Contacts of the strand formed by residues 178 - 182 (chain X) in PDB entry 2BQ8
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 TYR 178 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X VAL* 3.9 16.6 - - + -
128X SER 3.2 4.9 + - - -
129X VAL* 3.4 20.2 - - + -
130X ALA 3.0 24.0 + - - -
176X GLU* 3.5 6.1 - - - +
177X ASP* 1.3 79.8 - - - +
179X VAL* 1.3 63.4 + - - +
180X LEU* 4.2 2.2 - - + -
213X THR* 3.6 26.7 - - + +
276X ILE* 3.5 26.7 - - + -
277X SER 2.7 29.0 + - - -
279X LYS 3.5 0.2 - - - -
280X GLU 3.1 18.8 + - - -
281X MET* 4.0 19.5 - - + -
298X LEU 4.6 1.6 - - - -
299X PRO 4.9 0.2 - - - -
300X ARG* 3.2 44.6 - - + +
301X ARG* 5.7 0.7 - - + -
303X ARG* 4.3 1.3 - - - +
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Residues in contact with VAL 179 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130X ALA* 3.5 10.3 - - + -
132X PHE* 3.8 14.1 - - + -
171X LEU* 3.7 29.4 - - + -
174X ALA* 3.9 16.8 - - + -
176X GLU* 4.4 2.9 - - + +
178X TYR* 1.3 78.1 - - - +
180X LEU* 1.3 68.5 + - - +
211X GLY 4.4 4.9 + - - +
212X VAL* 3.4 12.2 - - + +
213X THR* 3.0 29.3 + - - -
303X ARG* 3.5 42.3 - - - +
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Residues in contact with LEU 180 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7X PHE* 3.7 30.7 - - + -
129X VAL* 4.7 5.4 - - + -
130X ALA 2.8 13.4 + - - +
131X ILE* 3.3 21.3 - - + -
132X PHE* 2.9 26.1 + - - -
178X TYR* 5.3 2.0 - - + -
179X VAL* 1.3 83.6 - - - +
181X VAL* 1.3 67.9 + - - +
182X ALA* 6.3 0.2 - - + -
212X VAL* 4.2 0.2 - - - -
213X THR* 3.8 6.1 - - - -
214X ALA* 3.5 23.8 - - + +
216X LEU* 4.6 9.6 - - + -
276X ILE* 4.1 17.5 - - + -
281X MET* 3.7 30.1 - - + -
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Residues in contact with VAL 181 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132X PHE* 3.4 13.0 - - + +
134X LEU* 3.6 33.0 - - + -
167X LEU* 4.8 2.0 - - + -
171X LEU* 3.9 27.4 - - + -
180X LEU* 1.3 80.2 - - - +
182X ALA* 1.3 63.5 + - - +
203X LEU* 4.3 8.3 - - + -
207X LEU* 4.1 12.3 - - + -
212X VAL* 3.8 16.8 - - + -
214X ALA 3.1 6.3 + - - +
215X TYR* 3.1 21.8 - - + -
216X LEU* 2.8 25.3 + - - +
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Residues in contact with ALA 182 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46X LEU* 4.8 3.6 - - + -
48X LEU* 4.0 17.5 - - + -
86X LEU* 3.4 2.9 - - + +
131X ILE* 4.4 7.4 - - + -
132X PHE 2.8 11.0 + - - +
133X MET* 3.8 25.8 - - - -
134X LEU* 2.7 35.5 + - - +
181X VAL* 1.3 75.0 - - - +
183X GLY* 1.3 53.5 + - - +
215X TYR* 3.9 4.5 - - - -
216X LEU* 3.2 15.3 - - + +
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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