Contacts of the helix formed by residues 168 - 193 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H GLU* 4.9 9.8 + - - +
91H GLU* 2.9 54.8 + - - +
92H GLY* 4.7 3.6 - - - +
95H SER* 5.9 2.8 - - - -
106H LEU 4.6 14.3 + - - -
153H LYS* 5.7 9.5 - - - +
157H PHE* 3.8 26.4 - - + -
167H LEU* 1.3 80.1 - - + +
169H PHE* 1.3 54.3 + - - +
171H LEU* 3.5 0.9 + - - +
172H THR* 2.6 51.3 + - + +
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Residues in contact with PHE 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H PHE* 3.4 42.2 - + - -
157H PHE* 3.7 39.2 - + + -
158H TYR* 5.2 15.3 - + + -
167H LEU 3.1 4.2 - - - +
168H ARG* 1.3 78.9 - - - +
170H CYS* 1.3 60.2 + - - +
172H THR* 2.6 20.4 + - - -
173H GLY* 2.8 16.4 + - - -
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Residues in contact with CYS 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H LEU* 3.4 13.5 + - + +
168H ARG 3.4 0.4 - - - -
169H PHE* 1.3 83.7 - - + +
171H LEU* 1.3 68.4 + - + +
173H GLY* 3.0 2.5 + - - -
174H LEU* 2.9 36.2 + - + +
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Residues in contact with LEU 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 3.8 14.4 - - + +
87H CYS* 3.6 48.5 - - + +
88H GLU* 3.8 14.1 - - + +
91H GLU* 3.3 38.8 - - + +
167H LEU* 3.5 15.2 + - + +
168H ARG 3.5 6.4 + - - +
170H CYS* 1.3 82.2 - - + +
172H THR* 1.3 58.3 + - + +
174H LEU* 3.7 7.7 + - + +
175H LEU* 3.1 32.6 + - - +
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Residues in contact with THR 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H GLU* 4.8 10.1 - - - +
91H GLU* 6.0 0.2 - - - +
150H LYS* 5.3 5.6 - - + +
153H LYS* 5.1 20.2 - - + -
154H PHE* 5.1 11.8 - - - -
157H PHE* 5.8 4.0 - - + +
168H ARG* 2.6 34.4 + - + +
169H PHE* 2.6 27.9 + - - -
171H LEU* 1.3 76.0 - - + +
173H GLY* 1.3 62.7 + - - +
175H LEU* 3.2 11.2 + - + +
176H VAL* 3.0 29.3 + - - +
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Residues in contact with GLY 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154H PHE* 5.1 13.2 - - - -
169H PHE* 2.8 20.7 + - - -
170H CYS* 3.6 2.7 - - - -
172H THR* 1.3 74.0 + - - +
174H LEU* 1.3 64.0 + - - +
176H VAL* 3.2 7.9 + - - +
177H ILE* 3.0 31.1 + - - +
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Residues in contact with LEU 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84H VAL* 4.8 17.9 - - + -
170H CYS* 2.9 27.9 + - + +
171H LEU* 4.1 10.5 - - + +
173H GLY* 1.3 73.7 - - - +
175H LEU* 1.3 65.5 + - - +
177H ILE* 3.3 18.8 + - + +
178H LEU* 2.9 34.3 + - + +
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81H LEU* 4.3 14.1 - - + -
84H VAL* 4.1 16.2 - - + +
85H LEU* 4.7 15.0 - - + -
88H GLU* 2.8 25.6 - - - +
113H ALA* 6.0 0.2 - - + -
150H LYS* 2.7 42.0 - - + +
171H LEU 3.1 16.7 + - - +
172H THR* 3.2 12.8 + - - +
174H LEU* 1.3 76.5 - - - +
176H VAL* 1.3 62.6 + - - +
178H LEU* 3.2 5.7 + - - +
179H TYR* 3.0 53.1 + - + +
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Residues in contact with VAL 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 3.7 28.1 - - + -
150H LYS* 3.3 40.4 - - + +
151H THR* 4.5 7.0 - - - +
154H PHE* 5.1 8.5 - - + -
172H THR* 3.0 17.4 + - - +
173H GLY* 3.2 8.5 + - - +
175H LEU* 1.3 75.5 - - - +
177H ILE* 1.3 65.0 + - + +
179H TYR* 3.4 6.4 + - - +
180H GLY* 2.9 21.1 + - - -
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Residues in contact with ILE 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H GLY* 3.0 18.6 + - - +
174H LEU* 3.7 22.4 - - + +
175H LEU 3.2 0.2 - - - -
176H VAL* 1.3 79.3 - - + +
178H LEU* 1.3 61.0 + - + +
180H GLY* 3.2 2.2 + - - -
181H MET* 3.0 46.1 + - + +
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Residues in contact with LEU 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77H LEU* 4.0 27.0 - - + +
80H ILE* 3.8 35.0 - - + +
81H LEU* 3.7 30.5 - - + -
84H VAL* 3.9 20.0 - - + -
174H LEU* 2.9 25.7 + - + +
175H LEU* 3.8 1.8 - - - +
177H ILE* 1.3 78.0 - - + +
179H TYR* 1.3 65.4 + - - +
181H MET* 3.2 10.3 + - - +
182H LEU* 3.1 29.3 + - + +
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Residues in contact with TYR 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36H HIS* 3.5 15.2 - + - -
81H LEU* 4.6 10.4 - - + +
113H ALA* 4.1 9.0 - - - +
142H TYR* 3.5 16.6 + - - -
143H TRP* 3.3 43.0 - + - -
146H ALA* 3.3 31.2 - - + -
147H PHE* 4.7 15.0 - - + -
150H LYS* 4.4 19.0 - - + -
175H LEU* 3.0 53.0 + - + +
176H VAL* 3.7 6.1 - - - +
178H LEU* 1.3 75.8 - - - +
180H GLY* 1.3 64.1 + - - +
182H LEU* 3.4 7.4 + - - +
183H LEU* 3.0 28.4 + - + +
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Residues in contact with GLY 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147H PHE* 4.5 10.2 - - - -
176H VAL 2.9 15.5 + - - -
177H ILE* 3.7 3.1 - - - -
178H LEU 3.2 0.2 - - - -
179H TYR* 1.3 76.8 - - - +
181H MET* 1.3 60.7 + - - +
183H LEU* 3.3 14.8 + - - +
184H LEU* 3.0 29.8 + - - +
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Residues in contact with MET 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73H LEU* 5.6 11.2 - - + -
77H LEU* 3.9 27.4 - - + -
177H ILE* 3.0 32.5 + - + +
178H LEU* 3.2 9.6 + - - +
180H GLY* 1.3 77.8 - - - +
182H LEU* 1.3 60.0 + - - +
184H LEU* 3.4 14.8 + - + +
185H VAL* 3.1 25.5 + - + +
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Residues in contact with LEU 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ARG* 4.0 39.9 + - + +
77H LEU* 4.0 29.4 - - + -
78H THR* 4.6 3.6 - - - +
81H LEU* 3.5 33.4 - - + -
143H TRP* 3.6 32.8 - - + -
178H LEU* 3.1 22.1 + - + +
179H TYR 3.8 3.6 - - - +
181H MET* 1.3 75.0 - - - +
183H LEU* 1.3 63.3 + - - +
185H VAL* 3.2 8.1 + - + +
186H GLU* 3.0 27.7 + - - +
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Residues in contact with LEU 183 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 3.7 14.4 - - + -
143H TRP* 3.5 31.1 - - + +
144H THR* 3.6 27.1 - - + -
147H PHE* 3.8 35.9 - - + -
179H TYR 3.0 17.4 + - - +
180H GLY* 3.4 12.8 - - - +
182H LEU* 1.3 77.3 - - - +
184H LEU* 1.3 60.2 + - + +
186H GLU* 3.1 7.8 + - - +
187H VAL* 2.9 36.1 + - + +
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Residues in contact with LEU 184 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180H GLY 3.0 20.5 + - - +
181H MET* 3.7 16.2 - - + +
182H LEU 3.3 0.4 - - - -
183H LEU* 1.3 76.9 - - + +
185H VAL* 1.3 59.0 + - + +
187H VAL* 3.3 13.2 + - + +
188H ASN* 2.9 28.9 + - - +
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Residues in contact with VAL 185 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H PRO 4.4 3.8 - - - +
70H GLY* 4.1 25.8 - - - +
73H LEU* 3.8 33.2 - - + -
74H ARG* 3.3 29.2 - - + +
77H LEU* 4.6 3.6 - - + -
181H MET 3.1 16.3 + - - +
182H LEU* 3.4 12.8 - - + +
184H LEU* 1.3 77.7 - - + +
186H GLU* 1.3 55.6 + - - +
188H ASN* 3.1 9.5 + - + +
189H VAL* 2.9 27.8 + - + +
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Residues in contact with GLU 186 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74H ARG* 2.8 35.3 + - - +
124H TYR* 5.4 0.2 - - - -
136H LEU* 4.0 26.0 - - - +
139H LEU* 3.6 19.4 - - - +
140H LEU* 4.1 21.2 - - + +
143H TRP* 3.2 28.7 + - + +
182H LEU 3.0 19.5 + - - +
183H LEU* 3.1 6.7 + - - +
185H VAL* 1.3 73.8 - - - +
187H VAL* 1.3 62.3 + - - +
189H VAL* 3.1 7.4 + - - +
190H ILE* 3.0 25.7 + - - +
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Residues in contact with VAL 187 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 4.8 14.1 - - + -
183H LEU* 2.9 23.3 + - + +
184H LEU* 3.6 17.3 - - + +
185H VAL 3.3 0.2 - - - -
186H GLU* 1.3 76.7 - - - +
188H ASN* 1.3 58.6 + - - +
190H ILE* 3.0 14.6 - - + +
191H ARG* 2.9 31.3 + - + +
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Residues in contact with ASN 188 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H PRO* 4.1 26.0 + - - +
70H GLY* 5.1 2.4 - - - +
184H LEU 2.9 14.4 + - - +
185H VAL* 3.3 12.6 - - - +
187H VAL* 1.3 77.2 - - - +
189H VAL* 1.3 56.7 + - - +
191H ARG* 3.0 36.1 + - - +
192H VAL* 2.9 34.2 + - - +
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Residues in contact with VAL 189 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68H PHE* 4.5 24.5 - - + -
69H PRO* 3.6 25.4 - - + +
74H ARG* 4.2 16.2 - - - +
124H TYR* 4.7 2.5 - - - +
136H LEU* 4.0 32.5 - - + -
185H VAL 2.9 18.2 + - - +
186H GLU* 3.1 13.0 + - - +
188H ASN* 1.3 76.4 - - - +
190H ILE* 1.3 62.1 + - - +
192H VAL* 3.2 15.9 + - - +
193H ARG* 3.5 18.7 + - + +
194H ARG 4.7 0.2 + - - -
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Residues in contact with ILE 190 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H LEU* 5.5 13.5 - - + -
186H GLU 3.0 14.3 + - - +
187H VAL* 3.0 29.2 - - + +
189H VAL* 1.3 77.7 - - - +
191H ARG* 1.3 62.2 + - - +
192H VAL 3.3 0.9 + - - -
193H ARG 3.9 5.5 + - - -
194H ARG 4.3 1.0 + - - -
195H TYR* 2.4 49.5 + - + +
196H ILE* 4.1 21.5 - - + +
197H PHE* 4.4 12.7 - - + +
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Residues in contact with ARG 191 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H VAL* 2.9 22.1 + - + +
188H ASN* 3.0 31.3 + - - +
190H ILE* 1.3 78.4 - - - +
192H VAL* 1.3 69.9 + - - +
197H PHE* 6.0 1.1 - - - -
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Residues in contact with VAL 192 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69H PRO* 3.9 33.7 - - + -
188H ASN* 2.9 32.7 + - - +
189H VAL* 3.6 7.6 - - - +
190H ILE 3.1 1.2 - - - -
191H ARG* 1.3 87.7 - - - +
193H ARG* 1.3 75.1 + - + +
201H PRO 4.7 2.9 - - - +
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Residues in contact with ARG 193 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66H LEU* 5.3 7.5 - - - +
67H HIS 5.6 1.2 + - - -
68H PHE* 3.4 40.8 - - + -
69H PRO* 6.3 0.7 - - + -
131H ASN* 3.9 24.1 - - - +
132H PHE 6.1 0.2 - - - -
136H LEU* 5.2 6.3 - - - -
189H VAL* 3.5 18.9 + - + +
190H ILE 3.9 3.3 + - - -
191H ARG 3.8 0.6 - - - -
192H VAL* 1.3 91.3 - - + +
194H ARG* 1.3 74.4 + - - +
195H TYR 4.2 0.2 - - - -
197H PHE* 4.4 8.9 - - - +
198H PHE 5.3 1.0 - - - +
200H THR 4.6 1.0 - - - +
201H PRO* 3.3 33.2 - - + +
202H ARG 5.9 0.2 - - - +
203H GLU* 3.1 34.5 - - - +
204H VAL* 4.6 16.1 - - + +
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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