Contacts of the helix formed by residues 185 - 209 (chain A) in PDB entry 5DLG
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 185 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLN* 3.6 37.7 + - - +
182A ASN* 3.4 26.8 + - - +
183A LEU 3.4 2.4 - - - -
184A THR* 1.3 75.8 - - - +
186A PRO* 1.3 71.7 - - - +
187A ASP* 3.5 10.7 + - - +
188A LEU* 3.0 11.5 + - - +
189A GLN* 3.0 22.5 + - - +
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Residues in contact with PRO 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLN* 3.2 49.6 - - + +
184A THR 3.2 9.6 - - - +
185A SER* 1.3 87.6 - - - +
187A ASP* 1.3 58.3 + - - +
189A GLN* 3.3 16.0 + - - +
190A LEU* 3.0 32.7 + - - +
218A HIS* 3.7 16.2 - - + +
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Residues in contact with ASP 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A GLN* 4.7 6.2 + - - -
174A TRP* 3.6 34.8 - - + -
178A LEU* 4.1 9.2 - - + -
179A GLN* 4.6 13.1 + - - +
185A SER* 3.2 8.6 + - - +
186A PRO* 1.3 81.4 - - - +
188A LEU* 1.3 54.1 + - - +
190A LEU* 3.5 7.4 + - - +
191A THR* 2.6 38.3 + - - -
239A SER* 3.9 12.8 - - - -
240A HIS 4.8 1.4 + - - -
241A GLY 5.3 1.6 + - - -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LEU* 3.6 28.5 - - + -
137A ILE* 3.9 12.8 - - + -
178A LEU* 3.7 23.6 - - + +
179A GLN* 3.7 10.3 - - + +
180A ILE* 3.7 36.6 - - + +
182A ASN 3.2 27.1 - - - +
183A LEU* 4.2 4.0 - - - +
185A SER* 3.0 17.2 + - - +
187A ASP* 1.3 75.4 - - - +
189A GLN* 1.3 65.9 + - - +
191A THR* 3.1 5.1 + - - -
192A VAL* 3.0 24.6 + - + +
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Residues in contact with GLN 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLN 3.5 21.1 + - - +
6A ASP* 4.7 7.2 + - - +
8A VAL* 3.7 22.8 - - + +
122A THR* 6.2 0.7 - - - +
125A VAL* 3.6 27.2 - - + +
126A GLN* 5.9 3.4 - - + +
129A LEU* 4.6 2.5 - - + -
183A LEU 4.4 10.3 + - - +
184A THR* 3.3 30.1 + - - +
185A SER 3.0 10.3 + - - +
186A PRO* 3.4 16.9 - - - +
188A LEU* 1.3 76.7 - - - +
190A LEU* 1.3 52.1 + - - +
192A VAL* 3.2 0.9 + - - -
193A GLY* 2.8 31.4 + - - -
218A HIS* 4.5 1.4 - - - -
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Residues in contact with LEU 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.2 13.0 - - + -
186A PRO 3.0 17.5 + - - +
187A ASP* 3.5 11.2 - - - +
189A GLN* 1.3 73.2 - - - +
191A THR* 1.3 57.3 + - - +
193A GLY* 3.2 2.5 + - - +
194A ALA* 2.8 29.6 + - - +
216A ILE* 3.9 7.6 - - + +
217A SER* 3.4 33.7 - - - +
218A HIS* 3.6 27.8 - - + +
237A LEU* 3.7 24.4 - - + +
238A VAL 3.8 6.5 - - - +
239A SER* 3.6 32.3 - - - -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 3.7 14.6 - - + -
142A LEU* 4.1 21.0 - - + +
174A TRP* 3.0 24.6 + - - +
175A LEU* 4.1 4.5 - - + -
178A LEU* 3.5 27.9 - - + +
187A ASP 2.6 21.6 + - - -
188A LEU 3.1 7.8 + - - -
190A LEU* 1.3 75.4 - - - +
192A VAL* 1.3 57.6 + - - +
194A ALA* 3.2 6.5 + - - +
195A VAL* 3.1 25.1 + - - +
237A LEU* 3.8 9.6 - - + +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.1 20.4 - - + +
128A ARG* 3.8 34.8 - - + -
129A LEU* 4.1 22.0 - - + +
132A LEU* 4.2 8.3 - - + -
137A ILE* 3.6 23.6 - - + -
188A LEU* 3.0 18.8 + - + +
189A GLN 3.8 3.6 - - - +
191A THR* 1.3 72.6 - - - +
193A GLY* 1.3 66.7 + - - +
195A VAL* 3.1 11.0 + - + +
196A ILE* 3.1 23.6 + - + +
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Residues in contact with GLY 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.1 12.3 - - - -
121A LEU* 3.9 5.9 - - - +
125A VAL* 3.5 18.4 - - - +
189A GLN 2.8 13.0 + - - -
190A LEU 3.5 4.5 - - - -
192A VAL* 1.3 77.8 - - - +
194A ALA* 1.3 56.3 + - - +
196A ILE* 3.2 6.9 + - - +
197A VAL* 3.0 33.6 + - - +
216A ILE* 4.4 3.4 - - - -
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A LEU* 3.8 14.1 - - + -
145A THR* 4.5 5.6 - - + +
190A LEU 2.8 14.9 + - - +
191A THR 3.2 10.3 + - - +
193A GLY* 1.3 71.5 - - - +
195A VAL* 1.3 64.5 + - - +
197A VAL 4.4 0.2 - - - +
198A GLU* 3.1 13.2 + - - +
216A ILE* 4.0 17.2 - - + +
235A GLN* 2.9 31.6 + - - +
237A LEU* 4.0 15.5 - - + -
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ARG* 3.8 14.4 - - + +
137A ILE* 4.1 15.3 - - + -
141A LEU* 4.1 33.9 - - + +
142A LEU* 3.6 23.6 - - + -
191A THR 3.1 16.7 + - - +
192A VAL* 3.1 16.0 + - + +
194A ALA* 1.3 76.3 - - - +
196A ILE* 1.3 65.3 + - - +
198A GLU* 3.3 6.2 - - - +
199A GLU* 3.2 37.7 + - + +
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PHE* 4.3 14.1 - - + -
121A LEU* 3.9 22.4 - - + -
124A ALA* 3.9 40.6 - - + +
125A VAL* 4.1 11.9 - - + +
128A ARG* 3.9 24.5 - - + +
192A VAL* 3.1 20.4 + - + +
193A GLY* 3.5 7.9 - - - +
195A VAL* 1.3 76.8 - - - +
197A VAL* 1.3 57.0 + - - +
199A GLU* 3.0 13.1 + - - +
200A MET* 2.8 35.0 + - + +
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.0 6.3 - - + -
12A VAL* 4.5 9.2 - - + -
121A LEU* 3.6 22.2 - - + -
193A GLY 3.0 16.6 + - - +
194A ALA 3.9 4.7 - - - +
195A VAL 3.4 0.2 - - - -
196A ILE* 1.3 75.5 - - - +
198A GLU* 1.3 53.4 + - - +
200A MET* 4.1 10.5 - - + -
201A ARG* 2.7 39.4 + - + +
214A ALA* 3.5 30.3 - - + -
216A ILE* 3.7 17.0 - - + -
235A GLN* 3.6 12.8 - - - +
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Residues in contact with GLU 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A LEU 3.6 20.2 - - - +
142A LEU* 4.1 1.6 - - + -
143A PRO* 3.3 22.2 - - + +
144A SER* 2.8 40.7 + - - -
145A THR* 2.8 20.6 + - - +
194A ALA 3.1 20.4 + - - +
195A VAL 3.3 9.2 - - - +
197A VAL* 1.3 75.4 - - - +
199A GLU* 1.3 57.9 + - + +
201A ARG* 3.8 5.7 + - - +
202A ALA* 2.9 29.9 + - - +
235A GLN* 3.4 10.5 + - - +
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Residues in contact with GLU 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A PHE* 4.2 13.3 - - + -
128A ARG* 2.5 45.8 + - - -
141A LEU* 5.8 1.7 - - - +
195A VAL* 3.4 21.8 - - + +
196A ILE* 3.0 13.7 + - - +
198A GLU* 1.3 73.0 - - + +
200A MET* 1.3 61.9 + - - +
202A ALA* 3.2 8.0 + - - +
203A ALA* 2.8 29.5 + - - +
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Residues in contact with MET 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.5 10.3 - - + -
102A ILE 5.6 0.2 - - - -
103A MET* 4.0 45.1 - - + +
106A PHE* 3.6 52.5 - - + -
119A VAL* 4.3 9.6 - - + -
121A LEU* 4.1 22.9 - - + -
196A ILE* 2.8 20.5 + - + +
197A VAL* 3.7 14.4 - - + +
199A GLU* 1.3 71.9 - - - +
201A ARG* 1.3 66.6 + - + +
203A ALA* 3.1 4.5 + - - +
204A ILE* 3.0 29.8 + - + +
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Residues in contact with ARG 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.9 5.4 - - + -
144A SER* 2.8 24.2 + - - -
197A VAL* 2.7 32.3 + - + +
198A GLU* 3.8 5.8 + - - +
200A MET* 1.3 73.6 - - + +
202A ALA* 1.3 62.7 + - - +
204A ILE* 3.4 6.2 + - + +
205A GLU* 3.2 22.2 + - - +
210A PHE 5.2 0.2 - - - +
212A CYS* 3.1 51.6 + - - +
213A SER* 4.3 1.0 - - - +
214A ALA* 3.9 14.6 - - + -
233A ASN* 3.4 34.2 + - - -
234A ARG 4.2 6.1 - - - -
235A GLN* 2.8 32.8 + - - +
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Residues in contact with ALA 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A GLU 2.9 18.7 + - - +
199A GLU* 3.2 8.7 + - - +
201A ARG* 1.3 76.8 - - - +
203A ALA* 1.3 57.4 + - - +
205A GLU* 3.3 7.0 + - - +
206A ARG* 2.8 32.9 + - - +
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Residues in contact with ALA 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 3.9 19.1 - - + -
105A ARG* 4.4 4.0 - - - +
106A PHE* 4.0 15.5 - - + -
199A GLU 2.8 13.2 + - - +
200A MET 3.1 9.2 + - - +
202A ALA* 1.3 76.8 - - - +
204A ILE* 1.3 55.6 + - - +
206A ARG* 3.4 4.8 + - - +
207A GLU* 2.9 46.6 + - - +
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Residues in contact with ILE 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A VAL* 4.4 4.7 - - + -
14A MET* 4.0 17.5 - - + -
99A VAL* 4.1 20.0 - - + +
102A ILE* 4.3 21.5 - - + -
103A MET* 3.8 29.8 - - + -
200A MET* 3.0 22.3 + - + +
201A ARG* 3.7 9.0 - - - +
202A ALA 3.3 0.2 - - - -
203A ALA* 1.3 75.0 - - - +
205A GLU* 1.3 56.3 + - - +
208A THR* 2.6 46.4 + - + +
210A PHE 3.6 14.1 - - - +
212A CYS* 4.1 20.6 - - - -
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Residues in contact with GLU 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201A ARG 3.2 13.9 + - - +
202A ALA* 3.9 5.4 - - - +
204A ILE* 1.3 79.3 - - - +
206A ARG* 1.3 60.9 + - - +
209A GLY* 2.9 31.2 + - - +
210A PHE 3.3 20.4 - - - +
211A GLN* 3.1 39.6 + - + +
233A ASN* 4.7 5.2 + - - +
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Residues in contact with ARG 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A ALA 2.8 18.1 + - - +
203A ALA* 3.9 5.4 - - - +
205A GLU* 1.3 78.4 - - - +
207A GLU* 1.3 90.4 + - - +
208A THR 3.9 0.2 + - - -
209A GLY 4.9 0.3 + - - -
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Residues in contact with GLU 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 4.5 4.2 - - - +
102A ILE* 3.7 18.8 - - + +
105A ARG* 3.1 43.3 + - - -
203A ALA* 2.9 23.2 + - - +
206A ARG* 1.3 114.6 + - - +
208A THR* 1.3 63.3 + - - +
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Residues in contact with THR 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ARG* 2.7 41.6 + - - +
98A GLU* 3.9 22.9 - - + +
99A VAL* 4.8 0.9 - - + +
102A ILE* 3.5 22.9 - - + -
204A ILE* 2.6 27.1 + - + +
207A GLU* 1.3 85.9 - - - +
209A GLY* 1.3 57.7 + - - +
210A PHE* 3.0 36.1 + - + +
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Residues in contact with GLY 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A GLN* 3.9 5.2 - - - +
24A ARG* 4.8 6.6 - - - +
205A GLU* 2.9 25.7 + - - +
206A ARG 4.7 0.8 + - - -
207A GLU 4.0 0.2 - - - -
208A THR* 1.3 76.9 - - - +
210A PHE* 1.3 64.7 + - - +
211A GLN* 3.8 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