Contacts of the helix formed by residues 118 - 130 (chain D) in PDB entry 2OUG
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 ILE 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65C HIS* 3.2 37.0 - - + +
92D VAL* 4.5 28.7 - - + -
115D LYS* 3.3 8.7 - - - +
117D ILE* 1.3 78.7 - - - +
119D THR* 1.3 71.3 + - - +
122D ALA* 3.1 23.0 + - - +
149D GLU* 3.3 17.3 - - - +
152D HIS* 2.7 23.6 - - + +
153D SER* 6.0 3.4 - - - +
156D ASN* 5.9 0.2 - - + -
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Residues in contact with THR 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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92D VAL* 6.2 0.7 - - - -
115D LYS* 2.3 38.3 + - - +
118D ILE* 1.3 79.3 - - - +
120D GLU* 1.3 56.7 + - - +
121D GLY 2.9 9.0 + - - -
122D ALA* 5.0 2.0 - - - -
123D PHE* 2.9 64.3 + - + +
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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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62C GLU* 3.6 18.7 - - - +
116D VAL 3.1 21.7 + - - +
117D ILE* 4.6 3.5 - - - +
118D ILE 3.5 0.4 - - - -
119D THR* 1.3 77.9 - - - +
121D GLY* 1.3 58.8 + - - +
123D PHE* 4.4 7.6 - - - -
124D GLU* 2.9 41.8 - - + +
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Residues in contact with GLY 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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117D ILE 3.4 11.4 + - - -
119D THR 2.9 1.0 - - - -
120D GLU* 1.3 79.5 - - - +
122D ALA* 1.3 67.2 + - - +
125D GLY* 2.9 18.5 + - - -
145D LEU* 3.1 17.1 - - - +
148D LYS* 6.2 3.1 - - - -
149D GLU* 3.4 13.5 - - - -
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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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92D VAL* 4.6 13.7 - - + +
93D ILE* 5.2 2.0 - - - -
96D LEU* 3.7 23.1 - - + -
118D ILE 3.1 17.0 + - - +
119D THR* 4.2 2.2 - - - +
121D GLY* 1.3 76.1 - - - +
123D PHE* 1.3 67.2 + - - +
126D PHE* 2.8 37.4 + - + -
145D LEU* 3.7 11.0 - - + -
149D GLU* 3.5 8.0 + - - +
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Residues in contact with PHE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D LEU* 4.1 19.4 - - + +
100D LYS* 3.8 25.4 - - + -
119D THR* 2.9 41.9 + - + +
120D GLU* 4.4 4.7 - - - -
122D ALA* 1.3 82.3 - - - +
124D GLU* 1.3 67.9 + - + +
126D PHE* 3.0 9.7 + - - +
127D GLN* 3.1 11.1 + - - +
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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* 2.9 46.3 + - + +
123D PHE* 1.3 82.7 - - + +
125D GLY* 1.3 64.7 + - - +
127D GLN* 3.1 21.5 + - - +
128D ALA* 3.1 15.2 + - - +
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Residues in contact with GLY 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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121D GLY 2.9 23.4 + - - -
122D ALA 3.4 0.2 - - - -
124D GLU* 1.3 79.8 - - - +
126D PHE* 1.3 57.0 + - - +
128D ALA* 3.2 6.0 + - - +
129D ILE* 3.1 33.7 + - - +
141D LEU* 5.3 1.0 - - - +
145D LEU* 4.3 11.4 - - - -
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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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51D PHE* 4.6 8.5 - + - -
93D ILE* 3.5 36.1 - - + -
96D LEU* 3.4 34.8 - - + -
97D SER* 4.7 10.5 - - - -
122D ALA* 2.8 40.2 + - + +
123D PHE 3.8 2.9 - - - +
125D GLY* 1.3 70.6 - - - +
127D GLN* 1.3 66.7 + - - +
128D ALA 3.1 0.7 - - - -
129D ILE* 3.8 20.4 - - + -
130D PHE* 2.9 59.7 + + + -
142D LEU* 4.1 9.4 - - + -
145D LEU* 3.4 21.3 - - + -
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Residues in contact with GLN 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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123D PHE 3.1 10.9 + - - +
124D GLU* 3.1 15.8 + - - +
126D PHE* 1.3 77.3 - - - +
128D ALA* 1.3 60.8 + - - +
130D PHE* 3.4 6.7 + - - +
131D THR* 3.0 34.0 + - - +
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Residues in contact with ALA 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 3.1 7.7 + - - +
125D GLY* 3.4 10.3 - - - +
127D GLN* 1.3 79.3 - - - +
129D ILE* 1.3 62.7 + - - +
131D THR* 3.2 13.5 + - - -
132D GLU* 3.3 15.9 + - - +
141D LEU* 4.3 21.1 - - + +
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Residues in contact with ILE 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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33D ILE* 5.9 0.2 - - - +
50D LEU* 3.7 7.9 - - + -
51D PHE* 3.3 25.8 - - + -
125D GLY 3.1 12.8 + - - +
126D PHE* 3.1 23.5 + - + +
128D ALA* 1.3 76.6 - - - +
130D PHE* 1.3 62.5 + - + +
131D THR 3.1 1.3 + - - -
132D GLU 3.5 1.7 + - - -
138D ARG* 2.9 50.9 + - + +
141D LEU* 3.9 19.1 - - + +
142D LEU* 3.9 21.5 - - + +
145D LEU* 3.6 30.5 - - + -
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Residues in contact with PHE 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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33D ILE* 4.6 21.5 - - + +
35D LEU* 5.3 8.6 - - - +
50D LEU* 3.6 33.7 - - + -
96D LEU* 3.9 18.8 - - + -
97D SER* 4.2 13.2 - - - -
100D LYS* 4.9 12.6 - - + -
126D PHE* 2.9 51.4 + + + +
127D GLN* 3.9 5.6 - - - +
129D ILE* 1.3 80.4 - - + +
131D THR* 1.3 60.6 + - - +
132D GLU 3.5 0.9 - - - -
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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