Contacts of the helix formed by residues 168 - 178 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199B GLU* 3.5 32.8 - - - +
147C ASN 5.2 0.8 + - - -
166C LYS* 3.6 22.9 - - + +
167C MET* 1.3 78.1 - - - +
169C GLU* 1.3 66.3 + - - +
170C HIS* 3.8 19.7 - - + +
171C HIS* 3.1 35.1 + - + +
172C ILE* 3.0 21.9 + - - +
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Residues in contact with GLU 169 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C MET 3.7 1.8 + - - -
168C MET* 1.3 72.5 - - - +
170C HIS* 1.3 59.3 + - - +
172C ILE* 3.2 14.0 + - + +
173C GLN* 3.0 28.7 + - + +
157F ASN* 5.3 5.0 - - - +
159F ASN* 5.1 8.0 + - - -
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Residues in contact with HIS 170 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168C MET* 3.8 16.9 - - + +
169C GLU* 1.3 79.3 - - - +
171C HIS* 1.3 95.3 + + - +
173C GLN* 3.6 14.8 + - - +
174C LYS* 3.0 33.7 + - + +
211C LEU 4.9 3.6 - - - -
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Residues in contact with HIS 171 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C ASN* 3.6 37.7 + - + +
167C MET* 4.8 7.0 - - + -
168C MET* 3.1 34.3 + - + +
170C HIS* 1.3 108.8 - + - +
172C ILE* 1.3 67.3 + - - +
174C LYS* 3.1 16.4 + - + +
175C PHE* 3.3 19.2 + - - -
211C LEU* 3.4 48.5 + - + +
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Residues in contact with ILE 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C MET* 4.0 33.7 - - + +
168C MET 3.0 19.2 + - - +
169C GLU* 3.5 12.1 - - + +
171C HIS* 1.3 77.2 - - - +
173C GLN* 1.3 59.1 + - - +
175C PHE* 3.0 12.5 + - - +
176C THR* 2.9 30.5 + - + +
182C CYS* 3.6 39.9 - - + -
184C ILE* 4.6 16.2 - - + -
190C VAL* 4.3 8.5 - - + -
192C LEU* 4.5 2.2 - - + -
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Residues in contact with GLN 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C GLU* 3.0 16.1 + - + +
170C HIS* 3.6 17.2 + - - +
171C HIS 3.2 0.4 - - - -
172C ILE* 1.3 78.4 - - - +
174C LYS* 1.3 57.0 + - + +
176C THR* 3.2 9.5 + - - +
177C ASP* 2.9 54.5 + - - +
157F ASN* 4.8 9.0 - - - +
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Residues in contact with LYS 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170C HIS* 3.0 25.0 - - + +
171C HIS* 3.1 13.9 + - + +
173C GLN* 1.3 78.2 - - + +
175C PHE* 1.3 60.7 + - - +
177C ASP* 3.6 18.9 - - - +
178C ILE* 3.8 13.9 + - - +
207C VAL* 3.8 20.9 - - + +
210C GLU* 3.2 30.1 + - - +
211C LEU* 3.9 20.4 + - + +
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Residues in contact with PHE 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149C ILE* 4.3 7.0 - - + -
162C ILE* 5.0 6.1 - - + -
167C MET* 3.8 24.9 - - + -
171C HIS 3.3 19.9 + - - -
172C ILE 3.0 6.1 + - - +
174C LYS* 1.3 75.4 - - - +
176C THR* 1.3 64.6 + - - +
177C ASP 3.1 1.6 - - - -
178C ILE* 3.1 25.1 + - + +
180C MET* 3.2 33.7 + - + +
192C LEU* 3.5 20.4 - - + -
204C VAL* 3.4 30.7 - - + -
207C VAL* 3.7 15.5 - - + -
208C ALA* 3.6 28.9 - - + -
211C LEU* 3.8 22.9 - - + -
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Residues in contact with THR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172C ILE* 2.9 20.1 + - + +
173C GLN* 3.2 18.4 + - - +
175C PHE* 1.3 76.2 - - - +
177C ASP* 1.3 62.6 + - - +
179C GLY* 3.0 11.4 + - - -
180C MET 3.3 22.3 + - - +
181C SER* 4.8 0.2 - - - -
182C CYS* 3.8 28.3 - - + +
192C LEU* 4.8 1.8 - - + -
195F LYS* 2.9 40.3 + - + +
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Residues in contact with ASP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C GLN* 2.9 46.0 + - - +
174C LYS* 3.6 13.2 - - - +
175C PHE 3.1 0.4 - - - -
176C THR* 1.3 79.9 + - - +
178C ILE* 1.3 61.5 + - + +
179C GLY 3.5 0.9 + - - -
195F LYS* 4.7 5.2 + - - +
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Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LYS 3.8 11.2 + - - +
175C PHE* 3.1 19.3 + - + +
176C THR 3.2 0.2 - - - -
177C ASP* 1.3 79.4 - - + +
179C GLY* 1.3 56.2 + - - +
180C MET* 4.4 6.3 - - + -
194C ILE* 4.0 11.8 - - + +
200C ASN* 5.2 2.1 - - - +
203C ALA* 3.9 30.3 - - + +
204C VAL* 3.9 17.0 - - + +
207C VAL* 3.6 31.4 - - + -
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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