Contacts of the helix formed by residues 189 - 207 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183C TYR* 2.8 19.8 + - + +
184C TYR* 4.3 0.6 + - - -
187C GLN* 4.3 12.8 - - + +
188C ASN* 1.3 72.1 - - - +
190C PRO* 1.4 65.3 - - - +
191C GLU* 3.3 3.1 - - - -
192C GLN* 3.5 31.6 + - + +
193C ALA* 3.0 21.8 + - - +
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Residues in contact with PRO 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C TYR* 3.6 35.8 - - + +
188C ASN* 3.4 18.4 - - - +
189C ALA* 1.4 84.9 - - - +
191C GLU* 1.4 58.3 + - + +
193C ALA* 3.5 0.8 - - + +
194C CYS* 2.9 39.6 + - - +
233C TRP 6.0 0.4 - - - +
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C ALA* 3.3 0.8 - - - -
190C PRO* 1.4 81.2 - - + +
192C GLN* 1.4 58.8 + - + +
194C CYS* 3.6 3.7 + - - +
195C HIS* 3.1 30.5 + - - +
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Residues in contact with GLN 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C TYR* 3.5 43.0 + - + -
187C GLN* 5.9 0.2 - - - +
189C ALA* 3.5 27.4 + - + +
190C PRO 3.4 0.4 - - - -
191C GLU* 1.4 74.7 - - + +
193C ALA* 1.4 60.1 + - - +
195C HIS* 3.9 5.3 - - - +
196C LEU* 3.1 31.2 + - - +
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Residues in contact with ALA 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180C SER* 3.3 35.6 - - - +
183C TYR* 3.7 8.0 - - - +
184C TYR* 3.6 20.6 - - + +
189C ALA 3.0 18.0 + - - +
190C PRO* 3.5 5.8 - - + +
192C GLN* 1.4 77.4 - - - +
194C CYS* 1.3 57.7 + - - +
197C ALA* 3.1 24.9 + - - +
233C TRP* 3.8 10.1 - - + -
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Residues in contact with CYS 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C PRO* 2.9 23.9 + - - +
191C GLU* 4.1 4.3 - - - +
193C ALA* 1.3 72.7 - - - +
195C HIS* 1.4 56.5 + - - +
197C ALA* 3.4 1.5 + - - +
198C LYS* 2.8 38.1 + - - +
230C LEU* 4.0 15.2 - - + +
233C TRP* 3.7 37.7 - - - -
234C THR* 4.2 19.7 - - + -
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Residues in contact with HIS 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C GLU 3.1 19.2 + - - +
192C GLN* 3.9 7.1 + - - +
194C CYS* 1.4 76.3 - - - +
196C LEU* 1.3 56.6 + - - +
198C LYS* 4.0 3.9 - - + +
199C THR* 2.6 57.8 + - + -
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Residues in contact with LEU 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C HIS* 3.4 35.9 - - + +
176C ALA* 3.9 15.9 - - + +
179C TYR* 3.6 26.2 - - + -
180C SER* 3.5 27.4 - - - +
183C TYR* 3.7 16.8 - - + -
192C GLN 3.1 17.3 + - - +
193C ALA 3.9 4.0 - - - +
195C HIS* 1.3 80.2 + - - +
197C ALA* 1.3 55.9 + - - +
199C THR* 4.0 3.6 - - - -
200C ALA* 3.1 30.7 + - + +
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Residues in contact with ALA 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176C ALA 5.1 0.2 - - - -
180C SER* 4.1 11.2 - - - +
193C ALA 3.1 18.6 + - - +
194C CYS 3.9 1.8 - - - +
196C LEU* 1.3 75.5 - - - +
198C LYS* 1.4 58.7 + - - +
200C ALA* 3.7 2.1 + - - +
201C PHE* 3.1 28.9 + - - +
226C LEU* 3.8 29.2 - - + +
229C ASN* 5.8 0.4 - - + -
230C LEU* 3.7 22.1 - - + +
233C TRP* 4.2 7.6 - - + -
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Residues in contact with LYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C CYS 2.8 21.9 + - - +
195C HIS* 4.0 5.2 - - + +
197C ALA* 1.4 70.6 - - - +
199C THR* 1.4 54.2 + - - +
201C PHE* 3.3 3.7 + - - +
202C ASP* 2.8 49.8 + - - +
230C LEU* 3.5 19.6 - - + +
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Residues in contact with THR 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C HIS* 2.6 47.5 + - + +
196C LEU* 4.0 5.6 - - - -
198C LYS* 1.4 73.4 - - - +
200C ALA* 1.4 54.6 + - - +
202C ASP* 3.7 5.1 - - - -
203C ASP* 2.8 59.9 + - - +
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Residues in contact with ALA 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C PRO* 4.5 2.1 - - - +
172C ARG* 6.3 1.1 - - - +
173C LEU* 3.9 11.0 - - + +
176C ALA* 3.5 27.4 - - + -
196C LEU* 3.1 21.0 + - + +
197C ALA 3.9 4.0 - - - +
199C THR* 1.4 73.6 - - - +
201C PHE* 1.3 61.1 + - - +
203C ASP* 4.1 5.7 - - - +
204C ALA* 3.2 24.9 + - - +
226C LEU* 4.4 9.6 - - + -
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Residues in contact with PHE 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173C LEU* 5.3 0.4 - - - -
197C ALA 3.1 19.9 + - - +
198C LYS* 3.7 4.9 - - - +
200C ALA* 1.3 73.9 - - - +
202C ASP* 1.4 71.4 + - - +
204C ALA* 3.4 5.4 + - - +
205C ILE* 2.9 54.9 + - + +
223C MET* 3.3 50.8 - - + +
226C LEU* 4.4 13.0 - - + +
227C ARG* 4.1 18.4 - - + -
230C LEU* 5.1 4.9 - - + -
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Residues in contact with ASP 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198C LYS* 2.8 34.1 + - - +
199C THR* 3.9 5.1 + - - +
201C PHE* 1.4 81.1 - - - +
203C ASP* 1.4 63.1 + - - +
205C ILE* 3.2 15.1 - - + +
206C ALA* 3.0 29.5 + - - +
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Residues in contact with ASP 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167C PRO* 3.6 21.8 - - + +
172C ARG* 4.1 14.8 + - - +
199C THR* 2.8 45.2 + - - +
200C ALA* 4.1 5.1 + - - +
202C ASP* 1.4 74.2 - - - +
204C ALA* 1.4 60.8 + - - +
206C ALA* 3.5 6.1 + - - +
207C GLU* 3.4 29.6 + - - +
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Residues in contact with ALA 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C PRO* 3.5 20.3 - - - +
168C THR* 3.4 23.4 - - + +
173C LEU* 3.8 13.0 - - + -
200C ALA 3.2 18.5 + - - +
201C PHE 3.8 3.8 - - - +
203C ASP* 1.4 73.4 - - - +
205C ILE* 1.4 63.1 + - - +
208C LEU* 3.2 20.4 + - - +
223C MET* 3.9 19.9 - - + +
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Residues in contact with ILE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C PHE* 2.9 35.6 + - + +
202C ASP* 3.2 23.8 - - + +
203C ASP 3.4 0.4 - - - -
204C ALA* 1.4 74.2 - - - +
206C ALA* 1.4 67.1 - - + +
207C GLU 3.3 0.9 + - - -
208C LEU* 3.4 19.2 + - + +
223C MET* 3.6 23.1 - - + +
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Residues in contact with ALA 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202C ASP 3.0 17.7 + - - +
203C ASP* 3.6 9.9 - - - +
205C ILE* 1.4 79.5 - - + +
207C GLU* 1.3 66.8 + - + +
208C LEU 3.7 1.0 + - - -
209C ASP* 4.6 6.2 - - - +
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Residues in contact with GLU 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166C GLN* 5.2 4.7 - - - +
167C PRO* 3.4 36.7 - - + +
168C THR* 3.3 11.9 - - + +
203C ASP* 3.4 16.4 + - - +
204C ALA 3.4 5.4 + - - +
205C ILE 3.2 0.2 - - - -
206C ALA* 1.3 86.5 - - + +
208C LEU* 1.4 57.4 + - - +
209C ASP* 3.0 15.9 - - - +
210C THR* 2.9 25.3 + - - -
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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