Contacts of the helix formed by residues 106 - 113 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102E ASP 3.0 15.3 + - - -
103E GLY* 3.3 13.1 + - - -
104E ASN 3.5 0.2 - - - -
105E GLY* 1.3 81.6 - - - +
107E LYS* 1.3 64.9 + - - +
108E GLU* 3.8 13.4 + - - +
109E PHE* 3.3 15.1 + - - +
110E LEU* 3.0 21.0 + - - +
120E GLU* 3.7 14.4 - - - -
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Residues in contact with LYS 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E SER* 1.3 73.1 - - - +
108E GLU* 1.3 59.6 + - + +
110E LEU* 4.4 4.3 - - + -
111E GLU* 2.8 60.6 + - + +
116E GLY 4.5 10.3 - - - -
118E ARG 3.8 16.8 - - - +
119E ARG* 5.1 2.3 - - - +
120E GLU* 3.4 48.4 + - + +
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Residues in contact with GLU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E SER* 3.3 11.6 + - - +
107E LYS* 1.3 78.1 - - + +
109E PHE* 1.3 60.1 + - - +
111E GLU* 3.8 5.3 - - - +
112E LYS* 2.8 31.4 + - - +
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Residues in contact with PHE 109 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ARG* 4.1 11.9 - - - -
103E GLY 3.5 20.4 - - - +
104E ASN* 3.3 41.1 - - - +
106E SER* 3.3 9.2 + - - +
107E LYS 3.2 0.4 - - - -
108E GLU* 1.3 81.8 - - - +
110E LEU* 1.3 63.1 + - - +
112E LYS* 2.9 35.6 + - + +
113E VAL* 3.0 41.8 + - + +
183E ALA* 3.3 27.4 - - + -
184E LEU* 4.5 2.7 - - + -
317E ALA* 3.5 35.4 - - + -
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Residues in contact with LEU 110 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104E ASN 3.7 16.8 - - - +
105E GLY* 3.4 23.3 - - - +
106E SER 3.0 17.0 + - - +
107E LYS* 3.8 6.3 - - + +
109E PHE* 1.3 74.0 - - - +
111E GLU* 1.3 58.3 + - + +
113E VAL* 3.1 12.4 + - - +
115E LEU* 2.7 54.4 + - + +
116E GLY* 5.2 0.2 - - - -
118E ARG* 4.4 9.0 - - + +
119E ARG 3.6 23.3 - - - +
120E GLU* 4.2 4.0 - - - -
121E GLY 4.1 0.7 - - - +
122E ASP 4.0 19.5 - - - +
183E ALA* 3.9 18.6 - - + -
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Residues in contact with GLU 111 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107E LYS* 2.8 51.9 + - - +
108E GLU* 3.9 4.6 - - - +
110E LEU* 1.3 73.7 - - + +
112E LYS* 1.3 63.0 + - - +
114E GLY* 3.2 12.1 + - - -
116E GLY* 3.6 29.4 - - - +
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Residues in contact with LYS 112 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ARG* 5.8 1.8 + - - +
41E THR* 5.7 3.4 + - - +
108E GLU 2.8 19.8 + - - +
109E PHE* 3.0 31.1 - - + +
111E GLU* 1.3 79.2 - - - +
113E VAL* 1.3 61.3 + - + +
114E GLY 3.3 1.1 + - - -
317E ALA* 4.6 15.0 + - - +
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Residues in contact with VAL 113 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E PHE* 3.0 46.0 + - + +
110E LEU* 3.2 15.5 - - - +
112E LYS* 1.3 81.1 - - + +
114E GLY* 1.3 58.7 + - - +
115E LEU* 3.8 27.4 - - + +
180E PRO 5.3 1.9 - - - +
182E MET 5.3 1.1 - - - +
183E ALA* 4.5 7.4 - - - +
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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