Contacts of the strand formed by residues 176 - 183 (chain X) in PDB entry 2AE0
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 ASN 176 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166X TYR* 3.1 7.5 - - - +
167X ILE 2.7 44.9 + - - +
169X PHE* 3.4 33.8 - - + +
173X SER* 4.4 6.7 + - - -
174X PRO 3.3 14.9 + - - -
175X LEU* 1.3 74.9 - - - +
177X PHE* 1.3 60.1 + - - +
178X PHE* 3.7 24.9 - - + -
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Residues in contact with PHE 177 (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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164X SER* 3.8 33.4 - - - -
165X GLY 3.4 15.0 - - - -
166X TYR* 3.4 49.4 - + + -
175X LEU 4.0 1.2 + - - -
176X ASN* 1.3 75.6 - - - +
178X PHE* 1.3 69.8 + - - +
179X SER* 4.7 3.8 - - - -
238X PRO* 3.8 1.9 - - - +
239X GLN* 2.9 71.6 + - + +
240X SER 3.9 7.6 - - - -
241X PHE* 4.3 13.0 - - + +
242X ALA* 4.8 8.3 - - + -
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Residues in contact with PHE 178 (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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120X ILE* 5.9 0.4 - - + -
147X LEU* 3.9 41.7 - - + -
159X MET* 3.8 18.8 - - + -
164X SER* 3.2 7.0 - - - -
165X GLY 3.0 33.4 + - - -
167X ILE* 3.6 37.5 - - + -
169X PHE* 4.6 10.8 - + - -
176X ASN* 3.7 31.6 - - + -
177X PHE* 1.3 79.0 - - - +
179X SER* 1.3 61.7 + - - +
236X PHE* 4.1 7.0 - - + -
237X LYS 3.3 7.6 - - - +
238X PRO* 3.8 30.7 - - + -
239X GLN* 4.6 0.2 - - - -
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Residues in contact with SER 179 (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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163X GLY 3.4 7.0 - - - -
164X SER* 4.0 8.1 - - - -
177X PHE* 4.7 4.3 - - - -
178X PHE* 1.3 74.2 - - - +
180X TYR* 1.3 63.7 + - - +
236X PHE* 3.2 7.4 - - - -
237X LYS* 2.9 46.7 + - - +
239X GLN* 2.7 38.8 + - - +
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Residues in contact with TYR 180 (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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163X GLY* 2.9 25.5 + - - +
179X SER* 1.3 75.4 + - - +
181X ALA* 1.3 61.7 + - - +
182X GLY* 3.3 39.8 - - - -
183X LYS* 3.5 19.2 + - + +
234X VAL* 3.9 22.2 - - + -
235X PHE 4.1 2.5 - - - -
236X PHE* 4.6 0.9 - - - -
237X LYS* 3.6 16.5 + - - -
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Residues in contact with ALA 181 (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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123X MET* 3.6 31.1 - - + +
179X SER 3.3 0.6 + - - -
180X TYR* 1.3 78.5 - - - +
182X GLY* 1.3 58.6 + - - +
235X PHE 3.0 8.6 + - - +
236X PHE 3.5 28.0 - - - +
237X LYS* 3.9 20.7 + - + +
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Residues in contact with GLY 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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123X MET* 3.7 15.6 - - - -
180X TYR* 3.3 26.6 - - - -
181X ALA* 1.3 81.5 - - - +
183X LYS* 1.3 60.3 + - - -
234X VAL* 3.8 1.0 - - - +
235X PHE* 2.9 28.5 + - - +
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Residues in contact with LYS 183 (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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123X MET* 4.5 1.7 - - - +
129X ARG* 3.9 14.6 + - - +
180X TYR* 3.5 16.2 + - + +
182X GLY* 1.3 74.5 - - - +
184X ASN* 1.3 79.1 + - - +
186X HIS 2.6 29.9 + - - -
187X ALA* 5.0 1.8 - - - +
188X TYR* 4.4 22.2 - - + +
232X SER* 2.7 22.4 + - - +
233X PHE 3.4 15.0 - - - +
234X VAL* 4.5 10.1 - - + -
235X PHE* 3.9 6.5 - - - -
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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