Contacts of the helix formed by residues 111 - 118 (chain A) in PDB entry 1OE5
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 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A PHE 4.7 0.4 - - - -
101A GLY* 3.9 9.0 - - - -
109A PHE 2.9 9.9 + - - -
110A GLY* 1.3 69.1 - - - +
112A VAL* 1.3 64.2 + - - +
113A ASN* 3.7 18.0 + - - +
114A HIS* 2.8 46.6 + - + +
115A VAL* 2.9 28.7 + - - +
145A SER* 3.0 21.7 + - - +
146A GLU* 3.4 33.4 - - + +
149A GLY* 3.6 6.0 - - - +
150A ALA* 3.5 25.0 - - - +
153A TRP* 4.8 0.6 - - + -
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A PHE 4.1 15.0 + - - +
104A GLN* 4.6 0.7 - - + -
105A THR* 3.8 23.1 - - + -
111A GLU* 1.3 74.2 - - - +
113A ASN* 1.3 66.2 + - - +
115A VAL* 3.3 1.1 + - - +
116A ARG* 2.8 44.1 + - + +
139A GLY 4.0 14.6 - - - +
140A PHE* 3.6 27.8 - - + +
142A CYS* 4.0 21.3 - - + +
144A GLN 4.6 7.1 + - - +
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Residues in contact with ASN 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 3.4 18.9 + - - +
112A VAL* 1.3 85.7 - - - +
114A HIS* 1.3 59.1 + - - +
116A ARG* 4.6 6.6 - - - +
117A ASP* 2.9 41.4 + - - +
145A SER* 5.9 0.5 - - - -
1284A IPA 3.9 20.1 - - + +
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Residues in contact with HIS 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLU* 2.8 40.6 + - + +
113A ASN* 1.3 79.7 - - - +
115A VAL* 1.3 64.9 + - - +
118A TRP* 2.9 22.3 + - + +
119A LEU* 3.3 9.6 + - - +
150A ALA* 3.7 18.4 + - - +
153A TRP* 3.7 30.2 + - + +
154A SER* 3.7 38.0 + - - -
157A LYS* 4.6 6.5 - - + +
1284A IPA 3.7 39.7 - - + +
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Residues in contact with VAL 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A THR* 4.1 3.1 - - + +
107A VAL* 4.1 22.0 - - + -
110A GLY* 3.4 29.2 - - - +
111A GLU 2.9 22.2 + - - +
112A VAL 3.7 3.1 - - - +
114A HIS* 1.3 78.5 - - - +
116A ARG* 1.3 58.4 + - - +
119A LEU* 3.6 13.4 - - + +
120A GLN 2.8 27.7 + - - -
121A ILE* 3.3 34.0 + - + +
140A PHE* 3.6 17.9 - - + -
153A TRP* 5.0 3.1 - - + +
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Residues in contact with ARG 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 2.8 36.8 + - - +
113A ASN* 4.0 7.6 - - - +
115A VAL* 1.3 71.6 - - - +
117A ASP* 1.3 68.5 + - - +
120A GLN* 3.3 22.9 + - - +
121A ILE 4.1 5.8 - - - -
122A GLU* 3.2 42.7 + - + +
140A PHE* 3.0 46.8 + - + +
141A GLU* 5.3 1.4 - - - +
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Residues in contact with ASP 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A ASN* 2.9 26.8 + - - +
116A ARG* 1.3 89.6 - - - +
118A TRP* 1.3 63.0 + - - +
120A GLN* 3.8 14.6 + - - +
1284A IPA 2.9 32.4 + - + +
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Residues in contact with TRP 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A HIS* 2.9 13.5 + - + +
117A ASP* 1.3 78.9 - - - +
119A LEU* 1.3 90.4 + - + +
120A GLN* 3.5 7.6 + - - +
153A TRP* 3.7 34.8 - + + -
156A PHE* 3.8 18.2 - - + -
157A LYS* 3.6 57.3 - - + +
161A GLY 2.9 24.6 + - - -
162A GLN* 3.4 8.5 - - - -
163A PRO* 3.2 55.8 - - + +
166A PHE* 4.3 13.0 - - + -
167A PHE* 5.2 0.2 - + - -
1284A IPA 4.3 7.0 - - + -
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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