Contacts of the helix formed by residues 107 - 118 (chain A) in PDB entry 1A7A
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 ASP 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ILE* 4.6 12.8 - - - +
106A THR* 1.3 72.9 - - - +
108A GLU* 1.3 70.8 + - - +
110A TYR* 3.4 11.4 - - - +
111A LEU* 3.2 22.5 + - - +
343A ARG* 4.6 15.6 + - - -
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Residues in contact with GLU 108 (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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106A THR* 3.8 14.4 + - - +
107A ASP* 1.3 86.8 + - - +
109A GLU* 1.3 60.1 + - + +
111A LEU* 3.1 9.8 + - - +
112A TRP* 2.8 28.8 + - - +
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Residues in contact with GLU 109 (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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8A LYS* 5.0 5.1 + - - +
102A TRP* 3.4 35.9 + - + -
104A GLY 4.0 1.7 - - - +
105A GLU* 3.3 12.2 - - + -
106A THR* 2.8 53.6 + - - +
108A GLU* 1.3 73.3 - - + +
110A TYR* 1.3 64.8 + - - +
112A TRP* 3.0 10.2 + - - +
113A CYS* 2.8 28.1 + - - -
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Residues in contact with TYR 110 (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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53A CYS* 4.0 1.6 - - - -
78A SER 3.1 24.0 + - - -
79A CYS* 3.0 20.2 + - - -
80A ASN* 3.4 15.3 - - - -
81A ILE* 3.5 34.1 - - + -
105A GLU* 3.2 17.6 + - - -
106A THR 2.7 10.4 + - - +
107A ASP* 3.4 14.4 - - - +
109A GLU* 1.3 76.6 - - - +
111A LEU* 1.3 66.2 + - + +
113A CYS* 3.1 11.4 + - + +
114A ILE* 3.4 29.7 + - + +
134A ASP* 2.7 37.0 + - - +
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Residues in contact with LEU 111 (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 ASP 3.2 9.3 + - - +
108A GLU* 3.1 10.4 + - - +
110A TYR* 1.3 86.6 - - + +
112A TRP* 1.3 63.8 + - + +
114A ILE* 3.7 8.9 + - + +
115A GLU* 3.0 48.6 + - - +
138A LEU* 4.0 31.6 - - + -
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Residues in contact with TRP 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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5A LEU* 3.9 21.1 - - + -
8A LYS* 3.3 40.6 - - + -
100A TYR* 3.8 23.1 - + - -
102A TRP* 4.4 5.4 - + - -
108A GLU 2.8 13.9 + - - +
109A GLU* 3.0 14.8 + - - +
111A LEU* 1.3 76.0 - - - +
113A CYS* 1.3 90.4 + - - +
115A GLU* 3.3 13.4 + - - +
116A GLN* 3.1 65.8 + - + +
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Residues in contact with CYS 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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77A SER* 3.9 8.1 - - - -
78A SER 5.5 1.1 - - - +
100A TYR* 3.0 47.6 - - + +
102A TRP* 3.9 15.0 - - - -
105A GLU* 3.7 15.3 - - - +
109A GLU 2.8 21.3 + - - -
110A TYR* 3.4 7.2 - - + +
112A TRP* 1.3 83.4 - - - +
114A ILE* 1.3 69.0 + - - +
116A GLN* 2.9 19.3 + - - +
117A THR* 3.5 7.6 + - - +
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Residues in contact with ILE 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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53A CYS* 4.1 16.8 - - - -
77A SER* 3.6 22.6 - - - +
78A SER 4.9 0.9 - - - +
110A TYR* 3.4 37.6 + - + +
111A LEU* 3.8 11.9 - - + +
112A TRP 3.5 0.2 - - - -
113A CYS* 1.3 75.3 - - - +
115A GLU* 1.3 62.9 + - - +
117A THR* 2.6 27.1 + - - +
118A LEU* 3.6 7.7 + - + +
134A ASP* 4.3 13.7 - - + +
135A LEU* 4.4 22.4 - - + -
138A LEU* 3.4 30.5 - - + -
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Residues in contact with GLU 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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4A LYS* 5.2 0.2 + - - -
111A LEU* 3.0 46.1 - - + +
112A TRP* 3.5 14.0 - - - +
113A CYS 3.2 0.8 - - - -
114A ILE* 1.3 75.9 - - - +
116A GLN* 1.3 67.5 + - - +
117A THR 3.0 5.5 + - - -
118A LEU* 3.1 27.8 + - + +
119A TYR* 4.4 5.5 + - - -
138A LEU* 4.4 9.3 - - + +
143A TYR* 3.2 27.1 + - - +
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Residues in contact with GLN 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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4A LYS* 3.1 47.2 + - - +
5A LEU 5.6 0.9 + - - -
75A GLN* 3.2 5.0 + - - -
100A TYR* 3.5 28.6 - - + -
112A TRP* 3.1 74.2 + - + +
113A CYS 2.9 9.8 + - - +
115A GLU* 1.3 84.3 + - - +
117A THR* 1.3 57.3 + - - +
118A LEU 3.5 0.2 - - - -
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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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51A ALA* 4.2 14.1 - - - +
52A GLY 4.6 4.3 + - - +
75A GLN* 3.1 24.4 + - + +
76A TRP* 3.4 40.4 - - - +
77A SER* 4.0 5.1 + - - +
100A TYR* 3.9 6.3 - - + -
113A CYS 3.7 13.0 - - - +
114A ILE* 2.6 21.3 + - - +
116A GLN* 1.3 78.7 - - - +
118A LEU* 1.3 67.5 + - - +
120A PHE* 3.0 24.3 - - - -
135A LEU* 5.3 1.9 - - - +
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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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51A ALA* 5.2 0.7 - - + -
114A ILE* 3.9 15.5 - - + +
115A GLU* 3.1 21.9 + - + +
117A THR* 1.3 82.2 + - - +
119A TYR* 1.3 71.1 + - + +
120A PHE* 3.7 1.6 - - - -
124A PRO* 3.6 1.9 - - - +
125A LEU* 3.1 43.4 + - + +
135A LEU* 4.2 24.9 - - + -
138A LEU* 5.0 3.8 - - + -
139A ILE* 4.3 15.7 - - + -
143A TYR* 3.4 52.0 - - + +
146A LEU* 4.6 2.5 - - + -
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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