Contacts of the helix formed by residues 170 - 181 (chain F) in PDB entry 1KR2
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 LYS 170 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94F GLU* 4.2 24.1 + - + +
97F LYS* 5.0 9.5 - - - +
169F TRP* 1.3 72.2 - - - +
171F SER* 1.3 57.8 + - - +
172F GLU* 3.8 21.7 + - - +
173F ASP* 2.7 70.6 + - - +
174F ILE* 3.2 4.5 + - - +
272F ARG* 6.3 0.2 - - - +
273F ASN* 3.3 28.3 - - + +
814F TAD 4.7 0.2 + - - -
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Residues in contact with SER 171 (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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169F TRP 3.3 6.1 + - - -
170F LYS* 1.3 71.2 - - - +
172F GLU* 1.3 72.4 + - - +
174F ILE* 3.2 15.8 + - - +
175F THR* 3.1 25.1 + - - -
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Residues in contact with GLU 172 (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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170F LYS* 3.8 26.0 + - - +
171F SER* 1.3 92.8 + - - +
173F ASP* 1.3 60.5 + - - +
175F THR* 3.8 7.4 - - - -
176F GLN* 3.0 43.8 + - + +
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Residues in contact with ASP 173 (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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94F GLU* 3.6 21.0 - - - +
96F LEU* 3.5 29.1 + - + +
169F TRP* 4.8 10.5 - - + -
170F LYS* 2.7 58.7 + - + +
172F GLU* 1.3 79.3 - - - +
174F ILE* 1.3 57.6 + - - +
176F GLN* 3.4 2.3 + - - +
177F ILE* 2.9 38.2 + - + +
814F TAD 4.5 5.9 + - - +
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Residues in contact with ILE 174 (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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163F PHE* 3.6 69.3 - - + +
169F TRP* 3.8 27.1 - - + +
170F LYS 4.1 1.8 - - - +
171F SER* 3.2 17.2 + - - +
173F ASP* 1.3 76.1 - - - +
175F THR* 1.3 65.4 + - - +
177F ILE* 3.1 16.1 + - - +
178F VAL* 3.1 15.9 + - + +
202F VAL* 5.1 8.7 - - + -
203F LEU* 4.1 14.8 - - + -
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Residues in contact with THR 175 (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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171F SER 3.1 11.4 + - - -
172F GLU* 3.8 10.6 - - - -
174F ILE* 1.3 79.7 - - - +
176F GLN* 1.3 62.5 + - + +
178F VAL* 3.3 8.2 - - - +
179F ALA* 2.8 41.2 + - + +
202F VAL* 3.6 26.2 - - + +
206F HIS* 4.8 6.5 - - - +
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Residues in contact with GLN 176 (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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96F LEU* 3.8 24.2 - - + +
100F ARG* 3.5 22.7 + - - +
172F GLU* 3.0 30.4 + - + +
173F ASP* 4.0 3.7 + - - +
175F THR* 1.3 79.5 - - + +
177F ILE* 1.3 61.7 + - - +
179F ALA* 4.4 1.6 - - - -
180F ASN* 2.7 55.6 + - + +
181F TYR* 3.7 3.7 + - - -
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Residues in contact with ILE 177 (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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95F THR* 4.1 4.5 - - + -
96F LEU* 4.0 28.5 - - + +
99F LEU* 3.8 27.1 - - + -
153F LEU* 4.6 5.2 - - + -
163F PHE* 5.3 6.1 - - + -
169F TRP* 3.9 28.7 - - + -
173F ASP* 2.9 30.1 + - + +
174F ILE* 3.1 5.6 + - - +
176F GLN* 1.3 75.8 - - - +
178F VAL* 1.3 59.6 + - + +
181F TYR* 2.9 15.5 + - - -
182F GLY 2.8 28.9 + - - +
183F LEU* 4.3 24.7 - - + -
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Residues in contact with VAL 178 (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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163F PHE* 4.4 4.9 - - + -
174F ILE 3.1 12.6 + - - +
175F THR* 3.3 14.4 - - - +
177F ILE* 1.3 78.8 - - + +
179F ALA* 1.3 60.7 + - - +
182F GLY* 4.4 6.1 - - - +
183F LEU* 4.2 18.2 - - + -
202F VAL* 4.7 5.6 - - + +
203F LEU* 3.8 28.0 - - + -
206F HIS* 3.8 31.8 - - + +
209F ASN* 3.1 33.1 - - - +
210F ILE* 3.9 18.6 - - + -
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Residues in contact with ALA 179 (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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175F THR* 2.8 26.7 + - + +
176F GLN* 4.3 1.1 - - - +
178F VAL* 1.3 81.8 - - - +
180F ASN* 1.3 70.2 + - - +
181F TYR 3.6 0.2 - - - -
206F HIS* 3.7 31.4 - - + +
209F ASN* 3.9 6.9 - - - +
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Residues in contact with ASN 180 (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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176F GLN* 2.7 53.2 + - - +
179F ALA* 1.3 82.9 - - - +
181F TYR* 1.3 78.3 + - + +
209F ASN* 4.7 0.4 - - - -
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Residues in contact with TYR 181 (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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96F LEU* 3.7 20.4 - - + -
99F LEU* 3.8 42.4 - - + -
100F ARG* 3.0 31.3 + - + +
103F GLN* 4.0 17.1 - - + +
150F LYS* 5.8 1.2 - - - +
151F VAL* 3.5 39.6 - - + +
152F LYS* 3.0 31.2 + - - +
176F GLN 3.7 9.6 - - - -
177F ILE* 2.9 12.0 + - - +
179F ALA 3.6 0.6 - - - -
180F ASN* 1.3 98.3 - - + +
182F GLY* 1.3 62.6 + - - +
209F ASN* 3.1 5.9 - - - +
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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