Contacts of the strand formed by residues 189 - 195 (chain F) 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 ASN 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199E GLU* 2.9 39.4 - - - +
203E ALA* 5.6 2.7 - - - +
150F ARG* 3.6 15.1 + - - +
163F PHE* 3.5 20.2 - - + -
164F GLY 3.3 9.4 + - - +
165F TYR* 3.2 25.0 - - - +
184F ILE* 3.7 0.9 - - - +
185F ALA* 2.9 25.8 + - - -
187F ASN* 2.9 19.0 + - - +
188F GLY* 1.3 80.8 - - - +
190F VAL* 1.3 62.0 + - - +
191F TYR* 4.0 4.9 - - + -
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Residues in contact with VAL 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162F ILE 3.6 0.7 - - - +
163F PHE* 3.5 7.8 - - - -
164F GLY 2.8 39.0 + - - +
166F LYS* 4.2 2.2 - - - +
167F MET* 4.2 34.5 - - + +
172F ILE* 4.8 8.3 - - + -
182F CYS* 3.4 31.4 - - - -
183F LYS 3.6 4.3 - - - +
184F ILE* 4.5 13.7 - - + -
188F GLY 3.8 9.0 - - - +
189F ASN* 1.3 82.3 - - - +
191F TYR* 1.3 69.4 + - - +
192F LEU* 4.1 9.2 - - + -
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Residues in contact with TYR 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199E GLU* 2.6 43.0 + - - -
161F ARG* 3.6 42.2 - - - +
162F ILE 3.6 3.1 - - - -
163F PHE* 3.3 31.9 - + - -
181F SER 3.7 1.4 - - - +
182F CYS* 3.6 1.2 - - - -
183F LYS* 2.9 54.5 + - + +
185F ALA* 4.2 11.9 - - + -
189F ASN* 4.0 11.0 - - + -
190F VAL* 1.3 75.8 - - - +
192F LEU* 1.3 63.2 + - - +
193F ASP* 4.2 2.7 + - - +
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Residues in contact with LEU 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F ARG* 3.2 8.2 - - - +
162F ILE* 2.9 49.5 + - + +
167F MET* 4.1 20.6 - - + -
172F ILE* 4.5 7.4 - - + -
175F PHE* 3.6 43.1 - - + -
176F THR* 4.9 1.3 - - + -
180F MET* 3.7 17.6 - - + +
181F SER 3.2 5.2 - - - +
182F CYS* 3.3 37.5 - - + -
190F VAL* 4.3 7.4 - - + -
191F TYR* 1.3 74.5 - - - +
193F ASP* 1.3 61.1 + - - +
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Residues in contact with ASP 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F ASN* 4.2 22.5 + - + +
160F MET 3.4 9.4 - - - +
161F ARG* 4.7 17.7 - - - +
179F GLY 4.5 0.3 - - - +
180F MET* 3.3 4.4 - - - -
181F SER* 2.9 60.1 + - - +
183F LYS* 4.9 7.1 - - - +
191F TYR 4.6 3.7 - - - +
192F LEU* 1.3 75.6 - - - +
194F ILE* 1.3 65.3 + - - +
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Residues in contact with ILE 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C CYS 5.7 3.1 - - - +
159F ASN* 3.3 7.6 - - - -
160F MET* 2.8 42.5 + - + +
178F ILE* 4.0 11.7 - - + +
179F GLY* 3.8 29.4 - - - +
180F MET* 4.1 11.9 - - + +
193F ASP* 1.3 81.3 - - - +
195F LYS* 1.3 70.2 + - + +
200F ASN* 3.5 36.3 - - + +
203F ALA* 6.3 0.4 - - + -
204F VAL* 4.0 24.2 - - + -
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Residues in contact with LYS 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C THR* 2.9 47.8 + - + +
177C ASP* 4.7 5.2 + - - +
179C GLY* 5.2 3.4 - - - +
180C MET 5.0 4.1 + - - +
181C SER* 6.4 0.9 - - - -
158F GLY* 3.9 6.5 - - - +
159F ASN* 3.6 11.5 + - - +
194F ILE* 1.3 78.5 - - - +
196F ARG* 1.3 72.3 + - - +
197F SER* 5.7 0.7 - - - -
200F ASN* 2.8 35.1 + - - +
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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