Contacts of the helix formed by residues 119 - 130 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113D ILE* 4.9 2.4 + - - +
117D GLU* 3.1 6.7 - - - +
118D LEU* 1.3 81.4 - - - +
120D GLU* 1.3 63.2 + - - -
121D GLU* 3.3 3.8 - - - -
122D ALA* 3.3 3.1 + - - +
123D MET* 3.0 26.8 + - - +
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Residues in contact with GLU 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ARG* 5.6 9.6 + - - -
119D GLY* 1.3 68.9 - - - -
121D GLU* 1.3 56.2 + - - +
123D MET* 3.7 7.0 - - - +
124D GLU* 2.7 40.3 + - + +
127D ARG* 3.2 26.9 + - - -
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Residues in contact with GLU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119D GLY* 3.3 1.3 - - - -
120D GLU* 1.3 76.6 - - - +
122D ALA* 1.3 60.7 + - - +
124D GLU* 2.8 42.5 - - - +
125D MET* 3.2 14.5 + - + +
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Residues in contact with ALA 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D TYR* 3.6 31.4 - - + +
98D LEU* 4.0 10.3 - - + +
118D LEU* 3.7 23.5 + - + +
119D GLY 3.3 9.3 + - - +
121D GLU* 1.3 81.7 - - - +
123D MET* 1.3 62.3 + - - +
125D MET* 3.3 8.0 + - - +
126D PHE* 3.1 21.0 + - - +
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Residues in contact with MET 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 4.7 0.2 - - - +
110D SER* 4.7 11.4 - - - +
113D ILE* 3.4 33.3 - - + +
114D ARG* 4.7 19.7 - - + -
119D GLY 3.0 17.9 + - - +
120D GLU* 3.7 10.3 - - - +
122D ALA* 1.3 72.2 - - - +
124D GLU* 1.3 55.7 + - - +
126D PHE* 3.1 39.7 + - + +
127D ARG* 2.7 75.0 + - + +
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Residues in contact with GLU 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D GLU* 2.7 24.3 + - + +
121D GLU* 2.8 25.6 + - - +
123D MET* 1.3 73.5 - - - +
125D MET* 1.3 67.4 - - - +
127D ARG* 3.2 28.8 + - - +
128D GLU* 3.4 12.9 + - - +
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Residues in contact with MET 125 (chain D).
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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96D GLY 5.5 6.7 - - - +
121D GLU* 3.2 13.9 + - + +
122D ALA* 3.3 10.1 + - - +
124D GLU* 1.3 83.6 - - + +
126D PHE* 1.3 55.7 + - - +
128D GLU* 4.8 6.5 - - - +
129D ASP* 2.3 45.0 + - - +
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Residues in contact with PHE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D LEU* 3.7 36.1 - - + -
99D ARG* 4.7 0.2 - - - -
100D ARG* 3.8 25.8 - - + -
106D LEU* 4.0 17.0 - - + -
109D PHE* 3.7 21.5 - + - -
110D SER* 4.1 4.0 - - - -
113D ILE* 3.7 13.9 - - + -
122D ALA 3.1 11.2 + - - +
123D MET* 3.1 29.6 + - + +
125D MET* 1.3 76.8 - - - +
127D ARG* 1.3 70.0 + - + +
129D ASP* 3.4 8.7 + - + +
130D GLU* 2.6 51.8 + - + +
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Residues in contact with ARG 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D ARG* 5.4 8.5 - - - +
120D GLU* 3.2 26.5 + - - -
123D MET* 2.7 52.8 + - + +
124D GLU* 3.2 19.8 + - - +
126D PHE* 1.3 74.4 - - - +
128D GLU* 1.3 67.3 + - + +
130D GLU* 2.9 14.0 + - - -
131D GLY 3.2 20.1 + - - -
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Residues in contact with GLU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124D GLU 3.4 10.7 + - - +
125D MET* 3.8 7.9 - - - +
127D ARG* 1.3 79.6 - - + +
129D ASP* 1.3 76.0 + - - +
130D GLU 3.2 8.3 + - - +
131D GLY 4.1 7.5 + - - -
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Residues in contact with ASP 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D MET* 2.3 35.5 - - - +
126D PHE* 3.6 8.5 - - + +
127D ARG 3.3 0.2 - - - -
128D GLU* 1.3 88.4 - - - +
130D GLU* 1.3 62.1 + - - +
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Residues in contact with GLU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ARG* 2.7 46.5 + - - +
106D LEU* 3.7 25.6 - - + -
126D PHE* 2.6 48.9 + - + +
127D ARG* 2.9 10.4 + - - +
128D GLU 3.5 3.9 - - - +
129D ASP* 1.3 80.3 - - - +
131D GLY* 1.3 62.0 + - - +
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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