Contacts of the helix formed by residues 206 - 229 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203D ASP* 2.9 34.4 + - - +
204D LEU 3.2 2.9 - - - -
205D SER* 1.3 79.1 - - - +
207D TYR* 1.3 63.5 + - - +
208D ARG* 3.2 14.0 + - - +
209D ASP* 2.9 24.5 + - - +
210D CYS* 3.2 12.7 + - - -
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Residues in contact with TYR 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D VAL* 3.8 9.6 - - + -
190D HIS* 3.5 35.9 + - + -
193D ILE* 3.6 48.2 - - + +
194D THR* 4.0 7.3 - - - +
204D LEU 5.2 1.6 - - - -
205D SER 5.4 2.5 - - - -
206D SER* 1.3 70.0 - - - +
208D ARG* 1.3 68.1 + - - +
210D CYS* 3.1 2.9 + - - +
211D LEU* 2.8 38.5 + - + +
304D HIS* 4.2 20.3 + - - +
305D ILE* 4.2 24.9 - - + -
306D PRO* 3.8 28.7 - - + +
309D VAL* 4.4 5.4 - - + -
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Residues in contact with ARG 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D SER* 3.2 9.6 + - - +
207D TYR* 1.3 77.8 - - - +
209D ASP* 1.3 51.9 + - - +
211D LEU* 3.2 5.9 + - - +
212D THR* 2.6 46.1 + - - +
308D ASP* 3.6 30.3 + - - +
309D VAL* 4.2 14.8 - - + +
311D ARG* 5.0 0.4 - - - +
312D ASP* 2.5 34.7 + - - +
316D ILE* 3.5 32.1 - - + +
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Residues in contact with ASP 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201D GLY 5.4 0.6 - - - +
202D PHE* 3.8 4.5 - - - -
203D ASP* 2.8 40.1 + - + +
206D SER* 2.9 26.2 + - - +
208D ARG* 1.3 73.7 - - - +
210D CYS* 1.3 58.9 + - - +
211D LEU 3.0 0.5 + - - -
212D THR* 3.0 9.7 + - - -
213D LYS* 2.7 52.1 + - - +
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Residues in contact with CYS 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D VAL* 3.8 22.1 - - + +
192D MET* 4.6 4.9 - - - -
193D ILE* 3.9 18.2 - - - -
202D PHE* 3.7 18.9 - - + -
203D ASP 3.0 39.0 - - - -
204D LEU* 4.1 5.2 - - - -
206D SER 3.2 6.3 + - - +
207D TYR 3.1 7.0 + - - +
209D ASP* 1.3 82.6 + - - +
211D LEU* 1.3 53.1 + - - +
213D LYS* 3.2 6.0 - - - +
214D TRP* 2.6 35.5 + - - +
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Residues in contact with LEU 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLY* 4.4 13.2 - - - +
186D ARG* 4.4 12.6 - - + +
189D VAL* 3.9 26.9 - - + -
207D TYR* 2.8 32.1 + - + +
208D ARG 4.5 0.2 - - - +
210D CYS* 1.3 72.4 - - - +
212D THR* 1.3 67.3 + - - +
213D LYS 3.0 1.1 - - - -
214D TRP* 3.5 11.1 - - + +
215D ASN* 2.9 25.6 + - - +
305D ILE* 5.1 4.5 - - + -
309D VAL* 3.6 29.4 - - + -
313D MET* 4.9 9.4 - - + -
316D ILE* 3.5 19.8 - - + +
317D ALA* 4.8 14.5 - - + +
320D LEU* 5.8 0.4 - - + -
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Residues in contact with THR 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208D ARG* 2.6 27.4 + - - +
209D ASP* 3.2 10.8 - - - -
211D LEU* 1.3 76.5 - - - +
213D LYS* 1.3 63.7 + - + +
215D ASN* 3.4 4.3 - - - +
216D LYS* 3.3 22.0 + - - +
316D ILE* 3.8 20.3 + - - +
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Residues in contact with LYS 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299B SER* 6.1 3.2 - - - -
302B THR* 5.9 4.6 - - - +
331B PRO* 6.0 3.6 - - - +
201D GLY* 3.4 21.3 + - - +
202D PHE* 3.2 42.1 - - + -
209D ASP* 2.7 30.5 + - - +
210D CYS* 3.2 2.2 - - - +
212D THR* 1.3 79.4 - - + +
214D TRP* 1.3 66.5 + - - +
215D ASN 3.3 0.2 + - - -
216D LYS* 3.3 7.7 + - - +
217D ALA* 3.0 23.9 + - - +
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Residues in contact with TRP 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D VAL* 4.0 31.2 - - + +
79D SER* 5.1 1.6 + - - -
182D VAL* 6.0 0.2 - - + -
183D ARG 3.8 12.1 + - - -
184D ASP* 5.2 0.2 - - - -
185D GLY* 3.3 40.5 - - - -
188D SER* 4.3 10.2 + - - -
189D VAL* 4.0 12.8 - - + -
192D MET* 5.9 0.4 - - + -
202D PHE* 3.6 9.1 - - + -
210D CYS 2.6 20.5 + - - +
211D LEU* 3.5 9.6 - - + +
213D LYS* 1.3 70.4 - - - +
215D ASN* 1.3 79.4 + - + +
217D ALA* 3.2 7.1 + - - +
218D ILE* 2.8 56.2 + - + +
317D ALA* 4.0 23.8 - - + -
319D MET* 4.1 9.0 - - + -
320D LEU* 4.2 23.6 - - + -
323D LEU* 4.3 15.3 - - + -
325D TYR* 5.9 0.4 - + - -
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Residues in contact with ASN 215 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211D LEU 2.9 17.5 + - - +
212D THR* 3.4 7.3 - - - +
214D TRP* 1.3 88.2 - - + +
216D LYS* 1.3 57.9 + - - +
218D ILE* 3.1 5.4 - - - +
219D GLU* 2.7 47.5 + - - +
316D ILE 4.0 12.3 - - - +
317D ALA* 3.7 3.6 - - - +
318D PRO* 3.6 18.2 - - - +
319D MET* 3.2 42.8 - - - +
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Residues in contact with LYS 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B GLN* 6.1 3.1 - - - +
349B LEU* 5.7 8.3 - - - +
212D THR* 3.3 10.1 + - + +
213D LYS* 3.3 10.1 + - - +
215D ASN* 1.3 83.4 + - - +
217D ALA* 1.3 68.5 + - - +
219D GLU* 3.4 33.8 + - - +
220D VAL* 3.1 46.1 + - + +
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Residues in contact with ALA 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D VAL* 4.0 15.9 - - + -
161D PHE* 4.6 17.0 - - + -
164D LYS* 5.0 11.5 - - - +
202D PHE* 4.8 7.6 - - + -
213D LYS 3.0 13.1 + - - +
214D TRP* 3.3 10.8 - - - +
216D LYS* 1.3 78.8 - - - +
218D ILE* 1.3 63.6 + - - +
220D VAL* 3.1 13.7 + - - +
221D MET* 3.2 19.6 + - + +
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Residues in contact with ILE 218 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D VAL* 4.4 13.5 - - + +
180D LEU* 5.4 4.5 - - + -
181D MET 5.6 4.9 - - - +
182D VAL* 4.9 12.1 - - + -
214D TRP* 2.8 41.4 + - + +
215D ASN* 3.1 16.4 - - - +
217D ALA* 1.3 72.3 - - - +
219D GLU* 1.3 67.8 + - - +
221D MET* 3.1 11.7 + - + +
222D TYR* 2.9 33.5 + - + +
319D MET* 3.8 22.9 - - + -
323D LEU* 3.6 33.2 - - + -
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215D ASN* 2.7 29.7 + - - +
216D LYS* 3.5 40.4 + - - +
218D ILE* 1.3 73.0 - - - +
220D VAL* 1.3 65.3 + - - +
222D TYR* 3.6 2.8 + - - +
223D ALA* 3.2 19.3 + - + +
319D MET* 3.8 30.4 - - + +
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Residues in contact with VAL 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D LYS* 4.1 34.1 - - - +
216D LYS* 3.1 39.9 - - + +
217D ALA* 3.1 7.8 + - - +
219D GLU* 1.3 75.4 - - - +
221D MET* 1.3 61.0 + - - +
222D TYR 3.0 1.6 - - - -
223D ALA* 2.7 30.0 + - + +
224D GLN* 3.0 21.1 + - + +
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Residues in contact with MET 221 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLY* 3.4 28.9 - - - -
76D VAL* 3.7 28.5 - - + +
160D PRO 4.3 0.7 - - - +
161D PHE* 3.5 41.5 - - + -
163D LEU* 4.1 24.8 - - - +
164D LYS* 3.9 15.3 - - + -
166D SER* 4.8 0.3 + - - -
180D LEU* 3.7 20.7 - - + +
217D ALA* 3.2 11.6 + - + +
218D ILE* 3.1 11.7 + - + +
220D VAL* 1.3 80.0 - - - +
222D TYR* 1.3 57.0 + - - +
224D GLN* 3.3 5.2 - - - +
225D CYS* 3.0 27.2 + - - +
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Residues in contact with TYR 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D LEU* 4.1 17.2 - - + +
182D VAL* 5.5 1.1 - - + -
218D ILE* 2.9 19.0 + - + +
219D GLU 3.7 6.1 - - - +
221D MET* 1.3 74.5 - - - +
223D ALA* 1.3 67.3 + - - +
225D CYS* 2.9 3.5 + - - +
226D MET* 2.8 67.7 + - + +
235D PRO* 4.5 17.5 - - + +
237D TYR* 4.9 5.8 + - - -
319D MET* 4.4 15.9 - - + -
322D GLN 5.5 3.6 + - - -
323D LEU* 3.6 31.3 - - + +
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Residues in contact with ALA 223 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219D GLU* 3.2 9.9 + - + +
220D VAL* 2.7 17.4 + - + +
222D TYR* 1.3 76.3 - - - +
224D GLN* 1.3 51.8 + - + +
226D MET* 3.3 7.0 + - - +
227D GLU* 2.8 40.5 + - - +
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Residues in contact with GLN 224 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LEU 3.9 4.5 - - - +
164D LYS 3.0 21.6 + - - +
165D SER* 3.0 2.2 - - - +
166D SER* 2.7 45.1 + - - +
167D VAL* 2.8 35.7 + - - +
220D VAL* 3.0 18.5 + - + +
221D MET* 3.3 9.9 - - - +
223D ALA* 1.3 77.0 - - + +
225D CYS* 1.3 52.7 + - - +
227D GLU* 3.0 7.3 + - - +
228D VAL* 2.6 41.5 + - - +
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Residues in contact with CYS 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D LEU* 6.0 0.7 - - + -
166D SER* 4.9 2.2 - - - +
180D LEU* 3.6 18.8 - - + -
221D MET 3.0 10.7 + - - +
222D TYR* 2.9 8.0 + - + +
224D GLN* 1.3 79.9 - - - +
226D MET* 1.3 64.1 + - + +
228D VAL* 3.4 5.9 - - - +
229D GLY* 3.0 24.9 + - - +
233D CYS* 2.0 59.2 - - - +
234D LEU 4.2 1.3 - - - -
235D PRO* 4.2 17.3 - - - -
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Residues in contact with MET 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222D TYR* 2.8 59.5 + - + +
223D ALA* 3.6 6.7 - - - +
225D CYS* 1.3 92.6 - - - +
227D GLU* 1.3 65.0 + - - +
229D GLY* 3.4 12.1 + - - +
230D LYS* 5.7 12.6 - - + +
233D CYS 5.8 1.6 - - - +
235D PRO* 4.5 11.0 - - + -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167D VAL* 4.0 28.4 - - + +
171D ARG* 5.3 3.6 + - - -
223D ALA* 2.8 19.8 + - - +
224D GLN* 3.4 6.6 + - - +
226D MET* 1.3 76.7 - - - +
228D VAL* 1.3 65.6 + - - +
229D GLY* 3.4 0.7 + - - -
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Residues in contact with VAL 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D SER* 4.1 13.5 - - - +
167D VAL* 3.9 32.1 - - + +
170D SER* 4.6 6.7 - - - -
178D PHE* 4.7 5.8 - - + -
224D GLN 2.6 24.4 + - - +
225D CYS* 3.4 6.5 - - - +
227D GLU* 1.3 76.0 - - - +
229D GLY* 1.3 59.0 + - - +
231D GLU* 6.0 0.3 - - - +
232D LYS* 3.5 40.6 - - + +
233D CYS* 3.5 18.2 - - + -
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Residues in contact with GLY 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D CYS 3.0 13.9 + - - -
226D MET* 3.4 9.8 + - - -
227D GLU 3.3 2.7 - - - -
228D VAL* 1.3 77.4 - - - +
230D LYS* 1.3 55.3 + - - -
231D GLU* 2.9 9.5 + - - -
232D LYS 3.0 3.4 + - - -
233D CYS* 2.8 33.0 + - - +
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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