Contacts of the helix formed by residues 204 - 227 (chain B) in PDB entry 1O2D
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 THR 204 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B HIS* 5.1 0.4 - - + +
2B TRP* 3.7 26.5 - - + -
3B GLU 4.1 13.8 + - - +
4B PHE* 5.5 0.2 - - - -
202B LYS 3.3 16.6 - - - +
203B SER* 1.3 73.2 - - - +
205B PRO* 1.3 69.0 - - - +
206B PRO* 3.4 9.5 - - - +
207B SER* 2.7 30.6 + - - +
208B ASP* 2.8 33.4 + - - -
249B GLN* 4.5 12.4 - - + +
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Residues in contact with PRO 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B HIS* 5.1 2.2 - - + -
2B TRP* 3.5 36.3 - - + +
204B THR* 1.3 87.8 - - - +
206B PRO* 1.3 70.9 - - + +
208B ASP* 3.3 7.9 + - + +
209B ALA* 3.1 22.7 + - - +
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Residues in contact with PRO 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B TRP* 3.7 30.1 - - + -
4B PHE* 3.7 31.6 - - + -
204B THR* 3.4 9.6 - - - +
205B PRO* 1.3 99.9 - - + +
207B SER* 1.3 61.5 + - - +
209B ALA* 3.3 8.3 + - + +
210B LEU* 3.2 28.8 + - + +
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Residues in contact with SER 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLY 4.9 0.8 + - - -
203B SER* 4.3 0.7 - - - -
204B THR* 2.7 37.3 + - - -
206B PRO* 1.3 78.4 - - - +
208B ASP* 1.3 58.0 + - - +
210B LEU* 3.3 5.2 + - - -
211B ALA* 2.8 32.1 + - - +
246B VAL* 3.4 18.5 - - - +
249B GLN* 4.0 23.5 - - - +
250B THR* 3.5 19.0 - - - +
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Residues in contact with ASP 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197B GLY 4.4 0.5 - - - +
198B TYR* 3.5 30.3 - - + +
203B SER* 4.4 2.9 - - - -
204B THR 2.8 29.3 + - - +
205B PRO* 3.6 6.9 - - + +
207B SER* 1.3 78.0 - - - +
209B ALA* 1.3 62.2 + - - +
211B ALA* 3.7 1.6 - - - +
212B ILE* 2.9 34.6 + - + +
292B LYS* 2.9 35.1 + - - -
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Residues in contact with ALA 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO 3.1 12.8 + - - +
206B PRO* 3.5 11.9 - - + +
207B SER 3.3 0.2 - - - -
208B ASP* 1.3 78.3 - - - +
210B LEU* 1.3 64.5 + - + +
212B ILE* 3.6 8.2 + - - +
213B GLU* 3.3 19.9 + - - +
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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
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4B PHE* 4.5 17.9 - - + -
206B PRO* 3.2 20.7 + - + +
207B SER* 4.5 3.8 - - - -
209B ALA* 1.3 80.0 - - + +
211B ALA* 1.3 57.9 + - - +
213B GLU* 3.4 5.2 + - - +
214B ALA* 3.0 28.6 + - - +
242B LEU* 3.8 35.2 - - + +
245B MSE 4.0 34.5 - - + -
246B VAL* 3.7 14.6 - - + -
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Residues in contact with ALA 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194B ALA* 3.5 28.9 - - - +
198B TYR* 4.0 15.5 - - + +
207B SER 2.8 19.1 + - - +
208B ASP* 3.7 5.2 - - - +
210B LEU* 1.3 75.4 - - - +
212B ILE* 1.3 59.1 + - - +
214B ALA* 3.2 2.0 + - - +
215B MSE 2.9 35.6 + - - +
246B VAL* 3.5 17.2 - - + +
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Residues in contact with ILE 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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198B TYR* 3.8 31.4 - - + +
208B ASP* 2.9 26.4 + - + +
209B ALA* 3.9 7.4 - - - +
211B ALA* 1.3 76.4 - - - +
213B GLU* 1.3 64.1 + - - +
215B MSE 3.3 13.1 + - + +
216B LYS* 3.0 49.4 + - + +
295B THR* 5.6 1.8 - - + -
299B ILE* 4.5 8.2 - - + +
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Residues in contact with GLU 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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209B ALA 3.3 11.7 + - - +
210B LEU* 3.8 8.5 - - - +
211B ALA 3.3 0.4 - - - -
212B ILE* 1.3 81.9 - - - +
214B ALA* 1.3 62.4 + - - +
216B LYS* 3.3 15.3 + - - +
217B ILE* 3.0 43.1 + - + +
242B LEU* 4.0 19.1 - - + -
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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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194B ALA* 3.9 16.4 - - + -
210B LEU 3.0 17.2 + - - +
211B ALA* 3.2 5.1 + - - +
213B GLU* 1.3 77.4 - - - +
215B MSE 1.3 57.6 + - - +
217B ILE* 3.3 2.0 + - - +
218B ILE* 2.9 38.7 + - + +
239B ALA* 3.8 29.8 - - + +
242B LEU* 4.1 11.4 - - + +
243B ALA* 4.4 4.3 - - + +
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Residues in contact with MSE 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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191B LEU* 6.1 0.2 - - - -
194B ALA* 3.9 15.0 - - + -
195B VAL* 3.8 25.4 - - + -
198B TYR* 3.7 35.0 - - + -
211B ALA* 2.9 27.2 + - + +
212B ILE* 3.7 17.7 - - + +
214B ALA* 1.3 76.1 - - - +
216B LYS* 1.3 63.1 + - - +
218B ILE* 4.6 3.1 - - - -
219B HIS* 3.0 26.0 + - - +
296B VAL* 3.9 17.0 - - + -
299B ILE* 3.8 27.5 - - + +
300B PHE* 3.8 26.1 - - + -
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Residues in contact with LYS 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212B ILE* 3.0 37.6 + - + +
213B GLU* 3.7 14.8 - - - +
215B MSE 1.3 75.2 - - - +
217B ILE* 1.3 65.2 + - + +
219B HIS* 3.5 4.3 + - - +
220B ARG* 3.2 23.2 + - - +
299B ILE* 4.0 28.3 - - + -
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Residues in contact with ILE 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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213B GLU* 3.0 44.8 + - + +
214B ALA 3.6 3.8 - - - +
216B LYS* 1.3 76.1 - - + +
218B ILE* 1.3 60.2 + - - +
220B ARG* 3.2 1.9 + - - -
221B ASN* 2.9 51.0 + - + +
235B LYS* 3.3 32.5 - - + +
236B MSE 4.5 1.3 - - - +
238B VAL* 4.2 16.2 - - + -
239B ALA* 3.7 10.3 - - + -
242B LEU* 4.1 15.7 - - + -
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Residues in contact with ILE 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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187B GLY 4.4 0.4 - - - +
190B ALA* 3.8 16.6 - - + +
191B LEU* 3.6 58.3 - - + +
194B ALA* 5.0 0.4 - - + -
214B ALA* 2.9 28.4 + - + +
215B MSE 3.9 6.1 - - - +
217B ILE* 1.3 74.3 - - - +
219B HIS* 1.3 66.5 + - - +
222B LEU* 2.9 42.2 + - + +
236B MSE 3.9 18.2 - - + -
239B ALA* 3.7 19.3 - - + +
300B PHE* 4.3 1.6 - - + -
307B PHE* 4.1 1.5 - - + -
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Residues in contact with HIS 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 MSE 3.0 16.6 + - - +
216B LYS* 3.9 4.6 + - - +
218B ILE* 1.3 80.4 - - - +
220B ARG* 1.3 66.5 + - - +
223B PRO* 3.9 6.8 - - - +
299B ILE* 3.3 23.1 + - + +
300B PHE* 3.6 26.3 + + + -
301B GLY* 3.7 18.7 + - - -
307B PHE* 3.6 36.7 - + - -
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Residues in contact with ARG 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 LYS 3.2 15.6 + - - +
217B ILE* 4.7 0.2 - - - -
218B ILE 3.2 0.6 - - - -
219B HIS* 1.3 84.9 - - - +
221B ASN* 1.3 75.5 + - - +
223B PRO* 4.6 3.4 - - - +
224B LYS* 4.8 14.0 + - - +
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Residues in contact with ASN 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 ILE* 2.9 34.3 + - + +
220B ARG* 1.3 97.0 - - - +
222B LEU* 1.3 67.2 + - - +
223B PRO* 3.4 2.7 - - - -
224B LYS* 3.3 4.6 + - - +
225B ALA* 2.9 23.0 + - - +
231B GLU* 5.6 0.5 - - - +
232B ALA* 3.5 29.7 - - + +
235B LYS* 3.5 37.2 - - + +
236B MSE 4.2 7.9 - - - -
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Residues in contact with LEU 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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183B THR* 3.9 25.4 - - + +
184B LEU* 4.7 0.4 - - - +
187B GLY* 4.1 7.0 - - - -
188B VAL* 4.1 16.2 - - + +
191B LEU* 4.9 1.6 - - + -
218B ILE* 2.9 33.4 + - + +
221B ASN* 1.3 76.2 - - - +
223B PRO* 1.3 69.0 - - + +
225B ALA* 3.1 1.5 + - - -
226B ILE* 3.0 37.9 + - + +
236B MSE 3.8 28.6 - - + -
307B PHE* 4.4 5.8 - - + -
311B LEU* 3.8 26.7 - - + -
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Residues in contact with PRO 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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218B ILE 4.3 0.2 - - - +
219B HIS 3.9 13.5 - - - +
220B ARG 4.6 2.2 - - - +
221B ASN* 3.6 4.0 - - - +
222B LEU* 1.3 94.7 - - + +
224B LYS* 1.3 62.1 + - + +
226B ILE* 3.3 12.5 + - + +
227B GLU* 3.2 27.5 + - - +
307B PHE* 4.2 18.2 - - + -
311B LEU* 4.3 12.3 - - + -
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Residues in contact with LYS 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 ARG 4.8 12.9 + - - +
221B ASN* 3.3 5.9 + - - +
222B LEU 3.2 0.6 - - - -
223B PRO* 1.3 79.2 - - + +
225B ALA* 1.3 64.6 + - - +
227B GLU* 3.2 22.0 + - - +
228B GLY 3.2 5.7 + - - -
229B ASN* 3.1 38.9 + - + +
232B ALA* 3.8 16.6 - - + -
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Residues in contact with ALA 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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183B THR* 3.8 10.5 - - + -
221B ASN 2.9 17.5 + - - +
222B LEU* 3.5 5.2 - - + +
224B LYS* 1.3 73.8 - - - +
226B ILE* 1.3 66.2 + - - +
228B GLY 3.0 5.9 + - - -
229B ASN 4.2 0.4 - - - -
232B ALA* 3.4 11.1 - - + +
233B ARG* 2.8 42.5 + - + -
236B MSE 3.7 23.8 - - + -
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Residues in contact with ILE 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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180B ASP* 3.2 48.9 - - + +
183B THR* 3.9 19.7 - - + -
184B LEU* 3.8 40.2 - - + +
222B LEU* 3.0 31.6 + - + +
223B PRO* 3.5 8.3 - - + +
225B ALA* 1.3 76.2 - - - +
227B GLU* 1.3 62.1 + - + +
228B GLY 3.4 0.7 + - - -
233B ARG* 3.7 3.3 + - - -
311B LEU* 4.0 15.3 - - + +
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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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180B ASP* 5.2 3.8 - - - -
223B PRO* 3.2 15.7 + - - +
224B LYS* 3.2 28.6 + - - +
225B ALA 3.2 0.4 - - - -
226B ILE* 1.3 77.3 - - + +
228B GLY* 1.3 57.0 + - - +
229B ASN* 3.6 2.3 - - + +
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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
------------------------------------------------------------
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