Contacts of the strand formed by residues 231 - 235 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151P VAL* 5.8 0.8 - - - +
155P LEU* 4.3 17.6 - - - +
162P ILE 2.9 10.2 + - - +
163P VAL* 3.2 7.8 - - - +
164P GLY 2.9 23.4 + - - -
230P SER* 1.3 76.7 - - - +
232P ILE* 1.3 64.5 + - - +
233P PHE* 3.5 9.6 - - - -
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Residues in contact with ILE 232 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113P TYR* 3.7 22.9 - - - +
115P SER* 5.1 0.7 - - - +
129P GLU* 3.4 27.6 - - + +
148P ASP* 3.8 35.0 - - + +
151P VAL* 4.3 10.1 - - + -
152P ARG* 3.9 25.4 - - + +
155P LEU* 5.1 3.1 - - + +
164P GLY 3.4 10.5 - - - +
166P ARG* 4.1 31.9 - - + +
231P GLY* 1.3 76.9 - - - +
233P PHE* 1.3 70.6 + - - +
282P ASN* 5.0 1.6 + - - +
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Residues in contact with PHE 233 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129P GLU* 3.4 2.0 - - - +
163P VAL* 4.0 8.1 - - + -
164P GLY 2.9 10.6 + - - +
165P PHE* 3.5 10.9 - - + -
166P ARG* 2.7 32.8 + - - -
224P PHE* 3.6 27.1 - + - -
229P VAL* 4.5 2.9 - - + -
230P SER 3.4 21.8 - - - -
231P GLY* 3.5 27.1 - - - -
232P ILE* 1.3 78.5 - - - +
234P ASN* 1.3 65.1 + - - +
282P ASN* 3.7 24.7 - - + -
283P LEU* 3.8 31.6 - - + -
286P ALA* 3.8 18.4 - - + -
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Residues in contact with ASN 234 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120P TYR* 2.6 28.8 + - - -
127P PHE 2.7 28.0 + - - -
129P GLU* 2.7 27.2 + - - +
165P PHE* 5.6 0.2 - - - -
166P ARG* 3.7 9.2 - - - -
168P PHE* 3.6 17.0 - - + -
233P PHE* 1.3 78.0 - - - +
235P LEU* 1.3 60.4 + - - +
236P GLY 4.0 0.4 - - - -
278P ALA* 4.1 6.5 - - + -
279P ASP 2.8 27.8 + - - +
280P LEU* 4.2 2.9 - - + +
283P LEU* 3.8 21.9 - - + +
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Residues in contact with LEU 235 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165P PHE* 4.1 10.5 - - + -
166P ARG 2.9 12.2 + - - +
167P TYR* 3.5 36.8 - - + -
168P PHE* 3.1 27.5 + - - -
212P VAL* 3.9 8.4 - - + +
217P VAL* 4.2 25.1 - - + +
220P VAL* 3.6 37.5 - - + -
221P ASN* 4.7 0.4 - - - +
233P PHE 4.4 3.1 - - - +
234P ASN* 1.3 74.6 - - - +
236P GLY* 1.3 60.4 - - - +
283P LEU* 5.0 3.1 - - + -
292P 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