Contacts of the helix formed by residues 189 - 207 (chain A) in PDB entry 4O46
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 ALA 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A TYR* 2.8 19.8 + - + +
184A TYR* 4.6 0.4 - - - -
187A GLN* 4.3 11.9 - - + +
188A ASN* 1.3 73.3 - - - +
190A PRO* 1.4 60.5 - - - +
191A GLU 3.3 3.3 + - - +
192A GLN* 3.5 34.5 + - + +
193A ALA* 3.0 26.0 + - - +
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Residues in contact with PRO 190 (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 TYR* 3.6 35.6 - - + -
188A ASN* 3.4 17.7 - - - +
189A ALA* 1.4 85.3 - - - +
191A GLU* 1.4 63.7 + - + +
193A ALA* 3.5 0.7 - - + +
194A CYS* 2.9 39.1 + - - -
233A TRP 5.9 1.3 - - - +
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Residues in contact with GLU 191 (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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189A ALA* 3.3 0.8 - - - -
190A PRO* 1.4 82.9 - - + +
192A GLN* 1.3 58.8 + - + +
194A CYS* 4.0 4.3 - - - +
195A HIS* 3.1 30.2 + - - +
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Residues in contact with GLN 192 (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 TYR* 3.5 39.8 + - + -
187A GLN* 5.8 0.6 - - - +
189A ALA* 3.5 30.1 + - + +
190A PRO 3.4 0.2 - - - -
191A GLU* 1.3 75.7 - - + +
193A ALA* 1.4 59.9 + - - +
195A HIS* 3.9 5.8 + - - +
196A LEU* 3.1 30.3 + - - +
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Residues in contact with ALA 193 (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 SER* 3.3 33.0 - - - +
183A TYR* 3.7 9.4 - - - +
184A TYR* 3.6 20.9 - - + +
189A ALA 3.0 18.2 + - - +
190A PRO* 3.5 6.1 - - + +
192A GLN* 1.4 76.0 - - - +
194A CYS* 1.4 57.4 + - - +
197A ALA* 3.1 25.1 + - - +
233A TRP* 3.8 10.3 - - + -
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Residues in contact with CYS 194 (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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190A PRO* 2.9 23.3 + - - +
191A GLU* 4.0 4.5 - - - +
193A ALA* 1.4 72.3 - - - +
195A HIS* 1.4 56.3 + - - +
197A ALA* 3.4 1.9 + - - +
198A LYS* 2.8 37.7 + - - +
230A LEU* 3.9 14.5 - - + +
233A TRP* 3.7 38.1 - - - -
234A THR* 4.1 19.7 - - + -
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Residues in contact with HIS 195 (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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191A GLU 3.1 19.4 + - - +
192A GLN* 3.9 6.5 + - - +
193A ALA 3.4 0.2 - - - -
194A CYS* 1.4 75.9 - - - +
196A LEU* 1.4 56.4 + - - +
198A LYS* 3.9 4.3 - - + +
199A THR* 2.6 57.3 + - + -
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Residues in contact with LEU 196 (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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158A HIS* 3.4 37.5 - - + +
176A ALA* 3.9 15.5 - - + +
179A TYR* 3.6 27.1 - - + -
180A SER* 3.5 26.9 - - - +
183A TYR* 3.7 15.9 - - + -
192A GLN 3.1 18.8 + - - +
193A ALA 3.9 3.4 - - - +
195A HIS* 1.4 78.7 + - - +
197A ALA* 1.3 56.2 + - - +
199A THR* 4.0 4.5 - - - -
200A ALA* 3.1 31.3 + - + +
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Residues in contact with ALA 197 (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 SER* 4.1 11.0 - - - +
193A ALA 3.1 19.1 + - - +
194A CYS 3.9 2.0 - - - +
196A LEU* 1.3 75.1 - - - +
198A LYS* 1.4 58.8 + - - +
200A ALA* 3.9 2.1 - - - +
201A PHE* 3.1 29.3 + - - +
226A LEU* 3.9 29.6 - - + +
229A ASN* 5.8 0.7 - - + -
230A LEU* 3.7 21.3 - - + +
233A TRP* 4.2 8.5 - - + -
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Residues in contact with LYS 198 (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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194A CYS 2.8 22.3 + - - +
195A HIS* 4.0 4.7 - - + +
197A ALA* 1.4 70.8 - - - +
199A THR* 1.4 55.0 + - - +
201A PHE* 3.2 3.8 + - + +
202A ASP* 2.8 61.1 + - - +
227A ARG* 5.5 6.3 - - - +
230A LEU* 3.5 22.1 - - + +
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Residues in contact with THR 199 (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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162A LYS* 5.8 8.5 - - - +
195A HIS* 2.6 47.4 + - + -
196A LEU* 4.0 5.6 - - - -
198A LYS* 1.4 73.6 - - - +
200A ALA* 1.3 54.3 + - - +
202A ASP* 3.4 5.5 + - - -
203A ASP* 2.8 59.7 + - - +
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Residues in contact with ALA 200 (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 PRO* 4.5 1.9 - - - +
172A ARG* 6.2 1.3 - - - +
173A LEU* 3.9 9.8 - - + +
176A ALA* 3.5 28.5 - - + -
196A LEU* 3.1 20.6 + - + +
197A ALA 3.9 4.9 - - - +
199A THR* 1.3 75.1 - - - +
201A PHE* 1.3 59.8 + - - +
203A ASP* 4.1 5.8 - - - +
204A ALA* 3.2 24.9 + - - +
226A LEU* 4.4 9.4 - - + -
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Residues in contact with PHE 201 (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 LEU* 5.3 0.4 - - - -
197A ALA 3.1 17.0 + - - +
198A LYS* 3.7 5.4 - - + +
200A ALA* 1.3 76.5 - - - +
202A ASP* 1.3 70.5 + - - +
204A ALA* 3.4 6.4 + - - +
205A ILE* 2.9 38.8 + - + +
223A MET* 3.3 54.6 - - + +
226A LEU* 4.4 11.4 - - + +
227A ARG* 3.4 53.6 - - + -
230A LEU* 5.1 3.8 - - + -
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Residues in contact with ASP 202 (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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198A LYS* 2.8 44.0 + - - +
199A THR* 3.9 5.6 + - - +
201A PHE* 1.3 80.5 - - - +
203A ASP* 1.4 62.5 + - - +
205A ILE* 3.4 6.3 + - - +
206A ALA* 2.9 29.1 + - - +
227A ARG* 5.4 2.9 + - - -
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Residues in contact with ASP 203 (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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162A LYS* 5.8 2.6 - - - -
167A PRO* 3.6 28.1 - - + +
172A ARG* 3.9 15.9 + - - +
199A THR* 2.8 46.8 + - - +
200A ALA* 4.1 5.2 - - - +
202A ASP* 1.4 74.6 - - - +
204A ALA* 1.4 60.7 + - - +
206A ALA* 3.5 7.1 + - - +
207A GLU* 3.3 16.6 + - - +
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Residues in contact with ALA 204 (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 PRO* 3.5 20.6 - - - +
168A THR* 3.4 23.8 - - + +
173A LEU* 3.9 9.9 - - + -
200A ALA 3.2 19.8 + - - +
201A PHE 3.7 3.8 - - - +
202A ASP 3.4 0.2 - - - -
203A ASP* 1.4 73.8 - - - +
205A ILE* 1.4 63.7 + - - +
207A GLU 3.4 0.2 - - - -
208A LEU* 3.2 22.7 + - - +
223A MET* 3.8 19.7 - - + -
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Residues in contact with ILE 205 (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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201A PHE* 2.9 29.3 + - + +
202A ASP* 3.7 8.7 - - - +
203A ASP 3.3 0.2 - - - -
204A ALA* 1.4 76.1 - - - +
206A ALA* 1.4 61.0 + - - +
207A GLU 3.3 0.5 + - - -
208A LEU* 3.4 33.2 + - + +
223A MET* 4.1 7.5 - - + +
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Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A ASP 2.9 17.7 + - - +
203A ASP* 3.6 9.9 - - - +
205A ILE* 1.4 75.9 - - - +
207A GLU* 1.3 57.1 + - + +
208A LEU 4.0 0.5 + - - -
209A ASP* 4.7 6.1 - - - +
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Residues in contact with GLU 207 (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 PRO* 4.1 17.5 - - + -
168A THR* 3.3 11.8 - - + +
203A ASP 3.3 12.6 + - - +
204A ALA 3.4 4.9 - - - -
205A ILE 3.2 0.8 - - - -
206A ALA* 1.3 78.5 - - + +
208A LEU* 1.4 56.8 + - - +
209A ASP* 3.0 14.6 - - - +
210A THR* 2.9 25.6 + - - -
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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