Contacts of the helix formed by residues 105 - 112 (chain R) in PDB entry 1HI0
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 ASN 105 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102R LEU* 4.2 14.6 - - + -
104R SER* 1.3 72.6 + - - +
106R LEU* 1.3 73.2 + - - +
107R LYS 3.3 2.5 - - - -
108R LYS* 3.2 8.0 + - + +
109R ARG* 2.8 37.5 + - + +
330R THR* 2.8 30.0 + - - +
331R PHE* 3.6 7.3 + - - +
332R TRP 3.2 24.4 + - - -
334R GLY 5.0 2.3 + - - +
388R GLU* 2.8 23.6 + - - +
389R VAL* 4.9 2.5 - - - -
390R GLY* 3.7 8.3 - - - -
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Residues in contact with LEU 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R SER* 3.4 18.4 + - - +
105R ASN* 1.3 88.6 + - - +
107R LYS* 1.3 58.2 + - - +
109R ARG* 3.3 11.1 + - - +
110R ALA* 2.9 28.3 + - - +
116R ASP* 6.6 0.2 - - + -
334R GLY* 5.5 5.2 - - - +
335R TRP* 6.2 2.5 - - + +
388R GLU* 4.3 24.5 - - + +
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Residues in contact with LYS 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104R SER* 5.0 1.0 + - - -
105R ASN 3.3 0.4 - - - -
106R LEU* 1.3 75.5 - - - +
108R LYS* 1.3 70.7 + - - +
110R ALA* 3.0 6.9 + - - -
111R ASP* 2.7 63.3 + - - +
236R GLY* 3.7 18.4 + - - +
237R GLY* 3.7 27.4 - - - -
238R GLU* 3.7 35.3 + - + +
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Residues in contact with LYS 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102R LEU* 4.0 27.8 - - + -
105R ASN 3.2 12.4 + - - +
107R LYS* 1.3 81.8 - - - +
109R ARG* 1.3 61.2 + - - +
111R ASP* 3.7 5.8 + - - +
112R ALA* 3.2 20.1 + - - +
232R TYR* 6.1 1.3 - - + +
236R GLY 4.2 5.4 + - - +
327R ASP* 3.9 9.5 + - - +
330R THR* 3.3 31.0 - - - +
331R PHE* 3.3 40.9 - - + -
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Residues in contact with ARG 109 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105R ASN* 2.8 29.9 + - - +
106R LEU* 3.5 11.9 - - + +
108R LYS* 1.3 73.9 - - - +
110R ALA* 1.3 65.0 + - - +
112R ALA* 3.1 9.9 + - - +
113R ASP 3.1 0.3 + - - -
114R LEU* 3.1 39.8 + - + +
115R ALA 3.1 27.1 + - - -
116R ASP* 5.5 0.8 - - - +
331R PHE* 2.7 53.5 + - + +
333R PRO* 3.7 25.3 - - - +
335R TRP* 3.9 10.8 - - - +
485R TYR* 2.8 34.6 + - - +
486R MET* 3.5 12.5 - - - -
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Residues in contact with ALA 110 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106R LEU 2.9 16.2 + - - +
107R LYS* 3.6 8.1 - - - +
109R ARG* 1.3 73.1 - - - +
111R ASP* 1.3 62.2 + - - +
112R ALA 2.9 1.3 - - - -
113R ASP* 2.6 29.6 + - - +
114R LEU 4.5 7.4 - - - -
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Residues in contact with ASP 111 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107R LYS* 2.7 60.0 + - - +
108R LYS* 4.1 6.1 + - - +
110R ALA* 1.3 77.2 - - - +
112R ALA* 1.3 59.0 + - - +
113R ASP* 3.3 7.4 + - - +
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Residues in contact with ALA 112 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108R LYS 3.2 17.1 + - - +
109R ARG 3.1 6.4 + - - +
110R ALA 2.9 1.4 - - - -
111R ASP* 1.3 75.3 - - - +
113R ASP* 1.3 70.8 + - - +
114R LEU* 3.7 14.1 + - + +
331R PHE* 3.9 21.5 - - + -
481R ASN* 5.6 0.5 + - - -
487R LYS* 3.9 30.0 + - - +
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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