Contacts of the helix formed by residues 125 - 134 (chain X) in PDB entry 2OU0
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 ARG 125 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120X MET* 3.0 15.1 + - + +
123X GLN* 3.3 54.5 + - - +
124X LYS* 1.3 76.0 - - - +
126X TRP* 1.3 53.7 + - - +
128X GLU* 3.2 27.3 + - + +
129X ALA* 2.8 33.3 + - - +
301X PO4 3.4 30.3 - - - +
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Residues in contact with TRP 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X LEU* 3.9 11.0 - - + -
92X ASP* 4.8 0.9 - - - -
95X ARG* 3.4 53.7 - - - +
121X LEU* 3.5 45.8 - - + -
124X LYS* 3.3 52.2 + - + +
125X ARG* 1.3 73.8 - - - +
127X ASP* 1.3 61.3 + - - +
129X ALA* 3.5 3.4 + - - +
130X ALA* 3.0 28.6 + - - +
153X PHE* 3.4 12.4 - - - +
154X ARG* 3.3 25.4 + - - +
301X PO4 3.4 6.2 + - - +
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Residues in contact with ASP 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X TRP* 1.3 77.7 - - - +
128X GLU* 1.3 63.6 + - + +
130X ALA* 3.3 7.2 + - - +
131X VAL* 3.1 29.4 + - + +
154X ARG* 3.4 28.3 + - - +
301X PO4 3.0 22.2 + - - +
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Residues in contact with GLU 128 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X MET* 3.4 23.4 - - + +
125X ARG* 3.6 36.6 + - + +
127X ASP* 1.3 75.2 - - + +
129X ALA* 1.3 64.6 + - - +
131X VAL* 3.3 7.7 + - - +
132X ASN* 3.0 18.5 + - - +
301X PO4 2.7 32.5 + - - +
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Residues in contact with ALA 129 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117X SER* 4.0 2.9 + - - +
120X MET* 3.6 23.8 - - + -
121X LEU* 3.7 34.3 - - + +
125X ARG 2.8 20.1 + - - +
126X TRP* 3.6 7.9 - - - +
128X GLU* 1.3 71.9 - - - +
130X ALA* 1.3 57.7 + - - +
132X ASN* 3.1 3.2 + - - +
133X LEU* 2.8 37.8 + - + +
153X PHE* 5.7 1.1 - - + -
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Residues in contact with ALA 130 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126X TRP 3.0 18.2 + - - +
127X ASP 3.5 6.3 - - - +
129X ALA* 1.3 78.1 - - - +
131X VAL* 1.3 62.5 + - + +
133X LEU* 3.5 4.5 + - - +
134X ALA* 3.4 19.6 + - - +
150X ILE* 3.5 35.9 - - + +
153X PHE* 6.0 1.1 - - - +
154X ARG* 4.1 22.9 - - + +
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Residues in contact with VAL 131 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127X ASP* 3.1 18.3 + - + +
128X GLU* 3.8 6.1 - - - +
129X ALA 3.3 0.2 - - - -
130X ALA* 1.3 76.1 - - + +
132X ASN* 1.3 62.7 + - - +
134X ALA* 3.4 13.3 + - - +
135X LYS* 3.4 37.4 + - - +
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Residues in contact with ASN 132 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114X PHE* 5.4 2.3 - - - -
116X ASN* 3.8 13.1 - - - +
117X SER* 2.5 35.8 + - - +
120X MET* 3.8 27.9 - - + +
128X GLU 3.0 16.8 + - - +
129X ALA 3.6 2.2 - - - +
131X VAL* 1.3 78.0 - - - +
133X LEU* 1.3 62.8 + - - +
135X LYS* 3.1 36.5 + - - +
136X SER* 5.2 0.2 - - - -
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Residues in contact with LEU 133 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102X MET* 4.1 20.4 - - + -
114X PHE* 3.8 21.1 - - + -
117X SER* 3.6 24.0 - - - +
121X LEU* 4.8 7.2 - - + -
129X ALA* 2.8 30.0 + - + +
130X ALA* 3.8 6.5 - - - +
132X ASN* 1.3 76.0 - - - +
134X ALA* 1.3 52.0 + - - +
136X SER* 2.7 31.2 + - - -
138X TRP* 3.7 11.4 - - + -
150X ILE* 3.8 22.4 - - + -
153X PHE* 3.7 37.0 - - + -
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Residues in contact with ALA 134 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X ALA 3.4 10.3 + - - +
131X VAL* 3.9 9.6 - - - +
132X ASN 3.2 0.8 - - - -
133X LEU* 1.3 74.5 - - - +
135X LYS* 1.3 57.9 + - + +
136X SER 3.0 11.5 + - - +
139X TYR* 3.3 55.1 - - + +
140X ASN* 4.4 2.6 - - - +
150X ILE* 3.9 4.4 - - + +
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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