Contacts of the helix formed by residues 106 - 120 (chain E) in PDB entry 2BZN
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 GLY 106 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104E GLY* 3.4 2.6 - - - -
105E THR* 1.3 83.5 + - - +
107E SER* 1.3 60.2 + - - -
108E SER 3.3 2.9 - - - -
109E ASP* 3.2 10.6 + - - +
110E PHE* 3.0 28.9 + - - +
27F ARG* 6.2 2.2 - - - -
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Residues in contact with SER 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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105E THR 3.7 1.4 + - - -
106E GLY* 1.3 71.6 - - - +
108E SER* 1.3 63.1 + - - +
110E PHE* 4.1 6.1 - - - +
111E GLU* 3.2 30.2 + - - +
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Residues in contact with SER 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 GLY* 3.3 1.0 - - - -
107E SER* 1.3 77.0 - - - +
109E ASP* 1.3 67.7 + - - +
111E GLU* 4.1 13.2 + - - +
112E GLN* 3.1 30.5 + - - +
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Residues in contact with ASP 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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78E LYS* 2.7 38.9 + - - +
102E SER 5.0 0.5 - - - +
103E SER* 3.4 18.6 + - - +
104E GLY* 2.9 17.8 + - - +
106E GLY* 3.2 15.0 + - - +
108E SER* 1.3 79.0 - - - +
110E PHE* 1.3 57.6 + - - +
112E GLN* 3.1 23.9 + - - +
113E LEU* 3.0 24.8 + - - +
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Residues in contact with PHE 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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103E SER* 3.6 8.3 - - - +
106E GLY 3.0 16.7 + - - +
107E SER* 4.1 5.2 - - - +
109E ASP* 1.3 75.5 - - - +
111E GLU* 1.3 63.2 + - + +
113E LEU* 3.1 13.7 + - + +
114E GLU* 2.8 55.0 + - + +
141E PHE* 4.2 28.0 - + + -
144E ASP* 5.6 2.7 - - + -
145E VAL* 3.9 21.8 - - + -
148E ARG* 4.1 20.4 - - + -
149E PHE* 4.1 15.3 - + - -
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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 SER* 3.2 19.7 + - - +
108E SER* 4.1 13.0 + - - +
110E PHE* 1.3 83.9 - - + +
112E GLN* 1.3 63.4 + - + +
114E GLU* 3.3 14.2 + - - +
115E GLN* 3.1 43.0 + - + +
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Residues in contact with GLN 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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78E LYS* 3.3 33.5 + - - +
80E TYR 5.3 5.0 - - - +
102E SER 5.2 3.0 + - - -
108E SER* 3.1 22.1 + - - +
109E ASP* 3.1 39.6 + - - +
111E GLU* 1.3 78.2 - - + +
113E LEU* 1.3 61.2 + - - +
115E GLN* 3.5 19.2 + - - +
116E ILE* 3.2 32.6 + - + +
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Residues in contact with LEU 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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101E ALA* 3.5 43.5 - - + +
102E SER 4.5 5.4 - - - +
103E SER* 3.7 24.0 - - - +
109E ASP 3.0 13.9 + - - +
110E PHE* 3.1 26.2 + - + +
112E GLN* 1.3 75.6 - - - +
114E GLU* 1.3 65.2 + - - +
116E ILE* 3.1 10.9 + - - +
117E LEU* 2.9 46.0 + - + +
126E ILE* 3.8 21.3 - - + -
128E LEU* 4.4 4.3 - - + -
145E VAL* 5.1 1.6 - - + -
149E PHE* 4.8 3.4 - - + -
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Residues in contact with GLU 114 (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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110E PHE* 2.8 38.6 + - + +
111E GLU* 3.3 16.5 - - - +
113E LEU* 1.3 76.7 - - - +
115E GLN* 1.3 57.8 + - + +
117E LEU* 3.3 1.0 + - - +
118E GLU* 2.9 44.6 + - - +
148E ARG* 2.7 37.5 + - - +
149E PHE* 3.9 24.4 - - + -
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Residues in contact with GLN 115 (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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82E LEU* 3.7 31.2 - - + +
111E GLU* 3.1 37.0 + - + +
112E GLN* 3.5 18.5 - - - +
114E GLU* 1.3 77.5 - - + +
116E ILE* 1.3 66.0 + - - +
118E GLU* 4.0 5.8 - - - +
119E ALA* 3.0 26.7 + - - +
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Residues in contact with ILE 116 (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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80E TYR 5.1 4.5 - - - +
82E LEU* 3.8 19.7 - - + +
85E TRP* 3.4 64.4 - - + +
101E ALA* 4.3 17.3 - - + -
102E SER 6.0 1.8 - - - +
112E GLN* 3.2 23.7 + - + +
113E LEU* 3.1 11.5 + - - +
115E GLN* 1.3 76.2 - - + +
117E LEU* 1.3 55.7 + - + +
119E ALA 3.2 1.0 + - - -
120E ILE* 2.8 40.9 + - + +
123E VAL* 4.8 3.8 - - + -
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Residues in contact with LEU 117 (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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101E ALA* 4.4 3.4 - - + -
113E LEU* 2.9 31.4 + - + +
114E GLU 3.9 3.1 - - - +
116E ILE* 1.3 78.1 - - - +
118E GLU* 1.3 61.2 + - - +
120E ILE 3.6 16.0 - - - +
121E PRO* 3.8 6.4 - - - +
123E VAL* 3.8 31.8 - - + +
126E ILE* 3.6 33.4 - - + -
149E PHE* 3.6 39.3 - - + -
152E HIS* 3.8 27.2 + - + +
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Residues in contact with GLU 118 (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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114E GLU* 2.9 30.4 + - - +
115E GLN* 4.0 5.7 - - - +
117E LEU* 1.3 79.5 - - + +
119E ALA* 1.3 61.3 + - - +
120E ILE 3.4 0.3 + - - -
121E PRO* 3.9 9.0 - - - +
148E ARG* 3.1 28.6 + - - +
149E PHE* 5.7 1.6 - - + -
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Residues in contact with ALA 119 (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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82E LEU* 3.9 17.0 - - + -
86E GLN* 4.0 17.0 - - - +
115E GLN 3.0 19.3 + - - +
116E ILE 3.7 2.7 - - - +
118E GLU* 1.3 76.4 - - - +
120E ILE* 1.3 68.7 - - + +
121E PRO* 3.4 7.5 - - - +
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Residues in contact with ILE 120 (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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82E LEU* 5.3 0.4 - - + -
85E TRP* 3.6 52.7 - - + +
86E GLN* 3.9 9.0 - - + +
89E ALA* 3.8 23.1 - - + -
96E LEU* 4.2 7.9 - - + -
116E ILE* 2.8 20.6 + - + +
117E LEU 3.6 9.3 - - - +
118E GLU 3.3 0.2 - - - -
119E ALA* 1.3 87.3 - - + +
121E PRO* 1.4 58.8 - - - +
122E GLN* 3.0 25.6 + - - +
123E VAL* 3.1 36.3 + - + +
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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