Contacts of the helix formed by residues 119 - 131 (chain A) in PDB entry 1QDV
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 GLY 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A ILE* 5.1 1.7 + - - +
117A GLU* 3.1 6.3 - - - +
118A LEU* 1.3 81.1 - - - +
120A GLU* 1.3 61.2 + - - -
121A GLU* 3.3 3.4 - - - -
122A ALA 3.3 2.4 + - - -
123A MET* 2.9 29.0 + - - +
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Residues in contact with GLU 120 (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 ARG* 4.6 9.0 + - - -
119A GLY* 1.3 68.7 - - - -
121A GLU* 1.3 57.6 + - - +
123A MET* 4.4 5.0 - - - +
124A GLU* 2.6 49.0 + - + +
127A ARG* 2.9 33.3 + - - -
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Residues in contact with GLU 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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119A GLY* 3.3 1.3 - - - -
120A GLU* 1.3 79.9 - - - +
122A ALA* 1.3 61.8 + - - +
124A GLU* 2.7 31.6 - - - +
125A MET* 3.2 40.3 + - - +
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Residues in contact with ALA 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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91A TYR* 3.7 24.9 - - + +
98A LEU* 4.0 12.3 - - + +
118A LEU* 3.6 33.3 + - + +
119A GLY 3.3 3.4 + - - +
121A GLU* 1.3 80.1 - - - +
123A MET* 1.3 60.3 + - - +
125A MET* 3.6 15.5 + - + +
126A PHE* 3.1 23.0 + - - +
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Residues in contact with MET 123 (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 SER* 3.9 22.9 - - - +
113A ILE* 3.8 30.2 - - + +
114A ARG* 3.9 36.8 - - - +
119A GLY 2.9 17.4 + - - +
120A GLU* 3.9 7.6 - - - +
121A GLU 3.3 0.2 - - - -
122A ALA* 1.3 74.1 - - - +
124A GLU* 1.3 65.9 + - - +
126A PHE* 3.2 29.9 + - + +
127A ARG* 2.9 56.2 + - + +
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Residues in contact with GLU 124 (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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120A GLU* 2.6 51.1 + - + +
121A GLU* 2.7 40.6 + - - +
123A MET* 1.3 73.9 - - - +
125A MET* 1.3 67.4 + - + +
127A ARG* 3.0 37.2 + - - +
128A GLU* 3.3 12.0 + - - +
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Residues in contact with MET 125 (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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91A TYR* 5.9 2.5 - - + +
96A GLY 5.4 7.2 - - - +
121A GLU* 3.2 40.3 + - - +
122A ALA* 3.8 17.9 - - + +
124A GLU* 1.3 85.9 - - + +
126A PHE* 1.3 60.3 + - - +
128A GLU* 3.3 24.3 + - - +
129A ASP* 3.0 17.6 - - - +
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Residues in contact with PHE 126 (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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98A LEU* 4.1 29.4 - - + +
100A ARG* 3.8 7.6 - - + -
106A LEU* 3.5 33.7 - - + -
109A PHE* 3.6 32.1 - + + -
110A SER* 3.7 12.8 - - - -
113A ILE* 3.6 22.9 - - + -
122A ALA 3.1 19.7 + - - +
123A MET* 3.2 19.3 + - + +
125A MET* 1.3 75.4 - - - +
127A ARG* 1.3 65.6 + - - +
128A GLU 3.4 0.3 + - - -
129A ASP* 3.5 17.3 + - + +
130A GLU* 3.5 28.5 - - + +
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Residues in contact with ARG 127 (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 ARG* 4.5 10.1 - - - +
120A GLU* 2.9 36.2 + - - -
123A MET* 2.9 54.0 + - + +
124A GLU* 3.0 30.2 + - - +
126A PHE* 1.3 80.3 - - - +
128A GLU* 1.3 52.0 + - - +
130A GLU* 3.7 4.2 + - - +
131A GLY 2.4 34.4 + - - +
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Residues in contact with GLU 128 (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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124A GLU 3.3 11.8 + - - +
125A MET* 3.3 16.7 + - - +
126A PHE 3.3 0.4 - - - -
127A ARG* 1.3 75.0 - - - +
129A ASP* 1.3 66.5 + - - +
131A GLY* 2.8 24.4 + - - +
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Residues in contact with ASP 129 (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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98A LEU 4.8 8.0 - - - +
125A MET 3.0 20.3 - - - +
126A PHE* 3.5 13.6 + - + +
127A ARG 3.4 0.4 - - - -
128A GLU* 1.3 81.6 - - - +
130A GLU* 1.3 63.9 + - + +
131A GLY 3.6 0.2 + - - -
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Residues in contact with GLU 130 (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 ARG* 2.2 64.8 + - - +
106A LEU* 3.5 31.2 - - + +
126A PHE* 3.5 23.7 - - + +
127A ARG* 3.7 5.1 + - - +
128A GLU 3.4 0.4 - - - -
129A ASP* 1.3 78.5 - - + +
131A GLY* 1.3 57.2 + - - +
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Residues in contact with GLY 131 (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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127A ARG* 2.4 27.1 + - - +
128A GLU* 2.8 22.9 - - - +
129A ASP 3.3 2.6 - - - -
130A GLU* 1.3 80.4 - - - +
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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