Contacts of the strand formed by residues 231 - 235 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151T VAL* 5.9 0.4 - - - -
155T LEU* 4.2 17.4 - - - +
162T ILE* 2.9 9.5 + - - +
163T VAL* 3.2 7.7 - - - +
164T GLY 2.9 23.4 + - - -
230T SER* 1.3 77.0 - - - +
232T ILE* 1.3 65.1 + - - +
233T PHE* 3.5 9.6 - - - -
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Residues in contact with ILE 232 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113T TYR* 3.7 23.8 - - - +
115T SER* 5.1 0.7 - - - +
129T GLU* 3.4 26.6 - - + +
148T ASP* 3.8 35.9 - - + +
151T VAL* 4.4 9.6 - - + -
152T ARG* 3.9 24.5 - - + +
155T LEU* 5.0 3.5 - - + +
164T GLY 3.4 10.3 - - - +
166T ARG* 4.1 32.1 - - + +
231T GLY* 1.3 75.9 - - - +
233T PHE* 1.3 70.2 + - - +
282T ASN* 5.0 1.6 + - - +
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Residues in contact with PHE 233 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129T GLU* 3.4 2.2 - - - +
163T VAL* 4.0 8.5 - - + -
164T GLY 2.9 11.0 + - - +
165T PHE* 3.5 11.9 - + + -
166T ARG* 2.7 32.6 + - - -
224T PHE* 3.6 26.2 - + - -
229T VAL* 4.5 2.5 - - + -
230T SER 3.4 22.4 - - - -
231T GLY* 3.5 26.0 - - - -
232T ILE* 1.3 79.4 - - - +
234T ASN* 1.3 65.6 + - - +
282T ASN* 3.7 23.8 - - + -
283T LEU* 3.8 31.4 - - + -
286T ALA* 3.8 19.3 - - + -
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Residues in contact with ASN 234 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120T TYR* 2.6 28.2 + - - -
127T PHE 2.7 27.6 + - - -
129T GLU* 2.7 27.5 + - - +
165T PHE* 5.6 0.2 - - - -
166T ARG* 3.7 9.2 - - - -
168T PHE* 3.6 16.8 - - + -
233T PHE* 1.3 79.0 - - - +
235T LEU* 1.3 59.9 + - - +
236T GLY 4.0 0.7 - - - -
278T ALA* 4.1 6.1 - - + -
279T ASP 2.8 27.5 + - - +
280T LEU* 4.2 2.9 - - + +
283T LEU* 3.7 21.1 - - - +
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Residues in contact with LEU 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165T PHE* 4.1 9.6 - - + -
166T ARG 2.9 12.2 + - - +
167T TYR* 3.5 37.3 - - + -
168T PHE* 3.1 28.0 + - - -
212T VAL* 3.9 7.8 - - + +
217T VAL* 4.1 26.0 - - + +
220T VAL* 3.6 39.3 - - + -
221T ASN* 4.7 0.2 - - - +
233T PHE 3.5 3.1 + - - +
234T ASN* 1.3 75.1 - - - +
236T GLY* 1.3 59.5 + - - +
283T LEU* 5.0 2.5 - - + -
292T 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