Contacts of the strand formed by residues 231 - 235 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151D VAL* 5.9 0.4 - - - -
155D LEU* 4.2 17.6 - - - +
162D ILE* 2.9 10.5 + - - +
163D VAL* 3.2 7.8 - - - +
164D GLY 2.9 23.7 + - - -
230D SER* 1.3 76.3 - - - +
232D ILE* 1.3 63.4 + - - +
233D PHE* 3.5 10.0 - - - -
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Residues in contact with ILE 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D TYR* 3.6 23.1 - - - +
115D SER* 5.1 0.9 - - - +
129D GLU* 3.4 26.9 - - + +
148D ASP* 3.8 34.8 - - + +
151D VAL* 4.4 10.3 - - + -
152D ARG* 3.9 24.9 - - + +
155D LEU* 5.1 3.7 - - + +
164D GLY 3.4 10.8 - - - +
166D ARG* 4.1 32.8 - - + +
231D GLY* 1.3 75.1 - - - +
233D PHE* 1.3 71.0 + - - +
282D ASN* 5.0 1.7 + - - +
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Residues in contact with PHE 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLU* 3.4 2.2 - - - +
163D VAL* 4.0 8.7 - - + -
164D GLY 2.9 10.4 + - - +
165D PHE* 3.5 11.0 - - + -
166D ARG* 2.7 33.1 + - - -
224D PHE* 3.6 25.8 - + - -
229D VAL* 4.5 2.2 - - + -
230D SER 3.4 21.5 - - - -
231D GLY* 3.5 27.1 - - - -
232D ILE* 1.3 80.4 - - - +
234D ASN* 1.3 65.5 + - - +
235D LEU 3.5 0.2 + - - -
282D ASN* 3.7 24.0 - - + -
283D LEU* 3.8 32.3 - - + -
286D ALA* 3.8 19.7 - - + -
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Residues in contact with ASN 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D TYR* 2.6 28.6 + - - -
127D PHE 2.7 27.3 + - - -
129D GLU* 2.7 26.6 + - - +
166D ARG* 3.7 8.6 - - - -
168D PHE* 3.6 17.4 - - + -
233D PHE* 1.3 77.1 - - - +
235D LEU* 1.3 60.8 + - - +
236D GLY 4.0 0.7 - - - -
278D ALA* 4.1 6.5 - - + -
279D ASP 2.8 27.9 + - - +
280D LEU* 4.2 2.9 - - + +
283D LEU* 3.7 21.5 - - + +
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Residues in contact with LEU 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165D PHE* 4.1 9.9 - - + -
166D ARG 2.9 12.6 + - - +
167D TYR* 3.5 37.9 - - + +
168D PHE* 3.1 28.4 + - - -
212D VAL* 3.9 7.3 - - + +
217D VAL* 4.1 26.0 - - + +
220D VAL* 3.6 37.0 - - + -
221D ASN* 4.7 0.4 - - - +
233D PHE 4.4 3.1 - - - +
234D ASN* 1.3 75.3 - - - +
236D GLY* 1.3 60.5 + - - +
283D LEU* 5.0 3.1 - - + -
292D PHE* 3.8 26.7 - - + -
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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