Contacts of the helix formed by residues 168 - 178 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D ASN* 4.4 14.3 + - - +
166D LYS 3.6 3.8 + - - +
167D MET* 1.3 74.5 - - - +
169D GLU* 1.3 66.1 + - - +
170D HIS* 3.5 31.6 - - + +
171D HIS* 2.9 45.0 + - + +
172D ILE* 3.0 12.0 + - - +
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Residues in contact with GLU 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LYS* 4.3 21.3 + - - +
167D MET 3.6 3.5 + - - +
168D MET* 1.3 71.8 - - - +
170D HIS* 1.3 58.5 + - - +
172D ILE* 3.3 11.9 + - + +
173D GLN* 3.0 29.8 + - - +
184D ILE* 6.3 2.5 - - + -
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Residues in contact with HIS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D MET* 3.5 38.2 - - + +
169D GLU* 1.3 79.6 - - - +
171D HIS* 1.3 88.5 + + - +
173D GLN* 3.8 13.8 - - - +
174D LYS* 3.1 38.2 + - - +
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Residues in contact with HIS 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D ASN* 3.5 35.4 + - + -
167D MET* 5.0 7.4 - - + -
168D MET* 2.9 46.3 + - + +
170D HIS* 1.3 105.4 + + - +
172D ILE* 1.3 65.8 + - - +
174D LYS* 3.0 20.5 + - - +
175D PHE* 3.4 12.1 - - - -
211D LEU* 3.8 48.8 + - + +
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D MET* 3.8 38.1 - - + +
168D MET 3.0 16.3 + - - +
169D GLU* 3.7 12.1 - - + +
171D HIS* 1.3 75.2 - - - +
173D GLN* 1.3 63.4 + - - +
175D PHE* 3.0 21.2 + - - +
176D THR* 3.0 19.8 + - + +
182D CYS* 3.7 21.8 - - - -
184D ILE* 3.9 25.6 - - + -
190D VAL* 4.2 16.8 - - + -
192D LEU* 4.1 8.5 - - + -
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Residues in contact with GLN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D GLU 3.0 15.9 + - - +
170D HIS* 3.8 17.3 + - - +
171D HIS 3.1 0.2 - - - -
172D ILE* 1.3 77.6 - - - +
174D LYS* 1.3 64.8 + - - +
176D THR* 3.2 10.4 + - - +
177D ASP* 2.8 56.5 + - - +
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Residues in contact with LYS 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D HIS* 3.1 31.4 + - - +
171D HIS* 3.0 11.4 + - - +
173D GLN* 1.3 88.6 - - - +
175D PHE* 1.3 61.2 + - - +
177D ASP* 3.6 20.3 + - - +
178D ILE* 3.7 14.4 - - - +
207D VAL* 3.7 24.2 - - + +
211D LEU* 4.2 12.3 - - + -
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Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D ILE* 4.4 2.0 - - + -
162D ILE* 3.5 20.0 - - + -
167D MET* 3.9 20.6 - - + -
171D HIS 3.4 23.3 - - - -
172D ILE* 3.0 8.9 + - - +
174D LYS* 1.3 74.8 - - - +
176D THR* 1.3 65.3 + - - +
177D ASP 3.1 1.3 - - - -
178D ILE* 3.1 23.4 - - + +
180D MET* 3.2 40.5 + - + +
192D LEU* 3.5 23.3 - - + -
204D VAL* 3.6 17.5 - - + -
207D VAL* 3.5 21.5 - - + -
208D ALA* 3.7 25.4 - - + -
211D LEU* 3.9 14.4 - - + -
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Residues in contact with THR 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A SER* 5.3 2.0 - - - +
195A LYS* 5.8 3.8 - - - -
172D ILE* 3.0 16.3 + - + +
173D GLN* 3.2 23.4 + - - +
175D PHE* 1.3 76.2 - - - +
177D ASP* 1.3 62.9 + - - +
179D GLY* 3.1 13.0 + - - -
180D MET 3.4 22.4 - - - +
182D CYS* 3.9 27.4 - - + +
192D LEU* 4.9 2.5 - - + -
186E LYS* 4.9 2.6 + - - -
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Residues in contact with ASP 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D GLN* 2.8 48.8 + - - +
174D LYS* 3.6 16.8 + - - +
175D PHE 3.1 0.4 - - - -
176D THR* 1.3 79.6 + - - +
178D ILE* 1.3 61.2 + - + +
179D GLY 3.3 0.4 - - - -
186E LYS* 3.6 27.4 + - - +
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Residues in contact with ILE 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D LYS 3.7 11.6 + - - +
175D PHE* 3.1 17.9 + - + +
177D ASP* 1.3 79.9 - - + +
179D GLY* 1.3 55.9 + - - +
180D MET* 4.4 8.3 - - + -
194D ILE* 4.1 12.2 - - + +
203D ALA* 4.1 24.9 - - + -
204D VAL* 4.1 17.9 - - + +
207D VAL* 3.9 27.8 - - + -
166E LYS* 6.3 0.4 - - - +
186E LYS* 4.0 21.7 - - - +
187E ASN* 3.9 30.7 + - + +
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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