Contacts of the helix formed by residues 110 - 122 (chain A) in PDB entry 2O23
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 110 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A SER* 4.9 0.8 + - - -
108A THR 4.4 5.8 - - - +
109A HIS* 1.3 97.4 + - - +
111A LEU* 1.3 63.5 - - - +
112A GLU* 3.8 7.5 + - - +
113A ASP* 3.0 38.6 + - - +
114A PHE* 3.5 1.4 + - - +
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Residues in contact with LEU 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A HIS 3.8 1.2 + - - -
110A THR* 1.3 74.1 - - - +
112A GLU* 1.3 58.9 + - - +
114A PHE* 3.2 19.3 + - + +
115A GLN* 3.0 34.4 + - + +
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Residues in contact with GLU 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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110A THR* 3.3 7.6 + - - +
111A LEU* 1.3 80.3 - - - +
113A ASP* 1.3 71.5 + - - +
115A GLN* 3.8 6.9 - - + +
116A ARG* 2.9 56.1 + - + +
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Residues in contact with ASP 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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96A VAL* 4.1 19.4 - - + +
98A SER* 4.6 8.8 + - - -
109A HIS* 3.6 17.3 - - + -
110A THR* 3.0 27.9 + - - +
112A GLU* 1.3 83.4 - - - +
114A PHE* 1.3 63.8 + - - +
116A ARG* 2.8 33.8 + - - +
117A VAL* 3.4 27.7 + - - +
167A ALA* 4.4 1.0 - - - +
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Residues in contact with PHE 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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109A HIS* 3.5 18.7 - + + +
110A THR 3.5 3.7 + - - +
111A LEU* 3.2 20.5 + - + +
113A ASP* 1.3 80.2 - - - +
115A GLN* 1.3 63.8 + - - +
116A ARG 3.4 0.2 + - - -
117A VAL* 3.4 2.4 + - - +
118A LEU* 3.1 47.9 + - + +
166A ALA* 4.2 7.4 - - + -
167A ALA* 3.6 33.3 - - + +
170A ALA* 3.7 24.2 - - + -
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Residues in contact with GLN 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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111A LEU* 3.0 24.3 + - + +
112A GLU* 3.8 9.2 - - + +
114A PHE* 1.3 80.1 - - - +
116A ARG* 1.3 55.7 + - - +
118A LEU* 3.4 13.9 + - - +
119A ASP* 2.9 65.3 + - - +
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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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94A ILE* 3.6 25.2 - - + +
95A ALA 4.7 10.5 + - - -
96A VAL* 4.7 8.1 - - - +
112A GLU* 2.9 39.5 + - - +
113A ASP* 2.8 32.7 + - - +
114A PHE 3.3 0.2 - - - -
115A GLN* 1.3 75.1 - - - +
117A VAL* 1.3 65.1 + - - +
119A ASP* 3.3 6.5 + - - +
120A VAL* 3.1 29.8 + - + +
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Residues in contact with VAL 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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94A ILE* 4.0 23.6 - - + +
95A ALA 4.4 1.3 - - - +
96A VAL* 3.8 30.3 - - + +
113A ASP 3.4 17.7 + - - +
114A PHE 3.4 3.3 + - - +
115A GLN 3.3 0.6 - - - -
116A ARG* 1.3 78.2 - - + +
118A LEU* 1.3 64.4 + - - +
121A ASN* 3.0 51.8 + - - +
167A ALA* 3.9 17.0 - - + +
168A TYR* 3.9 11.2 - - + -
171A SER* 3.9 9.0 - - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.1 45.3 + - + +
115A GLN* 3.7 15.0 - - - +
117A VAL* 1.3 75.8 - - - +
119A ASP* 1.3 66.6 + - - +
122A LEU* 3.0 38.0 + - + +
123A MET* 3.0 9.5 + - - +
167A ALA 4.7 1.8 + - - +
170A ALA* 4.2 12.3 - - + -
171A SER* 3.8 32.5 - - - +
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Residues in contact with ASP 119 (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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66A THR* 3.4 12.6 - - + +
115A GLN* 2.9 54.3 + - - +
116A ARG* 3.7 7.8 - - - +
117A VAL 3.2 0.4 - - - -
118A LEU* 1.3 78.0 - - - +
120A VAL* 1.3 59.0 + - + +
123A MET* 3.4 27.6 - - + +
124A GLY 2.8 26.5 + - - -
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Residues in contact with VAL 120 (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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65A VAL* 3.9 7.0 - - + +
66A THR* 3.8 13.2 - - + -
92A ALA 4.5 3.9 - - - +
93A GLY* 4.1 11.0 - - - +
94A ILE* 4.0 22.4 - - + -
116A ARG* 3.1 17.8 + - + +
119A ASP* 1.3 78.5 - - + +
121A ASN* 1.3 71.3 + - - +
124A GLY* 3.4 17.3 - - - -
125A THR* 3.9 1.4 + - - -
802A NAD 3.7 44.2 - - + +
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Residues in contact with ASN 121 (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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92A ALA 4.7 5.5 - - - +
93A GLY* 3.1 9.6 - - - -
94A ILE* 2.8 47.7 + - - +
117A VAL* 3.0 24.4 + - - +
120A VAL* 1.3 78.3 - - - +
122A LEU* 1.3 58.5 + - - +
125A THR* 3.2 23.4 + - - -
168A TYR* 3.7 12.9 - - - -
171A SER* 3.1 27.2 + - - +
172A LYS* 4.0 15.6 + - + +
175A ILE* 3.6 9.6 - - - +
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Residues in contact with LEU 122 (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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118A LEU* 3.0 30.6 + - + +
121A ASN* 1.3 77.6 - - - +
123A MET* 1.3 68.9 + - - +
124A GLY 3.2 0.7 - - - -
125A THR* 3.3 3.1 + - - -
126A PHE* 3.0 21.0 + - - +
170A ALA 4.4 2.0 - - - +
171A SER* 3.9 14.8 - - - +
174A GLY* 3.6 42.8 - - - +
175A ILE* 3.6 13.2 - - + +
178A MET* 4.0 13.8 - - - +
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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