Contacts of the helix formed by residues 116 - 132 (chain E) in PDB entry 4GKH
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 116 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113E TYR* 2.8 29.5 + - - +
115E ASP* 1.3 78.7 - - - +
117E GLY* 1.3 58.3 + - - +
118E GLU 3.3 2.7 - - - -
119E ASN* 3.2 19.6 + - - +
120E ILE* 2.9 40.1 + - - +
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Residues in contact with GLY 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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110E LEU* 3.6 26.0 - - - -
113E TYR 4.0 1.0 + - - -
114E PRO 3.5 7.9 + - - -
115E ASP 3.3 4.4 - - - -
116E SER* 1.3 77.6 - - - +
118E GLU* 1.3 57.3 + - - +
120E ILE* 3.3 2.1 + - - +
121E VAL* 2.9 37.0 + - - +
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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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115E ASP 5.0 2.2 + - - +
116E SER 3.3 0.4 - - - -
117E GLY* 1.3 75.8 - - - +
119E ASN* 1.3 66.6 + - - +
121E VAL* 3.9 4.5 - - - +
122E ASP* 2.9 35.5 + - - +
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Residues in contact with ASN 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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116E SER* 3.2 21.8 + - - +
118E GLU* 1.3 80.9 - - - +
120E ILE* 1.3 62.7 + - + +
122E ASP* 3.4 12.5 + - - +
123E ALA* 3.1 23.6 + - - +
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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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106E ALA* 4.8 16.6 - - + +
109E VAL* 4.0 21.8 - - + +
110E LEU* 3.8 39.7 - - + +
113E TYR* 4.4 1.1 - - + +
116E SER* 2.9 38.9 + - - +
117E GLY* 3.6 5.4 - - - +
119E ASN* 1.3 77.5 - - + +
121E VAL* 1.3 59.2 - - + +
123E ALA* 3.3 6.9 + - - +
124E LEU* 3.0 43.8 + - + +
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Residues in contact with VAL 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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110E LEU* 6.0 5.6 - - + -
117E GLY* 2.9 21.4 + - - +
118E GLU* 4.0 4.7 - - - +
120E ILE* 1.3 74.8 - - + +
122E ASP* 1.3 65.0 + - - +
124E LEU* 3.1 17.0 + - + +
125E ALA* 2.9 31.9 + - + +
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Residues in contact with ASP 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 GLU* 2.9 30.4 + - - +
119E ASN* 3.6 13.7 - - - +
121E VAL* 1.3 78.4 - - - +
123E ALA* 1.3 63.0 + - - +
125E ALA* 3.3 7.2 + - - +
126E VAL* 3.1 29.3 + - + +
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Residues in contact with ALA 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 ASN 3.1 13.4 + - - +
120E ILE* 3.6 10.3 - - - +
122E ASP* 1.3 73.0 - - - +
124E LEU* 1.3 66.2 + - - +
126E VAL* 3.3 8.4 + - - +
127E PHE* 3.0 24.1 + - - +
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Residues in contact with LEU 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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106E ALA* 4.4 21.5 - - + -
120E ILE* 3.0 36.2 + - + +
121E VAL* 3.1 19.3 + - + +
123E ALA* 1.3 76.5 - - - +
125E ALA* 1.3 57.3 + - - +
127E PHE* 3.4 8.3 + - + +
128E LEU* 3.0 30.5 + - - +
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Residues in contact with ALA 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 VAL* 2.9 19.6 + - + +
122E ASP* 3.6 7.0 - - - +
123E ALA 3.2 0.2 - - - -
124E LEU* 1.3 75.0 - - - +
126E VAL* 1.3 58.6 + - + +
128E LEU* 3.3 7.8 + - - +
129E ARG* 2.8 41.7 + - - +
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Residues in contact with VAL 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 ASP* 3.1 18.3 + - + +
123E ALA* 3.3 9.4 + - - +
125E ALA* 1.3 76.9 - - + +
127E PHE* 1.3 57.8 + - - +
129E ARG* 3.3 12.6 + - - +
130E ARG* 3.0 38.5 + - + +
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Residues in contact with PHE 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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79E MSE 3.4 26.9 - - + +
80E PRO* 3.8 35.4 - - + -
81E LEU* 5.9 1.6 - - + -
123E ALA 3.0 17.1 + - - +
124E LEU* 3.7 9.6 - - + +
126E VAL* 1.3 78.9 - - - +
128E LEU* 1.3 59.4 + - + +
130E ARG* 3.2 25.9 + - - +
131E LEU* 3.1 27.3 + - + +
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Residues in contact with LEU 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 LEU 3.0 18.0 + - - +
125E ALA* 3.7 6.5 - - - +
127E PHE* 1.3 78.8 - - + +
129E ARG* 1.3 64.9 + - + +
131E LEU* 3.3 15.8 + - + +
132E HIS* 3.0 62.1 + - + +
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Residues in contact with ARG 129 (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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125E ALA* 2.8 27.8 + - + +
126E VAL* 3.6 9.6 - - - +
128E LEU* 1.3 78.1 - - - +
130E ARG* 1.3 61.0 + - - +
132E HIS* 3.5 5.5 + - - +
133E SER* 2.8 30.9 + - - +
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Residues in contact with ARG 130 (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 PHE 4.3 6.1 + - - -
79E MSE 4.0 20.2 - - - +
80E PRO* 3.5 29.0 - - - +
126E VAL* 3.0 29.8 + - + +
127E PHE* 3.4 30.5 - - - +
128E LEU 3.2 0.2 - - - -
129E ARG* 1.3 75.5 - - - +
131E LEU* 1.3 64.9 + - - +
133E SER* 3.1 18.4 + - - -
134E ILE* 3.7 9.2 + - - +
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Residues in contact with LEU 131 (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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75E LEU* 4.1 17.5 - - + -
79E MSE 3.8 35.2 - - + +
127E PHE* 3.1 14.4 + - + +
128E LEU* 3.3 20.4 + - + +
130E ARG* 1.3 80.0 - - - +
132E HIS* 1.3 74.5 + - + +
133E SER 3.2 4.2 + - - -
134E ILE* 3.3 32.3 + - + +
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Residues in contact with HIS 132 (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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128E LEU* 3.0 51.2 + - + +
129E ARG* 3.7 6.1 - - - +
131E LEU* 1.3 90.3 - - + +
133E SER* 1.3 59.6 + - - +
134E ILE 3.4 4.3 + - - +
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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