Contacts of the strand formed by residues 162 - 167 (chain R) 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 ILE 162 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101R LEU* 3.8 18.8 - - + -
105R LEU* 3.7 26.7 - - + -
111R PHE* 3.3 15.9 - - + -
113R TYR* 4.2 12.1 - - + -
151R VAL* 3.7 26.9 - - + -
154R ILE* 3.9 13.5 - - + -
155R LEU* 4.0 13.2 - - + +
158R ALA* 3.7 18.6 - - + -
160R SER 3.7 5.2 - - - +
161R GLN* 1.3 79.1 - - - +
163R VAL* 1.3 64.0 + - - +
230R SER* 3.0 11.4 + - - -
231R GLY* 2.9 24.5 + - - +
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Residues in contact with VAL 163 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111R PHE 2.9 6.9 + - - -
112R LEU* 3.3 13.8 - - + +
113R TYR* 2.7 40.2 + - - +
161R GLN* 3.5 18.2 - - + +
162R ILE* 1.3 79.5 - - - +
164R GLY* 1.3 57.1 + - - +
165R PHE* 3.5 34.5 - - + -
224R PHE* 4.1 6.1 - - + -
229R VAL 3.0 29.2 - - - +
230R SER* 4.1 1.8 - - - -
231R GLY 3.2 9.9 - - - +
233R PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 164 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113R TYR* 3.4 33.8 - - - -
115R SER* 4.8 1.3 - - - -
151R VAL* 6.0 0.2 - - - +
162R ILE* 5.3 0.2 - - - +
163R VAL* 1.3 76.6 - - - +
165R PHE* 1.3 64.1 + - - -
166R ARG 3.7 0.6 + - - -
231R GLY 2.9 9.9 + - - +
232R ILE* 3.4 8.1 - - - +
233R PHE 2.9 28.4 + - - +
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Residues in contact with PHE 165 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112R LEU* 4.2 13.5 - - + -
113R TYR 2.9 18.3 + - - +
114R ALA* 3.8 2.1 - - - -
115R SER* 2.8 25.1 + - - +
163R VAL* 3.5 25.4 - - + -
164R GLY* 1.3 71.4 - - - -
166R ARG* 1.3 60.8 + - - +
167R TYR* 3.1 35.6 + + + +
220R VAL* 3.6 19.1 - - + -
221R ASN* 3.3 37.5 - - - -
224R PHE* 3.5 45.8 - + + -
233R PHE* 3.5 11.2 - + + -
235R LEU* 4.1 7.9 - - + -
283R LEU* 5.5 0.4 - - + -
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Residues in contact with ARG 166 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115R SER* 3.3 15.1 + - - +
116R SER 3.3 20.9 - - - +
117R ALA* 3.6 3.6 - - - +
119R THR* 3.2 17.8 + - - +
120R TYR* 3.1 44.0 + - - -
129R GLU* 3.8 7.8 - - - +
134R GLU* 2.8 38.2 + - - -
145R PHE* 5.6 0.4 - - - -
148R ASP* 2.8 29.7 + - - +
152R ARG* 4.0 2.4 - - - +
164R GLY 3.7 1.4 + - - -
165R PHE* 1.3 71.0 - - - +
167R TYR* 1.3 64.0 + - - +
168R PHE* 3.2 8.8 - - - -
232R ILE* 4.1 17.0 - - + +
233R PHE 2.7 18.3 + - - +
234R ASN* 3.7 7.6 - - - +
235R LEU 2.9 19.2 + - - +
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Residues in contact with TYR 167 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11R ILE* 3.5 15.6 - - + +
75R GLU* 2.7 31.7 + - - -
114R ALA* 3.5 18.5 - - + +
115R SER 4.1 3.2 + - - -
117R ALA* 3.0 21.7 + - - +
165R PHE* 3.1 30.0 + - + -
166R ARG* 1.3 71.2 - - - +
168R PHE* 1.3 63.4 + - - +
170R VAL* 3.7 12.6 - - + -
217R VAL* 3.6 20.6 - - + -
221R ASN* 3.1 21.2 + - - -
235R LEU* 3.5 29.2 - - + -
400R NAP 3.3 40.2 - + + -
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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