Contacts of the helix formed by residues 185 - 219 (chain A) in PDB entry 1CUN
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 HIS 185 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 5.4 10.1 + - - -
110A GLU* 5.5 1.3 - - - -
114A TYR* 3.5 62.6 + + + +
183A ASN 3.4 1.8 + - - -
184A HIS* 1.3 86.0 - - + +
186A VAL* 1.3 65.1 + - - +
187A GLU* 3.2 8.6 + - - -
188A ASN* 3.3 8.0 + - + +
189A ILE* 2.9 23.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 4.2 29.4 - - + -
182A ASN 4.1 4.5 - - - +
183A ASN* 2.9 62.9 + - + +
184A HIS 3.1 2.2 - - - +
185A HIS* 1.3 77.1 - - - +
187A GLU* 1.3 71.1 + - + +
189A ILE* 3.4 1.0 + - - +
190A THR* 2.8 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ASN 5.0 1.7 - - - +
185A HIS* 4.1 5.9 + - - -
186A VAL* 1.3 88.3 + - + +
188A ASN* 1.3 61.4 + - - +
190A THR* 3.9 4.3 - - - -
191A ALA* 3.1 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 2.9 24.9 + - - +
118A VAL* 5.0 1.0 - - - +
185A HIS* 3.3 12.3 + - + +
187A GLU* 1.3 78.6 + - - +
189A ILE* 1.3 59.1 + - - +
191A ALA* 3.8 4.9 - - - +
192A LYS* 2.9 61.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 3.6 33.0 - - + -
117A PHE* 3.9 17.0 - - + -
175A GLY* 3.6 34.3 - - - +
178A LEU* 4.0 23.3 - - + -
179A ILE* 3.7 17.5 - - + +
181A LYS* 5.9 0.4 - - - +
184A HIS 3.7 15.7 - - - +
185A HIS 2.9 21.0 + - - +
186A VAL 3.9 2.9 - - - +
188A ASN* 1.3 77.0 - - - +
190A THR* 1.3 61.5 + - - +
192A LYS* 3.3 2.5 + - - +
193A MET* 3.0 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ILE* 3.4 15.8 - - - +
186A VAL* 2.8 28.1 + - - +
187A GLU* 3.9 4.5 - - - -
189A ILE* 1.3 75.1 - - - +
191A ALA* 1.3 58.8 + - - +
193A MET* 3.4 15.4 + - + +
194A LYS* 3.0 30.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLU 3.1 18.4 + - - +
188A ASN* 3.9 6.5 - - - +
190A THR* 1.3 77.7 - - - +
192A LYS* 1.3 58.8 + - + +
194A LYS* 3.4 7.7 + - - +
195A GLY* 2.8 26.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 5.4 0.4 - - + +
117A PHE* 4.2 19.3 - - + -
118A VAL* 4.3 32.5 + - + +
121A VAL* 4.1 31.2 - - + +
125A GLU* 4.6 3.7 + - - +
188A ASN* 2.9 48.1 + - - +
189A ILE 3.8 3.8 - - - +
191A ALA* 1.3 74.4 - - + +
193A MET* 1.3 62.2 + - - +
195A GLY* 3.8 1.5 - - - -
196A LEU* 2.9 31.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A PHE* 3.9 17.5 - - + -
172A CYS* 3.4 47.2 - - + +
175A GLY* 3.8 5.4 - - - -
176A GLU* 3.7 23.8 - - + +
179A ILE* 3.8 27.1 - - + -
189A ILE* 3.0 23.6 + - + +
190A THR* 3.7 13.0 - - + +
192A LYS* 1.3 76.8 - - - +
194A LYS* 1.3 62.3 + - - +
196A LEU* 3.2 4.3 + - - +
197A LYS* 3.0 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A THR* 3.0 19.6 + - + +
191A ALA* 3.8 7.0 - - - +
193A MET* 1.3 76.6 - - - +
195A GLY* 1.3 63.1 + - - +
197A LYS* 3.4 9.9 + - - +
198A GLY* 3.0 21.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.9 7.0 - - - -
191A ALA 2.8 17.8 + - - -
192A LYS* 3.8 2.0 - - - -
194A LYS* 1.3 78.0 - - - +
196A LEU* 1.3 56.2 + - - +
198A GLY* 3.2 3.7 + - - -
199A LYS* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A VAL* 4.2 16.4 - - + +
124A GLU* 3.9 19.7 - - + -
125A GLU* 3.5 35.3 + - + +
128A ILE* 4.2 7.9 - - + -
168A VAL* 3.7 31.2 - - + -
171A VAL* 4.0 28.7 - - + -
172A CYS* 4.5 5.8 - - - -
192A LYS 2.9 16.8 + - - +
193A MET* 3.7 4.3 - - - +
195A GLY* 1.3 76.6 - - - +
197A LYS* 1.3 62.7 + - - +
199A LYS* 3.1 4.9 + - + +
200A VAL* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 5.0 5.1 - - + +
169A ASN* 4.7 11.9 + - - +
172A CYS* 3.9 35.2 - - - +
176A GLU* 5.2 8.2 + - - -
193A MET* 3.0 25.0 + - - +
194A LYS* 3.8 6.7 - - - +
196A LEU* 1.3 75.1 - - - +
198A GLY* 1.3 57.4 + - - +
200A VAL* 3.3 9.1 + - - +
201A SER* 3.0 32.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A LYS 3.0 15.2 + - - -
195A GLY* 3.6 4.3 - - - -
196A LEU 3.2 0.4 - - - -
197A LYS* 1.3 79.0 - - - +
199A LYS* 1.3 55.1 + - - +
201A SER* 3.4 6.6 + - - -
202A ASP* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLU* 3.5 36.0 + - + +
128A ILE* 3.8 24.2 - - + +
129A ASN* 2.9 36.5 + - - +
132A MET* 5.3 1.3 - - - +
195A GLY 2.9 16.0 + - - +
196A LEU* 3.1 8.3 + - - +
198A GLY* 1.3 75.9 - - - +
200A VAL* 1.3 64.6 + - - +
202A ASP* 3.3 9.9 + - - +
203A LEU* 3.0 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ILE* 3.8 20.4 - - + -
161A PHE* 3.7 22.3 - - + -
164A HIS 6.1 0.2 - - - -
165A LYS* 4.2 12.6 - - + -
168A VAL* 3.8 29.6 - - + -
196A LEU 3.0 17.4 + - - +
197A LYS* 3.3 8.0 + - - +
199A LYS* 1.3 75.7 - - - +
201A SER* 1.3 57.6 + - - +
203A LEU* 3.3 1.1 + - - -
204A GLU* 2.9 51.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LYS* 3.0 17.4 + - - +
198A GLY* 3.7 8.4 - - - -
199A LYS 3.3 0.2 - - - -
200A VAL* 1.3 77.4 - - - +
202A ASP* 1.3 59.6 + - - +
204A GLU* 3.3 16.1 + - - +
205A LYS* 3.0 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 202 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 3.9 19.8 - - + +
198A GLY 3.0 23.4 + - - +
199A LYS* 3.7 9.2 - - - +
200A VAL 3.3 0.2 - - - -
201A SER* 1.3 78.7 - - - +
203A LEU* 1.3 58.3 + - - +
205A LYS* 3.4 9.7 + - - +
206A ALA* 2.9 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 203 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP* 4.1 13.7 - - + -
128A ILE* 4.3 15.3 - - + -
131A LYS* 4.1 10.3 - - + +
132A MET* 3.6 38.3 - - - +
135A VAL* 4.3 11.0 - - + -
157A PHE* 3.8 26.0 - - + -
161A PHE* 3.5 34.5 - - + -
199A LYS 3.0 16.9 + - - +
200A VAL 3.3 0.2 + - - -
202A ASP* 1.3 74.1 - - - +
204A GLU* 1.3 60.9 + - - +
207A ALA* 2.8 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 204 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A PHE* 3.6 20.2 - - + -
165A LYS* 3.2 30.0 + - - +
200A VAL* 2.9 28.6 + - - +
201A SER* 3.3 18.8 + - - +
203A LEU* 1.3 75.7 - - - +
205A LYS* 1.3 62.2 + - - +
207A ALA* 3.8 3.3 - - - +
208A ALA* 3.0 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 205 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A SER 3.0 15.8 + - - +
202A ASP* 3.7 11.0 - - - +
204A GLU* 1.3 77.6 - - - +
206A ALA* 1.3 62.7 + - - +
208A ALA* 3.4 6.3 + - - +
209A GLN* 3.1 50.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 206 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A MET* 4.0 20.9 - - + +
135A VAL* 3.4 22.9 - - + +
136A ALA* 6.1 1.8 - - + -
202A ASP 2.9 17.4 + - - +
203A LEU 3.9 3.6 - - - +
205A LYS* 1.3 77.3 - - - +
207A ALA* 1.3 63.6 + - - +
209A GLN* 3.3 15.3 + - - +
210A ARG* 3.0 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 207 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A VAL* 3.6 11.8 - - + +
154A HIS* 3.2 14.6 + - - +
157A PHE* 3.8 22.0 - - + -
158A GLU* 3.8 20.9 - - - +
161A PHE* 5.0 1.3 - - + -
203A LEU 2.8 19.1 + - - +
204A GLU* 3.8 6.1 - - - +
206A ALA* 1.3 74.4 - - - +
208A ALA* 1.3 60.1 + - - +
210A ARG 3.3 0.9 + - - -
211A LYS* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A GLU* 5.5 1.3 - - - -
204A GLU 3.0 17.9 + - - +
205A LYS* 3.7 6.3 - - - +
206A ALA 3.3 0.2 - - - -
207A ALA* 1.3 76.2 - - - +
209A GLN* 1.3 63.3 + - + +
211A LYS* 3.4 7.2 + - - +
212A ALA* 3.0 25.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 209 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LYS* 3.1 47.0 + - + +
206A ALA* 3.6 15.3 + - - +
208A ALA* 1.3 78.9 - - + +
210A ARG* 1.3 61.6 + - - +
212A ALA* 3.5 6.9 + - - +
213A LYS* 3.1 34.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 210 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU 4.8 2.4 + - - -
135A VAL* 3.3 34.7 - - + +
137A SER* 3.4 32.4 + - - -
139A ASP* 3.0 28.7 + - - +
140A TYR* 3.7 16.4 - - + +
150A LEU* 3.6 29.9 + - - +
154A HIS* 4.3 14.0 - - + +
206A ALA 3.0 15.8 + - - +
207A ALA 3.7 4.3 - - - +
209A GLN* 1.3 76.1 - - - +
211A LYS* 1.3 65.5 + - - +
213A LYS* 3.2 8.5 + - - +
214A LEU* 3.0 36.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 211 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.2 20.9 - - + -
154A HIS* 3.8 26.9 + - + +
158A GLU* 5.2 0.9 - - - +
207A ALA 2.9 16.3 + - - +
208A ALA* 3.7 7.4 - - - +
210A ARG* 1.3 75.7 - - - +
212A ALA* 1.3 63.0 + - - +
214A LEU* 3.4 6.0 + - - +
215A ASP* 2.7 56.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 212 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA 3.0 17.3 + - - +
209A GLN* 3.6 8.1 - - - +
211A LYS* 1.3 79.4 - - - +
213A LYS* 1.3 55.9 + - + +
215A ASP* 3.4 5.5 + - - +
216A GLU* 3.0 45.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 213 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.2 54.0 + - + +
209A GLN* 3.1 21.9 + - - +
210A ARG 3.2 2.6 + - - +
212A ALA* 1.3 78.4 - - + +
214A LEU* 1.3 57.2 + - - +
216A GLU* 3.3 19.4 + - - +
217A ASN* 2.9 34.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 214 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.8 36.8 - - + +
147A ILE* 3.5 15.2 - - + +
150A LEU* 3.9 37.0 - - + +
151A LEU* 3.3 28.9 - - + -
154A HIS* 4.4 9.2 - - + -
210A ARG* 3.0 43.3 + - + +
211A LYS* 3.7 4.0 - - - +
213A LYS* 1.3 76.1 - - - +
215A ASP* 1.3 63.9 + - - +
217A ASN* 3.3 6.7 + - - +
218A SER 3.1 18.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 215 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 3.6 23.6 - - - +
211A LYS* 2.7 47.7 + - - +
212A ALA* 3.9 5.1 - - - +
214A LEU* 1.3 73.0 - - - +
216A GLU* 1.3 67.6 + - - +
218A SER* 3.1 8.5 + - - -
219A ALA* 2.9 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ALA* 3.0 35.1 + - - +
213A LYS* 3.3 20.4 + - - +
215A ASP* 1.3 77.3 - - - +
217A ASN* 1.3 63.8 + - - +
219A ALA* 3.3 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 217 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TYR* 3.7 32.0 - - - +
141A GLY 3.6 17.0 - - - +
144A LEU* 4.1 6.8 - - - +
147A ILE* 3.6 20.5 - - + +
213A LYS* 2.9 17.6 + - - +
214A LEU* 3.4 6.7 - - - +
215A ASP 3.2 0.2 - - - -
216A GLU* 1.3 77.1 - - - +
218A SER* 1.3 58.7 + - - +
219A ALA* 3.8 1.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 218 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 3.9 18.5 - - - +
147A ILE* 3.5 32.5 - - - +
148A GLN* 4.6 11.8 + - - -
151A LEU* 4.3 6.4 - - - +
214A LEU 3.1 7.6 + - - -
215A ASP* 3.1 12.5 + - - -
217A ASN* 1.3 75.6 - - - +
219A ALA* 1.3 63.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 219 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 5.9 0.2 - - - +
215A ASP* 2.9 17.7 + - + +
216A GLU* 3.3 14.5 + - - +
217A ASN 5.0 1.2 - - - +
218A SER* 1.3 81.9 - - - +
----------------------------------------------------------
Back to top of page
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