Contacts of the helix formed by residues 178 - 189 (chain A) in PDB entry 1WXQ
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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169A ALA* 4.2 2.2 - - - -
176A GLY 4.7 4.9 + - - -
177A VAL* 1.3 72.1 - - - +
179A GLU* 1.3 66.4 + - - +
180A ASN* 3.1 17.1 + - + +
181A ASP* 2.8 35.6 + - - +
182A VAL* 3.2 17.7 + - - +
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Residues in contact with GLU 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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163A LYS* 4.5 13.4 + - - +
165A GLU* 3.7 25.1 - - + +
166A SER* 3.5 30.3 + - - +
169A ALA* 3.8 17.0 - - + +
178A ASN* 1.3 75.7 + - - +
180A ASN* 1.3 57.2 + - - +
182A VAL* 3.7 3.0 + - - +
183A TRP* 3.1 24.8 + - - +
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Residues in contact with ASN 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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178A ASN* 3.0 15.0 + - + +
179A GLU* 1.3 78.5 - - - +
181A ASP* 1.3 70.2 + - - +
182A VAL 3.2 0.4 - - - -
183A TRP* 3.3 11.7 + - - +
184A GLU* 3.1 48.7 + - - +
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Residues in contact with ASP 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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176A GLY 4.1 3.6 - - - +
177A VAL* 3.8 13.8 - - + -
178A ASN* 2.8 40.2 + - - +
180A ASN* 1.3 83.2 - - - +
182A VAL* 1.3 64.2 + - - +
184A GLU* 3.8 10.8 - - - +
185A ALA* 3.0 25.9 + - - +
210A ILE* 4.3 8.9 - - + +
213A VAL* 4.1 25.4 - - + +
214A ASN* 5.2 5.4 + - + +
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Residues in contact with VAL 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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165A GLU* 3.5 29.6 - - + +
168A ILE* 4.1 18.6 - - + -
169A ALA* 3.9 19.7 - - - +
177A VAL* 3.5 18.8 - - + -
178A ASN 3.2 14.3 + - - +
179A GLU 3.8 7.0 - - - +
181A ASP* 1.3 75.4 - - - +
183A TRP* 1.3 65.6 + - - +
185A ALA* 3.4 0.9 + - - +
186A MSE 3.1 36.4 + - - +
206A PHE* 4.3 17.0 - - + -
210A ILE* 4.7 0.7 - - - -
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Residues in contact with TRP 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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163A LYS* 6.5 0.2 - - - -
165A GLU* 3.3 33.5 + - + +
179A GLU* 3.1 15.8 + - + +
180A ASN* 3.3 14.5 + - - +
182A VAL* 1.3 81.2 - - - +
184A GLU* 1.3 72.8 + - + +
186A MSE 3.8 3.5 - - - +
187A HIS* 3.0 70.7 + + + +
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Residues in contact with GLU 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 ASN* 3.1 41.8 + - - +
181A ASP* 3.8 12.5 - - - +
183A TRP* 1.3 88.1 - - + +
185A ALA* 1.3 56.7 + - - +
187A HIS* 3.1 3.9 + - - +
188A LYS* 2.7 37.9 + - - +
213A VAL* 5.3 8.0 - - - +
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Residues in contact with ALA 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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181A ASP 3.0 17.0 + - - +
182A VAL 3.8 0.2 - - - +
184A GLU* 1.3 75.5 - - - +
186A MSE 1.3 64.3 + - - +
188A LYS* 3.1 6.5 + - - +
189A LEU* 3.1 26.3 + - - +
206A PHE* 3.5 28.5 - - + -
209A GLU* 3.9 27.4 - - + -
210A ILE* 4.1 9.4 - - + -
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Residues in contact with MSE 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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164A LEU* 3.5 39.7 - - + -
165A GLU* 4.5 17.5 - - - +
168A ILE* 4.6 0.2 - - - -
182A VAL* 3.1 28.8 + - + +
183A TRP* 3.8 3.8 - - - +
185A ALA* 1.3 79.1 - - - +
187A HIS* 1.3 62.5 + - - +
189A LEU 3.1 6.8 + - - -
191A LEU* 3.0 45.2 + - + +
192A PRO 3.5 18.2 - - - +
193A GLU* 4.4 8.3 - - + +
198A TRP* 3.7 25.1 - - + -
206A PHE* 4.0 6.7 - - + -
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Residues in contact with HIS 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 TRP* 3.0 58.6 + + + +
184A GLU* 3.4 5.2 + - - +
186A MSE 1.3 76.6 - - - +
188A LYS* 1.3 65.8 + - - +
189A LEU 3.4 0.5 + - - -
190A ASN* 3.4 15.9 + - - +
191A LEU 5.8 0.4 - - - -
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Residues in contact with LYS 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 GLU 2.7 20.9 + - - +
185A ALA* 3.1 6.5 + - - +
187A HIS* 1.3 80.3 + - - +
189A LEU* 1.3 66.4 + - + +
190A ASN* 3.4 3.8 + - - -
209A GLU* 3.4 21.7 + - + +
212A ARG* 2.7 45.9 - - - +
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Residues in contact with LEU 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 ALA 3.1 18.0 + - - +
186A MSE 3.1 0.2 + - - -
188A LYS* 1.3 91.7 - - + +
190A ASN* 1.3 72.2 + - - +
191A LEU* 2.9 26.8 + - + +
202A ASP 5.1 0.2 - - - +
205A ALA* 3.7 35.4 - - + +
206A PHE* 3.9 15.5 - - - +
209A GLU* 4.2 14.6 - - + +
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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