Contacts of the helix formed by residues 119 - 131 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117C GLU* 3.2 6.1 - - - +
118C LEU* 1.3 78.5 - - - +
120C GLU* 1.3 61.3 + - - -
121C GLU* 3.3 3.4 - - - -
122C ALA 3.2 2.8 + - - -
123C MET* 2.9 40.9 + - - +
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Residues in contact with GLU 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C GLY* 1.3 71.2 - - - -
121C GLU* 1.3 62.2 + - + +
123C MET* 3.3 20.3 + - + +
124C GLU* 2.8 29.1 + - - +
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Residues in contact with GLU 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 5.9 0.7 - - - +
118C LEU 6.1 0.2 - - - +
119C GLY* 3.3 1.3 - - - -
120C GLU* 1.3 75.7 - - + +
122C ALA* 1.3 60.3 + - - +
124C GLU* 3.1 8.3 + - - +
125C MET* 2.9 30.4 + - - +
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Residues in contact with ALA 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 3.6 24.5 + - + +
98C LEU* 3.6 12.0 - - + +
113C ILE* 5.1 0.2 - - + -
118C LEU* 3.6 36.5 + - + +
119C GLY 3.2 3.6 + - - +
121C GLU* 1.3 77.4 - - - +
123C MET* 1.3 59.0 + - - +
125C MET* 3.2 15.5 - - - +
126C PHE* 3.0 28.8 + - - +
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Residues in contact with MET 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C ILE* 3.7 26.0 - - + +
114C ARG* 5.1 15.7 - - - -
119C GLY* 2.9 21.7 + - - +
120C GLU* 3.5 34.1 - - + +
121C GLU 3.2 0.4 - - - -
122C ALA* 1.3 76.7 - - - +
124C GLU* 1.3 59.3 + - - +
126C PHE* 3.4 10.1 + - + +
127C ARG* 3.2 44.4 + - - +
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Residues in contact with GLU 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120C GLU 2.8 19.7 + - - +
121C GLU* 3.1 7.6 + - - +
123C MET* 1.3 71.5 - - - +
125C MET* 1.3 56.9 + - - +
127C ARG* 3.2 17.7 + - - +
128C GLU* 1.9 82.5 + - - +
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Residues in contact with MET 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C TYR* 4.6 2.7 - - - -
96C GLY 3.1 22.2 - - - +
97C ARG* 4.0 6.3 - - + -
98C LEU* 3.3 44.1 - - + +
99C ARG* 5.9 2.2 - - - +
121C GLU 2.9 14.6 + - - +
122C ALA* 3.2 25.1 - - - +
124C GLU* 1.3 75.4 - - - +
126C PHE* 1.3 62.4 + - - +
128C GLU* 3.9 8.7 - - - +
129C ASP* 3.2 30.5 + - - +
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Residues in contact with PHE 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU* 4.3 11.0 - - + -
100C ARG* 4.2 5.6 - - + -
106C LEU* 3.4 33.2 - - + -
109C PHE* 3.7 27.1 - + - -
110C SER* 3.1 26.2 - - - -
113C ILE* 3.7 24.2 - - + -
122C ALA 3.0 18.1 + - - +
123C MET* 3.5 9.6 - - + +
125C MET* 1.3 79.1 - - - +
127C ARG* 1.3 72.4 + - + +
129C ASP* 3.4 3.0 + - - +
130C GLU* 3.1 52.1 + - + +
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Residues in contact with ARG 127 (chain C).
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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123C MET* 3.2 31.4 + - - +
124C GLU* 3.2 21.0 + - - +
126C PHE* 1.3 87.3 - - + +
128C GLU* 1.3 56.5 + - - +
130C GLU* 3.2 3.4 + - - +
131C GLY 2.9 39.8 + - - +
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Residues in contact with GLU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C GLU* 1.9 56.3 + - - +
125C MET* 3.9 7.6 + - - +
126C PHE 3.3 0.2 - - - -
127C ARG* 1.3 74.8 - - - +
129C ASP* 1.3 62.4 + - + +
130C GLU 3.4 0.9 + - - -
131C GLY* 3.8 9.3 + - - +
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Residues in contact with ASP 129 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C LEU 4.8 6.2 - - - +
99C ARG* 4.2 26.6 + - - -
125C MET* 3.2 19.0 + - - +
126C PHE* 4.1 4.0 - - - +
127C ARG 3.3 0.2 - - - -
128C GLU* 1.3 78.9 - - - +
130C GLU* 1.3 65.2 + - + +
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Residues in contact with GLU 130 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ARG* 2.9 60.0 + - - +
106C LEU* 3.0 21.0 - - + +
126C PHE* 3.1 38.8 + - + +
127C ARG* 4.0 3.4 - - - +
129C ASP* 1.3 84.1 - - + +
131C GLY* 1.3 59.1 + - - +
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Residues in contact with GLY 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127C ARG* 2.9 24.2 + - - +
128C GLU* 3.8 8.5 + - - +
129C ASP 3.7 1.0 - - - -
130C GLU* 1.3 80.9 - - - +
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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