Contacts of the helix formed by residues 164 - 197 (chain D) in PDB entry 1O9I
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 ASP 164 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP* 2.9 18.5 + - - -
16D ARG* 2.9 53.4 + - + +
18D ASP* 6.0 1.6 - - + +
80D LEU* 5.2 0.2 - - - +
162D THR* 2.9 14.3 + - - +
163D GLU* 1.3 76.8 - - - +
165D GLU* 1.3 58.7 + - - +
166D GLY 2.9 27.9 + - - -
167D VAL* 2.9 21.1 + - + +
168D ARG* 2.9 29.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 165 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ASP* 3.7 12.7 + - - +
16D ARG* 4.9 0.8 - - - +
159D TYR* 4.9 2.4 + - - -
163D GLU 3.2 10.0 + - - +
164D ASP* 1.3 71.9 + - - +
166D GLY* 1.3 61.2 + - - +
168D ARG* 3.1 46.0 + - - +
169D ASP* 2.9 28.4 + - - +
172D LYS* 4.3 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 166 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ASN* 3.6 10.7 + - - -
13D LYS 3.7 20.2 - - - +
15D ASP* 3.5 18.6 + - - -
76D MET* 4.1 2.6 - - - +
164D ASP* 2.9 8.0 + - - -
165D GLU* 1.3 75.6 - - - +
167D VAL* 1.3 65.3 + - - +
169D ASP* 3.3 7.6 + - - +
170D MET 3.3 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 167 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D PRO* 3.7 25.5 - - + +
21D MET* 4.1 14.6 - - + -
25D LEU* 4.6 12.3 - - + -
76D MET* 3.8 17.9 - - + -
80D LEU* 4.1 12.8 - - + -
162D THR* 3.9 19.5 - - + +
164D ASP* 2.9 28.3 + - + +
166D GLY* 1.3 74.2 - - - +
168D ARG* 1.3 63.3 + - - +
170D MET* 3.1 6.9 + - + +
171D LEU* 2.9 35.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 168 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D TYR* 2.9 70.7 + - + +
160D SER* 4.4 5.9 + - - +
162D THR* 3.2 28.5 + - + -
163D GLU* 4.4 13.6 - - - +
164D ASP 2.9 19.3 + - - +
165D GLU* 3.1 41.6 + - - +
167D VAL* 1.3 76.4 - - - +
169D ASP* 1.3 56.3 + - - +
171D LEU* 3.2 7.6 + - + +
172D LYS* 2.8 38.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 169 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 2.7 38.6 + - - -
11D ASN* 3.2 22.5 + - - +
165D GLU 2.9 18.3 + - - +
166D GLY* 3.5 7.6 - - - +
167D VAL 3.2 0.4 - - - -
168D ARG* 1.3 75.8 - - - +
170D MET* 1.3 62.7 + - - +
172D LYS* 3.3 16.7 + - - +
173D PHE 3.2 17.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 170 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D TYR* 4.5 3.4 - - - -
11D ASN* 3.3 23.9 + - - +
12D ALA* 3.9 17.5 - - - -
25D LEU* 4.5 5.8 - - + -
72D MET* 3.8 19.3 - - + +
73D ILE* 3.7 31.0 - - + -
76D MET* 3.8 42.4 - - + -
166D GLY 3.3 2.9 + - - +
167D VAL* 3.1 9.2 + - + +
169D ASP* 1.3 80.2 + - - +
171D LEU* 1.3 79.3 + - + +
173D PHE* 3.1 5.0 + - - +
174D LEU* 3.0 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D MET* 4.7 0.4 - - + -
25D LEU* 4.4 11.9 - - + -
73D ILE* 6.0 0.2 - - + -
155D VAL* 3.6 25.2 - - + +
158D LEU* 3.8 21.1 - - + +
159D TYR* 3.6 41.5 - - + +
162D THR* 4.7 1.6 - - + -
167D VAL* 2.9 33.2 + - + +
168D ARG* 3.6 11.4 - - - +
170D MET* 1.3 94.4 - - + +
172D LYS* 1.3 58.1 + - - +
174D LEU* 3.2 6.6 + - + +
175D LEU* 2.8 35.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 172 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D TYR* 3.9 26.8 + - + +
165D GLU* 4.3 13.7 + - - -
168D ARG* 2.8 30.7 + - - +
169D ASP* 3.7 20.5 - - - +
171D LEU* 1.3 75.3 - - - +
173D PHE* 1.3 60.9 + - - +
175D LEU* 3.6 15.0 + - + +
176D ALA* 3.3 20.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 173 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 3.6 37.5 - - + -
10D TYR* 3.5 63.7 - + + -
69D HIS* 4.2 4.7 - - - -
72D MET* 4.1 12.6 - - + -
169D ASP 3.2 4.4 + - - -
170D MET 3.1 7.7 + - - +
172D LYS* 1.3 74.1 - - - +
174D LEU* 1.3 69.7 - - + +
176D ALA* 3.1 9.5 + - + +
177D ARG* 3.0 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 4.5 7.0 - - - +
69D HIS* 3.8 44.0 - - + +
72D MET* 4.3 5.8 - - + -
73D ILE* 3.9 28.0 - - + -
155D VAL* 4.5 11.0 - - + -
170D MET* 3.0 34.0 + - + +
171D LEU* 3.7 12.8 - - + +
173D PHE* 1.3 82.2 - - + +
175D LEU* 1.3 65.0 + - - +
177D ARG* 3.3 2.4 + - - +
178D GLU* 2.8 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ARG* 3.0 50.7 + - + +
155D VAL* 3.6 19.7 - - + +
156D SER* 3.4 30.1 - - - +
159D TYR* 5.1 11.7 - - + -
171D LEU 2.8 26.6 + - - +
172D LYS* 3.7 20.0 - - + +
173D PHE 3.3 0.2 - - - -
174D LEU* 1.3 72.1 - - - +
176D ALA* 1.3 58.4 + - - +
178D GLU* 3.3 4.0 + - - -
179D THR* 3.0 16.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172D LYS 3.3 9.7 + - - +
173D PHE* 3.1 13.7 + - + +
175D LEU* 1.3 78.6 - - - +
177D ARG* 1.3 70.7 + - + +
179D THR* 3.1 10.1 + - - +
180D GLN* 3.1 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLN* 4.5 2.5 - - - +
65D GLU* 2.8 44.3 + - - +
69D HIS* 4.1 14.1 - - + -
173D PHE* 3.0 53.6 + - + +
174D LEU* 3.9 3.8 - - - +
176D ALA* 1.3 79.6 + - - +
178D GLU* 1.3 58.0 + - + +
180D GLN* 3.2 33.1 + - - +
181D HIS* 2.8 46.5 + - + -
184D GLN* 5.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D GLU* 4.2 14.7 - - - +
69D HIS* 6.2 2.2 - - + +
147D ARG* 5.6 1.3 - - - +
148D GLU* 3.4 26.6 - - - +
151D ALA* 3.8 12.3 - - + +
152D ARG* 3.1 50.7 - - + +
155D VAL* 3.5 26.4 - - - +
174D LEU* 2.8 31.9 + - + +
175D LEU* 3.8 0.3 - - - -
177D ARG* 1.3 73.7 - - + +
179D THR* 1.3 59.5 + - - +
181D HIS* 4.0 1.2 - - - +
182D GLN* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152D ARG* 3.1 31.5 + - - +
175D LEU 3.0 9.4 + - - -
176D ALA* 3.3 12.4 - - - -
178D GLU* 1.3 78.0 - - - +
180D GLN* 1.3 63.1 + - - +
182D GLN* 3.6 6.2 - - - +
183D LEU* 2.9 43.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176D ALA 3.1 9.1 + - - +
177D ARG* 3.5 42.0 - - - +
179D THR* 1.3 78.6 - - - +
181D HIS* 1.3 59.5 + - + +
183D LEU* 3.2 10.3 + - - +
184D GLN* 2.8 61.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 181 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D THR* 3.6 14.1 + - + +
65D GLU* 2.9 38.7 + - + -
66D GLU* 3.2 28.9 + - - -
69D HIS* 4.3 8.0 - + - -
148D GLU* 3.3 28.5 + - + +
177D ARG* 2.8 25.4 + - + +
178D GLU* 5.4 0.8 - - - +
180D GLN* 1.3 81.6 - - + +
182D GLN* 1.3 66.0 + - - +
184D GLN* 3.4 25.3 - - - +
185D PHE* 3.0 36.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 182 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D VAL* 4.0 6.3 - - + +
148D GLU* 3.2 37.2 + - + +
149D SER* 3.5 20.0 + - - +
152D ARG* 3.6 28.6 - - - +
178D GLU 2.8 20.2 + - - +
179D THR* 3.6 5.8 - - - +
181D HIS* 1.3 73.8 - - - +
183D LEU* 1.3 60.0 + - + +
185D PHE* 3.9 3.2 - - - +
186D MET* 2.9 46.4 + - + +
142E ARG* 3.2 19.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 183 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D THR* 2.9 38.5 + - + +
180D GLN* 3.7 10.3 - - - +
182D GLN* 1.3 79.5 - - + +
184D GLN* 1.3 63.3 + - - +
186D MET* 3.3 21.3 + - + +
187D LYS* 2.9 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58D LEU* 3.6 31.4 - - + +
62D THR* 2.7 30.1 + - - -
177D ARG* 5.4 0.5 + - - -
180D GLN* 2.8 44.5 + - - +
181D HIS* 3.4 29.0 - - - +
183D LEU* 1.3 73.2 - - - +
185D PHE* 1.3 75.7 + - + +
187D LYS* 3.4 7.4 + - - +
188D ALA* 3.0 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 185 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D PHE* 3.6 41.5 - + - -
58D LEU* 3.8 17.9 - - + -
59D LEU* 4.2 10.8 - - + -
62D THR* 3.9 11.9 - - + -
141D MET* 3.6 24.9 - - - +
144D ASN* 3.6 26.9 - - + -
145D VAL* 3.6 17.8 - - + +
148D GLU* 4.0 7.4 - - + -
181D HIS* 3.0 27.2 + - + +
184D GLN* 1.3 99.4 - - + +
186D MET* 1.3 59.2 + - - +
188D ALA* 3.4 3.4 + - - +
189D GLN* 2.8 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 186 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145D VAL* 3.6 17.2 - - + +
182D GLN* 2.9 38.2 + - + +
183D LEU* 3.3 21.7 + - + +
185D PHE* 1.3 77.4 - - - +
187D LYS* 1.3 58.2 + - - +
189D GLN* 3.3 9.0 + - - +
190D GLU* 2.9 41.7 + - + +
142E ARG* 3.4 42.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 5.1 4.0 - - - +
183D LEU 2.9 12.9 + - - +
184D GLN* 3.6 11.2 - - - +
186D MET* 1.3 74.9 - - - +
188D ALA* 1.3 66.5 + - - +
190D GLU* 3.3 14.2 + - + +
191D GLU* 2.7 68.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 6.4 0.2 - - - +
55D TYR* 3.8 33.0 - - + -
58D LEU* 4.4 5.4 - - + -
141D MET* 3.8 22.7 - - + -
184D GLN 3.0 17.7 + - - +
185D PHE 3.7 4.5 - - - +
187D LYS* 1.3 76.2 - - - +
189D GLN* 1.3 64.4 + - - +
191D GLU* 3.3 4.0 + - - +
192D LEU* 2.9 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137D LEU 5.5 0.2 - - - -
138D VAL* 4.7 4.0 - - + +
141D MET* 4.0 14.9 - - + +
142D ARG* 3.5 32.4 - - + +
145D VAL* 3.7 22.9 - - - +
185D PHE 2.8 17.2 + - - +
186D MET* 3.5 10.2 - - - +
187D LYS 3.3 0.2 - - - -
188D ALA* 1.3 76.8 - - - +
190D GLU* 1.3 60.7 + - + +
192D LEU* 3.3 5.4 + - - +
193D GLU* 2.8 62.1 + - + +
234D LYS* 5.9 1.8 - - - +
145E VAL* 6.1 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D MET* 2.9 27.4 + - + +
187D LYS* 3.9 13.7 - - + +
189D GLN* 1.3 77.2 - - + +
191D GLU* 1.3 66.6 + - + +
193D GLU* 3.3 17.8 + - - +
194D GLU* 3.0 27.7 + - - +
234D LYS* 5.0 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54D LYS* 2.8 33.6 + - - +
55D TYR* 2.6 38.8 + - - +
187D LYS* 2.7 49.3 + - - +
188D ALA* 3.7 3.5 - - - +
190D GLU* 1.3 76.0 - - - +
192D LEU* 1.3 64.3 + - - +
194D GLU* 3.2 9.9 + - - +
195D LYS* 3.0 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS 4.8 3.1 - - - +
265A GLN 4.1 1.8 - - - -
266A GLY* 3.7 35.2 - - - +
55D TYR* 3.7 24.7 - - + +
137D LEU* 3.6 32.3 - - + +
138D VAL* 3.9 15.4 - - + +
141D MET* 3.8 13.7 - - + -
188D ALA 2.9 22.6 + - - +
189D GLN* 3.7 4.0 - - - +
191D GLU* 1.3 77.9 - - - +
193D GLU* 1.3 55.9 + - - +
195D LYS* 3.2 3.7 + - + -
196D TYR* 2.9 46.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D VAL* 3.9 11.2 - - + -
142D ARG* 2.7 31.7 + - - +
189D GLN* 2.8 44.9 + - - +
190D GLU* 3.7 24.0 - - - +
192D LEU* 1.3 74.2 - - - +
194D GLU* 1.3 61.8 + - - +
197D GLY* 2.8 41.3 + - - +
198D ILE* 3.5 26.2 + - + +
234D LYS* 4.6 7.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 194 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190D GLU* 3.0 16.0 + - - +
191D GLU* 3.2 12.3 + - - +
193D GLU* 1.3 77.8 - - - +
195D LYS* 1.3 62.5 + - - +
197D GLY* 4.6 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 195 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A GLY* 3.4 24.6 + - - +
191D GLU 3.0 12.8 + - - +
192D LEU* 3.2 7.8 + - + +
193D GLU 3.2 0.2 - - - -
194D GLU* 1.3 80.7 - - - +
196D TYR* 1.3 101.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 196 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A HIS* 3.5 55.2 - + + +
265A GLN 3.6 3.1 + - - -
266A GLY* 2.9 38.9 + - - -
138D VAL* 3.9 14.6 - - + -
192D LEU* 2.9 32.9 + - + +
195D LYS* 1.3 111.9 - - + +
197D GLY* 1.3 60.5 + - - +
202D GLY* 3.2 27.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 197 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138D VAL* 4.3 7.6 - - - +
193D GLU* 2.8 35.3 + - - +
194D GLU 4.6 1.2 + - - -
195D LYS 3.8 0.2 - - - -
196D TYR* 1.3 75.5 - - - +
198D ILE* 1.3 64.3 + - - -
199D ILE 3.3 10.7 + - - +
202D GLY* 4.6 2.7 - - - -
----------------------------------------------------------
Back to top of page
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