Contacts of the helix formed by residues 205 - 228 (chain B) in PDB entry 4EOZ
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 PHE 205 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B ARG* 5.4 2.0 - - + -
165B LEU* 3.8 28.7 - - + -
166B LEU* 3.9 19.5 - - + +
169B ILE* 3.8 22.4 - - + -
183B ILE* 5.5 0.7 - - + -
187B CYS* 4.2 4.9 - - - -
190B LEU* 3.9 17.9 - - + -
201B TYR* 2.9 47.3 + + + +
203B GLU 3.5 0.2 - - - -
204B ASP* 1.3 80.9 - - - +
206B GLU* 1.3 63.4 + - + +
207B ALA 3.5 1.8 - - - -
208B PRO* 3.4 5.2 - - - +
209B PHE* 3.0 44.9 + + + +
252B LEU* 3.5 32.8 - - + -
256B THR* 5.3 0.2 - - - -
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Residues in contact with GLU 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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198B ARG* 2.5 36.2 + - - -
201B TYR* 3.0 16.1 + - + +
202B GLU* 3.6 25.1 - - + +
205B PHE* 1.3 79.8 - - + +
207B ALA* 1.3 66.3 + - - +
209B PHE* 3.1 3.3 + - + +
210B LEU* 2.9 42.7 + - + +
255B SER 4.3 0.5 - - - +
256B THR* 3.0 43.2 + - + +
259B PRO* 4.5 8.0 - - - +
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Residues in contact with ALA 207 (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 GLU* 2.9 34.0 + - - +
203B GLU* 4.3 6.3 - - - +
206B GLU* 1.3 72.5 - - - +
208B PRO* 1.3 69.3 - - + +
210B LEU* 4.0 7.0 - - - +
211B GLU* 3.3 22.9 + - - +
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Residues in contact with PRO 208 (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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162B ARG* 4.0 20.4 - - + +
166B LEU* 3.9 16.2 - - + -
203B GLU 3.8 12.8 - - - +
204B ASP 3.9 13.7 - - - +
205B PHE 3.4 15.5 - - - +
207B ALA* 1.3 94.0 - - + +
209B PHE* 1.3 54.3 + - - +
211B GLU* 3.7 11.6 - - + +
212B MSE 2.7 38.1 + - - +
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Residues in contact with PHE 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.4 1.7 - - - +
169B ILE* 3.8 32.5 - - + -
173B ARG* 3.8 15.5 - - - -
205B PHE* 3.0 34.4 + + + +
206B GLU* 3.3 6.5 - - + +
208B PRO* 1.3 75.8 - - - +
210B LEU* 1.3 65.0 + - + +
212B MSE 3.4 20.6 - - + +
213B SER* 2.7 51.6 + - - -
244B GLU* 4.5 3.8 - - - -
247B ARG* 4.9 1.6 - - - -
248B VAL* 5.7 0.2 - - + -
252B LEU* 3.6 24.2 - - + -
256B THR* 4.0 20.0 - - + -
260B ILE* 3.8 25.4 - - + -
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Residues in contact with LEU 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B GLU* 6.1 0.7 - - - +
206B GLU* 2.9 34.1 + - + +
207B ALA* 4.0 6.7 - - - +
209B PHE* 1.3 91.7 - - + +
211B GLU* 1.3 57.8 + - - +
213B SER* 3.5 3.7 - - - -
214B ALA* 2.7 36.6 + - - +
256B THR* 4.9 0.7 - - + -
259B PRO* 4.1 21.5 - - + +
260B ILE* 3.8 34.1 - - + +
263B VAL* 4.2 18.9 - - + +
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Residues in contact with GLU 211 (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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207B ALA 3.3 16.4 + - - +
208B PRO* 3.2 11.6 + - - +
210B LEU* 1.3 80.2 - - - +
212B MSE 1.3 61.9 + - - +
214B ALA* 3.4 7.2 + - - +
215B GLU* 3.3 34.2 + - - +
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Residues in contact with MSE 212 (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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166B LEU* 3.1 53.4 - - + +
169B ILE* 4.9 3.8 - - + -
170B ALA* 4.9 9.6 - - + -
173B ARG* 3.6 22.2 - - - -
208B PRO 2.7 14.8 + - - +
209B PHE* 3.4 34.5 - - + +
211B GLU* 1.3 74.4 - - - +
213B SER* 1.3 62.5 + - - +
215B GLU* 3.3 12.0 + - - +
216B PHE* 3.2 20.9 + - + +
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Residues in contact with SER 213 (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 ARG* 2.9 34.1 + - - +
209B PHE* 2.7 31.9 + - - -
210B LEU 3.2 4.5 + - - -
212B MSE 1.3 75.1 - - - +
214B ALA* 1.3 65.9 + - - +
216B PHE* 3.2 3.3 + - - +
217B PHE* 3.0 35.6 + - - -
260B ILE* 3.8 22.5 - - - +
263B VAL* 4.8 0.7 - - - -
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Residues in contact with ALA 214 (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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210B LEU 2.7 20.1 + - - +
211B GLU* 3.7 7.6 - - - +
213B SER* 1.3 74.3 - - - +
215B GLU* 1.3 63.2 + - - +
217B PHE* 3.3 0.7 + - - -
218B GLN* 3.1 24.8 + - - +
263B VAL* 3.8 20.2 - - + +
266B ARG* 3.9 15.3 - - - +
267B GLU* 3.8 15.7 - - + +
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Residues in contact with GLU 215 (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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211B GLU* 3.3 26.8 + - - +
212B MSE 3.3 12.6 + - - +
213B SER 3.2 0.8 - - - -
214B ALA* 1.3 78.2 - - - +
216B PHE* 1.3 65.0 + - - +
218B GLN* 3.4 4.9 + - - +
219B MSE 3.2 30.3 + - + +
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Residues in contact with PHE 216 (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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170B ALA 5.9 0.2 - - - -
173B ARG* 3.5 48.2 - - + +
174B LYS* 5.4 9.6 - - + -
212B MSE 3.2 11.2 + - + +
213B SER* 3.2 9.5 + - - +
215B GLU* 1.3 80.6 - - - +
217B PHE* 1.3 74.9 + + - +
219B MSE 3.5 23.1 + - + +
220B GLU* 2.9 54.8 + - - +
240B ARG* 3.9 23.3 - - - -
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Residues in contact with PHE 217 (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 ARG* 3.9 12.6 - - - -
213B SER* 3.0 34.5 + - - +
214B ALA 3.3 0.4 + - - +
216B PHE* 1.3 94.4 - + - +
218B GLN* 1.3 62.1 + - - +
220B GLU* 3.1 7.0 + - + +
221B SER* 2.8 28.9 + - - -
240B ARG* 3.3 34.1 - - + -
244B GLU* 3.8 16.6 - - + -
260B ILE* 4.0 7.4 - - + -
263B VAL* 3.8 17.9 - - + -
264B VAL* 3.7 31.0 - - + -
267B GLU* 3.8 17.5 - - + -
268B LEU* 3.7 15.2 - - + +
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Residues in contact with GLN 218 (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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214B ALA 3.1 16.2 + - - +
215B GLU* 3.8 5.4 - - - +
217B PHE* 1.3 77.7 - - - +
219B MSE 1.3 60.5 + - + +
221B SER* 2.8 29.7 + - - -
222B GLN* 3.4 17.2 + - + +
267B GLU* 2.9 44.4 - - - +
271B LYS* 3.9 9.8 - - - +
272B HIS* 2.9 32.1 + - - -
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Residues in contact with MSE 219 (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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215B GLU* 3.2 13.9 + - - +
216B PHE* 3.6 29.2 - - + +
218B GLN* 1.3 75.8 - - + +
220B GLU* 1.3 64.0 + - - +
222B GLN* 3.0 20.7 + - - +
223B LYS* 3.3 25.8 + - - +
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Residues in contact with GLU 220 (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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216B PHE* 2.9 41.2 + - + +
217B PHE* 3.3 15.7 - - + +
219B MSE 1.3 75.3 - - - +
221B SER* 1.3 64.2 + - - +
223B LYS* 3.1 24.7 + - - +
224B PHE* 3.0 61.5 + - + -
240B ARG* 3.5 23.8 + - - +
268B LEU* 5.0 2.9 - - + -
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Residues in contact with SER 221 (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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217B PHE 2.8 8.8 + - - -
218B GLN* 2.8 20.2 + - - -
220B GLU* 1.3 76.5 - - - +
222B GLN* 1.3 59.8 + - - +
224B PHE* 3.9 1.8 - - - +
225B LEU* 3.1 33.1 + - - +
233B TYR* 3.8 6.2 - - - -
267B GLU 4.5 1.1 - - - -
268B LEU* 3.5 26.8 - - - +
272B HIS* 2.8 37.2 + - - -
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Residues in contact with GLN 222 (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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218B GLN* 3.5 25.0 - - + +
219B MSE 3.0 13.5 + - - +
221B SER* 1.3 95.0 + - - +
223B LYS* 1.3 66.6 + - + +
225B LEU* 3.5 14.7 + - - +
226B ALA* 3.5 14.6 + - - +
272B HIS* 3.6 12.7 - - - -
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Residues in contact with LYS 223 (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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216B PHE* 6.5 0.2 - - - -
219B MSE 3.3 21.9 + - - +
220B GLU* 3.1 27.7 + - - +
222B GLN* 1.3 74.4 - - + +
224B PHE* 1.3 62.0 + - + +
226B ALA* 2.6 36.3 + - - +
227B GLU* 3.4 6.6 + - - +
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Residues in contact with PHE 224 (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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220B GLU* 3.0 52.0 + - + +
221B SER 3.9 0.4 - - - +
223B LYS* 1.3 79.5 - - + +
225B LEU* 1.3 60.5 + - - +
226B ALA 3.2 1.0 + - - -
227B GLU* 3.2 26.2 - - + +
228B ASN 3.7 2.6 + - - -
229B SER 5.1 1.6 + - - +
233B TYR* 3.3 44.1 - + + +
236B LYS* 3.5 67.3 - - + -
237B VAL* 4.2 4.5 - - + -
240B ARG* 5.0 6.5 - - + -
268B LEU* 4.3 19.3 - - + -
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Residues in contact with LEU 225 (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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221B SER 3.1 17.6 + - - +
222B GLN* 3.8 16.8 - - - +
223B LYS 3.0 1.2 + - - -
224B PHE* 1.3 77.9 - - - +
226B ALA* 1.3 58.0 + - - +
227B GLU 3.5 0.2 - - - -
228B ASN* 3.9 16.5 + - - +
233B TYR* 3.8 12.3 - - + -
272B HIS* 4.4 22.4 - - + +
275B THR* 4.4 20.9 - - + -
276B ILE* 3.6 29.4 - - + -
279B MSE 4.6 17.6 - - + +
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Residues in contact with ALA 226 (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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222B GLN 3.5 7.7 + - - +
223B LYS* 2.6 23.2 + - - +
225B LEU* 1.3 71.4 - - - +
227B GLU* 1.3 59.8 + - - +
228B ASN* 2.9 16.8 + - - +
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Residues in contact with GLU 227 (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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223B LYS 3.4 3.5 + - - +
224B PHE* 3.2 21.1 - - - +
226B ALA* 1.3 76.6 - - - +
228B ASN* 1.3 66.1 + - - +
229B SER* 3.4 5.2 + - - +
232B VAL* 3.9 22.9 - - + +
236B LYS* 3.6 33.8 + - + +
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Residues in contact with ASN 228 (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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224B PHE 3.7 5.1 + - - -
225B LEU 3.9 7.3 + - - +
226B ALA 2.9 12.2 + - - +
227B GLU* 1.3 81.3 - - - +
229B SER* 1.3 59.3 + - - +
279B MSE 3.0 33.6 - - - +
282B SER* 4.9 4.2 - - - -
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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