Contacts of the helix formed by residues 168 - 193 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 4.9 10.4 + - - +
91B GLU* 2.9 54.0 + - - +
92B GLY* 4.7 4.0 - - - +
95B SER* 5.9 2.4 - - - -
106B LEU 4.6 14.1 + - - -
153B LYS* 5.7 9.1 - - - +
157B PHE* 3.8 26.0 - - + -
167B LEU* 1.3 81.3 - - + +
169B PHE* 1.3 53.7 + - - +
171B LEU* 3.5 1.0 + - - +
172B THR* 2.6 52.2 + - + +
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Residues in contact with PHE 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 3.4 40.7 - + - -
157B PHE* 3.7 39.9 - + + -
158B TYR* 5.2 14.8 - + - -
167B LEU 3.1 3.5 - - - +
168B ARG* 1.3 78.7 - - - +
170B CYS* 1.3 61.7 + - - +
172B THR* 2.6 20.3 + - - -
173B GLY* 2.8 17.1 + - - -
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Residues in contact with CYS 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B LEU* 3.4 13.7 + - + +
168B ARG 3.4 0.4 - - - -
169B PHE* 1.3 83.3 - - + +
171B LEU* 1.3 66.9 + - + +
173B GLY* 3.0 2.0 + - - -
174B LEU* 2.9 36.9 + - + +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 3.8 17.7 - - + +
87B CYS* 3.4 53.8 - - + +
88B GLU* 3.5 17.0 - - + +
91B GLU* 3.6 32.1 - - + +
167B LEU* 3.5 13.4 + - + +
168B ARG 3.5 6.2 + - - +
170B CYS* 1.3 81.8 - - + +
172B THR* 1.3 57.9 + - + +
174B LEU* 3.7 9.1 + - + +
175B LEU* 3.1 31.1 + - - +
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Residues in contact with THR 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 4.8 10.3 - - - +
91B GLU* 6.0 0.2 - - - +
150B LYS* 5.3 5.3 - - + +
153B LYS* 5.1 21.1 - - + -
154B PHE* 5.1 12.2 - - - -
157B PHE* 5.8 4.4 - - + +
168B ARG* 2.6 33.7 + - + +
169B PHE* 2.6 27.5 + - - -
171B LEU* 1.3 75.8 - - + +
173B GLY* 1.3 63.2 + - - +
175B LEU* 3.2 11.4 + - + +
176B VAL* 3.0 29.8 + - - +
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Residues in contact with GLY 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B PHE* 5.1 14.1 - - - -
169B PHE* 2.8 20.4 + - - -
170B CYS* 3.0 3.1 + - - -
172B THR* 1.3 74.3 + - - +
174B LEU* 1.3 62.6 + - - +
176B VAL* 3.2 8.2 + - - +
177B ILE* 3.0 31.5 + - - +
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Residues in contact with LEU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B VAL* 4.8 17.0 - - + -
170B CYS* 2.9 27.4 + - + +
171B LEU* 4.1 10.5 - - + +
173B GLY* 1.3 74.6 - - - +
175B LEU* 1.3 66.4 + - - +
177B ILE* 3.3 17.3 + - + +
178B LEU* 2.9 35.3 + - + +
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Residues in contact with LEU 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B LEU* 4.3 14.8 - - + -
84B VAL* 4.1 16.9 - - + +
85B LEU* 4.7 14.8 - - + -
88B GLU* 2.8 25.1 - - - +
113B ALA* 6.0 0.4 - - + -
150B LYS* 2.7 40.4 - - + +
171B LEU 3.1 16.4 + - - +
172B THR* 3.3 13.2 - - + +
174B LEU* 1.3 76.8 - - - +
176B VAL* 1.3 62.4 + - - +
178B LEU* 3.2 5.4 + - - +
179B TYR* 3.0 53.5 + - + +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 3.7 27.9 - - + -
150B LYS* 3.3 39.9 - - + +
151B THR* 4.8 6.7 - - - +
154B PHE* 5.1 8.7 - - + -
172B THR* 3.0 16.3 + - - +
173B GLY* 3.2 9.2 + - - +
175B LEU* 1.3 74.9 - - - +
177B ILE* 1.3 65.0 + - + +
179B TYR* 3.4 6.1 + - - +
180B GLY* 2.9 20.8 + - - -
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B GLY* 3.0 17.5 + - - +
174B LEU* 3.7 20.6 - - + +
175B LEU 3.2 0.2 - - - -
176B VAL* 1.3 78.7 - - + +
178B LEU* 1.3 61.0 + - + +
180B GLY* 3.2 2.5 + - - -
181B MET* 3.0 45.8 + - + +
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Residues in contact with LEU 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 4.0 26.4 - - + +
80B ILE* 3.8 35.4 - - + +
81B LEU* 3.7 31.4 - - + -
84B VAL* 3.9 18.6 - - + -
174B LEU* 2.9 27.0 + - + +
175B LEU* 3.8 2.5 - - - +
177B ILE* 1.3 76.4 - - + +
179B TYR* 1.3 65.7 + - - +
181B MET* 3.2 10.5 + - - +
182B LEU* 3.1 29.8 + - + +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B HIS* 3.5 15.0 - + - -
81B LEU* 4.6 11.0 - - + +
113B ALA* 4.1 9.2 - - - +
142B TYR* 3.5 16.7 + - - -
143B TRP* 3.3 43.8 - + - -
146B ALA* 3.3 30.1 - - + -
147B PHE* 4.7 14.8 - - + -
150B LYS* 4.4 18.4 - - + -
175B LEU* 3.0 52.5 + - + +
176B VAL* 3.7 5.8 - - - +
178B LEU* 1.3 77.5 - - - +
180B GLY* 1.3 62.4 + - - +
182B LEU* 3.4 7.3 + - - +
183B LEU* 3.0 28.0 + - + +
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Residues in contact with GLY 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PHE* 4.5 10.4 - - - -
176B VAL 2.9 15.1 + - - -
177B ILE* 3.7 3.1 - - - -
178B LEU 3.2 0.2 - - - -
179B TYR* 1.3 77.2 - - - +
181B MET* 1.3 61.6 + - - +
183B LEU* 3.3 15.0 + - - +
184B LEU* 3.0 30.0 + - - +
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Residues in contact with MET 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.6 11.2 - - + -
77B LEU* 3.9 28.3 - - + -
177B ILE* 3.0 32.2 + - + +
178B LEU* 3.8 9.4 - - - +
180B GLY* 1.3 77.8 - - - +
182B LEU* 1.3 60.2 + - - +
184B LEU* 3.4 14.7 + - + +
185B VAL* 3.1 25.8 + - - +
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Residues in contact with LEU 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ARG* 4.0 41.2 + - + +
77B LEU* 4.0 28.9 - - + -
78B THR* 4.6 3.4 - - - +
81B LEU* 3.5 33.7 - - + -
143B TRP* 3.6 32.1 - - + +
178B LEU 3.1 22.7 + - - +
179B TYR 3.8 3.6 - - - +
181B MET* 1.3 74.3 - - - +
183B LEU* 1.3 61.4 + - - +
185B VAL* 3.2 8.6 + - + +
186B GLU* 3.0 28.4 + - - +
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Residues in contact with LEU 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B LEU* 3.7 13.7 - - + -
143B TRP* 3.5 31.8 - - + +
144B THR* 3.6 27.4 - - + -
147B PHE* 3.8 35.9 - - + -
179B TYR 3.0 18.2 + - - +
180B GLY* 3.4 13.0 - - - +
182B LEU* 1.3 75.7 - - - +
184B LEU* 1.3 59.3 + - + +
186B GLU* 3.1 8.6 + - - +
187B VAL* 2.9 34.4 + - + +
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180B GLY 3.0 20.6 + - - +
181B MET* 3.7 16.4 - - + +
182B LEU 3.3 0.2 - - - -
183B LEU* 1.3 77.3 - - + +
185B VAL* 1.3 58.7 + - + +
187B VAL* 3.3 14.1 + - + +
188B ASN* 2.9 28.2 + - - +
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Residues in contact with VAL 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO 4.4 4.3 - - - +
70B GLY* 4.1 25.1 - - - +
73B LEU* 3.8 33.4 - - + -
74B ARG* 3.3 29.8 - - + +
77B LEU* 4.6 3.1 - - + -
181B MET 3.1 15.2 + - - +
182B LEU* 3.2 13.9 + - + +
184B LEU* 1.3 76.6 - - + +
186B GLU* 1.3 56.7 + - - +
188B ASN* 3.1 9.2 + - + +
189B VAL* 2.9 27.3 + - + +
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Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ARG* 2.8 32.9 + - - +
124B TYR* 5.4 0.3 - - - -
136B LEU* 4.0 26.4 - - - +
139B LEU* 3.6 19.5 - - - +
140B LEU* 4.1 19.6 - - + +
143B TRP* 3.2 30.2 + - + +
182B LEU 3.0 18.5 + - - +
183B LEU* 3.1 7.8 + - - +
185B VAL* 1.3 75.4 - - - +
187B VAL* 1.3 63.1 + - - +
189B VAL* 3.1 8.2 + - - +
190B ILE* 3.0 24.2 + - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 4.8 14.4 - - + -
183B LEU* 2.9 23.7 + - + +
184B LEU* 3.6 16.6 - - + +
185B VAL 3.3 0.2 - - - -
186B GLU* 1.3 75.8 - - - +
188B ASN* 1.3 58.6 + - - +
190B ILE* 3.0 14.6 - - + +
191B ARG* 2.9 31.4 + - + +
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Residues in contact with ASN 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PRO* 4.1 26.0 + - - +
70B GLY* 5.1 2.0 - - - +
184B LEU 2.9 13.8 + - - +
185B VAL* 3.1 12.8 + - - +
187B VAL* 1.3 78.1 - - - +
189B VAL* 1.3 56.7 + - - +
191B ARG* 3.0 36.0 + - - +
192B VAL* 2.9 34.0 + - - +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B PHE* 4.5 24.9 - - + -
69B PRO* 3.6 25.4 - - + +
74B ARG* 4.2 16.2 - - - +
124B TYR* 4.7 2.5 - - + +
136B LEU* 4.0 32.8 - - + -
185B VAL 2.9 18.5 + - - +
186B GLU* 3.1 12.1 + - - +
188B ASN* 1.3 76.9 - - - +
190B ILE* 1.3 62.6 + - - +
192B VAL* 3.2 16.1 + - - +
193B ARG* 3.5 17.7 + - + +
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Residues in contact with ILE 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B LEU* 5.5 12.8 - - + -
186B GLU 3.0 15.0 + - - +
187B VAL* 3.0 28.5 - - + +
189B VAL* 1.3 79.4 - - - +
191B ARG* 1.3 61.7 + - - +
192B VAL 3.3 0.7 + - - -
193B ARG 3.9 5.5 + - - -
194B ARG 4.3 0.7 + - - -
195B TYR* 2.4 50.4 + - + +
196B ILE* 4.1 21.5 - - + +
197B PHE* 4.4 13.5 - - + +
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Residues in contact with ARG 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B VAL* 2.9 21.9 + - + +
188B ASN* 3.0 30.9 + - - +
190B ILE* 1.3 78.9 - - - +
192B VAL* 1.3 69.6 + - - +
197B PHE* 6.0 0.4 - - - -
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Residues in contact with VAL 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B PRO* 3.9 33.7 - - + -
188B ASN* 2.9 33.5 + - - +
189B VAL* 3.6 8.7 - - - +
190B ILE 3.1 0.6 - - - -
191B ARG* 1.3 88.6 - - - +
193B ARG* 1.3 74.3 + - + +
201B PRO 4.7 3.1 - - - +
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Residues in contact with ARG 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B LEU* 5.3 7.1 - - - +
67B HIS 5.6 1.2 + - - -
68B PHE* 3.4 40.7 - - + -
69B PRO* 6.3 0.7 - - + -
131B ASN* 3.9 23.5 - - - +
136B LEU* 5.2 5.8 - - - -
189B VAL* 3.5 18.7 + - + +
190B ILE 4.4 2.2 - - - -
191B ARG 3.8 0.6 - - - -
192B VAL* 1.3 90.1 - - + +
194B ARG* 1.3 73.0 + - - +
195B TYR 4.2 0.4 - - - -
197B PHE* 4.4 9.4 - - - +
198B PHE 5.3 0.9 - - - +
200B THR 4.6 1.4 - - - +
201B PRO* 3.3 34.2 - - + +
203B GLU* 3.1 34.7 - - - +
204B VAL* 4.6 16.4 - - + +
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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