Contacts of the helix formed by residues 154 - 176 (chain F) in PDB entry 5K58
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 154 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152F THR 4.0 0.6 + - - -
153F THR* 1.3 75.1 - - - +
155F GLU* 1.3 84.8 + - - +
156F THR* 3.2 16.0 + - - -
157F LEU* 3.5 17.2 - - + +
158F LEU* 2.6 35.6 + - - +
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Residues in contact with GLU 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137F ARG* 3.9 4.3 - - + +
140F MET* 3.5 26.5 - - + +
141F ARG* 3.7 38.0 + - + +
151F TYR* 6.3 0.4 - - + -
153F THR 3.4 4.5 + - - +
154F ASP* 1.3 92.7 + - - +
156F THR* 1.3 75.8 + - - +
158F LEU* 3.1 18.1 + - + +
159F ALA* 3.1 16.8 + - - +
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Residues in contact with THR 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180E TYR* 6.0 1.6 - - - +
189E ARG* 5.0 0.2 + - - -
133F GLU* 4.6 2.6 - - - +
137F ARG* 3.7 37.1 + - - +
141F ARG* 5.5 1.2 + - - -
154F ASP* 3.2 12.9 + - - -
155F GLU* 1.3 92.6 + - - +
157F LEU* 1.3 59.7 + - + +
160F SER* 3.3 22.9 + - - -
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Residues in contact with LEU 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184E ASP 5.3 0.2 - - - +
185E ASP* 4.2 24.5 - - + +
188E ALA* 4.1 14.6 - - + +
189E ARG* 2.8 78.9 + - + +
192E LEU* 4.4 9.0 - - + -
153F THR* 5.0 8.3 - - + -
154F ASP* 3.3 19.3 + - + +
156F THR* 1.3 78.5 - - + +
158F LEU* 1.3 66.9 + - - +
160F SER* 2.8 9.4 + - - -
161F GLN* 3.1 4.9 + - - +
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Residues in contact with LEU 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E LEU* 4.4 18.6 - - + -
140F MET* 2.9 37.7 - - + -
151F TYR* 3.7 42.0 - - + -
153F THR* 3.5 31.2 - - + +
154F ASP 2.6 17.5 + - - +
155F GLU* 3.1 2.7 + - - +
157F LEU* 1.3 78.4 - - - +
159F ALA* 1.3 65.6 + - - +
161F GLN* 3.0 16.2 - - - +
162F ILE* 3.1 11.9 - - + +
196F GLN 4.8 3.8 - - - +
197F LEU* 5.0 14.4 - - + -
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Residues in contact with ALA 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F GLU* 3.8 6.1 - - + +
136F LEU* 3.4 35.9 - - + +
137F ARG* 3.8 24.0 - - + -
140F MET* 3.1 13.6 - - - +
155F GLU 3.1 3.7 + - - +
158F LEU* 1.3 78.7 - - - +
160F SER* 1.3 55.4 + - - +
162F ILE* 2.7 30.6 + - - +
163F LEU* 2.9 12.8 + - - +
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Residues in contact with SER 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169E MET* 5.6 1.1 - - - +
172E ARG* 4.2 6.4 + - - +
180E TYR* 3.8 7.8 - - - -
189E ARG* 2.5 45.6 + - - -
133F GLU* 3.2 27.8 + - - -
156F THR 3.3 12.1 + - - -
157F LEU* 2.8 11.3 + - - -
158F LEU 3.4 0.2 - - - -
159F ALA* 1.3 77.2 - - - +
161F GLN* 1.3 51.6 + - - +
163F LEU* 3.7 3.5 - - - +
164F ALA* 2.8 34.7 + - - +
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Residues in contact with GLN 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E PHE* 3.9 18.1 - - - -
189E ARG* 3.2 42.9 + - - +
192E LEU* 3.2 20.9 - - + +
193E ILE* 3.3 26.5 - - - +
157F LEU 3.2 9.9 - - - +
158F LEU* 3.0 15.4 + - + +
160F SER* 1.3 82.6 + - - +
162F ILE* 1.3 63.9 + - + +
164F ALA* 3.3 16.1 - - - +
165F PHE* 3.4 8.0 + - - +
193F ILE* 5.8 0.2 - - - +
196F GLN* 2.8 30.6 + - - +
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Residues in contact with ILE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E LEU* 6.4 0.2 - - + -
88F LEU* 5.5 6.7 - - + +
92F VAL* 3.9 26.7 - - + -
136F LEU* 4.2 12.3 - - + -
140F MET* 4.5 5.2 - - + -
158F LEU* 3.1 20.4 - - + +
159F ALA* 2.7 25.8 + - - +
161F GLN* 1.3 80.4 - - + +
163F LEU* 1.3 57.5 + - - +
164F ALA 3.1 1.8 - - - -
165F PHE* 2.7 30.5 + - + +
166F CYS* 3.1 15.4 + - - -
193F ILE* 3.3 40.2 - - + -
196F GLN* 5.1 2.2 - - + +
197F LEU* 4.3 13.0 - - + -
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Residues in contact with LEU 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172E ARG* 4.2 19.1 - - - +
175E ARG* 4.7 0.9 - - - +
95F LEU* 3.9 19.3 - - + -
129F PHE* 3.7 38.1 - - + +
130F GLU* 6.2 0.2 - - - +
132F ILE* 3.5 33.7 - - + -
133F GLU* 4.3 10.5 - - + -
136F LEU* 4.6 9.5 - - + +
159F ALA 2.9 11.7 + - - +
160F SER* 3.8 9.9 - - - +
162F ILE* 1.3 76.8 - - - +
164F ALA* 1.3 62.5 + - - +
166F CYS* 3.2 12.9 + - + +
167F GLU* 3.2 22.2 + - - +
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165E PHE* 3.8 30.6 - - + +
168E GLY* 3.3 28.4 + - - -
169E MET* 4.2 17.0 - - + +
172E ARG* 5.6 4.6 - - - +
160F SER 2.8 18.3 + - - +
161F GLN* 3.3 10.1 - - - +
163F LEU* 1.3 77.0 - - - +
165F PHE* 1.3 63.1 + - - +
166F CYS 3.2 1.0 + - - -
167F GLU* 5.1 2.7 - - - -
168F GLY* 3.3 6.1 + - - -
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Residues in contact with PHE 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E GLN* 3.3 47.1 - - + -
164E ALA* 4.1 11.6 - - + +
165E PHE* 4.5 13.6 - - + +
92F VAL* 4.7 10.8 - - + -
96F LEU* 4.3 18.6 - - + -
161F GLN 3.4 6.7 + - - +
162F ILE* 2.7 23.5 + - + +
164F ALA* 1.3 74.3 - - - +
166F CYS* 1.3 65.9 + - - -
168F GLY* 3.9 1.4 + - - -
169F MET* 3.0 49.7 + - + +
186F PHE* 5.8 1.8 - + - -
189F ARG* 3.9 17.5 - - + -
193F ILE* 5.0 16.6 - - + -
196F GLN* 5.8 2.7 - - - +
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Residues in contact with CYS 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92F VAL* 4.6 15.5 - - - -
95F LEU* 3.6 35.9 - - + -
96F LEU* 3.7 26.9 - - + +
162F ILE* 3.1 18.6 + - - -
163F LEU* 3.7 9.2 - - + +
164F ALA 3.1 1.0 - - - -
165F PHE* 1.3 84.3 - - - +
167F GLU* 1.3 55.2 + - - +
169F MET* 2.9 5.2 + - - +
170F LEU* 2.7 41.7 + - + +
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168E GLY* 3.9 15.7 - - - +
171E SER* 3.2 22.0 + - - +
172E ARG* 3.0 31.1 - - - +
175E ARG* 3.1 31.6 + - - -
129F PHE* 3.8 28.2 - - + -
163F LEU* 3.2 20.0 + - - +
164F ALA 3.5 0.2 + - - -
166F CYS* 1.3 75.4 - - - +
168F GLY* 1.3 50.9 + - - +
170F LEU* 2.8 11.1 + - + +
171F SER* 2.6 41.9 + - - +
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Residues in contact with GLY 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E ALA* 3.1 26.4 - - - +
167E GLU* 3.8 9.1 - - - +
168E GLY* 3.6 11.9 - - - -
164F ALA 3.3 7.7 + - - -
165F PHE 4.2 0.2 - - - -
166F CYS 3.2 0.6 - - - -
167F GLU* 1.3 76.8 - - - +
169F MET* 1.3 60.9 + - - +
171F SER* 4.0 2.5 - - - -
172F ARG* 3.1 32.6 - - - +
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Residues in contact with MET 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160E SER* 5.8 1.6 - - - -
164E ALA* 3.6 22.7 - - + -
96F LEU* 4.4 14.1 - - + -
165F PHE* 3.0 35.7 - - + +
166F CYS* 2.9 11.2 + - - +
168F GLY* 1.3 77.8 - - - +
170F LEU* 1.3 63.2 + - - +
171F SER 3.4 0.9 - - - -
172F ARG* 4.3 13.9 - - - +
173F PHE* 3.8 9.2 + - - +
180F TYR 4.9 0.9 - - - +
181F ARG 5.0 2.0 - - - +
182F PRO* 3.6 41.9 - - + +
189F ARG* 3.3 45.5 - - - +
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Residues in contact with LEU 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F LEU* 4.9 11.0 - - + +
96F LEU* 4.8 15.3 - - + +
99F GLY* 4.9 9.0 - - - -
106F THR* 4.2 16.8 - - + +
109F LEU* 4.9 18.8 - - + -
110F THR* 3.2 28.9 - - + +
129F PHE* 4.9 11.9 - - + -
166F CYS* 2.7 30.4 + - + +
167F GLU* 2.8 17.4 + - + +
169F MET* 1.3 85.5 - - + +
171F SER* 1.3 59.9 + - - +
173F PHE* 4.0 5.5 - - - +
174F VAL* 3.5 12.5 + - - +
182F PRO* 4.6 12.8 - - + -
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Residues in contact with SER 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110E THR 5.8 2.9 - - - -
167E GLU* 3.2 34.7 + - - -
171E SER* 4.7 7.3 + - - -
110F THR* 4.7 5.2 - - - +
112F HIS* 5.0 10.4 - - - -
167F GLU* 2.6 28.7 + - - +
168F GLY* 4.4 0.4 - - - -
169F MET 3.4 0.2 - - - -
170F LEU* 1.3 72.7 - - - +
172F ARG* 1.3 60.1 + - - +
173F PHE 3.1 1.8 - - - -
174F VAL* 2.8 21.6 + - - +
175F ARG* 2.9 19.5 + - - +
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Residues in contact with ARG 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E PHE 4.9 1.0 + - - -
130E GLU* 4.2 3.4 + - - -
133E GLU* 2.4 35.1 + - - +
160E SER* 4.7 14.0 - - - +
163E LEU* 4.8 9.7 - - - +
164E ALA* 4.2 22.9 - - - +
167E GLU* 3.3 18.0 + - - +
168F GLY 3.1 22.5 + - - +
169F MET* 4.3 10.9 - - - -
170F LEU 3.6 0.2 - - - -
171F SER* 1.3 75.6 - - - +
173F PHE* 1.3 58.8 + - - +
174F VAL 3.5 0.3 + - - -
175F ARG* 3.4 26.4 + - - +
176F SER* 3.0 26.7 + - - -
180F TYR* 3.1 62.5 + - + +
189F ARG* 6.2 0.2 - - - +
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Residues in contact with PHE 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F GLY 3.9 3.4 - - - -
100F GLU* 3.7 35.2 - - + -
103F PRO* 3.9 23.6 - - + -
106F THR* 4.5 16.8 - - + -
169F MET 3.8 16.7 + - - +
170F LEU* 4.0 6.7 - - - +
171F SER 3.1 0.4 - - - -
172F ARG* 1.3 80.7 - - - +
174F VAL* 1.3 56.0 + - - +
176F SER* 4.0 0.7 + - - -
177F GLU 3.8 0.2 + - - -
178F PHE* 2.9 71.3 + + + -
180F TYR 3.2 25.1 + - - +
181F ARG* 3.5 28.0 - - + -
182F PRO* 3.6 11.4 - - + -
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Residues in contact with VAL 174 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106F THR* 4.4 8.5 - - + -
107F ARG* 4.3 34.5 + - + +
110F THR* 3.7 22.7 - - + +
112F HIS* 3.7 31.4 - - + +
170F LEU 3.5 15.5 - - - +
171F SER 2.8 10.6 + - - +
173F PHE* 1.3 76.6 - - - +
175F ARG* 1.3 70.2 + - + +
176F SER 3.1 1.8 - - - -
177F GLU* 2.9 17.3 + - - +
178F PHE* 4.8 8.1 - - + -
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Residues in contact with ARG 175 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109E LEU 5.3 0.2 - - - -
110E THR 5.0 11.4 - - - +
122E GLN* 4.4 5.5 + - - +
125E ILE* 4.8 3.6 - - - -
126E ASN* 3.1 60.3 + - - +
129E PHE* 3.3 29.5 - - - +
130E GLU* 3.8 13.3 + - - -
163E LEU* 5.7 0.2 - - - +
167E GLU* 2.8 34.8 + - - +
112F HIS* 5.9 2.0 - - - +
171F SER* 2.9 19.4 + - - +
172F ARG* 3.4 39.3 - - - +
174F VAL* 1.3 77.1 - - + +
176F SER* 1.3 60.4 + - - +
177F GLU* 3.2 14.4 - - - +
180F TYR* 5.0 3.2 - - - -
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Residues in contact with SER 176 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E ASN* 4.7 4.0 - - - +
172F ARG 3.0 18.2 + - - -
173F PHE 4.0 1.2 + - - -
174F VAL 3.1 0.4 - - - -
175F ARG* 1.3 82.0 - - - +
177F GLU* 1.3 71.2 + - - +
179F LYS* 3.6 20.4 + - - +
180F TYR* 3.1 37.4 + - - -
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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