Contacts of the helix formed by residues 154 - 191 (chain B) in PDB entry 6AGF
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 MET 154 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B ASP* 1.3 81.5 + - - +
155B ALA* 1.3 63.0 + - - +
156B SER 3.3 1.6 - - - -
157B ILE* 3.5 7.2 + - + +
158B VAL* 3.3 44.2 + - + +
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Residues in contact with ALA 155 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1060A VAL* 4.8 23.1 - - + +
1063A THR* 3.6 23.6 + - - +
1064A ILE* 5.7 1.6 - - + -
153B ASP* 3.8 10.2 + - - +
154B MET* 1.3 77.3 - - - +
156B SER* 1.3 55.9 + - - +
157B ILE 3.3 3.8 - - - -
158B VAL* 4.2 5.8 - - - +
159B SER* 3.2 33.0 + - - +
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Residues in contact with SER 156 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A THR* 5.3 7.0 - - - -
1067A TYR* 3.6 16.0 + - - -
152B ARG* 2.4 52.8 + - - -
153B ASP* 3.6 24.6 + - - +
154B MET 3.3 1.0 - - - -
155B ALA* 1.3 77.1 - - - +
157B ILE* 1.3 61.5 + - - +
160B GLU* 3.4 15.3 - - - +
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Residues in contact with ILE 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B ARG* 3.6 31.4 - - + -
153B ASP 3.2 26.5 - - - +
154B MET* 3.5 7.1 + - + +
155B ALA 3.3 0.2 - - - -
156B SER* 1.3 81.5 - - - +
158B VAL* 1.3 70.0 + - + +
159B SER 3.3 1.6 - - - -
160B GLU* 3.3 3.9 + - - +
161B ILE* 3.1 40.8 + - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B MET* 3.3 44.1 + - + +
155B ALA* 4.8 2.9 - - - -
157B ILE* 1.3 83.8 - - + +
159B SER* 1.3 59.0 + - - +
161B ILE* 3.5 9.7 + - + +
162B MET* 3.0 39.1 + - + +
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Residues in contact with SER 159 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1063A THR 4.1 4.8 + - - -
1064A ILE* 4.0 22.8 + - - +
1067A TYR* 3.6 28.5 - - - +
155B ALA* 3.2 24.1 + - - +
158B VAL* 1.3 78.5 - - - +
160B GLU* 1.3 60.9 + - - +
162B MET* 3.8 6.6 - - - +
163B MET* 3.2 21.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A TYR* 3.7 27.3 + - + -
152B ARG* 3.4 32.3 + - - -
156B SER 3.4 10.2 + - - +
157B ILE* 3.3 8.5 + - - +
158B VAL 3.3 0.4 - - - -
159B SER* 1.3 76.3 - - - +
161B ILE* 1.3 65.6 + - + +
163B MET* 3.6 4.3 + - + +
164B TYR* 3.2 50.8 + - + -
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Residues in contact with ILE 161 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ILE* 3.1 34.0 + - + +
158B VAL* 3.7 8.7 - - + +
160B GLU* 1.3 77.6 - - + +
162B MET* 1.3 63.4 + - + +
164B TYR* 3.2 8.3 + - - +
165B VAL* 2.9 41.8 + - + +
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Residues in contact with MET 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B VAL* 3.0 30.3 + - + +
159B SER* 3.6 7.4 + - - +
161B ILE* 1.3 78.3 - - + +
163B MET* 1.3 63.8 + - - +
165B VAL* 3.9 19.5 - - + -
166B LEU* 3.1 41.5 + - + +
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Residues in contact with MET 163 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067A TYR* 3.8 37.2 - - + +
1070A LYS* 3.7 33.9 - - + -
1071A VAL* 4.1 16.5 - - + +
159B SER 3.2 15.9 + - - +
160B GLU* 3.8 5.6 - - + +
161B ILE 3.2 0.2 - - - -
162B MET* 1.3 76.6 - - - +
164B TYR* 1.3 92.5 + - + +
166B LEU* 3.2 3.1 + - - +
167B ILE* 2.9 46.5 + - + +
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Residues in contact with TYR 164 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLU* 3.2 39.8 + - + -
161B ILE* 3.2 7.6 + - - +
163B MET* 1.3 99.8 - - + +
165B VAL* 1.3 65.6 + - + +
167B ILE* 4.5 13.5 - - + -
168B VAL* 3.2 34.5 + - + +
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Residues in contact with VAL 165 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ILE* 2.9 34.7 + - + +
162B MET* 4.1 20.6 - - + +
164B TYR* 1.3 79.5 - - + +
166B LEU* 1.3 61.8 + - + +
168B VAL* 4.0 2.1 - - - +
169B VAL* 3.0 41.9 + - + +
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Residues in contact with LEU 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071A VAL* 4.5 29.8 - - + +
162B MET* 3.1 38.7 + - + +
163B MET 3.2 2.9 + - - +
165B VAL* 1.3 76.7 - - + +
167B ILE* 1.3 64.8 + - - +
169B VAL* 4.8 5.2 - - + -
170B LEU* 3.2 43.5 + - + +
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Residues in contact with ILE 167 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070A LYS* 4.2 15.3 - - + +
1071A VAL* 4.7 10.3 - - + -
1074A TYR* 4.0 46.2 - - + +
163B MET* 2.9 38.4 + - + +
164B TYR* 4.2 13.9 - - + +
166B LEU* 1.3 76.9 - - - +
168B VAL* 1.3 69.5 + - + +
170B LEU* 3.4 4.5 + - - +
171B THR* 3.3 24.3 + - + +
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Residues in contact with VAL 168 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164B TYR* 3.2 23.6 + - + +
165B VAL* 4.2 2.2 - - - +
167B ILE* 1.3 80.0 - - + +
169B VAL* 1.3 67.6 + - + +
171B THR* 2.9 24.5 + - - +
172B ILE* 3.3 26.3 + - + +
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Residues in contact with VAL 169 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B VAL* 3.0 30.1 + - + +
166B LEU* 4.4 6.5 - - + +
168B VAL* 1.3 79.3 - - + +
170B LEU* 1.3 64.2 + - + +
172B ILE* 3.4 9.6 + - + +
173B TRP* 3.0 27.4 + - + +
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Residues in contact with LEU 170 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1036A PHE* 3.9 26.5 - - + -
1071A VAL* 6.4 1.8 - - + -
1074A TYR* 5.5 6.7 - - + -
1075A ILE* 4.9 17.9 - - + -
166B LEU* 3.2 43.2 + - + +
167B ILE* 3.9 4.5 - - - +
168B VAL 3.3 0.4 - - - -
169B VAL* 1.3 83.3 - - + +
171B THR* 1.3 63.7 + - + +
173B TRP* 3.5 32.5 + - + +
174B LEU* 3.3 23.1 + - + +
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Residues in contact with THR 171 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1074A TYR* 3.2 33.4 - - + +
1078A MET* 5.4 5.6 - - + -
167B ILE* 3.3 15.6 + - + +
168B VAL* 2.9 16.4 + - - +
170B LEU* 1.3 74.7 - - - +
172B ILE* 1.3 68.6 + - - +
174B LEU* 2.9 11.3 + - - +
175B VAL* 2.8 38.1 + - - +
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Residues in contact with ILE 172 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B VAL* 3.3 34.6 + - + +
169B VAL* 3.7 8.5 - - + +
171B THR* 1.3 81.3 - - - +
173B TRP* 1.3 60.7 + - - +
175B VAL* 4.5 6.1 - - + +
176B ALA* 3.2 27.9 + - + +
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Residues in contact with TRP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1032A TRP* 5.3 10.8 - - + -
1033A PHE* 5.4 12.8 - + - -
1036A PHE* 4.0 47.6 - + + -
169B VAL* 3.0 18.9 + - + +
170B LEU* 3.7 26.0 - - + +
171B THR 3.1 0.2 - - - -
172B ILE* 1.3 78.8 - - - +
174B LEU* 1.3 66.2 + - + +
176B ALA* 4.3 2.8 - - + +
177B GLU* 3.3 40.9 + - + +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A ILE* 5.0 14.3 - - + +
1033A PHE* 4.9 15.9 - - + -
1078A MET* 3.7 40.4 - - + +
1082A LEU* 4.8 21.5 - - + -
170B LEU* 3.3 11.1 + - + +
171B THR* 2.9 10.8 + - - +
173B TRP* 1.3 87.8 - - + +
175B VAL* 1.3 56.7 + - + +
176B ALA 3.2 2.0 - - - -
177B GLU* 2.8 7.6 + - + +
178B MET* 2.5 46.7 + - + +
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Residues in contact with VAL 175 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B THR* 2.8 27.7 + - - +
172B ILE* 4.7 3.8 - - + -
174B LEU* 1.3 75.4 - - + +
176B ALA* 1.3 59.4 + - - +
178B MET* 3.9 18.6 - - + -
179B ILE* 3.2 33.6 + - + +
----------------------------------------------------------
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Residues in contact with ALA 176 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ILE* 3.2 22.9 + - + +
173B TRP* 4.5 4.0 - - + +
174B LEU 3.2 0.4 - - - -
175B VAL* 1.3 78.5 - - - +
177B GLU* 1.3 61.9 + - + +
179B ILE* 3.8 1.3 - - - +
180B TYR* 2.9 27.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1027A ILE* 3.9 15.4 - - + +
173B TRP* 3.3 33.6 + - + +
174B LEU* 2.8 15.8 + - + +
176B ALA* 1.3 76.7 - - + +
178B MET* 1.3 62.4 + - - +
179B ILE 3.3 0.2 - - - -
180B TYR* 3.7 19.8 - - - +
181B CYS* 3.2 32.7 + - - -
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Residues in contact with MET 178 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1020A LEU* 4.7 19.5 - - + -
1023A ALA* 4.7 4.5 - - + +
1024A CYS* 4.6 13.5 - - - -
1027A ILE* 4.0 13.0 - - + +
1082A LEU* 3.9 27.4 - - + -
174B LEU* 2.5 33.3 + - + +
175B VAL* 4.1 17.7 - - + +
177B GLU* 1.3 73.1 - - - +
179B ILE* 1.3 70.3 + - + +
181B CYS* 4.1 1.9 - - - +
182B TYR* 3.2 25.3 + - - +
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B VAL* 3.2 31.2 + - + +
176B ALA* 4.4 1.1 - - - +
178B MET* 1.3 90.6 - - + +
180B TYR* 1.3 64.9 + - - +
181B CYS 3.4 0.4 - - - -
182B TYR* 3.9 19.7 - - + -
183B LYS* 3.2 33.3 + - + +
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B ALA 2.9 19.3 + - - +
177B GLU* 3.7 20.2 - - - +
178B MET 3.4 0.2 - - - -
179B ILE* 1.3 79.0 - - - +
181B CYS* 1.3 73.9 + - - +
183B LYS* 3.4 4.8 + - - +
184B LYS* 3.1 54.4 + - + +
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Residues in contact with CYS 181 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1023A ALA* 4.1 22.9 - - + +
1026A LYS* 5.1 17.7 - - + -
1027A ILE* 4.4 16.8 - - + -
177B GLU* 3.2 20.9 + - - +
178B MET 4.4 1.6 - - - +
180B TYR* 1.3 91.0 - - - +
182B TYR* 1.3 60.9 + - - +
184B LYS* 3.1 10.1 + - + +
185B ILE* 3.0 35.5 + - + +
----------------------------------------------------------
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Residues in contact with TYR 182 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1016A LYS* 3.3 33.7 - - - +
1019A THR* 3.2 31.3 + - + +
1020A LEU* 3.8 30.5 - - + -
1023A ALA* 4.0 8.9 - - + +
178B MET 3.2 19.5 + - - +
179B ILE* 4.1 20.6 - - + -
180B TYR 3.3 0.4 - - - -
181B CYS* 1.3 77.6 - - - +
183B LYS* 1.3 72.3 + - + +
185B ILE* 4.5 2.4 - - - +
186B ALA* 3.6 21.3 + - - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B ILE* 3.2 28.3 + - + +
180B TYR* 3.9 4.5 - - - +
181B CYS 3.2 0.2 - - - -
182B TYR* 1.3 88.8 - - + +
184B LYS* 1.3 63.5 + - - +
186B ALA* 4.2 3.9 - - + +
187B ALA* 3.3 24.3 + - - +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1026A LYS* 6.1 3.8 - - + -
180B TYR* 3.1 44.9 + - + +
181B CYS* 3.1 16.8 + - + +
183B LYS* 1.3 79.6 - - - +
185B ILE* 1.3 66.0 + - + +
187B ALA* 3.6 4.1 + - + +
188B ALA* 3.1 28.1 + - + +
----------------------------------------------------------
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Residues in contact with ILE 185 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A THR* 4.0 18.6 - - - +
1022A ARG* 3.3 46.0 - - + +
1023A ALA* 4.4 16.6 - - - +
1026A LYS* 3.9 27.8 - - + -
181B CYS* 3.0 18.4 + - + +
182B TYR* 4.5 1.8 - - - +
184B LYS* 1.3 85.7 - - + +
186B ALA* 1.3 60.3 + - - +
188B ALA* 3.2 9.3 + - + +
189B THR* 2.9 31.3 + - - +
----------------------------------------------------------
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Residues in contact with ALA 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1019A THR* 4.6 9.3 + - + +
182B TYR* 3.6 21.7 + - + +
183B LYS* 4.8 3.8 - - + +
185B ILE* 1.3 79.6 - - - +
187B ALA* 1.3 59.6 + - - +
188B ALA 3.3 0.2 - - - -
189B THR* 3.5 10.2 + - - -
190B GLU* 3.3 21.1 + - - +
----------------------------------------------------------
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Residues in contact with ALA 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B LYS 3.3 19.3 + - - +
184B LYS* 4.0 5.8 - - + +
185B ILE 3.2 0.4 - - - -
186B ALA* 1.3 76.8 - - - +
188B ALA* 1.3 62.1 + - - +
189B THR 3.2 0.4 - - - -
190B GLU* 3.3 17.6 + - + +
191B THR* 3.3 18.7 + - - +
----------------------------------------------------------
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B LYS* 3.1 20.6 + - + +
185B ILE* 3.2 11.6 + - + +
187B ALA* 1.3 74.5 - - - +
189B THR* 1.3 62.1 + - - +
191B THR* 2.9 23.9 + - - +
192B ALA* 3.6 11.1 + - - +
----------------------------------------------------------
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Residues in contact with THR 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1022A ARG* 4.6 6.9 + - - -
185B ILE* 2.9 20.0 + - - +
186B ALA* 3.6 13.4 - - - -
187B ALA 3.2 0.2 - - - -
188B ALA* 1.3 77.5 - - - +
190B GLU* 1.3 62.4 + - - +
192B ALA* 3.4 20.6 + - - +
----------------------------------------------------------
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B ALA 3.3 12.4 + - - +
187B ALA* 3.3 15.4 + - + +
189B THR* 1.3 78.7 - - - +
191B THR* 1.3 62.2 + - + +
192B ALA 3.3 3.6 + - - -
----------------------------------------------------------
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Residues in contact with THR 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B ALA 3.3 13.9 + - - +
188B ALA* 2.9 23.6 + - - +
190B GLU* 1.3 78.2 - - + +
192B ALA* 1.3 58.2 + - - +
----------------------------------------------------------
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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).
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