Contacts of the helix formed by residues 119 - 131 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B ILE* 5.1 2.7 + - - +
114B ARG* 5.5 0.2 + - - -
117B GLU* 3.2 6.1 - - - +
118B LEU* 1.3 80.9 - - - +
120B GLU* 1.3 59.7 + - - -
121B GLU* 3.5 5.8 - - - -
122B ALA* 3.6 3.1 - - - +
123B MET* 3.0 28.9 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ARG* 5.2 5.2 + - - -
119B GLY* 1.3 69.2 - - - -
121B GLU* 1.3 59.9 + - + +
123B MET* 3.2 6.1 + - - +
124B GLU* 2.6 64.8 + - - +
127B ARG* 2.9 28.2 + - - -
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 5.2 3.3 + - - -
118B LEU 5.0 3.8 - - - +
119B GLY* 5.6 1.8 - - - -
120B GLU* 1.3 76.6 + - + +
122B ALA* 1.3 67.0 + - - +
124B GLU* 3.5 12.2 + - - +
125B MET* 2.7 44.0 + - + +
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B TYR* 4.1 22.7 - - + +
96B GLY 5.8 1.8 - - - -
98B LEU* 3.8 15.2 - - + +
118B LEU* 3.5 32.8 - - + +
119B GLY 3.6 4.0 + - - +
120B GLU 3.2 0.2 - - - -
121B GLU* 1.3 85.9 + - - +
123B MET* 1.3 51.3 + - - +
125B MET* 3.6 5.8 - - - +
126B PHE* 2.7 34.7 + - - +
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.3 2.0 - - - +
106B LEU* 5.2 0.2 - - + -
110B SER* 3.8 13.7 - - - +
113B ILE* 3.9 25.1 - - + -
114B ARG* 2.8 50.7 - - - +
119B GLY 3.0 15.7 + - - +
120B GLU* 3.6 7.0 - - - +
122B ALA* 1.3 80.4 - - - +
124B GLU* 1.3 51.5 + - - +
126B PHE* 3.0 40.4 + - + +
127B ARG* 2.3 58.2 + - + +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B GLU* 2.6 55.3 + - - +
121B GLU* 3.5 9.5 + - - +
123B MET* 1.3 70.9 - - - +
125B MET* 1.3 59.4 + - + +
127B ARG* 2.9 30.7 + - - +
128B GLU* 2.8 43.4 + - - +
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Residues in contact with MET 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 5.6 0.4 - - + -
121B GLU* 2.7 32.7 + - + +
122B ALA* 3.6 5.2 - - - +
124B GLU* 1.3 73.3 - - + +
126B PHE* 1.3 58.5 + - - +
128B GLU* 3.8 18.2 - - + +
129B ASP* 2.4 43.7 + - - +
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Residues in contact with PHE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 3.8 41.9 + - + +
99B ARG* 4.6 0.4 - - - -
100B ARG* 3.5 33.4 - - + -
106B LEU* 3.3 35.4 - - + -
109B PHE* 4.0 9.6 - + - -
110B SER* 4.5 0.4 - - - -
113B ILE* 4.4 2.0 - - + -
122B ALA 2.7 15.5 + - - +
123B MET* 3.2 37.2 - - + +
125B MET* 1.3 75.3 - - - +
127B ARG* 1.3 70.4 + - - +
129B ASP* 3.5 4.7 + - + +
130B GLU* 3.2 45.1 + - + +
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Residues in contact with ARG 127 (chain B).
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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114B ARG* 5.3 4.2 - - - +
120B GLU* 2.9 31.7 + - - -
123B MET* 2.3 52.8 + - + +
124B GLU* 2.9 37.4 + - - +
126B PHE* 1.3 73.8 - - - +
128B GLU* 1.3 54.9 + - - +
130B GLU* 3.2 2.3 - - - +
131B GLY 2.3 49.0 + - - +
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Residues in contact with GLU 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLU* 2.8 35.7 + - - +
125B MET* 3.8 22.2 - - + +
127B ARG* 1.3 74.2 - - - +
129B ASP* 1.3 68.3 + - - +
131B GLY* 3.0 14.3 + - - -
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Residues in contact with ASP 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B ARG* 5.3 11.4 + - - -
98B LEU 5.1 3.6 - - - +
125B MET* 2.4 34.0 + - - +
126B PHE* 3.8 6.0 - - + +
128B GLU* 1.3 79.5 - - - +
130B GLU* 1.3 67.4 + - + +
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Residues in contact with GLU 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ARG* 3.2 42.4 + - - +
106B LEU* 3.0 30.0 - - + +
126B PHE* 3.2 37.4 + - + +
127B ARG* 3.0 7.1 + - - +
129B ASP* 1.3 85.4 - - + +
131B GLY* 1.3 58.9 + - - +
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Residues in contact with GLY 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ARG* 2.3 51.7 + - - +
128B GLU* 3.0 11.0 + - - -
130B GLU* 1.3 73.9 - - - +
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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