Contacts of the helix formed by residues 168 - 193 (chain D) in PDB entry 5YWB
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 ARG 168 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D GLU* 4.9 10.8 + - - +
91D GLU* 2.9 54.0 + - - +
92D GLY* 4.7 4.2 - - - +
95D SER* 5.9 2.8 - - - -
106D LEU 4.6 14.7 + - - -
153D LYS* 5.7 9.3 - - - +
157D PHE* 3.8 25.8 - - + -
167D LEU* 1.3 79.2 - - + +
169D PHE* 1.3 53.2 + - - +
171D LEU* 3.5 1.2 + - - +
172D THR* 2.6 51.9 + - + +
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Residues in contact with PHE 169 (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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154D PHE* 3.4 42.3 - + - -
157D PHE* 3.7 39.4 - + + -
158D TYR* 5.2 15.7 - + - -
167D LEU 3.1 4.3 - - - +
168D ARG* 1.3 78.1 - - - +
170D CYS* 1.3 60.3 + - - +
172D THR* 2.6 20.1 + - - -
173D GLY* 2.8 17.4 + - - -
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Residues in contact with CYS 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D LEU* 3.4 12.8 + - + +
168D ARG 3.4 0.4 - - - -
169D PHE* 1.3 83.5 - - + +
171D LEU* 1.3 68.1 + - + +
173D GLY* 3.0 2.8 + - - -
174D LEU* 2.9 36.9 + - + +
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Residues in contact with LEU 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL* 3.8 13.9 - - + +
87D CYS* 3.8 40.4 - - + +
88D GLU* 4.2 13.9 - - + +
91D GLU* 2.7 49.6 - - + +
167D LEU* 3.5 16.4 + - + +
168D ARG 3.5 5.8 + - - +
170D CYS* 1.3 81.1 - - + +
172D THR* 1.3 57.9 + - + +
174D LEU* 3.7 8.0 + - + -
175D LEU* 3.1 32.1 + - - +
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Residues in contact with THR 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU* 4.8 10.1 - - - +
91D GLU* 6.0 0.2 - - - +
150D LYS* 5.5 5.2 - - + +
153D LYS* 5.1 20.9 - - + -
154D PHE* 5.1 11.3 - - - -
157D PHE* 5.8 4.2 - - + +
168D ARG* 2.6 34.8 + - + +
169D PHE* 2.6 27.7 + - - -
171D LEU* 1.3 75.3 - - + +
173D GLY* 1.3 62.5 + - - +
175D LEU* 3.2 11.4 + - + +
176D VAL* 3.0 30.3 + - - +
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Residues in contact with GLY 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D PHE* 5.1 13.4 - - - -
169D PHE* 2.8 20.9 + - - -
170D CYS* 3.0 2.9 + - - -
172D THR* 1.3 73.6 + - - +
174D LEU* 1.3 63.0 + - - +
176D VAL* 3.2 7.8 + - - +
177D ILE* 3.0 31.1 + - - +
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Residues in contact with LEU 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84D VAL* 4.8 17.9 - - + -
170D CYS* 2.9 27.1 + - + +
171D LEU* 4.1 8.5 - - + +
173D GLY* 1.3 73.3 - - - +
175D LEU* 1.3 65.7 + - - +
177D ILE* 3.3 18.3 + - + +
178D LEU* 2.9 34.6 + - + +
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Residues in contact with LEU 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D LEU* 4.3 14.6 - - + -
84D VAL* 4.1 16.7 - - + +
85D LEU* 4.7 14.6 - - + -
88D GLU* 2.8 26.2 - - - +
113D ALA* 6.0 0.4 - - + -
150D LYS* 2.7 41.1 - - + +
171D LEU 3.1 16.7 + - - +
172D THR* 3.3 13.0 - - - +
174D LEU* 1.3 76.1 - - - +
176D VAL* 1.3 63.3 + - - +
178D LEU* 3.2 5.6 + - - +
179D TYR* 3.0 53.5 + - + +
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Residues in contact with VAL 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 3.7 28.6 - - + -
150D LYS* 3.3 41.1 - - + +
151D THR* 4.8 5.8 - - - +
154D PHE* 5.1 9.2 - - + -
172D THR* 3.0 16.3 + - - +
173D GLY* 3.7 8.3 - - - +
175D LEU* 1.3 74.7 - - - +
177D ILE* 1.3 65.1 + - + +
179D TYR* 3.4 5.9 + - - +
180D GLY* 2.9 20.4 + - - -
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Residues in contact with ILE 177 (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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173D GLY 3.0 18.4 + - - +
174D LEU* 3.7 21.3 - - + +
175D LEU 3.2 0.2 - - - -
176D VAL* 1.3 78.6 - - + +
178D LEU* 1.3 60.6 + - + +
180D GLY* 3.2 2.8 + - - -
181D MET* 3.0 45.4 + - + +
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77D LEU* 4.0 26.4 - - + +
80D ILE* 3.8 36.1 - - + +
81D LEU* 3.7 30.7 - - + +
84D VAL* 3.9 19.3 - - + -
174D LEU* 2.9 24.8 + - + +
175D LEU* 3.8 2.2 - - - +
177D ILE* 1.3 78.4 - - + +
179D TYR* 1.3 65.2 + - - +
181D MET* 3.2 9.7 + - - +
182D LEU* 3.1 30.8 + - + +
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Residues in contact with TYR 179 (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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36D HIS* 3.5 14.7 - - - -
81D LEU* 4.6 10.6 - - + +
113D ALA* 4.1 9.0 - - - +
142D TYR* 3.5 17.3 + - - -
143D TRP* 3.3 44.6 - + - -
146D ALA* 3.3 30.1 - - + -
147D PHE* 4.7 15.7 - - + -
150D LYS* 4.4 18.4 - - + -
175D LEU* 3.0 53.3 + - + +
176D VAL* 3.7 5.8 - - - +
178D LEU* 1.3 76.4 - - - +
180D GLY* 1.3 63.2 + - - +
182D LEU* 3.4 6.2 + - - +
183D LEU* 3.0 28.4 + - + +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PHE* 4.5 9.8 - - - -
176D VAL 2.9 14.8 + - - -
177D ILE* 3.2 4.0 + - - -
178D LEU 3.2 0.2 - - - -
179D TYR* 1.3 77.2 - - - +
181D MET* 1.3 60.7 + - - +
183D LEU* 3.3 15.1 + - - +
184D LEU* 3.0 29.6 + - - +
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Residues in contact with MET 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 5.6 12.3 - - + -
77D LEU* 3.9 27.8 - - + -
177D ILE* 3.0 32.2 + - + +
178D LEU* 3.2 10.0 + - - +
180D GLY* 1.3 77.2 - - - +
182D LEU* 1.3 59.1 + - - +
184D LEU* 3.4 14.3 + - + +
185D VAL* 3.1 26.3 + - - +
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Residues in contact with LEU 182 (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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74D ARG* 4.0 39.9 - - + +
77D LEU* 4.0 28.7 - - + -
78D THR* 4.6 4.0 - - - +
81D LEU* 3.5 34.1 - - + -
143D TRP* 3.6 32.8 - - + -
178D LEU 3.1 20.8 + - - +
179D TYR 3.8 3.4 - - - +
181D MET* 1.3 74.8 - - - +
183D LEU* 1.3 62.6 + - - +
185D VAL* 3.2 8.4 + - + +
186D GLU* 3.0 28.2 + - - +
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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
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140D LEU* 3.7 13.9 - - + -
143D TRP* 3.5 32.0 - - + +
144D THR* 3.6 27.1 - - + -
147D PHE* 3.8 35.9 - - + -
179D TYR 3.0 17.4 + - - +
180D GLY* 3.4 12.6 - - - +
182D LEU* 1.3 76.4 - - - +
184D LEU* 1.3 59.3 + - + +
186D GLU* 3.1 8.2 + - - +
187D VAL* 2.9 36.0 + - + +
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Residues in contact with LEU 184 (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 GLY 3.0 20.3 + - - +
181D MET* 3.7 16.6 - - + +
182D LEU 3.3 0.2 - - - -
183D LEU* 1.3 78.5 - - + +
185D VAL* 1.3 58.3 + - + +
187D VAL* 3.3 13.9 + - + +
188D ASN* 2.9 28.6 + - - +
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D PRO 4.4 4.5 - - - +
70D GLY* 4.1 25.4 - - - +
73D LEU* 3.8 33.0 - - + -
74D ARG* 3.3 28.5 - - + +
77D LEU* 4.6 3.1 - - + -
181D MET 3.1 16.3 + - - +
182D LEU* 3.2 14.1 + - + +
184D LEU* 1.3 76.8 - - + +
186D GLU* 1.3 56.6 + - - +
188D ASN* 3.1 9.3 + - + +
189D VAL* 2.9 27.5 + - - +
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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
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74D ARG* 2.8 35.5 + - - +
124D TYR* 5.4 0.2 - - - -
136D LEU* 4.0 26.3 - - - +
139D LEU* 3.6 18.7 - - - +
140D LEU* 4.1 21.0 - - + +
143D TRP* 3.2 29.4 + - + +
182D LEU 3.0 19.8 + - - +
183D LEU* 3.1 6.3 + - - +
185D VAL* 1.3 76.3 - - - +
187D VAL* 1.3 63.3 + - - +
189D VAL* 3.1 8.5 + - - +
190D ILE* 3.0 24.4 + - - +
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Residues in contact with VAL 187 (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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140D LEU* 4.8 14.1 - - + -
183D LEU* 2.9 23.0 + - + +
184D LEU* 3.6 17.0 - - + +
186D GLU* 1.3 75.8 - - - +
188D ASN* 1.3 57.4 + - - +
190D ILE* 3.0 14.8 - - + +
191D ARG* 2.9 30.7 + - + +
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Residues in contact with ASN 188 (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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69D PRO* 4.1 25.1 + - - +
70D GLY* 5.1 2.8 - - - +
184D LEU 2.9 13.7 + - - +
185D VAL* 3.3 12.2 - - - +
187D VAL* 1.3 76.4 - - - +
189D VAL* 1.3 57.3 + - - +
191D ARG* 3.0 37.9 + - - +
192D VAL* 2.9 34.3 + - - +
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Residues in contact with VAL 189 (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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68D PHE* 4.5 24.2 - - + -
69D PRO* 3.6 26.5 - - + +
74D ARG* 4.2 15.7 - - - +
124D TYR* 4.7 1.6 - - - +
136D LEU* 4.0 33.2 - - + -
185D VAL 2.9 18.7 + - - +
186D GLU* 3.1 12.1 + - - +
188D ASN* 1.3 76.8 - - - +
190D ILE* 1.3 61.9 + - - +
192D VAL* 3.2 15.5 + - + +
193D ARG* 3.5 18.2 + - + +
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Residues in contact with ILE 190 (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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136D LEU* 6.5 0.2 - - - -
140D LEU* 5.5 13.5 - - + -
186D GLU 3.0 14.2 + - - +
187D VAL* 3.0 29.6 - - + +
189D VAL* 1.3 78.8 - - - +
191D ARG* 1.3 63.1 + - - +
192D VAL 3.3 0.3 + - - -
193D ARG 3.9 5.9 + - - -
194D ARG 4.3 0.5 + - - -
195D TYR* 2.4 50.0 + - + +
196D ILE* 4.1 20.9 - - + +
197D PHE* 4.4 13.0 - - + +
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Residues in contact with ARG 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D VAL* 2.9 21.5 + - + +
188D ASN* 3.0 32.5 + - - +
190D ILE* 1.3 78.2 - - - +
192D VAL* 1.3 68.8 + - - +
197D PHE* 6.0 0.4 - - - -
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Residues in contact with VAL 192 (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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69D PRO* 3.9 32.8 - - + -
188D ASN* 2.9 34.0 + - - +
189D VAL* 3.6 7.2 - - - +
190D ILE 3.1 0.4 - - - -
191D ARG* 1.3 87.0 - - - +
193D ARG* 1.3 73.9 + - + +
201D PRO 4.7 2.9 - - - +
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Residues in contact with ARG 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66D LEU* 5.3 7.3 - - - +
67D HIS 5.6 1.0 + - - -
68D PHE* 3.4 41.0 - - + -
69D PRO* 6.3 0.4 - - + -
131D ASN* 3.9 23.5 - - - +
136D LEU* 5.2 6.5 - - - -
189D VAL* 3.5 19.1 + - + +
190D ILE 3.9 3.6 + - - -
191D ARG 3.8 0.4 - - - -
192D VAL* 1.3 88.8 - - + +
194D ARG* 1.3 73.7 + - - +
197D PHE* 4.4 9.3 - - - +
198D PHE 5.3 0.9 - - - +
200D THR 4.6 1.7 - - - +
201D PRO* 3.3 33.4 - - + +
203D GLU* 3.1 35.4 - - - +
204D VAL* 4.6 16.6 - - + +
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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