Contacts of the strand formed by residues 159 - 165 (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 159 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C GLU* 5.1 7.5 + - - -
153F GLU 4.1 0.2 - - - +
154F ILE* 3.9 0.2 - - - -
155F ASN* 3.0 28.9 + - + +
157F ASN* 2.9 27.2 + - - +
158F GLY* 1.3 84.1 - - - +
160F MET* 1.3 67.0 + - - +
161F ARG* 4.2 5.0 + - + +
193F ASP* 4.2 21.9 + - + +
194F ILE 3.3 16.7 - - - +
195F LYS* 3.6 10.0 + - - +
196F ARG* 3.2 9.1 - - - +
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Residues in contact with MET 160 (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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117F MET* 3.3 28.5 - - + -
152F PHE* 3.8 18.4 - - + -
153F GLU 3.2 12.1 - - - +
154F ILE* 3.7 9.6 - - + -
159F ASN* 1.3 74.5 - - - +
161F ARG* 1.3 64.3 + - - +
162F ILE* 4.8 4.0 - - + -
180F MET* 4.3 1.9 - - + +
193F ASP* 3.4 3.3 - - - -
194F ILE* 2.8 39.9 + - + +
196F ARG* 3.5 8.4 - - + +
201F ILE* 3.9 26.0 - - + -
204F VAL* 3.4 44.9 - - + -
205F ILE* 4.2 9.9 - - + -
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Residues in contact with ARG 161 (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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152F PHE* 3.4 3.6 - - - -
153F GLU* 2.8 73.3 + - + +
155F ASN* 6.2 2.5 - - + -
157F ASN* 5.6 4.7 + - - -
159F ASN* 4.1 5.5 + - + +
160F MET* 1.3 79.8 - - - +
162F ILE* 1.3 75.3 + - - +
163F PHE* 5.1 0.2 - - - -
180F MET* 4.9 0.2 - - - -
191F TYR* 3.6 43.4 - - - +
192F LEU 3.2 12.9 + - - +
193F ASP* 4.7 15.5 - - + +
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Residues in contact with ILE 162 (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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149F ILE* 4.0 31.4 - - + -
151F ASN 3.5 3.1 - - - -
152F PHE* 4.0 23.3 - - + -
160F MET* 4.8 1.1 - - + -
161F ARG* 1.3 80.9 - - - +
163F PHE* 1.3 66.4 + - - +
167F MET* 4.6 4.5 - - - -
175F PHE* 3.6 34.5 - - + -
180F MET* 4.1 13.4 - - + +
190F VAL 3.6 1.2 - - - +
191F TYR* 3.6 4.2 - - - -
192F LEU* 2.9 49.9 + - + -
204F VAL* 3.7 18.4 - - + -
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Residues in contact with PHE 163 (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* 4.6 6.7 - - + -
149F ILE* 3.8 1.4 - - - -
150F ARG* 2.7 69.5 + - + +
151F ASN* 3.1 42.2 + - - +
153F GLU* 3.8 8.7 - - - +
161F ARG* 4.9 1.6 - - + -
162F ILE* 1.3 74.6 - - - +
164F GLY* 1.3 53.0 + - - +
189F ASN* 3.5 30.3 - - + -
190F VAL 3.5 6.5 - - - -
191F TYR* 3.3 43.7 - + + -
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Residues in contact with GLY 164 (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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148F GLY 3.0 16.4 - - - -
149F ILE* 4.1 1.3 - - - -
150F ARG* 4.0 6.1 - - - -
162F ILE* 4.1 1.4 - - - +
163F PHE* 1.3 77.5 - - - +
165F TYR* 1.3 61.7 + - - +
167F MET* 4.2 10.1 - - - -
189F ASN* 3.3 10.2 + - - +
190F VAL* 2.8 34.4 + - - +
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Residues in contact with TYR 165 (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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203E ALA* 6.3 3.1 - - + -
206E THR* 4.3 20.6 - - + +
210E GLU* 4.6 5.8 + - - -
145F ARG* 3.3 23.5 - - - +
148F GLY* 2.7 24.5 + - - +
150F ARG* 3.6 28.0 - - - +
164F GLY* 1.3 75.2 - - - +
166F LYS* 1.3 120.6 + - + +
167F MET* 3.2 3.2 + - - +
187F ASN 4.1 12.3 - - - -
188F GLY 3.9 4.9 - - - -
189F ASN* 3.2 20.2 - - - +
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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