Contacts of the helix formed by residues 114 - 122 (chain A) in PDB entry 2A7P
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 SER 114 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A LEU* 4.2 0.7 - - - -
113A MET* 1.3 78.5 - - - +
115A ILE* 1.3 65.5 + - - +
116A GLU* 2.8 26.4 + - - -
117A ASP* 3.0 25.1 + - - -
118A LEU* 3.2 20.1 + - - +
182A LYS* 3.7 35.2 + - - +
183A ASN* 3.3 12.1 - - - -
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Residues in contact with ILE 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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107A LEU* 3.7 6.9 - - + +
113A MET 3.8 0.2 + - - -
114A SER* 1.3 73.6 - - - +
116A GLU* 1.3 72.2 + - - +
119A ALA* 3.3 8.8 + - - +
128A PHE* 3.5 41.3 - - + -
141A MET* 3.6 30.1 - - + +
144A LYS* 4.2 6.1 - - + -
145A ALA* 3.6 13.5 - - + +
148A THR* 3.6 10.1 - - - +
150A TYR* 2.8 49.1 + - + -
183A ASN* 3.0 18.6 + - + +
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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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114A SER* 2.8 23.4 + - - -
115A ILE* 1.3 89.4 + - - +
117A ASP* 1.3 67.9 + - - +
119A ALA* 3.2 3.5 + - - +
120A ARG* 3.0 24.5 + - - +
144A LYS* 3.1 44.7 - - + +
148A THR* 4.2 16.2 - - + -
183A ASN* 4.8 1.2 - - - +
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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 MET* 4.0 11.0 - - + +
114A SER* 3.0 23.1 + - - +
116A GLU* 1.3 77.6 - - - +
118A LEU* 1.3 63.1 + - - +
120A ARG* 3.2 27.6 + - - +
121A GLN* 3.0 42.4 + - - +
182A LYS* 3.5 17.0 + - - -
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASP* 4.3 3.8 - - + +
92A LEU* 3.8 27.1 - - + +
95A ALA* 3.8 20.2 - - + -
105A PHE* 3.8 26.0 - - + -
107A LEU* 4.2 16.2 - - + -
113A MET* 3.9 18.3 - - + -
114A SER 3.2 12.0 + - - +
117A ASP* 1.3 78.2 - - - +
119A ALA* 1.3 53.5 + - - +
121A GLN* 2.9 3.8 + - - -
122A CYS* 2.7 35.2 + - + +
126A LEU* 3.7 20.0 - - + -
150A TYR* 3.5 20.0 - - - +
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Residues in contact with ALA 119 (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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115A ILE 3.3 15.9 + - - +
116A GLU 3.2 5.1 + - - +
118A LEU* 1.3 79.9 - - - +
120A ARG* 1.3 58.6 + - - +
122A CYS 3.1 15.6 + - - +
123A ASP* 5.2 0.2 - - - -
126A LEU* 3.8 13.2 - - + -
148A THR* 3.7 30.3 - - - +
150A TYR* 3.8 13.0 + - + -
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Residues in contact with ARG 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 3.0 15.6 + - - +
117A ASP* 3.2 29.2 + - - +
119A ALA* 1.3 80.3 - - - +
121A GLN* 1.3 90.2 + - - +
122A CYS 3.5 0.2 - - - -
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Residues in contact with GLN 121 (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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89A LYS* 5.8 1.7 - - - +
92A LEU* 3.7 28.9 - - + +
96A ARG* 3.0 31.6 + - - +
113A MET* 4.1 13.5 - - - +
117A ASP* 3.0 29.2 + - - +
118A LEU 2.9 4.2 + - - +
120A ARG* 1.3 110.5 - - - +
122A CYS* 1.3 57.6 + - - +
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Residues in contact with CYS 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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92A LEU* 4.4 4.3 - - + -
95A ALA* 3.9 23.8 - - - -
96A ARG* 4.3 8.7 - - + +
99A THR* 3.3 29.6 - - - -
118A LEU* 2.7 33.0 + - + +
119A ALA* 3.1 20.6 - - - +
120A ARG 3.5 1.6 - - - -
121A GLN* 1.3 77.5 - - - +
123A ASP* 1.3 61.5 + - - +
124A GLY 3.5 3.8 + - - +
126A LEU* 4.0 13.4 - - + +
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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