Contacts of the helix formed by residues 189 - 207 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E TYR* 2.8 19.8 + - + +
184E TYR* 4.3 0.4 + - - -
187E GLN* 4.3 11.7 - - + +
188E ASN* 1.3 71.0 - - - +
190E PRO* 1.4 65.6 - - - +
191E GLU 3.3 2.5 - - - -
192E GLN* 3.4 34.7 + - + +
193E ALA* 3.1 21.8 + - - +
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Residues in contact with PRO 190 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184E TYR* 3.6 35.6 - - + +
188E ASN* 3.4 18.6 - - - +
189E ALA* 1.4 83.2 - - - +
191E GLU* 1.4 58.5 + - + +
193E ALA* 3.5 0.7 - - + +
194E CYS* 2.9 39.5 + - - +
233E TRP 6.0 1.3 - - - +
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Residues in contact with GLU 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E ALA* 3.3 1.2 - - - -
190E PRO* 1.4 81.2 - - + +
192E GLN* 1.4 57.5 + - + +
194E CYS* 4.0 3.9 - - - +
195E HIS* 3.1 29.8 + - - +
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Residues in contact with GLN 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E TYR* 3.5 40.0 + - + -
187E GLN* 5.8 0.6 - - - +
189E ALA* 3.4 28.5 + - + +
190E PRO 3.4 0.2 - - - -
191E GLU* 1.4 75.7 - - + +
193E ALA* 1.4 60.2 + - - +
195E HIS* 3.6 5.2 + - - +
196E LEU* 3.1 30.5 + - - +
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Residues in contact with ALA 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180E SER* 3.3 35.5 - - - +
183E TYR* 3.7 8.0 - - - +
184E TYR* 3.6 20.4 - - + +
189E ALA 3.1 17.8 + - - +
190E PRO* 3.5 6.5 - - + +
192E GLN* 1.4 75.7 - - - +
194E CYS* 1.4 57.7 + - - +
196E LEU 3.5 0.2 + - - -
197E ALA* 3.1 25.5 + - - +
233E TRP* 3.8 9.9 - - + -
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Residues in contact with CYS 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E PRO* 2.9 23.5 + - - +
191E GLU* 4.0 4.3 - - - +
193E ALA* 1.4 71.9 - - - +
195E HIS* 1.4 56.5 + - - +
197E ALA 3.4 0.3 + - - -
198E LYS* 2.8 38.3 + - - +
230E LEU* 3.4 18.6 - - + +
233E TRP* 3.7 35.7 - - - -
234E THR* 4.2 17.3 - - + -
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Residues in contact with HIS 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E GLU 3.1 19.3 + - - +
192E GLN* 3.9 6.0 + - - +
194E CYS* 1.4 75.3 - - - +
196E LEU* 1.3 57.0 + - - +
198E LYS* 4.0 4.3 - - + +
199E THR* 2.6 57.0 + - + -
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Residues in contact with LEU 196 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158E HIS* 3.4 36.8 - - + +
176E ALA* 3.9 15.7 - - + +
179E TYR* 3.6 26.7 - - + -
180E SER* 3.5 26.7 - - - +
183E TYR* 3.7 17.0 - - + -
192E GLN 3.1 17.5 + - - +
193E ALA 3.9 3.1 - - - +
195E HIS* 1.3 79.7 + - - +
197E ALA* 1.3 57.1 + - - +
199E THR* 4.0 4.1 - - - -
200E ALA* 3.1 31.2 + - + +
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Residues in contact with ALA 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ALA 5.1 0.2 - - - -
180E SER* 4.1 12.1 - - - +
193E ALA 3.1 17.5 + - - +
196E LEU* 1.3 74.3 - - - +
198E LYS* 1.4 61.1 + - - +
200E ALA* 3.9 1.9 - - - +
201E PHE* 3.1 29.1 + - - +
226E LEU* 3.9 35.1 - - + +
229E ASN* 5.9 0.7 - - + -
230E LEU* 3.8 18.6 - - + -
233E TRP* 4.2 6.7 - - + -
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Residues in contact with LYS 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194E CYS 2.8 23.2 + - - +
195E HIS* 4.0 4.5 - - + +
197E ALA* 1.4 70.0 - - - +
199E THR* 1.4 55.2 + - - +
201E PHE* 3.2 4.1 + - + +
202E ASP* 2.8 60.8 + - - +
227E ARG* 5.6 3.1 - - - +
230E LEU* 3.9 24.4 - - + +
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Residues in contact with THR 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E HIS* 2.6 46.8 + - + -
196E LEU* 4.0 5.8 - - - -
198E LYS* 1.4 75.0 - - - +
200E ALA* 1.4 53.8 + - - +
202E ASP* 3.8 4.7 - - - -
203E ASP* 2.8 59.6 + - - +
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Residues in contact with ALA 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E PRO* 4.5 2.1 - - - +
172E ARG* 6.2 1.8 - - - +
173E LEU* 3.9 9.4 - - + +
176E ALA* 3.5 28.7 - - + -
196E LEU* 3.1 20.0 + - + +
197E ALA 3.9 4.5 - - - +
199E THR* 1.4 76.1 - - - +
201E PHE* 1.3 60.6 + - - +
203E ASP* 4.1 5.0 - - - +
204E ALA* 3.2 24.8 + - - +
226E LEU* 4.4 9.0 - - + -
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Residues in contact with PHE 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173E LEU* 5.3 0.2 - - - -
197E ALA 3.1 19.1 + - - +
198E LYS* 3.7 5.6 - - + +
200E ALA* 1.3 75.0 - - - +
202E ASP* 1.4 70.1 + - - +
204E ALA* 3.4 5.6 + - - +
205E ILE* 2.9 56.6 + - + +
223E MET* 3.3 50.6 - - + +
224E GLN* 5.5 0.2 - - - -
226E LEU* 4.4 13.0 - - + +
227E ARG* 3.4 53.2 - - + -
230E LEU* 5.7 3.1 - - + -
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Residues in contact with ASP 202 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198E LYS* 2.8 48.3 + - - +
199E THR* 3.9 5.0 - - - +
201E PHE* 1.4 80.1 - - - +
203E ASP* 1.4 62.6 + - - +
205E ILE* 3.4 8.8 + - - +
206E ALA* 2.9 29.6 + - - +
227E ARG* 5.4 2.6 + - - -
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Residues in contact with ASP 203 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E PRO* 3.6 22.2 - - + +
172E ARG* 4.0 14.8 + - - +
199E THR* 2.8 46.1 + - - +
200E ALA* 4.1 4.5 + - - +
202E ASP* 1.4 74.8 - - - +
204E ALA* 1.4 62.1 + - - +
206E ALA* 3.5 6.0 + - - +
207E GLU* 3.3 29.9 + - - +
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Residues in contact with ALA 204 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E PRO* 3.5 19.9 - - - +
168E THR* 3.4 23.9 - - + +
173E LEU* 3.8 11.0 - - + -
200E ALA 3.2 18.9 + - - +
201E PHE 3.7 4.0 - - - +
203E ASP* 1.4 73.0 - - - +
205E ILE* 1.4 63.3 + - - +
208E LEU* 3.2 23.2 + - - +
223E MET* 3.8 17.9 - - + -
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Residues in contact with ILE 205 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201E PHE* 2.9 49.3 + - + +
202E ASP* 3.7 9.2 - - - +
203E ASP 3.4 0.2 - - - -
204E ALA* 1.4 73.8 - - - +
206E ALA* 1.3 64.7 + - - +
207E GLU 3.3 0.9 + - - -
208E LEU* 3.3 38.2 + - + +
223E MET* 3.6 18.8 - - + -
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Residues in contact with ALA 206 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E ASP 2.9 17.3 + - - +
203E ASP* 3.6 9.4 - - - +
205E ILE* 1.3 79.1 - - - +
207E GLU* 1.3 66.7 + - + +
208E LEU 3.7 0.6 + - - -
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Residues in contact with GLU 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLN* 5.5 1.7 + - - +
167E PRO* 3.4 34.0 - - + +
168E THR* 3.3 4.1 - - + +
203E ASP* 3.3 16.4 + - - +
204E ALA 3.4 5.6 - - - -
205E ILE 3.2 0.6 - - - -
206E ALA* 1.3 86.3 - - + +
208E LEU* 1.4 56.7 + - - +
209E ASP* 3.0 5.6 - - - +
210E THR* 2.6 54.1 + - + +
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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