.2 24.1 + - - +
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Residues in contact with ALA 158 (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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149B ILE* 4.9 7.2 - - + -
153B GLN* 3.4 6.3 - - - +
154B THR 3.0 5.0 + - - +
155B VAL 2.8 10.2 + - - +
157B SER* 1.3 74.8 - - - +
159B MSE 1.3 66.3 + - - +
161B VAL* 3.0 8.0 + - - +
162B LEU* 2.9 30.7 + - + +
175B VAL* 6.0 0.7 - - + -
193B LEU* 4.1 21.8 - - + -
202B ILE* 3.5 27.6 - - + -
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Residues in contact with MSE 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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194A ILE* 4.1 34.1 - - + -
155B VAL* 2.7 33.4 + - + +
156B ARG* 3.7 8.5 - - - +
158B ALA* 1.3 72.0 - - - +
160B TYR* 1.3 64.4 + - - +
162B LEU* 3.0 6.0 + - + +
163B LYS* 2.9 48.1 + - - +
190B LEU* 3.7 22.7 - - + -
193B LEU* 4.2 16.8 - - + +
194B ILE* 4.1 24.0 - - + -
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Residues in contact with TYR 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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156B ARG* 3.0 13.6 + - + +
157B SER* 3.3 13.7 - - - +
159B MSE 1.3 78.3 - - - +
161B VAL* 1.3 68.3 + - + +
163B LYS* 3.5 11.5 + - + +
164B ASN* 3.4 46.0 + - - -
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Residues in contact with VAL 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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147B VAL* 4.3 20.2 - - + -
148B SER 4.8 4.0 - - - +
149B ILE* 4.3 18.2 - - + -
153B GLN* 4.8 5.8 - - - +
157B SER 3.2 13.2 + - - +
158B ALA* 3.0 9.9 + - - +
160B TYR* 1.3 83.4 - - + +
162B LEU* 1.3 64.1 + - + +
164B ASN* 3.2 8.2 + - + +
165B GLN* 3.1 28.1 + - + +
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Residues in contact with LEU 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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194A ILE* 4.5 12.4 - - + +
147B VAL* 4.2 14.8 - - + -
149B ILE* 5.0 1.1 - - + -
158B ALA* 2.9 22.9 + - + +
159B MSE 3.3 13.5 - - - +
161B VAL* 1.3 79.8 - - + +
163B LYS* 1.3 63.5 + - - +
165B GLN* 3.1 5.9 + - - +
166B ALA* 2.9 23.7 + - - +
172B ILE* 3.2 53.7 - - + +
175B VAL* 3.7 29.4 - - + -
190B LEU* 4.8 8.5 - - + -
193B LEU* 4.4 13.7 - - + -
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Residues in contact with LYS 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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194A ILE* 3.5 36.4 + - + +
195A VAL* 3.9 21.1 - - + +
159B MSE 2.9 42.2 + - + +
160B TYR* 3.8 10.1 - - + +
162B LEU* 1.3 76.6 - - - +
164B ASN* 1.3 67.0 + - - +
165B GLN 3.4 0.5 + - - -
166B ALA* 3.4 15.0 + - - +
167B ASP* 4.7 4.7 + - - +
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Residues in contact with ASN 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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160B TYR* 3.4 42.0 + - - +
161B VAL* 3.2 11.6 + - + +
162B LEU 3.2 0.6 - - - -
163B LYS* 1.3 80.2 - - - +
165B GLN* 1.3 66.6 + - + +
167B ASP* 2.9 19.3 - - - +
168B MSE 4.1 3.6 - - - +
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Residues in contact with GLN 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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145B GLU 6.0 0.3 - - - -
146B PHE 4.6 10.6 - - - +
147B VAL* 4.1 30.5 - - + +
161B VAL* 3.1 24.3 + - + +
162B LEU 3.1 5.3 + - - +
164B ASN* 1.3 80.2 + - + +
166B ALA* 1.3 67.3 + - - +
167B ASP* 3.2 3.6 - - - -
168B MSE 2.8 39.6 + - - +
169B ALA* 2.8 35.1 + - + +
172B ILE* 4.3 1.3 - - + -
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Residues in contact with ALA 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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191A ARG* 2.5 44.3 + - + +
194A ILE* 5.3 2.2 - - + -
195A VAL* 3.6 23.3 - - + -
162B LEU 2.9 11.5 + - - +
163B LYS* 3.4 14.3 + - - +
165B GLN* 1.3 76.4 - - - +
167B ASP* 1.3 59.7 + - - +
168B MSE 3.3 0.2 + - - -
172B ILE* 4.1 16.2 - - + -
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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