Contacts of the strand formed by residues 111 - 114 (chain F) 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 PHE 111 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72F ILE* 3.7 9.6 - - + -
74F HIS* 3.7 37.2 - + + -
97F SER 4.1 13.2 - - - -
100F LEU* 3.7 20.6 - - + -
101F LEU* 3.8 25.6 - - + -
104F CYS* 3.8 24.7 - - + -
105F LEU* 6.3 0.2 - - + -
109F ILE 3.2 6.9 + - - +
110F PRO* 1.3 73.7 - - - +
112F LEU* 1.3 63.9 + - - +
113F TYR* 3.5 30.7 - + + -
147F PHE* 4.0 15.3 - + - -
161F GLN 3.0 12.3 + - - +
162F ILE* 3.3 8.0 + - + -
163F VAL 2.9 23.9 + - - -
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Residues in contact with LEU 112 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F ALA* 4.3 12.1 - - + -
72F ILE 2.9 14.3 + - - +
73F PHE* 3.2 26.5 - - + -
74F HIS* 2.7 30.8 + - - -
75F GLU* 3.7 4.1 - - - +
110F PRO* 4.0 17.5 - - + +
111F PHE* 1.3 79.8 - - - +
113F TYR* 1.3 54.0 + - - +
161F GLN* 4.0 16.2 - - - +
163F VAL* 3.3 15.0 - - + +
165F PHE* 4.2 14.4 - - + -
221F ASN 4.1 7.9 - - - +
224F PHE* 4.0 14.8 - - + -
225F LEU* 3.9 27.4 - - + +
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Residues in contact with TYR 113 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F HIS* 3.5 17.3 - + + +
75F GLU* 4.5 4.5 - - - -
97F SER* 5.9 0.2 - - - -
111F PHE* 3.5 37.7 - + + -
112F LEU* 1.3 74.4 - - - +
114F ALA* 1.3 77.7 + - - +
115F SER* 4.1 1.8 - - - -
147F PHE* 3.7 17.0 - + - -
148F ASP* 2.7 29.8 + - - -
151F VAL* 3.5 33.8 - - + +
162F ILE* 4.2 7.0 - - + -
163F VAL 2.7 27.1 + - - +
164F GLY* 3.4 23.8 - - - -
165F PHE* 2.9 31.3 + - - -
232F ILE* 3.7 15.9 - - - +
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Residues in contact with ALA 114 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F HIS 3.2 12.0 + - - +
75F GLU* 3.7 8.7 - - - +
113F TYR* 1.3 85.0 - - - +
115F SER* 1.3 58.8 + - - +
144F LYS* 3.0 21.5 + - - +
165F PHE 3.9 4.0 - - - -
167F TYR* 3.5 17.0 - - + -
400F NAP 3.4 38.1 - - - +
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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