Contacts of the helix formed by residues 119 - 128 (chain F) in PDB entry 1O1F
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 THR 119 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117F LYS 4.0 2.4 + - - +
118F MET* 1.3 72.1 - - - +
120F GLU* 1.3 59.1 + - - +
121F GLU* 3.4 12.6 + - - +
122F GLU* 2.9 41.7 + - - +
123F VAL* 3.0 25.2 + - - +
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Residues in contact with GLU 120 (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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108F ARG* 3.7 32.5 + - - +
109F HIS* 5.0 6.5 - - - -
112F ALA* 3.7 22.3 - - + +
118F MET 3.6 1.0 + - - -
119F THR* 1.3 69.9 - - - +
121F GLU* 1.3 59.5 + - - +
123F VAL* 3.7 13.2 - - - +
124F GLU* 3.0 59.6 + - - +
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Residues in contact with GLU 121 (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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119F THR* 3.1 10.6 + - - +
120F GLU* 1.3 77.0 - - - +
122F GLU* 1.3 62.6 + - + +
124F GLU* 3.2 12.1 + - - +
125F GLU* 3.0 48.5 + - + +
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Residues in contact with GLU 122 (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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798D LEU* 4.0 28.5 - - + +
118F MET* 4.0 12.0 - - + +
119F THR* 2.9 46.3 + - - +
121F GLU* 1.3 77.6 - - + +
123F VAL* 1.3 61.9 + - - +
125F GLU* 3.1 18.3 + - - +
126F LEU* 3.0 32.3 + - + +
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Residues in contact with VAL 123 (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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107F LEU 4.8 0.2 - - - +
108F ARG* 3.6 39.7 - - + +
111F LEU* 3.8 40.2 - - + -
112F ALA 4.3 1.1 - - - +
118F MET* 3.9 10.5 - - + +
119F THR 3.0 19.7 + - - +
120F GLU* 3.6 22.9 - - - +
121F GLU 3.3 0.2 - - - -
122F GLU* 1.3 75.1 - - - +
124F GLU* 1.3 62.6 + - - +
126F LEU* 3.1 10.1 + - - +
127F MET* 3.0 25.5 - - + +
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Residues in contact with GLU 124 (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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108F ARG* 5.3 7.4 - - - +
120F GLU* 3.0 49.9 + - - +
121F GLU* 3.6 8.7 - - - +
123F VAL* 1.3 75.2 - - - +
125F GLU* 1.3 58.5 + - + +
127F MET* 3.2 5.1 + - - +
128F LYS* 3.0 33.0 + - - +
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Residues in contact with GLU 125 (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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797D PHE* 5.7 0.7 - - - -
798D LEU* 6.1 0.5 - - - +
121F GLU* 3.0 37.4 + - + +
122F GLU* 3.1 28.9 + - - +
124F GLU* 1.3 77.0 - - + +
126F LEU* 1.3 64.1 + - + +
127F MET 3.5 0.4 + - - -
128F LYS* 4.1 34.3 - - - +
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Residues in contact with LEU 126 (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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794D CYS* 5.5 8.7 - - + -
797D PHE* 2.8 41.7 - - + -
798D LEU* 2.9 33.2 - - + -
111F LEU* 4.2 21.5 - - + -
118F MET* 6.2 2.2 - - + -
122F GLU* 3.0 18.3 + - + +
123F VAL* 3.1 5.3 + - - +
125F GLU* 1.3 83.1 - - + +
127F MET* 1.3 64.1 + - - +
128F LYS 3.5 0.2 - - - -
130F GLN* 3.1 24.2 + - - +
142F PHE* 3.2 15.0 - - + -
146F ILE* 4.1 9.7 - - + +
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Residues in contact with MET 127 (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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107F LEU* 3.9 22.9 - - + -
108F ARG* 4.4 13.7 - - + +
111F LEU* 5.3 1.8 - - - -
123F VAL* 3.0 29.0 + - + +
124F GLU* 4.1 4.9 - - - +
126F LEU* 1.3 86.3 - - - +
128F LYS* 1.3 57.7 + - - +
129F GLY 3.0 9.5 + - - -
130F GLN* 3.0 12.3 - - + +
131F GLU* 3.1 34.0 + - + +
137F ILE* 3.5 48.5 - - + -
142F PHE* 3.8 19.5 - - + -
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Residues in contact with LYS 128 (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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124F GLU 3.0 16.5 + - - +
125F GLU* 4.1 34.2 - - - +
126F LEU 3.5 0.6 - - - -
127F MET* 1.3 72.9 - - - +
129F GLY* 1.3 58.6 + - - +
130F GLN* 3.4 7.7 + - - +
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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