Contacts of the strand formed by residues 162 - 167 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 3.8 19.7 - - + -
105E LEU* 3.7 26.0 - - + -
111E PHE* 3.3 15.5 - - + -
113E TYR* 4.2 12.1 - - + -
151E VAL* 3.7 26.0 - - + -
154E ILE* 3.9 13.9 - - + -
155E LEU* 4.0 13.2 - - + +
158E ALA* 3.7 18.4 - - + -
160E SER 3.7 5.2 - - - +
161E GLN* 1.3 79.1 - - - +
163E VAL* 1.3 63.9 + - - +
164E GLY 5.3 0.2 - - - +
230E SER* 3.0 11.3 + - - -
231E GLY* 2.9 24.1 + - - +
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Residues in contact with VAL 163 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111E PHE 2.9 7.3 + - - -
112E LEU* 3.3 13.4 - - + -
113E TYR* 2.7 39.7 + - - +
161E GLN* 3.5 18.2 - - + +
162E ILE* 1.3 78.9 - - - +
164E GLY* 1.3 59.3 + - - +
165E PHE* 3.5 34.3 - - + -
224E PHE* 4.1 6.3 - - + -
229E VAL 3.0 28.9 - - - +
230E SER* 4.1 1.8 - - - -
231E GLY 3.2 9.4 - - - +
233E PHE* 4.0 11.7 - - + -
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Residues in contact with GLY 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E TYR* 3.4 32.9 + - - -
115E SER* 4.8 2.0 - - - -
151E VAL* 6.0 0.2 - - - +
163E VAL* 1.3 76.7 - - - +
165E PHE* 1.3 63.8 + - - -
166E ARG 3.7 0.2 + - - -
231E GLY 2.9 10.1 + - - +
232E ILE* 3.4 7.8 - - - +
233E PHE 2.9 28.4 + - - +
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Residues in contact with PHE 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E LEU* 4.2 12.6 - - + -
113E TYR 2.9 17.2 + - - +
114E ALA* 3.8 1.9 - - - -
115E SER* 2.8 24.4 + - - +
163E VAL* 3.5 25.6 - - + -
164E GLY* 1.3 73.5 - - - -
166E ARG* 1.3 61.7 + - - +
167E TYR* 3.1 35.6 + + + -
220E VAL* 3.6 19.3 - - + -
221E ASN* 3.3 38.1 - - - -
224E PHE* 3.5 46.4 - + + -
233E PHE* 3.5 11.9 - + + -
235E LEU* 4.1 7.6 - - + -
283E LEU* 5.8 0.2 - - + -
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Residues in contact with ARG 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115E SER* 3.3 14.5 + - - +
116E SER 3.3 21.5 - - - +
117E ALA* 3.6 3.4 - - - +
119E THR* 3.2 16.4 + - - +
120E TYR* 3.1 46.1 + - + -
129E GLU* 3.8 8.4 - - - +
134E GLU* 2.8 37.2 + - - -
145E PHE* 5.6 0.4 - - - -
148E ASP* 2.8 29.9 + - - +
152E ARG* 3.9 2.4 - - - +
164E GLY 3.7 1.2 + - - -
165E PHE* 1.3 70.4 - - - +
167E TYR* 1.3 62.7 + - - +
168E PHE* 3.2 8.7 - - - -
232E ILE* 4.1 17.2 - - + +
233E PHE 2.7 19.0 + - - +
234E ASN* 3.7 8.1 - - - +
235E LEU* 2.9 19.6 + - - -
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Residues in contact with TYR 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E ILE* 3.5 24.6 - - + +
75E GLU* 2.8 30.7 + - - -
114E ALA* 3.5 17.9 - - + +
115E SER 4.1 3.2 + - - -
117E ALA* 3.0 22.3 + - - +
165E PHE* 3.1 31.3 + - + -
166E ARG* 1.3 72.1 - - - +
168E PHE* 1.3 62.6 + - - +
170E VAL* 3.7 12.3 - - + -
217E VAL* 3.5 21.3 - - + -
221E ASN* 3.1 21.2 + - - -
235E LEU* 3.5 29.4 - - + -
400E NAP 3.6 32.4 - + + -
402E BMA 4.6 0.3 + - - -
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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