Contacts of the helix formed by residues 189 - 207 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B TYR* 2.8 19.1 + - + +
184B TYR* 4.3 0.4 + - - -
187B GLN* 4.3 13.2 - - + +
188B ASN* 1.3 71.7 - - - +
190B PRO* 1.4 65.6 - - - +
191B GLU 3.3 2.9 - - - -
192B GLN* 3.4 32.0 + - + +
193B ALA* 3.1 21.5 + - - +
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Residues in contact with PRO 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TYR* 3.6 36.5 - - + +
188B ASN* 3.4 17.9 - - - +
189B ALA* 1.4 83.8 - - - +
191B GLU* 1.4 59.0 + - + +
193B ALA* 3.5 1.0 - - + +
194B CYS* 2.9 39.1 + - - -
233B TRP 5.9 0.9 - - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 3.3 0.8 - - - -
190B PRO* 1.4 80.8 - - + +
192B GLN* 1.4 59.6 + - + +
194B CYS* 3.6 4.5 + - - +
195B HIS* 3.1 29.9 + - - +
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Residues in contact with GLN 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B TYR* 3.5 40.7 + - + -
187B GLN* 5.8 0.2 - - - +
189B ALA* 3.4 27.6 + - + +
190B PRO 3.4 0.4 - - - -
191B GLU* 1.4 74.9 - - + +
193B ALA* 1.4 60.1 + - - +
195B HIS* 3.9 4.9 + - - +
196B LEU* 3.1 31.0 + - - +
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Residues in contact with ALA 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER* 3.3 36.1 - - - +
183B TYR* 3.8 7.4 - - - +
184B TYR* 3.6 20.0 - - + +
189B ALA 3.1 17.8 + - - +
190B PRO* 3.5 6.5 - - + +
192B GLN* 1.4 75.9 - - - +
194B CYS* 1.4 57.9 + - - +
197B ALA* 3.1 25.8 + - - +
233B TRP* 3.8 10.1 - - + -
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Residues in contact with CYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B PRO* 2.9 24.0 + - - +
191B GLU* 4.0 4.9 - - - +
193B ALA* 1.4 72.5 - - - +
195B HIS* 1.3 59.6 + - - +
197B ALA* 3.4 1.6 + - - +
198B LYS* 2.8 33.8 + - - +
230B LEU* 3.9 15.0 - - + +
233B TRP* 3.7 37.7 - - - -
234B THR* 4.1 19.7 - - + -
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Residues in contact with HIS 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLU 3.1 19.7 + - - +
192B GLN* 3.9 5.8 + - - +
193B ALA 3.4 0.2 - - - -
194B CYS* 1.3 76.5 - - - +
196B LEU* 1.4 56.0 + - - +
198B LYS* 4.0 4.3 - - + +
199B THR* 2.6 58.1 + - + -
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Residues in contact with LEU 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B HIS* 3.4 36.6 - - + +
176B ALA* 3.9 15.5 - - + +
179B TYR* 3.6 26.5 - - + -
180B SER* 3.5 26.9 - - - +
183B TYR* 3.7 16.6 - - + -
192B GLN 3.1 17.5 + - - +
193B ALA 3.9 3.4 - - - +
195B HIS* 1.4 80.5 + - - +
197B ALA* 1.3 56.5 + - - +
199B THR* 4.0 3.7 - - - -
200B ALA* 3.1 31.2 + - + +
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Residues in contact with ALA 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B SER* 4.1 11.4 - - - +
193B ALA 3.1 17.7 + - - +
194B CYS 3.8 2.0 - - - +
196B LEU* 1.3 75.5 - - - +
198B LYS* 1.4 63.2 + - - +
200B ALA* 3.7 2.1 + - - +
201B PHE* 3.1 24.6 + - - +
226B LEU* 3.8 30.5 - - + +
229B ASN* 5.8 0.7 - - + -
230B LEU* 3.7 22.6 - - + +
233B TRP* 4.2 7.6 - - + -
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Residues in contact with LYS 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B CYS 2.8 22.5 + - - +
195B HIS* 4.0 4.5 - - + +
197B ALA* 1.4 71.8 - - - +
199B THR* 1.4 55.9 + - - +
201B PHE* 3.3 4.0 + - + +
202B ASP* 2.8 72.3 + - - +
230B LEU* 3.5 21.9 - - + +
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Residues in contact with THR 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B HIS* 2.6 47.2 + - + -
196B LEU* 4.0 6.1 - - - -
198B LYS* 1.4 74.9 - - - +
200B ALA* 1.3 53.7 + - - +
202B ASP* 3.7 5.1 - - - -
203B ASP* 2.8 59.4 + - - +
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Residues in contact with ALA 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B PRO* 4.4 2.6 - - - +
172B ARG* 6.3 0.9 - - - +
173B LEU* 3.9 11.7 - - + +
176B ALA* 3.5 27.6 - - + -
196B LEU* 3.1 20.2 + - + +
197B ALA 3.8 4.3 - - - +
199B THR* 1.3 76.7 - - - +
201B PHE* 1.4 60.7 + - - +
203B ASP* 4.1 4.8 - - - +
204B ALA* 3.2 24.6 + - - +
226B LEU* 4.4 9.4 - - + -
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Residues in contact with PHE 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173B LEU* 5.3 0.4 - - - -
197B ALA 3.1 18.1 + - - +
198B LYS* 3.7 7.0 - - + +
200B ALA* 1.4 74.8 - - - +
202B ASP* 1.4 70.9 + - - +
204B ALA* 3.4 5.4 + - - +
205B ILE* 2.9 57.4 + - + +
223B MET* 3.3 51.1 - - + -
224B GLN* 5.5 0.4 - - - -
226B LEU* 4.4 12.5 - - + +
227B ARG* 3.4 51.6 - - + -
230B LEU* 5.1 4.7 - - + -
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Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B LYS* 2.8 62.2 + - - +
199B THR* 3.9 5.0 - - - +
201B PHE* 1.4 80.5 - - - +
203B ASP* 1.4 63.4 + - - +
205B ILE* 3.4 8.8 + - - +
206B ALA* 2.9 29.6 + - - +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 3.6 19.3 - - + +
172B ARG* 4.1 14.9 + - - +
199B THR* 2.8 45.4 + - - +
200B ALA* 4.1 4.9 - - - +
202B ASP* 1.4 74.8 - - - +
204B ALA* 1.4 60.5 + - - +
206B ALA* 3.4 7.1 - - - +
207B GLU* 3.3 29.3 + - - +
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Residues in contact with ALA 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B PRO* 3.6 18.8 - - - +
168B THR* 3.4 20.6 - - + +
173B LEU* 3.9 10.8 - - + -
200B ALA 3.2 18.8 + - - +
201B PHE 3.7 4.5 - - - +
202B ASP 3.4 0.2 - - - -
203B ASP* 1.4 72.6 - - - +
205B ILE* 1.3 65.0 + - - +
207B GLU 3.4 3.3 - - - -
208B LEU* 3.1 23.2 + - - +
223B MET* 3.8 18.8 - - + -
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Residues in contact with ILE 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B PHE* 2.9 48.2 + - + +
202B ASP* 3.7 8.3 - - - +
203B ASP 3.4 0.2 - - - -
204B ALA* 1.3 75.2 - - - +
206B ALA* 1.3 62.5 + - - +
207B GLU 3.3 1.0 + - - -
208B LEU* 3.4 37.1 + - + +
223B MET* 3.6 19.7 - - + -
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Residues in contact with ALA 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B ASP 2.9 18.0 + - - +
203B ASP* 3.4 11.4 - - - +
204B ALA 3.3 0.2 - - - -
205B ILE* 1.3 78.1 - - - +
207B GLU* 1.3 62.3 + - + +
208B LEU 3.7 0.4 + - - -
209B ASP* 4.1 6.2 - - - +
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Residues in contact with GLU 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B GLN* 3.5 15.8 - - - +
167B PRO* 3.4 23.1 - - + +
168B THR* 3.3 3.1 - - - +
203B ASP 3.3 18.9 + - - +
204B ALA 3.4 4.5 - - - +
205B ILE 3.2 0.4 - - - -
206B ALA* 1.3 84.2 - - + +
208B LEU* 1.4 56.6 + - - +
209B ASP* 3.0 11.9 - - - +
210B THR* 2.6 49.7 + - + +
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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
------------------------------------------------------------
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