Contacts of the helix formed by residues 112 - 124 (chain E) in PDB entry 1KAF
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 GLU 112 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109E ASP* 2.8 27.4 + - + +
110E MET* 2.5 25.6 + - + +
111E GLU* 1.3 69.2 - - - +
113E ASP* 1.3 80.1 + - - +
114E LYS* 2.9 7.9 - - - +
115E ASP* 3.1 24.2 + - + +
116E LEU* 3.4 10.4 + - - +
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Residues in contact with ASP 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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110E MET* 2.9 26.9 - - - +
111E GLU 2.5 7.8 + - - +
112E GLU* 1.3 90.7 + - - +
114E LYS* 1.3 56.4 + - - +
116E LEU* 3.3 7.2 + - - +
117E MET* 2.9 23.9 + - - +
154E ILE* 3.9 3.4 - - + -
196E ARG* 2.9 35.1 + - + -
197E SER* 3.6 12.8 - - - -
198E ALA* 3.8 15.0 + - - +
201E ILE* 3.3 28.9 - - + +
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Residues in contact with LYS 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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111E GLU* 3.0 46.8 + - + +
112E GLU* 2.9 1.3 - - - -
113E ASP* 1.3 76.9 - - - +
115E ASP* 1.3 64.5 + - - +
117E MET* 3.2 3.5 + - - +
118E LEU* 3.0 26.9 + - - +
133E ILE* 5.7 4.0 - - - +
134E TYR 5.8 1.6 + - - -
137E ASN 5.9 0.8 - - - -
138E TYR* 3.6 50.1 + - + +
154E ILE* 3.5 34.5 + - + -
156E ASN* 4.9 8.8 + - - -
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Residues in contact with ASP 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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112E GLU* 3.1 18.5 + - + +
114E LYS* 1.3 79.4 - - - +
116E LEU* 1.3 63.2 + - - +
118E LEU* 3.4 10.2 + - - +
119E LYS* 3.0 50.8 + - - +
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Residues in contact with LEU 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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112E GLU* 3.4 6.9 + - - +
113E ASP* 3.3 15.1 + - - +
115E ASP* 1.3 80.1 + - - +
117E MET* 1.3 65.8 + - - +
119E LYS* 3.1 11.5 + - + +
120E LEU* 2.9 48.1 + - + +
198E ALA* 3.8 42.4 - - + +
201E ILE* 4.2 11.7 - - + -
202E GLU* 5.5 1.6 - - + +
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Residues in contact with MET 117 (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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113E ASP 2.9 13.5 + - - +
114E LYS 3.2 6.9 + - - +
116E LEU* 1.3 76.6 - - - +
118E LEU* 1.3 57.6 + - + +
120E LEU* 3.3 3.3 + - - +
121E LEU* 2.9 45.5 + - + +
138E TYR* 3.9 29.8 - - + -
140E ALA* 4.0 11.4 - - + -
152E PHE* 3.6 33.4 - - - +
153E GLU* 4.4 0.9 - - - +
154E ILE* 3.8 24.5 - - + -
160E MET* 3.7 29.8 - - + -
201E ILE* 4.0 15.0 - - + +
205E ILE* 4.6 2.9 - - + -
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Residues in contact with LEU 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 LYS 3.0 12.4 + - - +
115E ASP* 3.7 11.9 - - - +
117E MET* 1.3 77.1 - - + +
119E LYS* 1.3 63.1 + - + +
121E LEU* 3.5 8.0 + - + +
122E ASP* 3.1 24.4 + - - +
128E LEU* 5.3 7.9 - - + +
131E VAL* 3.7 26.7 - - + -
138E TYR* 2.8 35.0 - - + +
140E ALA* 4.7 10.5 - - + -
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Residues in contact with LYS 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 ASP* 3.0 41.2 + - - +
116E LEU* 3.5 16.4 - - + +
118E LEU* 1.3 79.2 - - + +
120E LEU* 1.3 60.8 + - + +
122E ASP* 3.4 5.6 + - - +
123E LYS* 2.9 30.2 + - - +
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Residues in contact with LEU 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 LEU* 2.9 40.5 + - + +
117E MET 3.9 3.1 - - - +
119E LYS* 1.3 74.0 - - + +
121E LEU* 1.3 65.7 + - - +
123E LYS* 3.8 17.4 - - + +
124E ASN* 2.9 35.1 + - - +
201E ILE* 4.2 8.1 - - + +
202E GLU* 3.6 46.0 - - + +
205E ILE* 3.9 17.7 - - + +
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Residues in contact with LEU 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 MET* 2.9 34.2 + - + +
118E LEU* 3.8 8.1 - - + +
120E LEU* 1.3 77.0 - - - +
122E ASP* 1.3 61.8 + - - +
124E ASN 3.3 1.7 + - - -
125E GLY 3.3 3.6 + - - -
126E PHE* 2.9 64.1 + - + +
128E LEU* 4.3 13.7 - - + -
140E ALA* 3.7 29.8 - - + -
152E PHE* 3.9 19.7 - - + -
205E ILE* 3.5 28.5 - - + -
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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 LEU 3.1 17.7 + - - +
119E LYS* 3.7 5.2 - - - +
121E LEU* 1.3 78.0 - - - +
123E LYS* 1.3 66.0 + - - +
125E GLY* 3.2 13.0 + - - -
126E PHE 5.0 3.8 - - - +
128E LEU* 5.2 6.2 - - + +
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Residues in contact with LYS 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 LYS 2.9 17.7 + - - +
120E LEU* 3.8 20.2 - - + +
121E LEU 3.4 0.2 - - - -
122E ASP* 1.3 80.2 + - - +
124E ASN* 1.3 70.6 + - - +
125E GLY 3.6 0.9 + - - -
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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 LEU* 2.9 31.3 + - - +
122E ASP 3.2 0.6 - - - -
123E LYS* 1.3 90.5 + - - +
125E GLY* 1.3 61.5 + - - +
126E PHE* 3.3 29.9 + - + -
205E ILE* 3.8 12.0 - - + +
206E THR* 5.6 1.1 - - - +
209E SER* 3.4 28.0 + - - -
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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