Contacts of the helix formed by residues 168 - 181 (chain A) in PDB entry 1A9Q
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 ARG 168 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ASP* 2.9 48.3 + - - +
166A TYR 3.7 7.6 - - - -
167A ASP* 1.3 92.8 + - - +
169A ASP* 1.3 75.7 + - - +
171A ARG* 3.2 23.7 + - - +
172A GLN* 3.1 24.3 + - - +
229A ARG* 5.2 4.4 - - - +
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Residues in contact with ASP 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ASP* 3.3 11.4 + - - +
168A ARG* 1.3 83.9 + - - +
170A MET* 1.3 65.6 + - + +
172A GLN* 3.2 11.6 + - - +
173A LYS* 3.0 40.6 + - - +
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Residues in contact with MET 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 5.3 3.1 - - + -
167A ASP* 3.0 27.8 + - + +
168A ARG 3.2 0.4 - - - -
169A ASP* 1.3 80.7 - - + +
171A ARG* 1.3 57.8 + - - +
173A LYS* 3.2 18.6 + - + +
174A ALA* 2.9 27.7 + - - +
234A ARG* 3.6 30.1 - - - -
236A PHE* 3.6 38.0 - - + -
278A LEU* 5.0 6.4 - - + +
281A SER 3.8 23.3 - - - +
282A ILE* 3.9 26.9 - - + +
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 4.1 12.3 - - + -
132A ILE 3.6 20.8 + - - +
133A ARG* 3.7 28.5 + - - +
166A TYR* 2.9 31.9 + - + +
167A ASP 3.3 11.3 + - - +
168A ARG* 3.2 26.6 + - - +
170A MET* 1.3 75.3 - - - +
172A GLN* 1.3 63.6 + - - +
174A ALA* 3.5 7.1 + - - +
175A HIS* 3.1 31.8 + - + -
189A GLU* 3.0 31.3 + - - +
236A PHE* 4.4 13.2 - - + -
237A GLY 5.8 0.2 - - - +
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Residues in contact with GLN 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ARG 3.1 14.3 + - - +
169A ASP* 3.4 14.1 - - - +
170A MET 3.2 0.2 - - - -
171A ARG* 1.3 75.1 - - - +
173A LYS* 1.3 70.9 + - - +
175A HIS* 3.1 22.6 + - - +
176A SER* 3.2 17.0 + - - -
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Residues in contact with LYS 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASP* 3.0 31.7 + - + +
170A MET* 3.5 25.1 - - + +
172A GLN* 1.3 80.9 - - - +
174A ALA* 1.3 61.7 + - - +
176A SER* 3.2 9.9 + - - +
177A THR* 3.0 29.6 + - - -
278A LEU* 4.4 4.7 - - + -
281A SER* 4.2 32.1 - - - +
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Residues in contact with ALA 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.8 28.9 - - + -
170A MET 2.9 16.5 + - - +
171A ARG 3.6 6.5 - - - +
172A GLN 3.2 0.2 - - - -
173A LYS* 1.3 76.9 - - - +
175A HIS* 1.3 61.0 + - - +
177A THR 3.6 0.2 + - - -
178A TRP* 3.1 24.3 + - - +
187A LEU* 3.7 4.5 - - - +
236A PHE* 3.9 14.4 - - + -
274A PHE* 3.7 8.6 - - + -
278A LEU* 3.7 14.8 - - + +
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Residues in contact with HIS 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU* 3.5 15.1 - - + +
171A ARG* 3.1 22.8 + - + -
172A GLN* 3.1 17.9 + - - +
174A ALA* 1.3 75.9 - - - +
176A SER* 1.3 64.6 + - - +
178A TRP* 3.4 4.0 + - - +
179A LYS* 3.1 38.5 + - - +
187A LEU* 3.7 42.3 - - + +
188A GLN 4.8 2.0 - - - -
189A GLU* 3.7 22.0 + - + -
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Residues in contact with SER 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLN* 3.2 11.7 + - - -
173A LYS* 3.2 12.4 + - - +
175A HIS* 1.3 73.8 - - - +
177A THR* 1.3 66.5 + - - +
179A LYS* 3.1 18.6 + - - +
180A GLN* 3.0 33.2 + - - +
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Residues in contact with THR 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A LYS 3.0 18.9 + - - -
174A ALA 3.9 4.3 - - - -
176A SER* 1.3 76.7 - - - +
178A TRP* 1.3 61.5 + - - +
180A GLN* 3.1 17.1 + - + +
181A MET* 3.1 20.8 + - - +
274A PHE* 4.2 17.5 - - + -
277A LEU* 3.5 42.2 + - + -
278A LEU* 4.0 11.3 - - - +
281A SER* 4.5 11.4 + - - -
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Residues in contact with TRP 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE* 3.7 39.3 - - + -
174A ALA 3.1 18.1 + - - +
175A HIS 3.6 5.4 - - - +
177A THR* 1.3 76.4 - - - +
179A LYS* 1.3 67.5 + - + +
181A MET* 3.1 22.5 + - + +
182A GLY 3.7 2.9 + - - -
183A GLU* 3.6 36.8 + - + +
185A ARG* 2.8 37.0 + - + -
186A GLU* 3.8 4.5 - - - +
187A LEU* 3.2 40.8 - - + +
270A LYS* 4.2 18.6 - - + -
274A PHE* 4.0 28.6 - + + -
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Residues in contact with LYS 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A HIS* 3.1 25.0 + - - +
176A SER* 3.1 18.8 + - - +
178A TRP* 1.3 79.2 - - + +
180A GLN* 1.3 60.9 + - + +
182A GLY* 3.0 21.1 + - - -
183A GLU 5.7 0.2 - - - +
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Residues in contact with GLN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A SER* 3.0 22.6 + - - +
177A THR* 3.1 19.2 + - + +
179A LYS* 1.3 77.1 - - + +
181A MET* 1.3 57.3 + - - +
182A GLY 3.2 1.9 + - - -
277A LEU* 6.1 1.6 - - + -
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A THR 3.1 13.6 + - - +
178A TRP* 3.1 17.6 + - + +
179A LYS 3.1 1.0 - - - -
180A GLN* 1.3 77.2 - - - +
182A GLY* 1.3 64.9 + - - +
183A GLU* 3.4 29.3 + - + +
270A LYS* 4.0 16.4 - - + +
273A GLN* 3.8 35.7 - - + +
274A PHE* 3.7 30.5 - - + -
277A LEU* 3.6 27.6 - - + -
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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