Contacts of the strand formed by residues 181 - 185 (chain B) in PDB entry 2QU7
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 VAL 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B THR* 4.8 3.1 - - + -
173B VAL* 3.8 30.3 - - + -
174B LEU* 3.6 33.2 - - + -
178B CYS* 4.2 4.9 - - - +
179B LYS 3.9 0.6 + - - -
180B GLU* 1.3 73.6 - - - +
182B GLY* 1.3 76.7 + - - +
183B LEU 3.6 0.3 + - - -
200B TYR* 2.5 42.7 + - + +
204B ILE* 4.7 5.8 - - + +
215B LEU* 3.8 10.0 - - - +
246B GLY 3.6 10.8 - - - +
248B VAL* 3.9 21.1 - - + -
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Residues in contact with GLY 182 (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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181B VAL* 1.3 76.5 - - - +
183B LEU* 1.3 59.1 + - - -
184B LEU 4.3 0.2 - - - -
215B LEU* 3.4 11.4 - - - +
239B LEU* 4.0 26.9 - - - -
244B ILE* 3.7 7.6 - - - +
246B GLY 2.9 13.7 + - - -
247B ILE* 3.4 4.1 - - - -
248B VAL* 2.9 26.5 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ALA* 5.9 0.9 - - + -
181B VAL 3.6 0.4 + - - -
182B GLY* 1.3 73.9 - - - -
184B LEU* 1.3 62.8 + - - +
185B LEU* 3.8 35.0 - - + -
196B ARG 4.9 1.1 - - - +
197B LYS* 4.5 5.8 - - - -
200B TYR* 3.7 55.9 - - + -
215B LEU 2.8 14.1 + - - +
216B ILE* 4.1 11.4 - - + -
217B HIS* 2.9 31.2 + - - +
239B LEU* 4.6 0.6 - - - +
248B VAL* 3.6 31.6 - - + +
250B THR* 3.9 11.0 - - + -
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Residues in contact with LEU 184 (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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183B LEU* 1.3 76.8 - - - +
185B LEU* 1.3 55.2 + - - +
217B HIS* 3.9 3.8 - - + -
231B SER 5.8 0.2 - - - -
232B GLY* 4.2 6.5 - - - +
235B ALA* 3.5 32.1 - - + -
236B THR* 3.5 22.9 - - - +
239B LEU* 4.1 13.0 - - + -
247B ILE* 4.0 9.9 - - + -
248B VAL 2.9 14.5 + - - +
249B ALA* 3.7 25.6 - - + -
250B THR* 2.7 36.8 + - - +
254B LEU* 3.3 24.0 - - + +
258B ALA* 3.9 11.7 - - + -
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Residues in contact with LEU 185 (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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183B LEU* 3.8 22.4 - - + -
184B LEU* 1.3 71.5 - - - +
186B ALA* 1.3 62.5 + - - +
193B THR* 3.7 30.5 - - + +
196B ARG* 4.2 3.6 - - + -
197B LYS* 3.8 26.7 - - + +
216B ILE* 3.6 18.8 - - + -
217B HIS 2.8 13.1 + - - +
218B TYR* 3.2 32.1 - - + -
219B SER* 3.0 20.8 + - - -
231B SER* 4.6 0.2 + - - -
250B THR* 3.6 20.6 - - + +
254B LEU* 3.4 13.0 - - - +
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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