Contacts of the helix formed by residues 112 - 126 (chain A) in PDB entry 1BUO
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 GLU 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LYS* 6.4 0.4 - - - +
110A GLU* 3.7 3.8 + - + -
111A ILE* 1.3 70.0 - - - +
113A TYR* 1.3 69.6 + - - +
115A GLU* 3.3 19.4 + - - +
116A GLU* 2.4 58.8 + - - +
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Residues in contact with TYR 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A TYR* 3.3 36.6 - + - +
90A ALA 5.5 1.1 - - - -
92A LEU* 6.5 0.2 - - + -
111A ILE* 3.3 3.4 - - + +
112A GLU* 1.3 84.5 - - - +
114A LEU* 1.3 76.7 + - + +
116A GLU* 3.4 5.0 + - + +
117A GLN* 2.9 67.9 + - + +
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A ILE* 4.1 19.7 - - + -
86A TYR* 3.7 34.8 - - + -
92A LEU* 4.0 29.4 - - + -
102A LEU* 5.8 1.6 - - + -
106A ALA* 3.7 15.5 - - + -
111A ILE* 3.1 26.5 + - + +
113A TYR* 1.3 95.5 - - + +
115A GLU* 1.3 61.7 - - - +
117A GLN* 4.7 2.0 - - + -
118A CYS* 2.9 42.7 + - - -
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Residues in contact with GLU 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.7 16.1 - - + +
106A ALA* 3.5 26.0 - - - +
107A GLU* 3.8 18.5 - - + +
110A GLU* 3.3 31.7 - - - +
111A ILE 3.0 17.2 + - - +
112A GLU* 3.7 18.1 + - - +
114A LEU* 1.3 78.1 - - - +
116A GLU* 1.3 62.6 + - - +
119A LEU* 2.9 29.8 + - + +
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Residues in contact with GLU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A GLU* 2.4 54.6 + - - +
113A TYR* 3.7 4.9 - - + +
115A GLU* 1.3 74.4 - - - +
117A GLN* 1.3 71.0 + - + +
119A LEU* 3.7 6.6 - - - +
120A LYS* 2.9 32.7 + - + +
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 2.9 60.0 + - + +
114A LEU* 4.2 3.4 - - + +
116A GLU* 1.3 87.6 + - + +
118A CYS* 1.3 64.6 + - - +
120A LYS* 3.9 29.4 - - - +
121A MET* 3.0 31.0 + - - +
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Residues in contact with CYS 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A LEU* 6.1 2.0 - - - -
99A LEU* 4.1 24.4 - - + +
102A LEU* 3.7 33.0 - - - -
103A LEU* 4.0 24.0 - - + -
114A LEU* 2.9 32.8 + - - +
117A GLN* 1.3 76.6 - - - +
119A LEU* 1.4 65.0 + - - +
121A MET* 3.3 1.0 + - - +
122A LEU* 2.9 31.0 + - + +
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Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A LEU* 3.9 27.7 - - + +
107A GLU* 5.3 4.3 - - - +
115A GLU* 2.9 22.5 + - + +
116A GLU* 3.7 6.1 - - - +
118A CYS* 1.4 79.2 - - - +
120A LYS* 1.3 56.5 + - - +
122A LEU* 3.4 6.4 + - + +
123A GLU* 2.9 61.5 + - + +
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 2.9 21.8 + - + +
117A GLN* 3.9 31.0 - - - +
118A CYS 3.3 0.2 - - - -
119A LEU* 1.3 72.3 - - - +
121A MET* 1.3 58.1 + - - +
123A GLU* 3.9 6.1 - - - +
124A THR* 3.0 49.0 + - + +
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Residues in contact with MET 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A LEU* 3.8 29.8 - - + -
117A GLN* 3.0 21.4 + - + +
118A CYS 3.7 2.9 - - - +
120A LYS* 1.3 74.8 - - - +
122A LEU* 1.3 63.9 + - - +
124A THR* 4.7 4.3 - - - +
125A ILE* 3.0 47.4 + - + +
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Residues in contact with LEU 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA 5.8 0.4 - - - +
99A LEU* 4.0 42.1 - - + +
100A ASP* 4.4 10.5 - - + +
103A LEU* 3.9 27.6 - - + -
118A CYS 2.9 24.4 + - - +
119A LEU* 3.7 7.4 - - + +
121A MET* 1.3 71.0 - - - +
123A GLU* 1.3 59.0 + - + +
125A ILE* 3.9 5.2 - - + +
126A GLN* 3.0 42.4 + - - +
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A LEU* 2.9 44.4 + - + +
120A LYS* 3.9 6.1 - - - +
122A LEU* 1.3 75.6 - - + +
124A THR* 1.3 62.5 + - + +
126A GLN* 2.8 35.2 + - - +
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Residues in contact with THR 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LYS* 3.0 40.4 + - + +
121A MET* 4.1 6.5 + - - +
123A GLU* 1.3 72.2 - - + +
125A ILE* 1.3 78.0 + - - +
126A GLN* 3.1 7.2 - - - +
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Residues in contact with ILE 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A ALA* 6.5 0.7 - - + -
99A LEU* 4.9 7.0 - - + -
121A MET* 3.0 48.0 + - + +
122A LEU* 4.0 4.7 - - + +
124A THR* 1.3 88.7 + - - +
126A GLN* 1.3 63.7 + - - +
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Residues in contact with GLN 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LEU* 3.0 35.3 + - - +
123A GLU* 2.8 30.8 - - - +
124A THR 3.1 8.5 - - - +
125A ILE* 1.3 80.0 - - - +
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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