Contacts of the helix formed by residues 169 - 195 (chain D) in PDB entry 5E9W
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 ILE 169 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER 3.3 1.9 - - - +
168D ARG* 1.3 85.2 - - + +
170D PHE* 1.3 58.5 - - - +
171D TYR 3.3 2.5 - - - -
172D LEU* 3.1 18.3 + - + +
173D ARG* 2.8 67.1 + - + +
340D ILE* 3.4 47.1 - - + -
362D LEU* 3.5 23.6 - - + -
363D GLU* 4.9 17.9 - - + -
460D GLU* 5.5 0.4 - - + -
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Residues in contact with PHE 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER* 3.7 29.9 + - - +
168D ARG 3.4 1.0 - - - -
169D ILE* 1.3 79.3 - - - +
171D TYR* 1.3 89.1 + + + +
173D ARG* 3.4 10.4 + - + +
174D ASN* 3.0 50.9 + - - +
416D GLN* 3.3 40.8 - - + -
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Residues in contact with TYR 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER 5.2 3.8 - - - -
168D ARG 4.6 4.1 + - - -
169D ILE* 3.3 0.6 - - - +
170D PHE* 1.3 105.6 - + + +
172D LEU* 1.3 61.4 + - - +
174D ASN* 3.4 4.5 + - + +
175D PHE* 2.9 29.5 + - - +
416D GLN* 4.0 36.3 + - + -
455D THR 5.3 5.4 - - - +
456D LEU* 3.9 11.2 - - + +
460D GLU* 4.0 24.5 - - - +
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Residues in contact with LEU 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ILE* 3.1 41.1 + - + +
171D TYR* 1.3 76.6 - - - +
173D ARG* 1.3 65.2 + - - +
175D PHE* 3.3 4.9 + - + +
176D ASN* 3.1 32.8 + - - +
340D ILE* 4.2 2.9 - - + -
362D LEU* 4.0 21.1 - - + -
456D LEU* 4.6 8.2 - - + +
460D GLU* 3.9 22.0 + - + +
463D ALA* 4.1 19.3 - - + -
464D THR* 3.8 32.5 - - - +
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Residues in contact with ARG 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D SER 5.8 3.0 - - - +
169D ILE* 2.8 41.8 + - + +
170D PHE* 3.8 8.2 - - + +
172D LEU* 1.3 72.9 - - - +
174D ASN* 1.3 67.2 + - - +
176D ASN* 3.3 10.6 + - - +
177D ASN* 3.0 30.5 + - - +
363D GLU 4.8 10.3 + - - -
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Residues in contact with ASN 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D PHE* 3.0 51.1 + - + +
171D TYR* 3.7 8.7 - - - +
172D LEU 3.3 0.2 - - - -
173D ARG* 1.3 76.2 - - - +
175D PHE* 1.3 58.4 + - - +
177D ASN* 3.3 9.1 + - - +
178D TRP* 2.9 28.6 + - - +
412D LEU* 5.2 3.1 - - + +
415D MET* 2.7 50.7 + - - +
416D GLN* 4.7 7.9 - - - -
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Residues in contact with PHE 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D TYR 2.9 19.0 + - - +
172D LEU* 3.6 6.1 - - + +
173D ARG 3.2 0.2 - - - -
174D ASN* 1.3 73.9 - - - +
176D ASN* 1.3 61.5 + - - +
178D TRP* 3.2 17.7 + + - +
179D MET* 2.9 64.2 + - + +
395D PHE* 4.3 5.6 - + + -
399D TYR* 3.7 29.4 - + + -
412D LEU* 4.5 5.1 - - + +
455D THR* 4.1 16.8 - - + -
456D LEU* 3.8 20.9 - - + -
461D TRP* 3.8 23.6 - + - -
464D THR* 3.6 32.8 - - + -
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Residues in contact with ASN 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D LEU* 3.1 26.5 + - - +
173D ARG* 3.6 12.5 - - - +
175D PHE* 1.3 75.1 - - - +
177D ASN* 1.3 59.0 + - - +
179D MET* 3.3 7.9 + - - +
180D LYS* 2.9 36.2 + - - +
285D PHE* 3.9 32.5 - - + -
362D LEU* 5.8 5.1 - - - +
395D PHE* 3.9 8.5 - - - -
464D THR* 3.7 19.2 + - - -
467D TYR* 6.3 0.2 - - - -
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Residues in contact with ASN 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D ARG* 3.0 22.1 + - - +
174D ASN* 3.5 11.8 - - - +
175D PHE 3.2 0.2 - - - -
176D ASN* 1.3 77.7 - - - +
178D TRP* 1.3 52.1 + - - +
180D LYS* 3.5 15.9 + - - +
181D SER* 2.7 37.5 + - - -
210D GLY* 4.2 3.1 - - - +
214D LYS* 2.8 31.9 + - - +
415D MET* 3.8 13.5 - - + -
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Residues in contact with TRP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174D ASN 2.9 15.9 + - - +
175D PHE* 3.6 11.7 - + - +
177D ASN* 1.3 73.8 - - - +
179D MET* 1.3 104.7 + - + +
181D SER* 3.3 2.7 + - - -
182D VAL* 3.1 42.4 + - + +
398D PHE* 5.6 0.2 - + - -
399D TYR* 3.9 18.8 - + - -
402D LYS* 3.8 22.0 - - + -
403D ILE* 3.8 25.8 - - + -
408D ASN* 2.7 36.8 + - + -
411D LEU* 3.8 17.1 - - + +
412D LEU* 3.4 42.1 - - + +
415D MET* 3.7 12.7 - - - +
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Residues in contact with MET 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D PHE* 2.9 54.1 + - + +
176D ASN* 3.5 7.0 - - - +
178D TRP* 1.3 94.4 - - + +
180D LYS* 1.3 56.9 + - + +
182D VAL 3.5 0.2 + - - -
183D LEU* 3.0 30.1 + - - +
395D PHE* 3.5 61.5 - - + +
398D PHE* 3.4 37.3 - - + -
399D TYR* 4.5 2.2 - - - -
469D VAL* 4.1 3.1 - - + -
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Residues in contact with LYS 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ASN* 2.9 22.1 + - - +
177D ASN* 3.6 24.4 + - - +
178D TRP 3.3 0.2 - - - -
179D MET* 1.3 73.7 - - + +
181D SER* 1.3 59.5 + - - +
183D LEU* 3.7 6.2 - - - +
184D ILE* 2.8 40.1 + - + +
210D GLY* 4.9 2.4 + - - -
211D ASP* 3.0 21.5 + - - +
214D LYS* 4.0 9.9 - - + -
284D GLN* 3.6 43.3 - - + +
285D PHE* 3.9 17.0 - - + -
317D THR* 5.3 2.5 - - + -
501D SAH 2.9 28.2 + - - +
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Residues in contact with SER 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D ASN 2.7 25.0 + - - -
178D TRP* 3.5 8.9 - - - -
179D MET 3.3 0.2 - - - -
180D LYS* 1.3 76.7 - - - +
182D VAL* 1.3 53.1 + - - +
184D ILE* 4.0 2.1 - - - +
185D GLY* 2.8 31.5 + - - -
214D LYS* 3.2 25.3 - - - +
411D LEU* 4.2 19.7 - - - -
415D MET* 4.7 6.8 - - - +
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Residues in contact with VAL 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178D TRP* 3.1 46.1 + - + +
179D MET* 4.0 2.9 - - - +
181D SER* 1.3 73.7 - - - +
183D LEU* 1.3 60.8 + - - +
185D GLY* 3.8 1.1 - - - -
186D GLU* 2.9 29.7 + - + +
398D PHE* 4.3 3.8 - - + -
402D LYS* 3.4 42.2 - - + +
408D ASN* 3.9 23.8 - - - +
411D LEU* 4.7 6.7 - - + -
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Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D MET 3.0 19.0 + - - +
180D LYS* 3.7 5.2 - - - +
182D VAL* 1.3 79.0 - - - +
184D ILE* 1.3 62.2 + - - +
186D GLU* 3.4 1.8 + - - +
187D PHE* 3.2 57.5 + - + -
284D GLN* 3.9 31.0 - - - +
315D ILE* 4.3 10.5 - - + -
316D GLY 4.1 21.1 - - - +
317D THR* 4.6 7.0 - - + -
391D TYR* 3.7 16.6 - - + +
398D PHE* 4.0 17.2 - - + -
469D VAL* 4.6 8.7 - - + -
470D PHE 4.8 4.3 - - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180D LYS* 2.8 26.5 + - + +
181D SER* 4.0 2.9 - - - +
183D LEU* 1.3 70.1 - - - +
185D GLY* 1.3 66.8 + - - +
187D PHE* 3.3 2.1 + - - +
188D LEU* 2.9 33.6 + - + +
211D ASP* 4.2 12.6 - - - +
214D LYS* 4.0 31.0 - - + +
215D TRP* 3.5 53.8 - - + -
280D ILE* 5.3 0.2 - - - +
282D SER* 4.2 12.3 - - - +
284D GLN* 4.7 5.6 - - - +
315D ILE* 4.3 12.8 - - + -
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Residues in contact with GLY 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181D SER 2.8 23.2 + - - -
182D VAL* 3.8 2.5 - - - -
183D LEU 3.3 0.2 - - - -
184D ILE* 1.3 75.9 - - - +
186D GLU* 1.3 60.9 + - - +
188D LEU* 3.8 7.3 - - - +
189D GLU* 3.2 24.1 + - - +
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Residues in contact with GLU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D VAL* 2.9 17.2 + - + +
183D LEU 3.6 4.0 - - - +
184D ILE 3.2 0.2 - - - -
185D GLY* 1.3 76.5 - - - +
187D PHE* 1.3 64.5 + - + +
189D GLU* 3.4 6.5 + - - +
190D LYS* 3.0 55.6 + - + +
391D TYR* 2.9 38.4 + - - -
398D PHE* 4.4 2.1 - - - -
401D GLU* 5.1 1.2 - - - +
402D LYS* 3.2 29.5 + - - +
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Residues in contact with PHE 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D LEU* 3.2 33.0 - - + +
184D ILE 3.3 4.6 + - - +
186D GLU* 1.3 84.9 - - + +
188D LEU* 1.3 61.1 + - - +
189D GLU 3.2 1.3 - - - -
190D LYS* 3.7 23.4 - - + +
191D VAL* 2.9 33.6 + - - +
280D ILE* 3.9 13.5 - - + -
313D TYR* 3.6 38.6 - + + -
315D ILE* 3.8 20.0 - - + -
390D VAL* 4.4 6.7 - - + -
391D TYR* 3.3 32.8 - + - -
471D ALA* 3.2 27.6 - - + -
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D ILE* 2.9 37.0 + - + +
185D GLY* 3.8 7.2 - - - +
187D PHE* 1.3 78.0 - - - +
189D GLU* 1.3 57.0 + - - +
191D VAL* 3.6 3.1 + - + +
192D ARG* 3.1 47.1 + - - +
199D ILE* 4.1 11.9 - - + -
214D LYS 4.4 2.9 - - - +
215D TRP* 3.8 19.1 - - + -
218D GLY* 3.7 27.1 - - - -
220D ILE* 3.6 24.9 - - + -
280D ILE* 4.0 16.5 - - + +
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Residues in contact with GLU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLY 3.2 16.4 + - - +
186D GLU* 3.7 5.4 - - - +
187D PHE 3.2 0.2 - - - -
188D LEU* 1.3 76.4 - - - +
190D LYS* 1.3 59.6 + - - +
192D ARG* 3.4 12.5 + - + +
193D GLN* 2.6 67.0 + - - +
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Residues in contact with LYS 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B ASN* 4.5 7.5 - - - +
367B ASP* 3.8 35.0 + - + +
186D GLU* 3.0 50.4 + - + +
187D PHE* 3.3 32.5 + - + +
189D GLU* 1.3 75.9 - - - +
191D VAL* 1.3 61.3 + - - +
193D GLN* 3.2 23.0 + - - +
194D LYS* 3.3 17.9 + - - +
313D TYR* 3.8 22.9 - - + +
390D VAL* 5.5 2.9 - - + -
391D TYR* 5.4 1.3 - - - -
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Residues in contact with VAL 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D PHE 2.9 19.8 + - - +
188D LEU* 3.7 4.9 - - - +
190D LYS* 1.3 75.1 - - - +
192D ARG* 1.3 55.7 + - - +
194D LYS* 3.1 6.6 + - - +
195D LYS* 2.7 54.5 + - - +
199D ILE* 3.4 37.5 - - + -
279D ASP* 4.0 6.7 - - + +
280D ILE* 3.7 18.6 - - + -
311D GLY 5.1 0.9 - - - +
313D TYR* 3.6 26.0 - - + -
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Residues in contact with ARG 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LYS* 5.5 2.3 + - - -
188D LEU* 3.1 37.3 + - - +
189D GLU* 3.4 14.0 + - - +
190D LYS 3.3 0.2 - - - -
191D VAL* 1.3 77.2 - - - +
193D GLN* 1.3 62.1 + - - +
194D LYS 3.2 1.2 + - - -
195D LYS 3.7 0.2 + - - -
196D LYS* 3.3 37.5 + - + +
199D ILE* 4.4 24.6 - - + +
218D GLY* 2.1 39.6 + - - -
219D ARG* 3.1 27.9 + - - +
220D ILE* 3.8 6.1 - - - +
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Residues in contact with GLN 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LYS* 5.3 7.2 + - - +
363B GLU 3.8 26.2 + - - +
367B ASP 5.6 4.7 + - - +
189D GLU* 2.6 47.0 + - - +
190D LYS* 3.6 17.7 + - - +
191D VAL 3.2 0.6 - - - -
192D ARG* 1.3 77.4 - - - +
194D LYS* 1.3 59.8 + - + +
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Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B LYS* 5.7 3.5 + - - -
229B ALA* 5.0 12.3 - - - +
231B VAL* 5.4 1.2 - - - +
232B SER* 5.3 2.8 + - - -
367B ASP 5.2 4.5 + - - +
368B VAL* 5.0 18.4 - - + -
190D LYS 3.3 11.6 + - - +
191D VAL* 3.1 7.2 + - - +
192D ARG 3.1 1.5 - - - +
193D GLN* 1.3 80.9 - - - +
195D LYS* 1.3 75.1 + - + +
196D LYS* 4.9 1.0 - - - +
311D GLY* 2.9 30.2 + - - -
313D TYR* 2.9 21.7 + - - -
473D GLU* 2.7 29.5 + - - -
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Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B VAL* 3.2 23.0 - - - +
191D VAL* 2.7 44.1 + - + +
194D LYS* 1.3 81.4 - - + +
196D LYS* 1.3 69.3 + - - +
197D ARG* 3.0 19.2 + - + +
198D ASP 5.6 0.7 - - - +
199D ILE* 4.4 3.4 - - + -
279D ASP* 3.0 44.2 + - - +
309D SER* 4.5 6.4 - - - -
310D PRO 4.0 18.2 + - - -
311D GLY* 4.3 3.8 + - - -
312D GLY* 4.1 14.8 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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