Contacts of the helix formed by residues 106 - 113 (chain O) in PDB entry 2AAZ
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 SER 106 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102O ASP 3.0 15.9 + - - -
103O GLY* 3.2 14.7 + - - -
104O ASN 3.5 0.4 - - - -
105O GLY* 1.3 80.8 - - - +
107O LYS* 1.3 64.7 + - - +
108O GLU* 3.8 8.3 + - - +
109O PHE* 3.2 15.1 + - - +
110O LEU* 3.0 21.5 + - - +
120O GLU* 3.7 12.3 - - - -
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Residues in contact with LYS 107 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105O GLY 4.5 0.4 - - - -
106O SER* 1.3 72.2 - - - +
108O GLU* 1.3 62.5 + - - +
110O LEU* 3.9 6.1 - - + +
111O GLU* 3.1 63.9 + - - +
116O GLY* 3.1 25.5 + - - -
118O ARG 3.5 21.4 + - - +
119O ARG* 4.8 2.2 - - - +
120O GLU* 3.2 37.8 + - + +
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Residues in contact with GLU 108 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O SER* 3.0 8.6 - - - +
107O LYS* 1.3 78.0 - - - +
109O PHE* 1.3 62.3 + - - +
111O GLU* 3.9 6.3 - - - +
112O LYS* 3.0 31.4 + - + +
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Residues in contact with PHE 109 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O ARG* 4.3 11.0 - - - -
103O GLY 3.6 7.6 - - - +
104O ASN* 3.2 46.0 - - - +
106O SER* 3.1 19.1 + - - +
108O GLU* 1.3 76.8 - - - +
110O LEU* 1.3 67.5 + - - +
112O LYS* 2.9 38.1 + - + +
113O VAL* 3.0 39.1 + - + +
183O ALA* 3.2 27.8 - - + -
184O LEU* 4.6 2.7 - - + -
317O ALA* 3.7 34.1 - - + -
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Residues in contact with LEU 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ASN 3.8 16.2 - - - +
105O GLY* 3.5 21.3 - - - +
106O SER 3.0 16.8 + - - +
107O LYS* 3.9 6.5 - - + +
109O PHE* 1.3 75.6 - - + +
111O GLU* 1.3 57.4 + - + +
113O VAL* 3.1 12.3 + - - +
115O LEU* 2.7 52.7 + - + +
116O GLY* 5.2 0.2 - - - -
118O ARG* 4.3 9.4 - - + +
119O ARG 3.7 24.2 - - - +
120O GLU* 4.2 4.3 - - - -
121O GLY 4.1 1.8 - - - +
122O ASP 4.0 19.5 - - - +
183O ALA* 3.9 19.3 - - + -
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Residues in contact with GLU 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O LYS* 3.1 57.0 + - - +
108O GLU* 3.9 5.7 - - - +
110O LEU* 1.3 76.4 - - - +
112O LYS* 1.3 62.6 + - - +
114O GLY* 3.3 11.3 + - - -
116O GLY* 3.6 19.3 - - - +
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Residues in contact with LYS 112 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40O ARG* 5.9 1.2 + - - +
41O THR* 5.8 1.8 + - - +
108O GLU* 3.0 19.2 + - + +
109O PHE* 3.0 36.6 - - + +
111O GLU* 1.3 79.1 - - - +
113O VAL* 1.3 60.0 + - + +
114O GLY 3.3 2.3 + - - -
317O ALA* 4.5 16.2 + - - +
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Residues in contact with VAL 113 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O PHE* 3.0 45.8 + - + +
110O LEU* 3.2 16.2 - - - +
112O LYS* 1.3 80.4 - - + +
114O GLY* 1.3 59.0 + - - +
115O LEU* 3.7 27.9 - - + +
180O PRO 5.4 1.9 - - - +
182O MET 5.4 1.3 - - - +
183O ALA* 4.6 7.0 - - - +
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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