Contacts of the strand formed by residues 231 - 235 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151Q VAL* 5.8 0.6 - - - +
155Q LEU* 4.2 17.8 - - - +
162Q ILE* 2.9 10.4 + - - +
163Q VAL* 3.2 7.6 - - - +
164Q GLY 2.9 23.0 + - - -
230Q SER* 1.3 75.3 - - - +
232Q ILE* 1.3 64.6 + - - +
233Q PHE* 3.5 10.1 - - - -
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Residues in contact with ILE 232 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113Q TYR* 3.7 23.6 - - - +
115Q SER* 5.1 1.1 - - - +
129Q GLU* 3.4 26.7 - - + +
148Q ASP* 3.8 34.8 - - + +
151Q VAL* 4.4 10.1 - - + -
152Q ARG* 3.9 24.7 - - + +
155Q LEU* 5.1 3.3 - - + +
164Q GLY 3.4 10.1 - - - +
166Q ARG* 4.1 32.3 - - + +
231Q GLY* 1.3 76.7 - - - +
233Q PHE* 1.3 71.1 + - - +
282Q ASN* 5.0 1.6 + - - +
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Residues in contact with PHE 233 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129Q GLU* 3.4 2.2 - - - +
163Q VAL* 4.0 8.7 - - + -
164Q GLY 2.9 10.8 + - - +
165Q PHE* 3.5 11.0 - - + -
166Q ARG* 2.7 32.3 + - - -
224Q PHE* 3.6 26.5 - + - -
229Q VAL* 4.5 2.7 - - + -
230Q SER 3.4 21.3 - - - -
231Q GLY* 3.5 26.2 - - - -
232Q ILE* 1.3 79.6 - - - +
234Q ASN* 1.3 65.5 + - - +
235Q LEU 3.5 0.2 + - - -
282Q ASN* 3.7 24.2 - - + -
283Q LEU* 3.8 31.0 - - + -
286Q ALA* 3.8 19.7 - - + -
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Residues in contact with ASN 234 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Q TYR* 2.6 28.2 + - - -
127Q PHE 2.7 27.2 + - - -
129Q GLU* 2.7 26.8 + - - +
165Q PHE* 5.6 0.2 - - - -
166Q ARG* 3.7 9.0 - - - -
168Q PHE* 3.6 16.4 - - + -
233Q PHE* 1.3 78.4 - - - +
235Q LEU* 1.3 60.8 + - - +
236Q GLY 4.0 0.7 - - - -
278Q ALA* 4.1 6.7 - - + -
279Q ASP 2.8 28.4 + - - +
280Q LEU* 4.2 2.4 - - + +
283Q LEU* 3.7 21.9 - - + +
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Residues in contact with LEU 235 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165Q PHE* 4.1 9.9 - - + -
166Q ARG 2.9 12.0 + - - +
167Q TYR* 3.5 37.5 - - + -
168Q PHE* 3.1 28.0 + - - -
212Q VAL* 3.9 7.7 - - + +
217Q VAL* 4.1 26.0 - - + +
220Q VAL* 3.6 38.6 - - + -
221Q ASN* 4.7 0.7 - - - +
233Q PHE 3.5 3.3 + - - +
234Q ASN* 1.3 76.2 - - - +
236Q GLY* 1.3 61.1 + - - +
283Q LEU* 5.0 2.7 - - + -
292Q PHE* 3.8 26.5 - - + -
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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