Contacts of the helix formed by residues 118 - 128 (chain E) in PDB entry 4Q96
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 118 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117E TYR* 1.3 80.6 - - - +
119E GLY* 1.3 66.0 + - - -
120E GLU 3.4 2.7 - - - -
121E PHE* 3.4 7.3 + - - +
122E ILE* 3.1 18.5 + - - +
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Residues in contact with GLY 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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112E GLN* 6.2 1.8 - - - -
118E GLY* 1.3 67.9 - - - -
120E GLU* 1.3 67.0 + - - +
122E ILE* 3.3 8.6 + - - +
123E GLN* 3.0 22.5 + - - +
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Residues in contact with GLU 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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118E GLY 3.4 1.3 - - - -
119E GLY* 1.3 74.9 - - - +
121E PHE* 1.3 61.9 + - - +
123E GLN* 3.2 9.7 + - - +
124E GLN* 3.1 29.9 + - - +
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Residues in contact with PHE 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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82D GLU* 3.4 57.0 - - + +
85D LEU* 4.3 8.5 - - + -
86D VAL* 3.8 26.9 - - + -
117E TYR* 3.7 33.9 - + + -
118E GLY* 3.4 11.0 + - - +
119E GLY 3.3 0.4 - - - -
120E GLU* 1.3 77.7 - - - +
122E ILE* 1.3 64.6 + - - +
124E GLN* 3.2 24.2 + - - +
125E LEU* 3.0 44.8 + - + +
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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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108E LEU* 4.2 17.5 - - + +
111E TRP* 3.7 34.1 - - + -
112E GLN* 4.4 21.5 - - + +
117E TYR* 3.8 24.0 - - + +
118E GLY 3.1 17.5 + - - +
119E GLY* 3.3 8.9 + - - +
121E PHE* 1.3 75.0 - - - +
123E GLN* 1.3 58.5 + - - +
125E LEU* 3.1 17.1 + - + +
126E LYS* 2.9 49.1 + - + +
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Residues in contact with GLN 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 GLY 3.0 12.9 + - - +
120E GLU* 3.4 12.1 - - - +
122E ILE* 1.3 77.5 - - - +
124E GLN* 1.3 53.4 + - - +
126E LYS* 3.2 20.3 + - - +
127E LEU* 2.7 71.1 + - + +
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Residues in contact with GLN 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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86D VAL* 4.0 23.0 - - + +
120E GLU* 3.1 16.0 + - - +
121E PHE* 3.2 34.4 + - - +
123E GLN* 1.3 76.0 - - + +
125E LEU* 1.3 51.7 + - - +
127E LEU* 3.3 9.7 + - - +
128E SER* 2.8 35.4 + - - -
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Residues in contact with LEU 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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85D LEU* 3.6 38.4 - - + +
86D VAL* 3.7 13.0 - - + +
89D PHE* 4.0 9.4 - - + +
108E LEU* 3.7 30.5 - - + +
111E TRP* 3.8 21.3 - - + -
121E PHE* 3.0 40.0 + - + +
122E ILE* 3.1 14.6 + - + +
124E GLN* 1.3 72.4 - - - +
126E LYS* 1.3 65.0 + - - +
128E SER* 2.7 22.6 + - - -
129E MET* 3.6 9.9 + - - +
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Residues in contact with LYS 126 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E GLU* 4.9 6.6 + - - +
108E LEU* 3.6 29.5 - - + +
109E ASN* 3.3 26.4 + - - +
112E GLN* 4.2 16.8 + - - +
122E ILE* 2.9 31.9 + - + +
123E GLN* 3.5 26.9 - - - +
125E LEU* 1.3 76.9 - - - +
127E LEU* 1.3 64.2 + - + +
129E MET* 3.1 22.6 + - + +
130E GLU* 3.9 8.7 + - - +
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Residues in contact with LEU 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 GLN* 2.7 46.9 + - + +
124E GLN* 3.6 8.1 - - - +
126E LYS* 1.3 72.5 - - - +
128E SER* 1.3 62.6 + - - +
129E MET 3.0 1.6 + - - -
130E GLU* 3.2 45.9 + - + +
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Residues in contact with SER 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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86D VAL* 3.7 30.4 + - - -
89D PHE* 3.5 21.8 - - - +
90D SER* 3.4 24.9 + - - +
93D ALA* 4.7 0.2 - - - +
124E GLN 2.8 16.3 + - - -
125E LEU* 2.7 18.9 + - - -
126E LYS 3.1 0.8 - - - -
127E LEU* 1.3 76.3 - - - +
129E MET* 1.3 58.7 + - - +
130E GLU 3.5 1.9 + - - -
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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