Contacts of the strand formed by residues 174 - 178 (chain A) in PDB entry 2OUX
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 174 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A VAL* 4.4 5.7 + - - +
171A THR* 4.4 8.0 + - + +
172A ILE* 3.8 10.9 - - - +
173A TYR* 1.3 80.8 - - - +
175A VAL* 1.3 63.3 + - - +
176A TYR* 3.4 33.1 - - + +
187A VAL* 4.4 11.2 - - + -
188A ILE 3.9 1.8 - - - -
189A SER* 4.0 24.9 - - - -
230A ASP 4.8 1.6 + - - -
231A PHE* 3.3 33.0 - + - -
232A LEU* 3.5 50.0 + - + +
233A ALA* 3.9 7.2 - - + -
405A MG 3.5 20.9 - - - -
173B TYR* 5.6 1.3 - + - -
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147A VAL* 3.8 20.6 - - + -
149A ILE* 3.8 36.6 - - + -
158A ALA* 5.6 1.6 - - + -
162A LEU* 4.3 18.6 - - + -
172A ILE 3.9 12.1 - - - +
174A TYR* 1.3 77.5 - - - +
176A TYR* 1.3 64.8 + - - +
177A VAL* 4.4 1.0 - - - +
187A VAL* 3.5 2.8 - - - -
188A ILE* 2.9 47.4 + - + +
190A LEU* 5.2 4.0 - - + +
193A LEU* 4.4 18.6 - - + -
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Residues in contact with TYR 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A PHE* 4.5 13.0 - - + -
147A VAL 2.9 18.9 + - - +
148A SER* 3.0 6.3 - - - -
149A ILE* 2.8 26.7 + - - +
171A THR* 5.9 2.5 - - + -
174A TYR* 3.4 29.5 - - + +
175A VAL* 1.3 73.8 - - - +
177A VAL* 1.3 60.9 + - - +
184A LEU* 4.0 11.4 - - + -
186A GLY 3.8 2.0 - - - -
187A VAL* 4.0 19.3 - - + -
210A VAL* 4.8 1.1 - - + -
233A ALA* 4.0 6.9 - - - +
235A PRO* 3.5 33.0 - - + +
243A LEU* 3.7 26.2 - - + -
246A ILE* 3.7 26.1 - - + +
405A MG 2.7 29.7 - - - -
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Residues in contact with VAL 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ILE* 3.1 12.1 - - + +
150A VAL 3.8 0.9 - - - -
151A ALA* 3.4 40.6 - - + +
175A VAL 4.4 5.2 - - - +
176A TYR* 1.3 78.7 - - - +
178A VAL* 1.3 65.6 + - - +
184A LEU* 3.8 1.6 - - - +
185A VAL* 2.9 33.7 + - + +
186A GLY* 2.9 30.2 + - - +
187A VAL* 4.2 4.3 - - - +
188A ILE* 5.0 1.8 - - + +
202A ILE* 4.0 21.1 - - + -
206A LEU* 4.2 13.7 - - + -
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Residues in contact with VAL 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A SER* 4.3 14.1 - - - +
149A ILE* 2.8 22.6 + - - +
150A VAL* 3.5 18.4 - - + +
151A ALA 4.2 1.2 + - - -
177A VAL* 1.3 80.6 - - - +
179A ASP* 1.3 71.2 + - - +
182A ASN* 3.7 28.9 - - - +
183A HIS 2.9 20.9 - - - +
184A LEU* 4.0 2.9 - - - -
185A VAL* 4.0 5.8 - - - +
243A LEU* 3.9 24.9 - - + -
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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
------------------------------------------------------------
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