Contacts of the strand formed by residues 231 - 235 (chain E) in PDB entry 2X86
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 GLY 231 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E VAL* 5.8 0.8 - - - +
155E LEU* 4.2 17.8 - - - +
162E ILE* 2.9 10.7 + - - +
163E VAL* 3.2 7.8 - - - +
164E GLY 2.9 23.0 + - - -
230E SER* 1.3 76.1 - - - +
232E ILE* 1.3 66.2 + - - +
233E PHE* 3.5 9.4 - - - -
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Residues in contact with ILE 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 3.7 24.0 - - - +
115E SER* 5.1 0.7 - - - +
129E GLU* 3.4 26.4 - - + +
148E ASP* 3.8 34.5 - - + +
151E VAL* 4.4 9.9 - - + -
152E ARG* 3.9 24.9 - - + +
155E LEU* 5.1 3.5 - - + +
164E GLY 3.4 11.4 - - - +
166E ARG* 4.1 32.1 - - + +
231E GLY* 1.3 76.3 - - - +
233E PHE* 1.3 69.9 + - - +
282E ASN* 5.0 1.7 + - - +
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Residues in contact with PHE 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E GLU* 3.5 2.7 - - - +
163E VAL* 4.0 8.3 - - + -
164E GLY 2.9 11.0 + - - +
165E PHE* 3.5 11.3 - - + -
166E ARG* 2.7 32.6 + - - -
224E PHE* 3.6 26.5 - + - -
229E VAL* 4.5 2.9 - - + -
230E SER 3.4 20.9 - - - -
231E GLY* 3.5 26.2 - - - -
232E ILE* 1.3 79.2 - - - +
234E ASN* 1.3 63.8 + - - +
235E LEU 3.5 0.2 + - - -
282E ASN* 3.7 23.6 - - + -
283E LEU* 3.8 33.0 - - + -
286E ALA* 3.8 18.8 - - + -
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Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E TYR* 2.6 28.3 + - - -
127E PHE 2.7 28.0 + - - -
129E GLU* 2.7 26.9 + - - +
165E PHE* 5.6 0.2 - - - -
166E ARG* 3.7 9.5 - - - -
168E PHE* 3.6 17.0 - - + -
233E PHE* 1.3 78.2 - - - +
235E LEU* 1.3 61.1 + - - +
236E GLY 4.0 0.7 - - - -
278E ALA* 4.1 6.5 - - + -
279E ASP 2.8 28.2 + - - +
280E LEU* 4.2 2.9 - - + +
283E LEU* 3.7 21.4 - - + +
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Residues in contact with LEU 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E PHE* 4.1 10.1 - - + -
166E ARG 2.9 12.8 + - - +
167E TYR* 3.5 37.7 - - + -
168E PHE* 3.1 27.7 + - - -
212E VAL* 3.9 8.0 - - + +
217E VAL* 4.1 25.4 - - + +
220E VAL* 3.6 37.2 - - + -
233E PHE 4.4 3.4 - - - +
234E ASN* 1.3 75.0 - - - +
236E GLY* 1.3 60.6 + - - +
283E LEU* 5.0 2.9 - - + -
292E PHE* 3.8 26.9 - - + -
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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