Contacts of the helix formed by residues 113 - 129 (chain E) in PDB entry 2X1X
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 HIS 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E TYR* 1.3 79.5 + - + +
115E ASN* 3.1 28.8 + - + +
116E THR* 3.2 27.7 + - - -
117E GLU* 4.0 1.6 + - - +
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Residues in contact with TYR 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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113E HIS* 1.3 88.7 - - + +
115E ASN* 1.3 61.4 + - - +
116E THR 3.2 0.2 - - - -
117E GLU* 3.1 30.1 + - + +
118E ILE* 3.4 16.2 + - + +
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Residues in contact with ASN 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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113E HIS* 3.1 20.0 + - + +
114E TYR* 1.3 77.7 - - - +
116E THR* 1.3 59.6 + - - +
118E ILE* 3.4 9.9 + - - +
119E LEU* 2.9 42.4 + - + +
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Residues in contact with THR 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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113E HIS* 3.2 22.6 + - - +
115E ASN* 1.3 75.1 - - - +
117E GLU* 1.3 59.8 + - - +
119E LEU* 4.2 7.2 - - + -
120E LYS* 2.8 34.4 + - + +
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Residues in contact with GLU 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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113E HIS 4.0 0.8 + - - -
114E TYR* 3.1 19.9 + - + +
116E THR* 1.3 79.2 - - - +
118E ILE* 1.3 65.2 + - + +
120E LYS* 3.9 9.7 - - - +
121E SER* 3.4 21.5 + - - -
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Residues in contact with ILE 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 TYR* 3.4 20.9 + - + +
115E ASN* 3.4 13.1 + - - +
116E THR 3.3 0.4 - - - -
117E GLU* 1.3 79.6 - - + +
119E LEU* 1.3 74.4 + - + +
121E SER* 2.9 22.9 + - - +
122E ILE* 3.1 22.2 + - + +
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Residues in contact with LEU 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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115E ASN* 2.9 33.4 + - + +
116E THR* 3.8 8.1 - - + +
118E ILE* 1.3 84.0 - - + +
120E LYS* 1.3 65.6 + - - +
122E ILE* 3.2 16.0 + - + +
123E ASP* 3.1 27.3 + - + +
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Residues in contact with LYS 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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116E THR* 2.8 26.4 + - + +
117E GLU* 3.9 10.1 - - - +
119E LEU* 1.3 72.2 - - - +
121E SER* 1.3 80.6 + - - +
123E ASP* 3.6 4.6 + - - +
124E ASN* 3.2 35.8 + - - +
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Residues in contact with SER 121 (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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117E GLU 3.4 10.7 + - - -
118E ILE* 2.9 19.3 + - - +
119E LEU 3.3 0.4 - - - -
120E LYS* 1.3 94.2 - - - +
122E ILE* 1.3 58.5 + - - +
124E ASN* 3.4 8.4 + - - +
125E GLU* 2.9 33.3 + - - +
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Residues in contact with ILE 122 (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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118E ILE* 3.1 21.8 + - + +
119E LEU* 3.2 25.8 + - + +
121E SER* 1.3 80.4 + - - +
123E ASP* 1.3 68.5 + - + +
125E GLU* 3.3 10.2 + - + +
126E TRP* 3.2 47.2 + - + -
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Residues in contact with ASP 123 (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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119E LEU* 3.1 17.1 + - + +
120E LYS* 4.0 4.5 - - - +
122E ILE* 1.3 75.8 - - + +
124E ASN* 1.3 69.2 + - - +
126E TRP* 3.3 14.7 + - + +
127E ARG* 3.1 26.6 + - - +
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Residues in contact with ASN 124 (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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120E LYS* 3.2 27.8 + - - +
121E SER* 3.4 11.7 + - - +
123E ASP* 1.3 84.0 + - - +
125E GLU* 1.3 63.0 + - - +
127E ARG* 2.8 34.8 + - - +
128E LYS* 3.1 31.0 + - - +
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Residues in contact with GLU 125 (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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121E SER* 2.9 18.4 + - - +
122E ILE* 3.4 17.2 - - + +
123E ASP 3.2 0.4 - - - -
124E ASN* 1.3 79.1 + - - +
126E TRP* 1.3 57.5 + - - +
128E LYS* 3.4 5.9 + - - +
129E THR* 2.6 50.2 + - + +
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Residues in contact with TRP 126 (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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122E ILE* 3.2 41.8 + - + -
123E ASP* 3.3 12.3 + - + +
125E GLU* 1.3 78.4 - - - +
127E ARG* 1.3 59.8 + - - +
129E THR* 3.4 8.4 + - - -
130E GLN* 3.2 25.3 + - - +
167E ASN* 3.0 33.8 + - - -
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Residues in contact with ARG 127 (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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123E ASP* 3.1 18.8 + - - +
124E ASN* 2.8 39.9 + - - +
126E TRP* 1.3 77.4 - - - +
128E LYS* 1.3 70.9 + - - +
129E THR 3.4 0.7 + - - -
130E GLN* 3.4 36.5 + - - +
132E MET* 4.4 4.3 - - - +
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Residues in contact with LYS 128 (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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124E ASN* 3.1 20.6 + - - +
125E GLU* 3.4 7.8 + - - +
127E ARG* 1.3 87.2 - - - +
129E THR* 1.3 62.9 + - + +
130E GLN 3.5 0.4 - - - -
132E MET* 3.4 12.7 - - - +
134E ARG* 3.2 18.9 + - - -
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Residues in contact with THR 129 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125E GLU* 2.6 37.8 + - + +
126E TRP* 3.4 11.7 + - - -
127E ARG 3.2 0.2 - - - -
128E LYS* 1.3 81.9 - - + +
130E GLN* 1.3 61.7 + - - +
134E ARG* 3.3 5.8 - - - +
164E GLY* 3.1 3.6 - - - -
165E CYS* 2.9 39.5 + - - +
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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