Contacts of the strand formed by residues 231 - 235 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151M VAL* 5.8 0.6 - - - +
155M LEU* 4.2 17.2 - - - +
162M ILE* 2.9 9.5 + - - +
163M VAL* 3.2 8.4 - - - +
164M GLY 2.9 23.2 + - - -
230M SER* 1.3 76.1 - - - +
232M ILE* 1.3 65.1 + - - +
233M PHE* 3.5 10.8 - - - -
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Residues in contact with ILE 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113M TYR* 3.7 23.6 - - - +
115M SER* 5.1 0.9 - - - +
129M GLU* 3.4 25.8 - - + +
148M ASP* 3.8 35.9 - - + +
151M VAL* 4.4 9.6 - - + -
152M ARG* 3.9 24.7 - - + +
155M LEU* 5.1 3.7 - - + +
164M GLY 3.4 10.8 - - - +
166M ARG* 4.1 32.1 - - + +
231M GLY* 1.3 75.9 - - - +
233M PHE* 1.3 72.4 + - - +
282M ASN* 5.0 1.6 + - - +
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Residues in contact with PHE 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129M GLU* 3.4 2.2 - - - +
163M VAL* 4.0 7.2 - - + -
164M GLY 2.9 10.8 + - - +
165M PHE* 3.5 11.5 - - + -
166M ARG* 2.7 33.1 + - - -
224M PHE* 3.6 26.9 - + + -
229M VAL* 4.5 2.7 - - + -
230M SER 3.4 21.3 - - - -
231M GLY* 3.5 26.9 - - - -
232M ILE* 1.3 78.4 - - - +
234M ASN* 1.3 65.2 + - - +
282M ASN* 3.7 24.5 - - + -
283M LEU* 3.8 31.4 - - + -
286M ALA* 3.8 19.3 - - + -
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Residues in contact with ASN 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120M TYR* 2.6 29.3 + - - -
127M PHE 2.7 27.8 + - - -
129M GLU* 2.7 26.1 + - - +
165M PHE* 5.6 0.2 - - - -
166M ARG* 3.7 9.5 - - - -
168M PHE* 3.6 15.8 - - + -
233M PHE* 1.3 78.7 - - - +
235M LEU* 1.3 60.4 + - - +
236M GLY 4.0 0.4 - - - -
278M ALA* 4.1 6.1 - - + -
279M ASP 2.8 27.7 + - - +
280M LEU* 4.4 2.9 - - + -
283M LEU* 3.7 21.7 - - - +
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Residues in contact with LEU 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165M PHE* 4.1 9.9 - - + -
166M ARG 2.9 13.6 + - - +
167M TYR* 3.5 38.0 - - + +
168M PHE* 3.1 28.1 + - - -
212M VAL* 3.9 7.4 - - + +
217M VAL* 4.1 26.5 - - + +
220M VAL* 3.6 39.0 - - + -
221M ASN* 4.7 0.2 - - - +
233M PHE 4.4 3.1 - - - +
234M ASN* 1.3 74.7 - - - +
236M GLY* 1.3 59.9 + - - +
283M LEU* 5.0 2.7 - - + -
292M PHE* 3.8 26.0 - - + -
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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