Contacts of the strand formed by residues 166 - 170 (chain B) in PDB entry 2OQH
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 ALA 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE 4.3 2.2 + - - -
131B THR* 3.5 9.8 - - + +
132B ALA 3.0 21.5 + - - -
164B PHE* 3.4 6.3 - - - +
165B ASP* 1.3 82.5 - - - +
167B VAL* 1.3 69.8 + - - +
192B VAL* 4.1 1.1 - - - -
193B ASN* 3.3 20.6 - - + +
195B ARG* 3.5 34.3 - - - +
322B ALA* 4.0 5.6 - - + -
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Residues in contact with VAL 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 4.0 1.6 - - - -
132B ALA* 3.3 16.8 - - + +
134B ILE* 3.7 36.6 - - + -
155B ALA* 4.9 7.2 - - + +
158B VAL* 6.2 0.4 - - + -
159B VAL* 3.6 30.7 - - + -
166B ALA* 1.3 81.7 - - - +
168B LYS* 1.3 64.3 + - - +
185B VAL* 5.0 1.6 - - + -
189B LEU* 5.0 3.4 - - + -
192B VAL* 4.1 12.6 - - + -
193B ASN 2.8 11.2 + - - +
194B LEU* 3.5 15.3 - - + +
195B ARG* 2.9 26.0 + - - +
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Residues in contact with LYS 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B THR* 3.7 14.7 - - + +
132B ALA 2.9 10.4 + - - +
133B LEU* 3.4 26.4 - - + +
134B ILE* 2.9 28.0 + - - -
167B VAL* 1.3 75.4 - - - +
169B LEU* 1.3 69.2 + - - +
170B LYS* 6.0 0.4 - - - +
195B ARG* 3.5 24.2 - - + +
197B ASP* 3.4 25.0 + - + -
223B GLU* 3.4 27.1 + - - +
297B HIS* 5.3 5.5 - - - -
324B ASP* 2.7 33.4 + - - +
326B MSE 5.7 3.1 - - - +
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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
----------------------------------------------------------
133B LEU* 4.8 0.2 - - - -
134B ILE* 3.4 22.6 - - + +
135B THR* 4.7 1.6 - - - -
136B ARG* 5.2 1.3 - - + +
151B MSE 3.7 24.7 - - + -
167B VAL* 4.2 0.6 - - - +
168B LYS* 1.3 76.4 - - - +
170B LYS* 1.3 79.7 + - - +
171B GLY 3.2 0.5 + - - -
178B ASP* 3.9 14.4 - - + +
181B ILE* 3.7 28.3 - - + -
182B LEU* 3.7 31.9 - - + -
185B VAL* 6.4 0.2 - - + -
194B LEU* 5.3 1.1 - - + +
195B ARG 3.0 14.8 + - - +
196B VAL* 3.4 10.7 - - + -
197B ASP* 2.9 26.3 + - - -
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Residues in contact with LYS 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.4 13.1 - - + +
134B ILE 3.0 8.3 + - - +
135B THR* 3.7 37.8 - - + -
136B ARG* 5.1 3.6 + - - +
168B LYS* 3.9 1.0 + - - +
169B LEU* 1.3 81.7 - - - +
171B GLY* 1.3 71.0 + - - +
172B THR* 4.1 8.6 - - + +
178B ASP* 4.9 0.9 - - - +
197B ASP* 3.8 8.7 - - - +
199B ASN* 3.4 23.6 - - - +
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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