Contacts of the helix formed by residues 215 - 237 (chain J) in PDB entry 6AHU
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 215 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213J SER* 3.6 1.6 - - - -
214J GLU* 1.3 100.2 + - - +
216J ASP* 1.3 64.6 + - - +
217J ALA 3.2 5.2 - - - -
218J LYS* 3.3 22.8 + - - +
219J ALA* 3.8 2.9 + - - +
136L PHE 5.7 0.9 + - - -
137L SER* 5.5 9.8 + - - -
138L GLY 5.6 0.5 + - - -
332L ARG* 4.3 26.6 - - - +
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Residues in contact with ASP 216 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182J GLY 4.5 11.4 - - - +
183J LYS 4.6 2.2 - - - +
212J LEU* 5.0 7.1 - - - +
213J SER* 3.3 22.7 + - - +
215J SER* 1.3 78.1 + - - +
217J ALA* 1.3 53.9 + - - +
218J LYS 3.2 1.1 - - - -
219J ALA* 3.0 21.9 + - - +
220J ALA* 2.5 34.0 + - - +
223J THR* 5.4 2.3 - - - +
224J ASN* 3.2 22.5 + - - +
137L SER* 3.8 16.8 - - - +
138L GLY* 5.5 0.8 - - - -
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Residues in contact with ALA 217 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187J ILE* 5.6 2.9 - - - +
204J ALA* 3.4 34.4 - - + +
207J GLY* 4.2 8.4 - - - +
208J LEU* 4.1 25.1 - - + +
211J GLY 4.5 5.8 - - - +
212J LEU* 4.3 6.0 - - + +
213J SER* 4.1 9.0 - - - +
214J GLU 5.4 0.4 - - - -
215J SER 3.2 2.6 - - - +
216J ASP* 1.3 77.2 - - - +
218J LYS* 1.3 60.8 + - - +
220J ALA* 3.5 18.2 + - - +
221J VAL* 4.0 4.9 + - - +
333L LYS* 5.1 1.3 - - - +
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Residues in contact with LYS 218 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4J PHE* 4.4 26.9 - - + -
201J TYR* 5.7 3.0 - - + -
204J ALA* 4.0 17.8 - - + +
215J SER 3.3 12.7 + - - +
216J ASP 3.2 0.2 - - - -
217J ALA* 1.3 77.1 - - - +
219J ALA* 1.3 64.2 + - + +
221J VAL* 3.3 20.8 - - - +
222J SER* 3.5 10.4 + - - -
102L ASP* 3.8 27.2 + - - +
331L PHE* 3.1 33.1 + - - -
332L ARG* 4.9 8.5 - - + +
333L LYS* 5.1 16.0 - - + +
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Residues in contact with ALA 219 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215J SER 3.8 1.7 + - - +
216J ASP* 3.0 32.0 + - - +
218J LYS* 1.3 78.3 - - + +
220J ALA* 1.3 59.1 + - - +
221J VAL 3.2 2.2 - - - -
222J SER* 4.5 1.8 - - - -
223J THR* 2.8 47.3 + - + +
224J ASN* 2.8 15.4 + - - +
137L SER* 3.7 16.2 - - - +
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Residues in contact with ALA 220 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185J VAL 3.4 19.1 - - - +
186J ILE* 3.4 31.7 - - - +
187J ILE* 4.4 10.2 + - + -
207J GLY* 6.3 0.2 - - - -
212J LEU* 3.8 18.4 - - + -
216J ASP 2.5 18.7 + - - +
217J ALA 3.6 9.4 - - - +
218J LYS 3.3 0.6 - - - -
219J ALA* 1.3 74.9 - - - +
221J VAL* 1.3 56.7 + - - +
224J ASN* 3.6 13.9 - - - +
225J CYS* 3.5 2.8 - - - -
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Residues in contact with VAL 221 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J VAL 4.3 1.0 - - - +
4J PHE* 3.7 24.7 - - + -
5J ALA* 3.7 20.8 + - - -
6J ASP 3.9 20.9 + - - +
30J TYR* 5.7 2.5 - - + -
187J ILE* 4.6 14.8 - - + +
200J PRO* 4.8 12.6 - - + +
203J VAL* 4.8 16.8 - - + -
204J ALA* 5.4 4.0 - - + -
217J ALA 4.0 6.1 + - - +
218J LYS* 3.3 17.9 - - - +
220J ALA* 1.3 78.6 - - - +
222J SER* 1.3 56.1 + - - +
225J CYS* 3.3 23.6 - - - +
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Residues in contact with SER 222 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ALA* 3.7 19.8 + - - +
3J VAL 2.9 33.2 + - - +
4J PHE* 3.6 24.5 - - - +
218J LYS* 3.5 14.7 + - - -
219J ALA* 3.5 3.4 + - - -
221J VAL* 1.3 80.8 - - - +
223J THR* 1.3 67.0 + - - +
224J ASN 3.6 0.2 - - - -
225J CYS 4.1 0.6 - - - -
226J ARG* 3.3 18.5 + - - +
102L ASP 4.8 1.4 + - - -
142L MET* 5.6 0.2 - - - -
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Residues in contact with THR 223 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2J ALA* 5.8 0.3 - - - +
216J ASP* 5.4 1.8 - - - +
219J ALA* 2.8 32.1 + - + +
222J SER* 1.3 75.2 + - - +
224J ASN* 1.3 62.4 + - - +
226J ARG* 3.1 19.7 + - - +
227J ALA* 3.2 13.7 + - - +
137L SER* 4.3 4.9 + - - +
140L LYS* 3.9 30.0 - - + +
142L MET* 3.5 43.1 - - + +
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Residues in contact with ASN 224 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J ALA* 5.0 1.9 - - - +
183J LYS 3.2 23.9 + - - +
184J ASN* 3.8 19.7 - - + +
185J VAL 4.2 4.4 + - - +
186J ILE* 3.7 20.6 - - + +
212J LEU* 5.9 1.2 - - - +
216J ASP* 3.2 26.3 + - - +
219J ALA 2.8 12.2 + - - +
220J ALA* 3.6 18.9 - - - +
223J THR* 1.3 74.7 - - - +
225J CYS* 1.3 60.7 + - - +
227J ALA* 3.6 5.9 + - - +
228J ALA* 3.2 27.4 + - - +
140L LYS* 4.5 11.4 + - - +
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Residues in contact with CYS 225 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6J ASP* 3.3 35.6 - - + +
76J ARG* 5.3 1.6 + - - -
186J ILE* 3.7 21.8 - - - -
187J ILE 5.2 3.4 - - - -
220J ALA 3.5 16.7 + - - -
221J VAL* 3.3 32.1 - - - +
222J SER 3.9 2.7 + - - +
223J THR 3.3 0.4 - - - -
224J ASN* 1.3 75.1 - - - +
226J ARG* 1.3 59.8 + - - +
228J ALA* 3.8 4.6 - - - +
229J LEU* 3.0 29.1 + - - +
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Residues in contact with ARG 226 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219D ASP* 3.4 27.7 + - - -
220D LEU 3.5 24.2 + - - +
2J ALA 4.6 4.6 - - - +
3J VAL* 4.7 21.5 - - + +
6J ASP* 4.4 2.7 + - - -
222J SER 3.3 15.6 + - - +
223J THR* 3.1 12.6 + - - +
225J CYS* 1.3 77.0 - - - +
227J ALA* 1.3 58.1 + - - +
229J LEU* 3.5 5.2 + - - +
230J LEU* 3.0 43.4 + - - +
121L LYS* 4.1 15.5 - - - +
122L ASP* 2.4 40.0 + - - +
142L MET* 3.4 29.9 - - + +
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Residues in contact with ALA 227 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217D THR* 4.4 12.4 - - - +
219D ASP* 4.8 9.6 - - + +
149J GLY 4.6 4.6 - - - +
184J ASN* 6.2 2.5 - - + -
223J THR 3.2 9.3 + - - +
224J ASN* 4.1 5.8 - - - +
225J CYS 3.4 0.2 - - - -
226J ARG* 1.3 81.1 - - - +
228J ALA* 1.3 57.0 + - - +
230J LEU* 4.0 7.8 - - - +
231J HIS* 3.4 22.9 + - - +
140L LYS* 3.5 28.9 - - + +
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Residues in contact with ALA 228 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76J ARG* 5.5 2.0 - - - +
102J VAL* 4.6 3.6 - - - +
123J ASP* 4.8 0.6 - - - +
124J LEU* 3.7 46.0 - - + +
149J GLY 5.4 1.3 - - - -
151J ALA* 4.0 13.2 - - + -
186J ILE* 4.9 2.5 - - + -
224J ASN 3.2 17.9 + - - +
225J CYS* 4.0 6.7 - - - +
226J ARG 3.2 0.2 - - - -
227J ALA* 1.3 76.6 - - - +
229J LEU* 1.3 62.8 + - - +
230J LEU 3.3 0.2 - - - -
231J HIS* 3.6 15.2 + - - +
232J GLY 3.8 3.6 + - - -
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Residues in contact with LEU 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3J VAL* 5.8 5.6 - - + -
6J ASP* 4.8 9.2 - - - +
32J VAL* 4.6 21.8 - - + -
72J LYS* 6.2 2.7 - - + -
74J LEU* 3.8 26.5 - - + -
76J ARG* 3.4 28.8 - - - +
101J ASP* 5.6 2.6 - - - +
102J VAL* 3.9 14.4 - - + +
225J CYS 3.0 18.3 + - - +
226J ARG* 4.0 5.2 - - - +
228J ALA* 1.3 75.1 - - - +
230J LEU* 1.3 63.3 + - - +
232J GLY* 3.2 11.8 + - - -
233J GLU* 3.6 9.2 + - - +
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Residues in contact with LEU 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D TYR* 6.0 1.1 - - - +
217D THR* 4.6 9.9 - - - +
218D ILE 3.3 30.3 - - - +
219D ASP* 3.8 24.5 - - + +
220D LEU 4.5 4.5 - - - +
226J ARG* 3.0 30.0 + - + +
227J ALA* 4.2 5.8 - - - +
228J ALA 3.3 0.2 - - - -
229J LEU* 1.3 74.8 - - - +
231J HIS* 1.3 63.0 + - - +
233J GLU* 3.3 38.0 + - + +
234J THR* 3.4 20.0 + - + +
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Residues in contact with HIS 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D GLY 5.1 3.4 + - - -
217D THR* 3.5 25.8 - - + +
121J ASP* 5.9 0.7 - - - -
122J VAL 3.1 20.9 - - - -
123J ASP* 2.5 42.7 + - + +
148J ARG* 4.4 17.9 + - - +
149J GLY* 3.7 26.4 + - - +
150J LEU* 4.8 2.1 + - - +
227J ALA 3.4 16.7 + - - +
228J ALA* 3.7 9.0 - - - +
229J LEU 3.2 0.4 - - - -
230J LEU* 1.3 79.5 - - - +
232J GLY* 1.3 58.0 + - - +
234J THR* 3.2 16.7 + - - -
235J ARG* 3.4 13.7 + - + +
239J PHE* 5.9 5.6 - + - -
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Residues in contact with GLY 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101J ASP* 2.9 30.0 - - - +
102J VAL* 4.0 6.3 - - - -
123J ASP* 3.3 22.1 + - - -
228J ALA 3.8 4.2 + - - -
229J LEU 3.2 9.5 + - - -
230J LEU 3.2 0.8 - - - -
231J HIS* 1.3 77.9 - - - +
233J GLU* 1.3 57.7 + - - +
235J ARG* 3.8 2.1 - - - -
236J LYS 3.1 17.7 + - - -
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Residues in contact with GLU 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D TYR* 4.9 3.3 + - - -
101J ASP* 4.3 7.8 - - - +
229J LEU 3.6 6.8 + - - +
230J LEU* 3.3 35.0 + - + +
232J GLY* 1.3 76.6 - - - +
234J THR* 1.3 64.1 + - + +
235J ARG 3.2 0.4 - - - -
236J LYS* 3.4 10.8 + - + +
237J THR* 3.6 19.5 + - + +
238J ALA 4.2 0.2 - - - +
242J ILE* 3.9 28.6 - - + +
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Residues in contact with THR 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D TYR* 6.0 3.8 - - + -
216D GLY 4.3 9.2 + - - +
217D THR* 4.4 6.6 - - - +
218D ILE* 4.7 20.9 - - + +
230J LEU* 3.4 18.1 + - + +
231J HIS* 3.2 18.9 + - - -
233J GLU* 1.3 77.9 - - + +
235J ARG* 1.3 57.3 + - - +
238J ALA* 2.9 34.0 - - - +
239J PHE* 3.2 37.4 - - - +
242J ILE* 5.4 8.1 - - + -
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Residues in contact with ARG 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J LEU 5.3 2.4 + - - -
93J THR* 4.8 12.5 + - - -
94J SER* 5.6 8.9 - - - +
98J ARG* 6.0 0.5 - - - -
99J LEU 5.6 1.4 + - - -
101J ASP 5.3 3.3 + - - +
103J VAL* 3.5 37.0 - - - +
120J LEU* 6.1 0.8 - - - +
121J ASP* 2.8 40.1 + - + +
122J VAL* 4.3 2.1 - - - +
123J ASP* 3.4 24.4 + - - +
231J HIS* 3.4 17.6 + - + +
232J GLY* 4.0 4.5 - - - +
233J GLU 3.2 0.4 - - - -
234J THR* 1.3 79.3 + - - +
236J LYS* 1.3 66.9 + - - +
237J THR 4.7 1.6 - - - +
238J ALA* 4.9 1.0 - - - -
239J PHE* 4.2 22.2 - - + -
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Residues in contact with LYS 236 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLN* 3.9 18.1 + - - +
98J ARG* 2.7 41.1 + - + +
99J LEU* 3.4 26.5 - - - +
100J TYR 4.6 0.4 - - - +
101J ASP* 3.3 29.3 - - - +
232J GLY 3.1 18.7 + - - +
233J GLU* 3.4 8.4 + - + +
235J ARG* 1.3 81.0 - - - +
237J THR* 1.3 75.7 + - + +
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Residues in contact with THR 237 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124D GLN* 4.4 13.3 - - + +
127D GLN* 3.0 32.8 + - - +
98J ARG* 4.8 5.0 + - - -
233J GLU* 3.6 7.6 + - + +
235J ARG 4.7 1.3 - - - -
236J LYS* 1.3 91.6 - - + +
238J ALA* 1.3 69.9 + - - +
242J ILE* 3.4 35.7 - - + +
243J SER 5.6 3.6 - - - +
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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