Contacts of the helix formed by residues 116 - 125 (chain F) in PDB entry 4OA5
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 GLU 116 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F LYS* 4.3 14.9 - - + +
115F GLY* 1.3 71.8 - - - -
117F ALA* 1.3 73.8 + - - +
118F LEU* 3.0 38.7 + - - +
119F ALA* 3.2 14.8 + - + +
120F GLN* 3.0 19.1 + - - +
138F ASN* 4.7 9.4 + - - +
141F SER* 5.1 0.7 + - - -
145F TYR* 4.1 11.6 + - - -
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Residues in contact with ALA 117 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63F VAL* 3.6 20.0 - - + -
87F ILE* 3.7 18.2 - - + -
89F LYS* 5.6 0.2 - - - +
115F GLY 3.6 2.8 + - - -
116F GLU* 1.3 76.1 + - - +
118F LEU* 1.3 59.1 + - - +
120F GLN* 3.1 1.0 + - - +
121F LEU* 2.7 39.1 + - + +
145F TYR* 3.4 32.8 - - + +
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Residues in contact with LEU 118 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLU* 3.0 18.9 + - - +
117F ALA* 1.3 74.7 - - - +
119F ALA* 1.3 62.7 + - - +
121F LEU* 3.8 8.6 - - + +
122F ASN* 3.1 21.8 + - - +
141F SER* 4.2 18.2 - - - +
144F ALA* 3.8 33.0 - - + +
145F TYR* 3.9 22.0 - - + -
148F TRP* 5.8 2.8 - - + -
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Residues in contact with ALA 119 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116F GLU* 3.2 18.8 + - + +
118F LEU* 1.3 79.3 - - - +
120F GLN* 1.3 69.2 + - - +
122F ASN* 3.2 19.5 + - - +
123F THR* 3.3 12.6 + - - +
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Residues in contact with GLN 120 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87F ILE* 3.7 33.7 - - + -
113F LEU* 3.6 21.8 - - + +
114F HIS 3.6 19.8 + - - +
115F GLY* 3.8 19.4 - - - +
116F GLU 3.0 15.8 + - - +
117F ALA 3.9 0.2 - - - +
119F ALA* 1.3 79.8 + - - +
121F LEU* 1.3 66.4 + - - +
123F THR* 2.8 39.8 + - - +
124F LEU* 3.1 9.5 + - - +
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Residues in contact with LEU 121 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61F VAL* 3.6 31.2 - - + -
63F VAL* 4.4 10.5 - - + -
87F ILE* 3.7 13.7 - - + -
117F ALA 2.7 25.9 + - - +
118F LEU* 3.8 9.0 - - + +
120F GLN* 1.3 71.7 - - - +
122F ASN* 1.3 61.8 + - - +
124F LEU* 3.0 16.5 + - + +
125F LYS* 3.2 6.8 + - - +
133F ILE* 4.8 1.6 - - + -
145F TYR* 3.7 32.3 - - + -
148F TRP* 3.1 60.2 + - + +
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Residues in contact with ASN 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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118F LEU 3.1 13.8 + - - +
119F ALA* 3.3 13.9 - - - +
120F GLN 3.1 0.2 - - - -
121F LEU* 1.3 76.7 - - - +
123F THR* 1.3 60.9 + - - +
125F LYS* 3.2 54.7 + - - +
126F GLU* 3.6 4.7 - - - +
148F TRP* 4.8 3.0 - - - +
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Residues in contact with THR 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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113F LEU* 4.4 4.9 - - - +
119F ALA 3.3 13.4 + - - +
120F GLN* 2.8 36.3 + - - +
122F ASN* 1.3 76.7 - - + +
124F LEU* 1.3 65.5 + - - +
125F LYS 3.5 0.3 + - - -
126F GLU* 3.5 20.7 + - - +
127F MET* 4.9 3.8 + - - +
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Residues in contact with LEU 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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61F VAL* 4.0 26.2 - - + -
85F TYR* 3.6 57.9 - - + -
87F ILE* 4.2 12.1 - - + -
113F LEU* 3.8 18.8 - - + -
120F GLN 3.1 9.1 + - - +
121F LEU* 3.0 12.7 + - + +
123F THR* 1.3 78.1 + - - +
125F LYS* 1.3 60.3 + - - +
126F GLU 3.1 3.1 - - - -
127F MET* 2.9 29.6 + - + +
128F ALA 3.4 6.9 + - - -
130F PHE* 3.5 12.7 - - + -
148F TRP* 4.3 6.3 - - + -
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Residues in contact with LYS 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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121F LEU 3.2 8.4 + - - +
122F ASN* 3.2 45.2 + - - +
123F THR 3.3 1.4 - - - -
124F LEU* 1.3 77.2 - - - +
126F GLU* 1.3 80.1 + - - +
128F ALA* 3.2 24.7 + - - +
148F TRP* 4.3 3.8 - - + +
152F TYR* 3.5 48.3 + - + +
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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