Contacts of the helix formed by residues 117 - 125 (chain D) in PDB entry 2DFS
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 THR 117 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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827A ARG* 5.1 2.7 - - - +
110D THR* 4.2 0.9 - - - -
115D LYS 3.9 1.1 + - - +
116D LEU* 1.3 76.7 - - - +
118D ASP* 1.3 63.8 + - - +
119D GLU* 3.1 31.6 - - + +
120D GLU* 2.7 29.2 + - - +
121D VAL* 3.1 21.1 + - - +
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Residues in contact with ASP 118 (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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106D ARG* 2.7 44.4 + - - +
110D THR* 3.8 15.5 + - - +
116D LEU 4.0 0.4 + - - -
117D THR* 1.3 71.5 - - - +
119D GLU* 1.3 53.9 + - - +
121D VAL* 3.1 3.4 + - - +
122D ASP* 2.7 41.8 + - - +
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Residues in contact with GLU 119 (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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117D THR* 3.1 29.9 + - - +
118D ASP* 1.3 76.5 - - - +
120D GLU* 1.4 61.9 + - + +
122D ASP* 3.9 8.1 - - - +
123D GLU* 3.1 22.2 + - - +
126D ARG* 4.2 5.2 + - - -
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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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826A GLN* 4.2 3.9 - - - +
827A ARG* 2.6 48.9 + - - +
830A VAL* 5.9 1.4 - - - +
116D LEU* 3.2 12.5 - - + +
117D THR* 2.7 43.7 + - - +
119D GLU* 1.4 75.7 - - + +
121D VAL* 1.3 62.0 + - - +
123D GLU* 3.2 8.9 + - - +
124D MET* 3.0 41.8 + - + +
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Residues in contact with VAL 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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105D LEU* 5.8 1.1 - - + -
106D ARG* 4.0 34.8 - - + +
109D MET* 3.7 31.2 - - + -
110D THR* 3.5 22.9 - - + -
116D LEU* 3.8 12.3 - - + -
117D THR 3.1 11.2 + - - +
118D ASP* 3.1 8.9 + - - +
120D GLU* 1.3 74.8 - - - +
122D ASP* 1.3 56.5 + - - +
124D MET* 3.0 9.9 + - - +
125D ILE* 3.0 36.6 + - + +
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Residues in contact with ASP 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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106D ARG* 2.6 41.4 + - - -
118D ASP* 2.7 25.8 + - - +
119D GLU* 3.9 8.3 + - - +
121D VAL* 1.3 71.2 - - - +
123D GLU* 1.3 57.9 + - - +
125D ILE* 3.7 12.4 - - - +
126D ARG* 3.0 41.2 + - - +
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Residues in contact with GLU 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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119D GLU 3.1 11.8 + - - +
120D GLU* 3.3 13.0 - - - +
122D ASP* 1.3 75.8 - - - +
124D MET* 1.3 70.5 + - + +
126D ARG* 2.6 70.7 + - - +
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Residues in contact with MET 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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826A GLN* 3.2 52.0 - - + +
830A VAL* 5.9 7.4 - - + -
109D MET* 5.1 2.9 - - - -
116D LEU* 4.2 3.4 - - - -
120D GLU* 3.0 38.0 + - + +
121D VAL* 3.0 11.0 + - - +
123D GLU* 1.3 84.6 - - + +
125D ILE* 1.3 60.5 + - - +
126D ARG 3.4 4.4 + - - +
128D ALA* 4.1 4.9 - - - +
141D PHE* 3.3 31.9 - - + -
145D MET* 5.6 9.6 - - + -
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Residues in contact with ILE 125 (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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102D ALA* 5.8 11.4 - - + -
105D LEU* 4.6 9.6 - - + -
106D ARG* 3.4 26.9 - - - +
121D VAL* 3.0 26.7 + - + +
122D ASP* 3.7 15.5 - - - +
123D GLU 3.3 0.2 - - - -
124D MET* 1.3 76.6 - - - +
126D ARG* 1.3 62.2 + - - +
127D GLU 3.5 0.9 + - - -
128D ALA* 3.5 24.4 + - + +
141D PHE* 4.0 18.8 - - + -
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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