Contacts of the strand formed by residues 210 - 214 (chain B) in PDB entry 2QQ6
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 GLU 210 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B ARG* 2.8 30.9 + - - +
164B ASP 2.9 17.7 + - - +
165B ALA* 3.1 4.3 - - - +
166B ILE* 2.6 34.1 + - - +
202B ARG* 5.2 0.7 - - - +
208B GLU 4.2 8.1 - - - +
209B VAL* 1.3 76.0 - - - +
211B VAL* 1.3 55.5 + - - +
212B ALA 4.2 0.2 + - - -
237B LEU* 3.4 40.4 - - + +
339B VAL* 5.9 0.9 - - - +
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Residues in contact with VAL 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.3 23.6 - - + +
168B LEU* 5.1 8.7 - - + -
198B VAL* 6.2 0.7 - - + -
201B VAL* 5.2 7.9 - - + -
202B ARG* 2.9 50.5 - - + +
209B VAL* 4.4 2.0 - - + +
210B GLU* 1.3 75.1 - - - +
212B ALA* 1.3 68.4 + - - +
213B ILE* 4.5 12.3 - - + -
236B LEU* 3.4 12.9 - - + +
237B LEU* 2.8 28.6 + - - +
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Residues in contact with ALA 212 (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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123B TYR* 6.0 1.8 - - + -
166B ILE 2.8 9.7 + - - +
167B LYS* 3.3 11.7 - - + -
168B LEU 2.9 23.0 + - - -
211B VAL* 1.3 75.8 - - - +
213B ILE* 1.3 68.3 + - - +
237B LEU* 3.8 20.8 - - + +
238B TRP* 3.6 39.7 - - + +
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Residues in contact with ILE 213 (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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167B LYS* 5.4 0.9 - - - -
168B LEU* 3.1 17.7 - - + +
170B VAL* 3.6 32.8 - - + -
198B VAL* 3.4 44.4 - - + -
211B VAL* 4.5 9.0 - - + -
212B ALA* 1.3 81.5 - - - +
214B ASP* 1.3 56.2 + - - +
227B PHE* 5.0 1.8 - - + -
231B MSE 4.0 1.1 - - - -
236B LEU* 3.7 23.1 - - + -
238B TRP* 3.3 7.0 + - - -
239B LEU* 3.5 21.3 - - + +
240B GLU* 2.7 34.7 + - - +
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Residues in contact with ASP 214 (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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167B LYS* 3.6 16.5 - - - +
168B LEU 2.7 9.8 + - - +
169B ASP* 3.5 18.6 - - - +
170B VAL* 3.4 26.7 + - - +
171B ASP* 4.2 2.1 - - - +
213B ILE* 1.3 73.2 - - - +
215B MSE 1.3 63.8 + - - +
216B HIS* 2.6 47.1 + - - -
240B GLU* 2.5 24.7 - - + +
241B GLU* 4.0 2.3 - - - +
409B MG 2.2 30.5 - - - -
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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