Contacts of the strand formed by residues 162 - 168 (chain B) in PDB entry 3QEK
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 HIS 162 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B TRP* 3.4 0.7 - - - -
161B ASN* 1.3 96.8 + - + +
163B VAL* 1.3 65.8 + - - +
211B LYS* 3.6 4.5 - - + -
213B ASP* 2.7 37.1 + - - +
237B ALA* 4.0 16.4 - - + +
238B ARG 4.6 0.3 + - - -
239B VAL* 4.0 15.4 + - - +
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Residues in contact with VAL 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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155B MSE 2.9 45.1 - - + -
160B TRP* 4.4 6.3 - - + +
162B HIS* 1.3 82.8 - - - +
164B ILE* 1.3 67.5 + - - +
165B LEU* 4.9 0.9 - - + +
180B LEU* 5.0 4.7 - - + -
184B LEU* 5.1 1.1 - - + -
211B LYS 3.1 16.4 + - - +
212B ALA* 3.5 15.7 - - + -
213B ASP* 2.8 29.5 + - - +
214B LYS 3.8 0.2 + - - -
237B ALA* 4.2 1.6 - - - -
239B VAL* 3.4 25.8 - - + +
241B ILE* 4.4 8.1 - - + -
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Residues in contact with ILE 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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163B VAL* 1.3 76.5 - - - +
165B LEU* 1.3 64.2 + - - +
166B ILE* 3.9 4.9 + - + -
213B ASP* 4.7 1.3 - - + -
214B LYS* 3.6 12.1 - - + +
216B LEU* 4.1 26.9 - - + -
232B ALA* 4.2 10.3 - - + +
235B LEU* 3.2 37.2 - - + -
237B ALA* 3.6 30.3 - - + +
239B VAL 2.8 8.0 + - - +
240B ILE* 3.4 29.5 - - + +
241B ILE* 2.8 29.2 + - - +
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Residues in contact with LEU 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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151B TRP* 4.6 7.9 - - + -
163B VAL* 4.1 2.3 + - + +
164B ILE* 1.3 74.1 - - - +
166B ILE* 1.3 56.8 + - - +
167B VAL* 3.7 22.4 - - + -
177B GLN* 3.7 40.2 - - + +
180B LEU* 4.1 23.1 - - + -
181B GLU* 5.3 3.1 - - + -
212B ALA* 5.0 8.1 - - + -
214B LYS 3.0 11.3 + - - +
215B VAL* 3.4 14.3 - - + +
216B LEU* 2.8 32.2 + - - +
241B ILE* 3.5 35.7 - - + +
242B LEU 4.8 0.2 - - - +
243B SER 5.1 1.3 - - - +
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Residues in contact with ILE 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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164B ILE* 4.4 6.5 - - + -
165B LEU* 1.3 76.3 - - - +
167B VAL* 1.3 65.6 + - - +
216B LEU* 3.3 22.9 - - + +
218B PHE* 3.9 19.3 - - + -
228B LEU* 4.4 13.9 - - + -
229B LEU* 3.9 28.0 - - + -
232B ALA* 4.9 3.1 - - + -
240B ILE* 3.9 24.2 - - + -
241B ILE 2.7 14.3 + - - +
242B LEU* 3.2 22.8 - - + +
243B SER 2.9 24.3 + - - -
252B VAL* 5.0 7.0 - - + -
261B MSE 5.9 0.2 - - + -
268B TRP* 4.8 4.3 - - + -
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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
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165B LEU* 3.7 28.7 - - + -
166B ILE* 1.3 81.0 - - - +
168B SER* 1.3 70.6 + - - +
173B GLY* 3.5 28.0 - - - +
174B ARG* 4.5 1.1 - - + +
177B GLN* 3.9 25.4 - - + +
215B VAL* 4.7 2.0 - - + -
216B LEU 2.9 8.5 + - - +
217B GLN* 3.2 17.8 - - + +
218B PHE* 3.1 26.5 + - - -
243B SER* 3.3 14.8 - - - +
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Residues in contact with SER 168 (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 VAL* 1.3 76.9 - - - +
169B ASP* 1.3 57.8 + - - +
170B ASP* 2.7 42.5 + - - +
172B GLU* 5.2 0.9 - - - +
173B GLY* 3.3 22.3 + - - -
174B ARG* 3.7 1.2 + - - +
218B PHE* 3.5 30.1 - - - -
220B PRO* 4.4 5.6 - - - -
243B SER 3.1 12.3 + - - -
244B ALA* 4.3 7.1 - - - -
245B SER 5.0 2.1 + - - -
248B ASP* 4.5 5.6 - - - -
273B ARG* 5.5 1.9 + - - -
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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