Contacts of the helix formed by residues 108 - 119 (chain A) in PDB entry 1O69
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 ASP 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ASP 3.1 18.2 + - - +
101A CYS 4.0 5.4 - - - -
102A ASP* 3.7 20.1 - - - +
106A ASN 3.3 1.0 + - - -
107A ILE* 1.3 80.0 - - - +
109A VAL* 1.3 61.5 + - - +
110A ASP* 3.2 16.3 + - - +
111A LEU* 3.0 33.1 + - + +
112A LEU 3.0 23.7 + - - -
137A LYS* 5.7 1.4 + - - -
295A ASN* 4.8 6.6 + - - +
349A ASN* 3.8 22.9 + - - +
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Residues in contact with VAL 109 (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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102A ASP* 4.7 1.4 + - - -
107A ILE 3.5 1.5 + - - +
108A ASP* 1.3 72.5 + - - +
110A ASP* 1.3 69.3 + - - +
112A LEU* 3.3 8.8 + - - +
113A LYS* 3.0 41.6 + - - +
137A LYS* 4.1 30.3 - - + +
140A GLU* 3.8 29.6 - - + -
141A ILE* 4.3 12.8 - - + -
144A ILE* 3.7 20.2 - - + -
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Residues in contact with ASP 110 (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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108A ASP* 3.2 12.7 + - - +
109A VAL* 1.3 80.8 - - - +
111A LEU* 1.3 59.4 + - + +
113A LYS* 3.3 21.6 + - - +
114A LEU* 3.0 27.4 + - - +
298A GLN* 4.7 15.4 - - - +
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Residues in contact with LEU 111 (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 ILE* 3.5 14.9 - - + +
100A ASP* 3.4 38.1 - - + +
108A ASP* 3.0 20.2 + - + +
109A VAL 3.3 0.2 - - - -
110A ASP* 1.3 73.4 - - + +
112A LEU* 1.3 61.9 + - - +
114A LEU* 3.6 8.4 - - + +
115A ALA* 2.9 30.5 + - - +
298A GLN* 3.8 33.4 - - + +
299A LYS 5.1 0.7 - - - +
347A TYR* 3.4 25.8 - - + +
348A LEU 3.7 14.1 - - - +
349A ASN* 3.7 17.9 - - + +
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Residues in contact with LEU 112 (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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76A LEU* 3.8 13.0 - - + -
99A ILE* 3.6 27.3 - - + +
107A ILE* 4.0 8.5 - - + -
108A ASP 3.0 14.2 + - - +
109A VAL* 3.5 7.6 - - - +
111A LEU* 1.3 77.1 - - - +
113A LYS* 1.3 62.6 + - - +
115A ALA* 3.3 1.4 + - - +
116A ILE* 3.1 47.0 + - + +
126A LEU* 4.2 15.5 - - + -
141A ILE* 3.9 38.8 - - + -
144A ILE* 4.1 21.1 - - + -
145A CYS* 5.2 1.8 - - - -
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Residues in contact with LYS 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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109A VAL* 3.0 38.0 + - + +
110A ASP* 3.6 17.7 + - - +
111A LEU 3.3 0.2 - - - -
112A LEU* 1.3 77.4 - - - +
114A LEU* 1.3 62.7 + - - +
116A ILE* 3.3 7.5 + - - +
117A LYS* 3.0 25.9 + - - +
140A GLU* 6.2 0.6 - - - +
144A ILE* 3.8 29.8 - - + -
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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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110A ASP 3.0 16.6 + - - +
111A LEU* 3.6 10.3 - - + +
113A LYS* 1.3 77.4 - - - +
115A ALA* 1.3 56.9 + - - +
117A LYS* 3.3 25.4 + - - +
118A GLU* 3.0 63.1 + - - +
298A GLN* 4.0 35.2 - - + +
299A LYS* 5.5 4.9 - - - +
300A ASP* 5.8 0.4 - - + +
347A TYR* 3.8 25.6 - - + -
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Residues in contact with ALA 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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76A LEU* 4.3 10.8 - - + -
97A VAL* 4.4 0.7 - - + -
99A ILE* 4.3 18.6 - - + -
111A LEU 2.9 20.8 + - - +
112A LEU 3.7 4.3 - - - +
114A LEU* 1.3 74.0 - - - +
116A ILE* 1.3 63.1 + - - +
118A GLU 3.4 2.1 + - - -
119A CYS* 3.1 28.8 + - - -
347A TYR* 3.5 37.7 + - + -
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Residues in contact with ILE 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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76A LEU* 3.7 19.7 - - + -
112A LEU* 3.1 29.7 + - + +
113A LYS* 3.8 4.5 - - - +
114A LEU 3.3 0.2 - - - -
115A ALA* 1.3 74.8 - - - +
117A LYS* 1.3 65.5 + - - +
119A CYS* 3.1 24.8 + - - +
123A PRO* 4.5 8.8 - - + +
144A ILE* 3.4 32.1 - - + -
148A ASN* 3.5 31.6 - - + +
150A ILE* 3.7 20.2 - - + -
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Residues in contact with LYS 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 LYS 3.0 15.6 + - - +
114A LEU* 3.6 32.9 - - - +
116A ILE* 1.3 80.3 - - - +
118A GLU* 1.3 70.1 + - + +
119A CYS 3.6 4.9 + - - +
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Residues in contact with GLU 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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114A LEU* 3.0 38.1 + - + +
115A ALA 3.7 1.1 - - - -
116A ILE 3.2 0.2 - - - -
117A LYS* 1.3 91.3 - - + +
119A CYS* 1.3 62.6 + - - +
120A GLU* 3.3 3.6 + - - +
300A ASP* 4.2 12.0 - - - +
347A TYR* 3.3 34.0 + - - +
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Residues in contact with CYS 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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74A ILE* 4.2 16.2 - - + -
76A LEU* 4.5 7.0 - - - -
97A VAL* 4.8 9.0 - - - -
115A ALA 3.1 22.5 + - - -
116A ILE 3.1 12.7 + - - +
117A LYS 3.3 5.0 - - - +
118A GLU* 1.3 75.8 - - - +
120A GLU* 1.3 64.5 + - - +
121A LYS 3.0 21.2 + - - +
122A LYS* 5.0 0.2 - - - -
123A PRO* 3.7 27.1 - - + -
347A TYR* 5.9 0.4 - - - -
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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