Contacts of the strand formed by residues 162 - 167 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101N LEU* 3.8 18.8 - - + -
105N LEU* 3.7 26.5 - - + -
111N PHE* 3.3 15.5 - - + -
113N TYR* 4.2 12.3 - - + -
151N VAL* 3.7 26.5 - - + -
154N ILE* 3.9 13.2 - - + -
155N LEU* 4.0 14.2 - - + +
158N ALA* 3.7 18.2 - - + -
160N SER 3.3 5.8 + - - +
161N GLN* 1.3 79.2 - - - +
163N VAL* 1.3 64.4 + - - +
230N SER* 3.0 11.2 + - - -
231N GLY* 2.9 24.1 + - - +
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Residues in contact with VAL 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N PHE 2.9 7.1 + - - -
112N LEU* 3.3 13.3 - - + -
113N TYR* 2.7 40.1 + - - -
161N GLN* 3.5 17.7 - - + +
162N ILE* 1.3 80.2 - - - +
164N GLY* 1.3 59.2 + - - +
165N PHE* 3.5 34.4 - - + -
224N PHE* 4.1 5.6 - - + -
229N VAL 3.0 29.2 - - - +
230N SER* 4.1 1.6 - - - -
231N GLY 3.2 9.4 - - - +
233N PHE* 4.0 12.8 - - + -
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Residues in contact with GLY 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N TYR* 3.4 32.8 - - - -
115N SER* 4.8 1.3 - - - -
162N ILE* 5.3 0.2 - - - +
163N VAL* 1.3 77.8 - - - +
165N PHE* 1.3 64.3 + - - -
166N ARG 3.7 0.2 + - - -
231N GLY 2.9 10.3 + - - +
232N ILE* 3.4 8.5 - - - +
233N PHE 2.9 27.9 + - - +
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Residues in contact with PHE 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112N LEU* 4.2 12.6 - - + -
113N TYR 2.9 18.3 + - - +
114N ALA* 3.8 2.1 - - - -
115N SER* 2.8 24.9 + - - +
163N VAL* 3.5 25.8 - - + -
164N GLY* 1.3 73.1 - - - -
166N ARG* 1.3 60.4 + - - +
167N TYR* 3.1 36.2 + + + -
220N VAL* 3.6 18.6 - - + -
221N ASN* 3.3 37.7 - - - -
224N PHE* 3.5 46.2 - + + -
233N PHE* 3.5 11.0 - + + -
235N LEU* 4.1 7.4 - - + -
283N LEU* 5.8 0.4 - - + -
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Residues in contact with ARG 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N SER* 3.3 16.2 + - - +
116N SER 3.3 21.8 - - - +
117N ALA* 3.6 3.6 - - - +
119N THR* 3.2 17.8 + - - -
120N TYR* 3.1 44.6 + - + -
129N GLU* 3.8 7.4 - - - +
134N GLU* 2.8 37.8 + - - -
145N PHE* 5.6 0.2 - - - -
148N ASP* 2.8 29.3 + - - +
152N ARG* 3.9 2.4 - - - +
164N GLY 3.7 1.6 + - - -
165N PHE* 1.3 71.3 - - - +
167N TYR* 1.3 63.5 + - - +
168N PHE* 3.2 8.5 - - - -
232N ILE* 4.1 16.1 - - + +
233N PHE 2.7 19.0 + - - +
234N ASN* 3.7 7.9 - - - +
235N LEU 2.9 18.8 + - - -
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Residues in contact with TYR 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N ILE* 3.5 24.7 - - + +
75N GLU* 2.8 32.1 + - - -
114N ALA* 3.5 17.6 - - + +
115N SER 4.1 3.0 + - - -
116N SER* 4.2 0.2 + - - -
117N ALA* 3.0 22.3 + - - +
165N PHE* 3.1 30.2 + - + -
166N ARG* 1.3 71.9 - - - +
168N PHE* 1.3 62.8 + - - +
170N VAL* 3.7 15.5 - - + -
217N VAL* 3.6 20.2 - - + -
221N ASN* 3.1 21.5 + - - -
235N LEU* 3.5 29.6 - - + -
400N NAP 3.7 29.0 - + + -
402N 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