Contacts of the strand formed by residues 162 - 167 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101O LEU* 3.8 19.3 - - + -
105O LEU* 3.7 26.5 - - + -
111O PHE* 3.3 15.5 - - + -
113O TYR* 4.2 11.4 - - + -
151O VAL* 3.7 26.7 - - + -
154O ILE* 3.9 13.0 - - + -
155O LEU* 4.0 13.8 - - + +
158O ALA* 3.7 18.8 - - + -
160O SER 3.3 5.4 + - - +
161O GLN* 1.3 78.4 - - - +
163O VAL* 1.3 64.4 + - - +
230O SER* 3.0 11.4 + - - -
231O GLY* 2.9 24.3 + - - +
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Residues in contact with VAL 163 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111O PHE 2.9 8.1 + - - -
112O LEU* 3.3 12.9 - - + -
113O TYR* 2.7 40.2 + - - +
161O GLN* 3.5 17.7 - - + +
162O ILE* 1.3 80.2 - - - +
164O GLY* 1.3 58.3 + - - +
165O PHE* 3.5 35.3 - - + -
224O PHE* 4.1 6.1 - - + -
229O VAL 3.0 28.9 - - - +
230O SER* 4.1 2.0 - - - -
231O GLY 3.2 9.2 - - - +
233O PHE* 4.0 12.3 - - + -
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Residues in contact with GLY 164 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113O TYR* 3.4 33.8 + - - -
115O SER* 4.8 1.1 - - - -
162O ILE* 5.3 0.2 - - - +
163O VAL* 1.3 76.6 - - - +
165O PHE* 1.3 64.3 + - - -
166O ARG 3.7 0.6 + - - -
231O GLY 2.9 9.7 + - - +
232O ILE* 3.4 7.4 - - - +
233O PHE* 2.9 28.1 + - - +
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Residues in contact with PHE 165 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112O LEU* 4.2 13.2 - - + -
113O TYR 2.9 17.4 + - - +
114O ALA* 3.8 1.9 - - - -
115O SER* 2.8 25.1 + - - +
163O VAL* 3.5 25.4 - - + -
164O GLY* 1.3 72.2 - - - -
166O ARG* 1.3 61.0 + - - +
167O TYR* 3.1 35.3 + + + -
220O VAL* 3.6 18.6 - - + -
221O ASN* 3.3 37.7 - - - -
224O PHE* 3.5 47.3 - + + -
233O PHE* 3.5 11.4 - + + -
234O ASN 5.6 0.2 - - - -
235O LEU* 4.1 7.0 - - + -
283O LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 166 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115O SER* 3.4 16.4 + - - +
116O SER 3.3 22.0 - - - +
117O ALA* 3.6 3.6 - - - +
119O THR* 3.2 16.9 + - - -
120O TYR* 3.1 44.4 + - + -
129O GLU* 3.8 7.6 - - - +
134O GLU* 2.8 37.8 + - - -
145O PHE* 5.6 0.4 - - - -
148O ASP* 2.8 29.7 + - - +
152O ARG* 3.9 2.8 - - - +
164O GLY 3.7 1.4 + - - -
165O PHE* 1.3 70.0 - - - +
167O TYR* 1.3 64.0 + - - +
168O PHE* 3.2 8.3 - - - -
232O ILE* 4.1 17.7 - - + +
233O PHE 2.7 19.6 + - - +
234O ASN* 3.7 8.1 - - - +
235O LEU* 2.9 19.9 + - - +
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Residues in contact with TYR 167 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O ILE* 3.5 25.3 - - + +
75O GLU* 2.8 29.9 + - - -
114O ALA* 3.5 18.5 - - + +
115O SER 4.1 3.2 + - - -
116O SER* 4.2 0.2 + - - -
117O ALA* 3.0 22.2 + - - +
165O PHE* 3.1 31.3 + - + -
166O ARG* 1.3 71.5 - - - +
168O PHE* 1.3 63.5 + - - +
170O VAL* 3.7 12.6 - - + -
217O VAL* 3.6 21.8 - - + -
221O ASN* 3.1 21.0 + - - -
235O LEU* 3.5 29.2 - - + -
400O NAP 3.6 32.3 - + + -
402O BMA 4.6 0.2 + - - -
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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