Contacts of the helix formed by residues 178 - 189 (chain A) in PDB entry 1QRJ
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 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 5.5 0.6 - - - +
138A GLN* 2.5 30.9 + - - +
139A GLY* 2.8 4.4 - - - +
140A LEU* 2.5 58.1 + - + +
177A ALA* 1.3 86.9 - - - +
179A LYS* 1.3 63.0 + - - +
181A CYS* 3.6 10.3 - - + +
182A GLN* 2.7 26.3 + - - +
205A TRP* 5.5 0.4 - - + -
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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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140A LEU* 5.2 2.0 - - + -
178A ASN* 1.3 79.5 - - - +
180A GLU* 1.3 57.3 + - - +
181A CYS 2.6 15.7 + - - -
182A GLN* 2.8 7.9 + - - +
183A LYS* 2.7 25.7 + - - +
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Residues in contact with GLU 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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140A LEU* 3.5 26.5 - - + +
178A ASN 3.6 0.2 - - - -
179A LYS* 1.3 78.1 - - - +
181A CYS* 1.3 57.7 + - - +
183A LYS* 3.7 33.0 + - - +
184A LEU* 3.0 25.8 + - - +
205A TRP* 3.8 24.2 + - + +
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Residues in contact with CYS 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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138A GLN* 3.8 12.8 - - - +
144A TYR* 3.2 43.3 - - - -
177A ALA* 3.7 10.8 - - + -
178A ASN* 3.2 29.2 - - + +
179A LYS 2.6 4.9 + - - -
180A GLU* 1.3 72.5 - - - +
182A GLN* 1.3 57.8 + - - +
183A LYS 2.9 0.7 - - - -
184A LEU* 2.5 28.2 + - - +
185A LEU* 2.9 14.8 + - - +
202A CYS* 4.2 7.0 - - - -
205A TRP* 4.6 10.0 - - + -
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Residues in contact with GLN 182 (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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174A TYR* 3.6 42.5 + - + +
175A SER* 3.9 14.5 - - - +
177A ALA* 3.4 21.0 - - + +
178A ASN 2.7 16.2 + - - +
179A LYS* 2.8 5.1 + - - +
181A CYS* 1.3 72.9 - - - +
183A LYS* 1.3 60.9 + - - +
185A LEU* 4.0 5.3 - - - +
186A GLN* 3.0 42.4 + - - +
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Residues in contact with LYS 183 (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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179A LYS 2.7 14.3 + - - +
180A GLU* 3.7 38.3 + - - +
182A GLN* 1.3 75.3 - - - +
184A LEU* 1.3 61.1 + - + +
186A GLN* 3.9 5.0 - - - +
187A ALA* 2.7 46.2 + - + +
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Residues in contact with LEU 184 (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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180A GLU 3.0 13.4 + - - +
181A CYS* 2.5 20.7 + - - +
183A LYS* 1.3 73.1 - - + +
185A LEU* 1.3 53.9 + - - +
187A ALA* 3.1 6.2 + - - +
188A ARG* 2.6 47.9 + - - +
201A ALA* 3.2 33.0 - - + +
202A CYS* 4.1 12.6 - - - -
205A TRP* 3.1 56.5 - - + -
206A THR 5.6 0.2 - - - +
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Residues in contact with LEU 185 (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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144A TYR* 3.9 14.1 - - + +
173A ALA 4.5 1.1 - - - +
174A TYR* 3.5 35.9 - - + -
177A ALA* 5.3 3.1 - - + -
181A CYS* 2.9 9.6 + - - +
182A GLN 4.0 7.2 - - - +
184A LEU* 1.3 76.9 - - + +
186A GLN* 1.3 58.7 + - - +
188A ARG* 3.0 9.7 + - - +
189A GLY 2.9 22.0 + - - -
190A HIS* 2.7 59.6 + - + +
191A THR* 4.4 9.4 - - + +
198A MET* 3.4 32.8 - - + -
201A ALA* 4.7 2.7 - - + -
202A CYS* 5.7 2.0 - - - -
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Residues in contact with GLN 186 (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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174A TYR* 3.1 37.6 + - - -
182A GLN* 3.0 40.2 + - - +
183A LYS* 3.9 5.6 - - - +
185A LEU* 1.3 72.6 - - - +
187A ALA* 1.3 55.3 + - - +
188A ARG 2.7 5.2 + - - -
189A GLY* 2.5 28.3 + - - +
191A THR* 4.1 15.2 - - + +
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Residues in contact with ALA 187 (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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183A LYS* 2.7 35.3 + - + +
184A LEU* 3.6 6.3 - - - +
186A GLN* 1.3 73.3 - - - +
188A ARG* 1.3 69.0 + - - +
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Residues in contact with ARG 188 (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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184A LEU* 2.6 28.6 + - + +
185A LEU* 3.0 14.4 - - - +
186A GLN 2.8 0.2 - - - -
187A ALA* 1.3 89.2 + - - +
189A GLY* 1.3 63.5 + - - +
190A HIS* 3.6 22.5 - - + +
200A ARG 4.9 1.9 + - - -
201A ALA* 3.2 32.3 + - + +
204A THR* 5.8 8.1 - - - +
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Residues in contact with GLY 189 (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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185A LEU 2.9 5.2 + - - -
186A GLN* 2.5 24.0 + - - -
187A ALA 3.4 0.2 - - - -
188A ARG* 1.3 76.1 - - - +
190A HIS* 1.3 58.8 + - - +
191A THR* 3.8 2.9 - - - -
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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