Contacts of the helix formed by residues 206 - 229 (chain B) in PDB entry 3AP3
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 SER 206 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE* 4.2 5.7 - - - +
203B ASP* 3.2 19.0 + - - +
204B LEU 3.9 0.8 - - - -
205B SER* 1.3 79.5 - - - +
207B TYR* 1.3 58.4 + - - +
208B ARG* 3.3 14.6 + - - +
209B ASP* 3.0 22.1 + - - +
210B CYS* 3.1 32.6 + - - -
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Residues in contact with TYR 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.6 19.7 - - + -
190B HIS* 3.4 33.4 + - + -
193B ILE* 3.4 45.2 - - + +
194B THR* 4.2 3.1 - - - +
206B SER* 1.3 69.0 + - - +
208B ARG* 1.3 65.9 + - - +
210B CYS* 3.2 0.9 + - - +
211B LEU* 3.0 37.8 + - + +
304B HIS* 4.4 15.3 + - - +
305B ILE* 4.2 25.4 - - + -
306B PRO* 4.0 30.1 - - + -
309B VAL* 4.4 8.5 - - + -
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Residues in contact with ARG 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B SER* 3.4 8.7 - - - +
207B TYR* 1.3 78.6 - - - +
209B ASP* 1.3 56.4 + - - +
212B THR* 2.7 38.2 + - - +
308B ASP* 3.3 29.7 + - - -
309B VAL* 3.8 19.3 - - + +
311B ARG* 4.4 1.6 - - - +
312B ASP* 2.6 36.3 + - - +
316B ILE* 3.6 31.7 - - + +
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 4.2 1.0 - - - -
203B ASP* 3.1 55.7 + - - +
206B SER* 3.0 13.3 + - - +
208B ARG* 1.3 74.7 - - - +
210B CYS* 1.3 67.4 + - - +
212B THR* 3.6 5.5 + - - -
213B LYS* 3.1 36.9 + - - +
213C LYS* 5.4 0.3 + - - -
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Residues in contact with CYS 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B VAL* 3.4 27.8 - - + +
192B MET* 4.5 14.8 - - - -
193B ILE* 3.5 22.2 - - - -
202B PHE* 4.2 10.4 - - - -
203B ASP 3.2 29.8 - - - -
206B SER 3.1 19.2 + - - +
207B TYR 3.2 0.9 + - - +
209B ASP* 1.3 77.6 + - - +
211B LEU* 1.3 53.1 + - - +
213B LYS* 3.5 4.8 - - - +
214B TRP* 2.8 32.7 + - - +
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B GLY* 3.8 32.8 - - - +
186B ARG* 4.1 14.1 - - + +
189B VAL* 3.7 18.8 - - + -
207B TYR* 3.0 27.3 + - + +
210B CYS* 1.3 71.5 - - - +
212B THR* 1.3 57.1 + - - +
213B LYS 2.8 1.9 + - - -
214B TRP* 2.9 10.7 + - + +
215B ASN* 2.6 36.8 + - - +
305B ILE* 5.3 2.5 - - + -
309B VAL* 3.7 25.6 - - + -
313B MET* 4.6 16.6 - - + -
316B ILE* 3.6 14.8 - - + -
317B ALA* 5.1 6.5 - - + -
320B LEU* 5.3 1.3 - - + -
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Residues in contact with THR 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B ARG* 2.7 26.5 + - - +
209B ASP* 3.9 6.2 - - - -
211B LEU* 1.3 77.0 - - - +
213B LYS* 1.3 57.7 - - + +
215B ASN* 3.0 6.2 - - + +
216B LYS* 2.9 28.3 + - + +
316B ILE* 3.3 28.6 + - - +
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Residues in contact with LYS 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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201B GLY* 3.2 39.5 + - - +
202B PHE* 4.1 21.3 - - + -
209B ASP* 3.1 31.8 + - - +
210B CYS* 3.5 5.4 - - - +
211B LEU 2.8 1.0 + - - -
212B THR* 1.3 75.5 - - + +
214B TRP* 1.3 66.4 + - - +
215B ASN 3.0 1.3 - - - -
216B LYS* 3.2 10.3 + - - +
217B ALA* 2.9 26.5 + - - +
209C ASP* 5.1 3.2 + - - -
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Residues in contact with TRP 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 3.8 27.4 - - + +
79B SER* 5.1 1.2 + - - -
182B VAL* 5.9 0.2 - - + -
183B ARG 3.7 13.2 + - - -
184B ASP* 4.9 0.4 - - - -
185B GLY* 3.2 36.1 - - - -
188B SER* 4.4 11.7 + - - -
189B VAL* 4.0 12.1 - - + -
192B MET* 5.3 0.7 - - + -
202B PHE* 3.8 12.6 - - + -
210B CYS 2.8 18.5 + - - +
211B LEU* 3.2 14.4 - - + +
213B LYS* 1.3 71.1 - - - +
215B ASN* 1.3 78.5 + - + +
217B ALA* 3.3 4.0 + - - +
218B ILE* 2.8 58.0 + - + +
317B ALA* 3.7 26.0 - - + -
319B MET* 4.1 7.6 - - + -
320B LEU* 3.4 25.8 - - + -
323B LEU* 4.0 16.8 - - + -
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Residues in contact with ASN 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 LEU 2.6 15.3 + - - +
212B THR* 3.0 15.3 - - - +
214B TRP* 1.3 82.4 - - + +
216B LYS* 1.3 72.9 + - - +
218B ILE* 3.8 2.0 - - - +
219B GLU* 2.9 34.3 + - - +
316B ILE 3.6 15.8 - - - +
317B ALA* 3.3 22.6 - - - +
318B PRO* 3.5 12.4 - - - +
319B MET* 3.3 27.8 - - - +
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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 THR* 2.9 18.1 + - + +
213B LYS* 3.2 12.1 + - - +
215B ASN* 1.3 79.1 + - - +
217B ALA* 1.3 62.0 + - - +
219B GLU* 3.3 35.7 + - - +
220B VAL* 3.2 44.5 + - + +
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Residues in contact with ALA 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B VAL* 4.0 15.0 - - + -
161B PHE* 4.7 13.2 - - + -
164B LYS* 5.2 10.0 - - - +
202B PHE* 4.4 15.3 - - + -
213B LYS* 2.9 17.5 + - + +
214B TRP 3.5 3.6 - - - +
216B LYS* 1.3 77.3 - - - +
218B ILE* 1.3 61.2 + - - +
220B VAL* 3.4 8.1 + - - +
221B MET* 3.3 28.2 + - + +
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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
----------------------------------------------------------
76B VAL* 3.9 21.0 - - + +
180B LEU* 4.7 15.9 - - + -
181B MET 5.1 4.5 - - - +
182B VAL* 4.2 26.2 - - + -
183B ARG 6.3 0.4 - - - +
214B TRP* 2.8 51.7 + - + +
215B ASN 3.8 7.6 - - - +
217B ALA* 1.3 71.9 - - - +
219B GLU* 1.3 65.6 + - - +
221B MET* 4.1 5.8 - - - +
222B TYR* 3.3 23.7 + - + +
319B MET* 4.1 14.3 - - + +
323B LEU* 4.2 18.2 - - + -
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Residues in contact with GLU 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 ASN* 2.9 25.5 + - - +
216B LYS* 3.3 40.6 + - - +
217B ALA 3.3 0.2 - - - -
218B ILE* 1.3 78.2 - - - +
220B VAL* 1.3 60.9 + - - +
222B TYR* 4.2 1.9 - - - +
223B ALA* 3.5 20.8 + - - +
319B MET* 3.9 30.6 - - + +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B LYS* 4.4 31.2 - - - +
216B LYS* 3.2 34.6 + - + +
217B ALA* 3.8 7.6 - - - +
218B ILE 3.2 0.6 - - - -
219B GLU* 1.3 77.4 - - - +
221B MET* 1.3 60.5 + - - +
222B TYR 3.1 2.4 + - - -
223B ALA* 3.2 6.4 + - - +
224B GLN* 2.9 44.0 + - + +
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Residues in contact with MET 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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75B GLY* 3.7 37.7 - - - +
76B VAL* 3.9 13.7 - - + +
160B PRO 4.0 11.4 - - - +
161B PHE* 3.9 20.0 - - + -
163B LEU* 3.9 25.2 - - + +
164B LYS* 3.9 27.8 - - + +
166B SER* 4.9 0.5 + - - -
180B LEU* 3.5 22.3 - - + +
217B ALA 3.3 18.3 + - - +
218B ILE* 4.2 7.0 - - - +
219B GLU 3.7 0.2 - - - -
220B VAL* 1.3 75.5 - - - +
222B TYR* 1.3 57.4 + - - +
224B GLN* 3.4 4.5 - - - +
225B CYS* 2.8 27.9 + - - +
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Residues in contact with TYR 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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180B LEU* 3.7 22.2 - - + +
182B VAL* 5.1 0.4 - - + -
218B ILE* 3.3 18.7 + - + +
219B GLU 4.2 3.4 - - - +
220B VAL 3.1 0.6 - - - -
221B MET* 1.3 77.1 - - - +
223B ALA* 1.3 55.7 + - - +
225B CYS* 3.0 2.9 + - - +
226B MET* 2.6 66.0 + - + +
235B PRO* 4.0 25.9 - - + +
237B TYR* 4.8 6.4 + - - -
319B MET* 4.6 15.0 - - + -
322B GLN* 5.2 9.1 + - + -
323B LEU* 4.0 29.5 - - + +
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Residues in contact with ALA 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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219B GLU 3.5 12.9 + - - +
220B VAL* 3.2 9.1 + - - +
222B TYR* 1.3 78.1 - - - +
224B GLN* 1.3 53.4 + - + +
226B MET* 3.2 7.8 + - - +
227B GLU* 2.8 39.2 + - - +
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Residues in contact with GLN 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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163B LEU 4.2 1.1 - - - +
164B LYS 3.2 23.4 + - - +
165B SER* 3.3 2.4 - - - -
166B SER* 3.2 20.9 + - - +
167B VAL* 3.1 47.7 + - - +
220B VAL* 2.9 25.0 + - + +
221B MET* 3.4 11.7 - - - +
223B ALA* 1.3 72.8 - - + +
225B CYS* 1.3 60.4 + - - +
226B MET 2.9 0.7 + - - -
227B GLU* 3.1 6.1 + - - +
228B VAL* 2.8 35.5 + - - +
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Residues in contact with CYS 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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163B LEU* 5.9 0.4 - - + -
166B SER* 4.2 2.8 + - - +
180B LEU* 3.9 14.4 - - + -
221B MET 2.8 22.8 + - - +
222B TYR* 3.0 6.0 + - + +
224B GLN* 1.3 73.0 - - - +
226B MET* 1.3 74.9 + - + +
228B VAL* 4.0 3.1 - - - -
229B GLY* 3.4 16.5 + - - +
233B CYS* 2.0 64.5 - - - +
235B PRO* 4.1 14.1 - - - -
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Residues in contact with MET 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 TYR* 2.6 51.3 + - + +
223B ALA* 3.5 9.0 - - - +
224B GLN 3.0 0.2 - - - -
225B CYS* 1.3 93.3 - - + +
227B GLU* 1.3 65.8 + - - +
228B VAL 3.2 1.3 - - - -
229B GLY* 3.4 11.4 + - - -
230B LYS* 5.7 13.2 - - + +
233B CYS 5.2 2.5 - - - +
235B PRO* 4.4 17.0 - - + -
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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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167B VAL* 4.3 26.1 - - + +
171B ARG* 5.4 3.3 + - - -
223B ALA* 2.8 20.9 + - - +
224B GLN* 3.7 5.3 + - - +
226B MET* 1.3 71.8 - - - +
228B VAL* 1.3 67.9 + - - +
229B GLY* 3.3 1.0 + - - -
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Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B SER* 3.8 27.8 - - - +
167B VAL* 4.1 19.5 - - + +
170B SER* 5.1 4.0 - - - -
178B PHE* 4.8 6.1 - - + -
224B GLN 2.8 23.8 + - - +
225B CYS* 3.4 7.9 - - - +
227B GLU* 1.3 78.9 - - - +
229B GLY* 1.3 58.1 + - - +
232B LYS* 3.3 43.3 - - + +
233B CYS* 3.4 17.5 - - + -
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Residues in contact with GLY 229 (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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225B CYS 3.4 9.2 + - - -
226B MET* 3.4 10.2 + - - -
227B GLU 3.3 3.5 - - - -
228B VAL* 1.3 79.1 - - - +
230B LYS* 1.3 64.8 - - - -
231B GLU* 2.8 10.2 + - - -
232B LYS 2.8 13.5 + - - -
233B CYS 2.8 12.5 + - - +
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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