Contacts of the helix formed by residues 109 - 121 (chain N) in PDB entry 6AH0
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 109 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ARG* 5.8 3.6 - - - +
108N LEU* 1.3 75.0 - - - +
110N LYS* 1.3 57.9 + - - +
112N MET* 3.2 3.2 + - - +
113N ASP* 2.9 26.0 + - - -
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Residues in contact with LYS 110 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108N LEU 3.2 2.6 - - - +
109N ASP* 1.3 76.5 - - - +
111N ARG* 1.3 55.8 + - - +
113N ASP* 3.2 3.1 + - - +
114N GLU* 2.9 26.0 + - - -
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Residues in contact with ARG 111 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A VAL* 5.6 1.3 - - - -
108N LEU* 3.2 11.3 + - - +
110N LYS* 1.3 74.7 - - - +
112N MET* 1.3 56.4 + - - +
114N GLU* 3.2 3.1 + - - +
115N ARG* 2.9 25.5 + - - -
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Residues in contact with MET 112 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ARG 4.9 4.9 - - - -
87A VAL* 4.6 17.3 - - - +
90A GLY* 5.3 10.0 - - - -
108N LEU 2.9 13.2 + - - -
109N ASP* 3.2 4.4 + - - +
111N ARG* 1.3 76.3 - - - +
113N ASP* 1.3 54.9 + - - +
115N ARG* 3.2 3.7 + - - +
116N ARG* 2.9 25.6 + - - -
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Residues in contact with ASP 113 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109N ASP 2.9 14.3 + - - -
110N LYS* 3.2 4.7 + - - +
112N MET* 1.3 76.3 - - - +
114N GLU* 1.3 55.8 + - - +
116N ARG* 3.2 3.6 + - - +
117N LYS* 2.9 25.8 + - - -
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Residues in contact with GLU 114 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110N LYS 2.9 13.7 + - - -
111N ARG* 3.2 4.7 + - - +
113N ASP* 1.3 73.8 - - - +
115N ARG* 1.3 57.3 + - - +
117N LYS* 3.2 3.5 + - - +
118N GLU* 2.9 25.6 + - - -
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Residues in contact with ARG 115 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLY 6.0 4.0 - - - -
111N ARG 2.9 13.2 + - - -
112N MET* 3.2 4.9 + - - +
114N GLU* 1.3 73.9 - - - +
116N ARG* 1.3 62.4 + - - +
118N GLU* 3.2 16.7 + - - +
119N ARG* 3.6 3.6 + - - -
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Residues in contact with ARG 116 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLY* 5.9 2.6 + - - -
112N MET 2.9 13.6 + - - -
113N ASP* 3.6 4.5 - - - +
115N ARG* 1.3 75.2 - - - +
117N LYS* 1.3 57.6 + - - +
119N ARG* 2.9 18.4 + - - -
120N ARG* 3.1 10.9 + - - -
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Residues in contact with LYS 117 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113N ASP 2.9 13.5 + - - -
114N GLU* 3.6 4.5 - - - +
116N ARG* 1.3 71.8 - - - +
118N GLU* 1.3 53.0 + - - +
119N ARG 2.6 15.9 + - - -
120N ARG* 3.1 2.4 + - - +
121N GLU* 3.0 23.4 + - - -
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Residues in contact with GLU 118 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114N GLU 2.9 14.0 + - - -
115N ARG* 3.2 9.3 + - - +
117N LYS* 1.3 72.3 - - - +
119N ARG* 1.3 54.7 + - - +
121N GLU* 4.6 5.3 - - - +
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Residues in contact with ARG 119 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N ARG 3.6 2.4 + - - -
116N ARG 2.9 8.4 + - - -
117N LYS 2.6 7.9 + - - -
118N GLU* 1.3 75.6 - - - +
120N ARG* 1.3 63.5 + - - +
121N GLU* 3.2 6.6 + - - -
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Residues in contact with ARG 120 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116N ARG 3.1 11.4 + - - -
117N LYS* 3.1 3.9 + - - +
119N ARG* 1.3 76.5 - - - +
121N GLU* 1.3 62.9 + - - +
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Residues in contact with GLU 121 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117N LYS 3.0 14.2 + - - -
118N GLU* 5.2 3.8 - - - +
119N ARG* 3.2 7.8 - - - +
120N ARG* 1.3 81.1 - - - +
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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