Contacts of the helix formed by residues 115 - 122 (chain A) in PDB entry 1GTA
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 PHE 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A VAL 5.9 0.2 - - - -
109A ILE* 3.8 29.2 - - + +
110A ALA* 4.5 1.3 - - - -
112A SER 3.0 19.3 + - - +
113A LYS 3.2 2.4 - - - +
114A ASP* 1.3 71.7 - - - +
116A GLU* 1.3 73.0 + - + +
118A LEU* 2.9 13.4 + - - +
119A LYS* 2.6 61.0 + - + +
165A MET* 4.3 17.9 - - + -
209A THR* 3.9 19.7 - - + -
210A PHE* 3.4 45.8 - + + -
218A LYS* 3.9 17.5 - - + -
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Residues in contact with GLU 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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113A LYS 4.6 3.9 + - - +
114A ASP 3.0 2.0 + - - -
115A PHE* 1.3 90.2 - - + +
117A THR* 1.3 61.4 + - + +
119A LYS* 2.8 52.1 + - - +
120A VAL* 3.2 17.7 - - - +
218A LYS* 5.2 6.9 - - - +
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Residues in contact with THR 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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114A ASP* 3.2 21.7 + - - +
116A GLU* 1.3 79.5 - - + +
118A LEU* 1.3 68.0 + - - +
119A LYS 3.4 0.4 - - - -
120A VAL* 3.4 18.9 - - + +
121A ASP* 3.6 10.9 + - - +
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Residues in contact with LEU 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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109A ILE* 3.7 37.2 - - + +
112A SER* 3.5 23.3 - - - +
114A ASP* 3.1 37.2 + - + +
115A PHE* 3.1 13.0 - - - +
117A THR* 1.3 79.6 - - - +
119A LYS* 1.3 62.9 + - - +
121A ASP* 3.2 15.5 + - + +
122A PHE* 3.2 9.9 + - - +
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Residues in contact with LYS 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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109A ILE* 3.9 11.4 - - - +
115A PHE* 2.6 36.2 + - + +
116A GLU* 2.8 46.0 + - - +
118A LEU* 1.3 68.5 - - - +
120A VAL* 1.3 72.5 + - - +
122A PHE* 3.2 4.2 + - - +
123A LEU* 3.0 47.6 + - + +
165A MET* 3.9 16.4 - - + +
218A LYS* 5.9 4.9 - - + -
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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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116A GLU 3.2 21.3 - - - +
117A THR* 3.4 18.8 - - + +
119A LYS* 1.3 81.6 - - - +
121A ASP* 1.3 67.8 + - + +
123A LEU* 3.7 7.2 + - - +
124A SER* 3.4 18.7 + - - -
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Residues in contact with ASP 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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117A THR 3.6 9.7 + - - +
118A LEU* 3.2 11.1 + - + +
120A VAL* 1.3 84.1 - - + +
122A PHE* 1.4 60.8 + - - +
124A SER* 2.9 26.2 + - - -
125A LYS* 2.9 36.6 + - - -
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Residues in contact with PHE 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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101A ASP 4.8 1.1 - - - -
102A ILE* 3.9 30.1 - - + -
105A GLY* 4.0 20.9 - - - -
106A VAL* 4.0 14.4 - - + -
109A ILE* 3.7 23.1 - - + -
118A LEU 3.2 4.0 + - - +
119A LYS 3.2 6.2 + - - +
121A ASP* 1.4 72.4 + - - +
123A LEU* 1.3 58.3 + - + +
125A LYS* 2.9 29.3 + - + +
126A LEU* 3.0 35.1 + - + +
129A MET* 5.0 10.1 - - + -
162A VAL* 4.4 8.3 - - + -
165A MET* 3.4 36.3 - - + -
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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