Contacts of the helix formed by residues 168 - 177 (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 MET 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147E ASN* 5.0 8.4 + - - +
166E LYS 5.0 3.1 - - - +
167E MET* 1.3 74.7 - - - +
169E GLU* 1.3 60.7 + - - +
170E HIS* 3.5 29.6 - - + +
171E HIS* 2.9 56.0 + - + +
172E ILE* 2.9 11.7 + - - +
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Residues in contact with GLU 169 (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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167E MET 3.7 2.2 + - - -
168E MET* 1.3 73.1 - - - +
170E HIS* 1.3 58.3 + - - +
172E ILE* 4.4 22.8 - - - +
173E GLN* 2.9 47.5 + - - +
184E ILE* 5.0 7.6 - - - +
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Residues in contact with HIS 170 (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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168E MET* 3.5 32.8 - - + +
169E GLU* 1.3 78.3 - - - +
171E HIS* 1.3 93.1 + + - +
173E GLN* 3.8 14.3 + - - +
174E LYS* 3.6 22.2 + - - +
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Residues in contact with HIS 171 (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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147E ASN* 3.1 45.8 + - + +
167E MET* 4.7 12.8 - - + -
168E MET* 2.9 42.9 + - + +
170E HIS* 1.3 103.7 - + - +
172E ILE* 1.3 65.8 + - - +
173E GLN 3.1 0.9 - - - -
174E LYS* 3.1 15.0 + - + +
175E PHE* 3.4 18.1 - - - -
211E LEU* 4.0 39.0 + - + +
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Residues in contact with ILE 172 (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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167E MET* 3.7 43.1 - - + +
168E MET 2.9 15.8 + - - +
169E GLU* 3.9 21.3 - - - +
171E HIS* 1.3 75.2 - - - +
173E GLN* 1.3 58.1 + - - +
175E PHE* 3.0 26.3 + - - +
176E THR* 3.0 19.7 + - + -
182E CYS* 3.7 24.2 - - - -
184E ILE* 4.2 23.3 - - + -
190E VAL* 4.3 12.3 - - + -
192E LEU* 4.0 10.3 - - + -
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Residues in contact with GLN 173 (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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169E GLU* 2.9 33.0 + - - +
170E HIS* 3.8 14.4 + - - +
171E HIS 3.1 0.2 - - - -
172E ILE* 1.3 78.3 - - - +
174E LYS* 1.3 58.1 + - + +
176E THR* 3.2 10.5 + - - +
177E ASP* 2.9 52.2 + - - +
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Residues in contact with LYS 174 (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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170E HIS 3.6 15.3 - - - +
171E HIS* 3.1 10.9 + - + +
173E GLN* 1.3 78.4 - - + +
175E PHE* 1.3 60.3 + - - +
177E ASP* 3.4 21.5 - - - +
178E ILE* 3.9 9.2 + - - +
207E VAL* 3.3 50.4 + - + +
210E GLU* 3.7 23.8 + - - +
211E LEU* 3.7 15.5 - - + +
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Residues in contact with PHE 175 (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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149E ILE* 4.1 3.8 - - + -
162E ILE* 3.3 29.2 - - + -
167E MET* 4.0 16.6 - - + -
171E HIS 3.4 21.1 - - - -
172E ILE 3.0 6.3 + - - +
174E LYS* 1.3 75.0 - - - +
176E THR* 1.3 64.6 + - - +
177E ASP 3.1 1.8 - - - -
178E ILE* 3.1 23.7 + - + +
180E MET* 3.3 33.0 + - + +
192E LEU* 3.8 22.4 - - + -
204E VAL* 3.6 22.2 - - + -
207E VAL* 3.7 14.6 - - + -
208E ALA* 3.7 24.2 - - + -
211E LEU* 3.7 22.2 - - + -
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Residues in contact with THR 176 (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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183B LYS* 3.8 32.1 + - + -
172E ILE* 3.0 20.5 + - + +
173E GLN* 3.2 21.1 + - - +
175E PHE* 1.3 77.5 - - - +
177E ASP* 1.3 63.9 + - - +
179E GLY* 3.1 13.7 + - - -
180E MET 3.7 20.7 + - - +
182E CYS* 3.9 24.0 - - + -
192E LEU* 4.6 2.5 - - + -
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Residues in contact with ASP 177 (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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173E GLN* 2.9 43.4 + - - +
174E LYS* 3.4 19.6 - - + +
175E PHE 3.1 0.4 - - - -
176E THR* 1.3 80.4 + - - +
178E ILE* 1.3 60.2 + - + +
179E GLY 3.8 0.3 + - - -
186F LYS* 3.3 13.2 - - - +
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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