Contacts of the strand formed by residues 113 - 118 (chain F) in PDB entry 1O94
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 GLY 113 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E MET 3.1 14.8 - - - -
112F TYR* 1.3 79.6 - - - +
114F PHE* 1.3 58.4 + - - +
145F PHE* 3.8 13.2 - - - -
148F LYS* 3.8 18.0 - - - +
150F THR 3.0 14.2 + - - -
151F VAL* 4.0 4.3 - - - -
152F VAL* 2.8 26.0 + - - +
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Residues in contact with PHE 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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96E ASP* 5.4 0.9 - - - +
98E ILE* 3.4 19.3 - - + -
129E SER* 3.5 20.9 - - - -
226E MET* 3.1 19.6 + - + +
227E SER* 3.6 17.2 - - - -
103F ALA* 3.7 24.0 - - + -
104F SER* 3.7 32.1 - - - -
107F ALA* 3.6 17.7 - - + -
113F GLY* 1.3 75.2 - - - +
115F ALA* 1.3 65.5 + - - +
116F THR* 3.5 25.4 - - + -
145F PHE* 3.7 5.2 - - - -
152F VAL* 3.1 33.7 - - + -
154F THR* 4.6 2.9 - - + -
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Residues in contact with ALA 115 (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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227E SER* 4.9 2.0 - - - -
114F PHE* 1.3 77.2 - - - +
116F THR* 1.3 66.8 + - - +
118F VAL* 4.0 17.5 - - + +
132F ARG* 4.6 10.5 - - - +
143F VAL* 4.2 12.6 - - + -
145F PHE* 3.9 22.7 - - + -
152F VAL 3.2 5.5 + - - +
153F LEU* 3.3 8.0 - - + +
154F THR 3.1 21.1 + - - -
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Residues in contact with THR 116 (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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126E ALA 4.2 0.3 + - - -
127E TYR* 2.8 24.8 + - - +
128E ALA 5.2 1.8 - - - +
129E SER* 3.4 21.9 + - - +
95F HIS* 4.0 7.2 - - + +
100F LEU* 6.3 0.7 - - + -
103F ALA* 5.5 0.7 - - + -
114F PHE* 3.5 25.8 - - + -
115F ALA* 1.3 75.0 - - - +
117F ASP* 1.3 70.6 + - - +
118F VAL* 3.3 4.6 + - - +
132F ARG* 2.8 41.8 + - - +
154F THR* 3.2 17.3 - - + +
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Residues in contact with ASP 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ALA* 4.9 6.6 - - - +
95F HIS* 3.5 39.2 + - + -
116F THR* 1.3 75.5 - - - +
118F VAL* 1.3 61.6 + - - +
119F TYR* 3.6 13.7 - - - -
132F ARG* 3.9 16.2 + - + +
133F GLY 4.8 0.3 + - - -
137F GLN* 4.4 5.2 - - - +
154F THR* 2.9 15.7 + - - -
156F ARG* 2.9 52.4 + - - +
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Residues in contact with VAL 118 (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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115F ALA* 4.0 27.4 - - + +
116F THR 3.8 10.5 - - - +
117F ASP* 1.3 75.7 - - - +
119F TYR* 1.3 59.5 + - - +
120F ILE 3.3 28.7 - - - +
121F VAL* 4.2 5.6 - - + -
130F ALA* 3.8 18.6 - - + -
131F THR 3.5 9.0 - - - +
132F ARG* 4.8 3.4 - - + -
153F LEU* 4.3 7.9 - - + -
154F THR 3.0 15.9 + - - +
155F ILE* 3.6 22.9 - - + +
156F ARG* 3.0 20.3 + - - +
160F PHE* 4.0 2.9 - - - -
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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