Contacts of the helix formed by residues 159 - 196 (chain A) in PDB entry 3KQG
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 159 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP* 1.3 60.1 + - - +
161A LEU* 3.6 12.6 + - - +
162A GLU* 3.2 36.5 + - - +
163A LYS* 2.9 50.6 + - - +
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Residues in contact with ASP 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 1.3 73.2 + - - +
161A LEU* 1.3 61.9 + - - +
163A LYS* 3.8 25.0 + - - +
164A ALA* 3.4 20.1 + - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 3.2 7.4 + - - +
160A ASP* 1.3 76.1 - - - +
162A GLU* 1.3 66.9 + - + +
164A ALA* 3.4 9.6 + - + +
165A SER* 3.2 28.1 + - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 3.2 33.0 + - - +
161A LEU* 1.3 77.9 - - + +
163A LYS* 1.3 59.3 + - + +
165A SER* 3.3 7.2 + - - -
166A ALA* 2.9 32.9 + - - +
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Residues in contact with LYS 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A SER* 2.9 42.3 + - - +
160A ASP* 3.9 23.7 + - - +
161A LEU 3.3 0.2 - - - -
162A GLU* 1.3 75.8 - - + +
164A ALA* 1.3 57.8 + - - +
166A ALA* 4.1 4.6 - - - +
167A LEU* 3.1 31.6 + - - +
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Residues in contact with ALA 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160A ASP 3.4 11.6 + - - +
161A LEU* 3.4 14.1 + - + +
162A GLU 3.2 0.6 - - - -
163A LYS* 1.3 76.8 - - - +
165A SER* 1.3 64.9 + - - +
167A LEU* 3.8 5.2 - - - +
168A ASN* 3.0 32.4 + - - +
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Residues in contact with SER 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 3.2 15.8 + - - +
162A GLU* 3.3 10.4 + - - -
164A ALA* 1.3 78.2 - - - +
166A ALA* 1.3 64.9 + - - +
168A ASN* 3.1 5.7 + - - +
169A THR* 2.9 32.2 + - - +
172A ARG* 5.1 2.0 - - - +
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A GLU 2.9 20.0 + - - +
163A LYS* 4.1 4.7 - - - +
165A SER* 1.3 71.5 - - - +
167A LEU* 1.3 65.7 + - - +
169A THR* 2.8 23.9 + - - -
170A LYS* 2.9 27.1 + - - +
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Residues in contact with LEU 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LYS 3.1 18.8 + - - +
164A ALA* 3.8 5.6 - - - +
166A ALA* 1.3 78.3 - - - +
168A ASN* 1.3 66.6 + - - +
170A LYS* 3.4 8.9 + - + +
171A ILE* 3.0 41.8 + - + +
168C ASN* 4.6 9.4 - - - +
171C ILE* 4.0 26.7 - - + -
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Residues in contact with ASN 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A ALA* 3.0 21.9 + - - +
165A SER* 3.5 2.2 - - - +
167A LEU* 1.3 87.1 - - - +
169A THR* 1.3 62.4 + - - +
171A ILE* 3.1 10.4 + - - +
172A ARG* 2.9 53.3 + - - +
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Residues in contact with THR 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER* 2.9 25.2 + - - +
166A ALA* 2.8 21.4 + - - -
168A ASN* 1.3 70.8 - - - +
170A LYS* 1.3 59.6 + - - +
172A ARG* 3.0 30.7 - - - +
173A ALA* 3.0 26.9 + - - +
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Residues in contact with LYS 170 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A ALA* 2.9 30.5 + - + +
167A LEU* 3.6 7.9 - - + +
169A THR* 1.3 79.0 + - - +
171A ILE* 1.3 59.9 + - - +
173A ALA* 3.2 8.7 + - - +
174A LEU* 3.0 32.4 + - - +
168C ASN* 5.4 8.4 - - - +
171C ILE* 4.8 15.6 - - + +
175C GLN* 4.1 25.6 + - - +
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Residues in contact with ILE 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.0 39.4 + - + +
168A ASN* 3.1 9.8 + - - +
170A LYS* 1.3 73.9 - - - +
172A ARG* 1.3 67.0 + - + +
174A LEU* 3.3 6.9 + - - +
175A GLN* 3.0 35.0 + - - +
167B LEU 6.2 0.2 - - - +
170B LYS* 5.3 13.2 - - + +
171B ILE* 4.6 17.7 - - + -
174B LEU* 4.3 14.3 - - + +
171C ILE* 3.6 23.6 - - + -
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Residues in contact with ARG 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A SER* 3.8 3.2 + - - +
168A ASN* 2.9 37.6 + - - +
169A THR* 3.0 45.1 - - - +
171A ILE* 1.3 76.9 - - + +
173A ALA* 1.3 58.2 + - - +
175A GLN* 3.3 20.5 + - - +
176A GLY* 2.9 25.1 + - - -
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Residues in contact with ALA 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A THR 3.0 15.9 + - - +
170A LYS* 3.3 13.0 - - - +
171A ILE 3.1 0.4 - - - -
172A ARG* 1.3 77.2 - - - +
174A LEU* 1.3 58.9 + - + +
176A GLY* 3.0 3.7 + - - -
177A SER* 2.8 32.5 + - - +
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Residues in contact with LEU 174 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LYS 3.0 15.3 + - - +
171A ILE 3.3 7.4 + - - +
173A ALA* 1.3 75.6 - - + +
175A GLN* 1.3 55.3 + - - +
177A SER* 3.4 3.2 + - - +
178A LEU* 2.8 40.2 + - + +
174B LEU* 4.1 13.7 - - + -
171C ILE* 3.6 31.0 - - + -
174C LEU* 3.8 27.1 - - + -
175C GLN* 3.7 33.4 - - + +
178C LEU* 3.6 25.6 - - + -
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Residues in contact with GLN 175 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A ILE* 3.0 23.5 + - - +
172A ARG* 3.4 27.7 - - - +
173A ALA 3.2 0.2 - - - -
174A LEU* 1.3 76.1 - - - +
176A GLY* 1.3 62.2 + - - +
178A LEU* 3.9 2.0 - - - +
179A GLU* 3.1 42.5 + - - +
170B LYS* 3.0 41.3 + - - +
174B LEU* 3.5 27.3 - - + +
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Residues in contact with GLY 176 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A ARG 2.9 14.2 + - - -
173A ALA* 3.0 4.4 + - - -
175A GLN* 1.3 77.5 - - - +
177A SER* 1.3 56.6 + - - +
179A GLU* 3.4 8.6 + - - +
180A ASN* 3.0 27.5 + - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ALA* 2.8 21.7 + - - +
174A LEU* 3.8 1.3 - - - +
176A GLY* 1.3 70.4 - - - +
178A LEU* 1.3 55.7 + - - +
180A ASN* 3.1 9.0 + - - +
181A MET* 2.7 39.9 + - - +
178C LEU* 3.6 29.7 - - - +
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Residues in contact with LEU 178 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A LEU* 2.8 27.0 + - + +
175A GLN* 3.9 5.2 - - - +
177A SER* 1.3 72.8 - - - +
179A GLU* 1.3 59.1 + - + +
181A MET* 4.3 0.9 - - - -
182A SER* 3.2 22.3 + - - -
174B LEU* 3.6 37.5 - - + +
177B SER* 3.1 25.8 - - - +
178B LEU* 3.5 29.4 - - + -
181B MET* 3.4 29.2 - - + +
178C LEU* 3.9 22.2 - - + -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A GLN* 3.1 31.0 + - - +
176A GLY* 3.7 6.3 - - - +
177A SER 3.1 0.8 - - - -
178A LEU* 1.3 78.2 - - + +
180A ASN* 1.3 64.8 + - - +
182A SER* 3.4 8.9 + - - -
183A LYS* 3.2 19.9 + - - +
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Residues in contact with ASN 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A GLY 3.0 15.6 + - - +
177A SER* 3.1 12.8 + - - +
179A GLU* 1.3 73.9 - - - +
181A MET* 1.3 71.5 + - - +
183A LYS* 3.1 18.9 + - - +
184A LEU* 3.0 45.8 + - - +
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Residues in contact with MET 181 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER* 2.7 21.6 + - - +
178A LEU* 3.7 8.3 - - - +
180A ASN* 1.3 74.7 - - - +
182A SER* 1.3 61.3 + - - +
184A LEU* 3.1 15.2 + - + +
185A LEU* 2.9 34.3 + - + +
181B MET* 3.7 7.2 - - + -
178C LEU* 4.0 20.0 - - + -
181C MET* 3.5 33.7 - - + -
182C SER* 4.4 25.1 - - - -
185C LEU* 4.2 21.3 - - + -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178A LEU 3.2 12.4 + - - -
179A GLU* 3.5 11.7 - - - -
181A MET* 1.3 79.0 - - - +
183A LYS* 1.3 62.2 + - - +
185A LEU* 3.3 7.5 + - - +
186A LYS* 3.1 44.1 + - - +
181B MET* 3.6 16.6 - - - +
184B LEU* 5.8 1.0 - - - +
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Residues in contact with LYS 183 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A GLU 3.2 9.2 + - - +
180A ASN* 3.1 20.6 + - - +
182A SER* 1.3 80.2 - - - +
184A LEU* 1.3 66.4 + - + +
186A LYS* 3.3 14.3 + - + +
187A ARG* 3.2 19.4 + - - +
327A GLU* 2.8 43.8 + - + +
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Residues in contact with LEU 184 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180A ASN* 3.0 43.0 + - - +
181A MET* 3.1 15.9 + - + +
183A LYS* 1.3 79.6 - - + +
185A LEU* 1.3 60.4 + - - +
187A ARG* 3.4 17.3 + - + +
188A GLN* 3.0 31.8 + - - +
185C LEU* 3.8 23.3 - - + -
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181A MET* 2.9 19.4 + - + +
182A SER* 3.3 7.6 + - - +
184A LEU* 1.3 74.7 - - - +
186A LYS* 1.3 56.0 + - - +
188A GLN* 3.3 3.2 + - - +
189A ASN 2.8 28.8 + - - -
181B MET* 3.8 46.7 - - + +
184B LEU* 4.1 20.4 - - + -
185B LEU* 3.5 37.0 - - + -
188B GLN* 3.0 26.2 + - - +
181C MET* 4.6 5.4 - - + -
185C LEU* 4.0 17.0 - - + -
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Residues in contact with LYS 186 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A SER* 3.1 33.7 + - - +
183A LYS* 3.4 15.5 - - + +
185A LEU* 1.3 75.9 - - + +
187A ARG* 1.3 58.5 + - - +
189A ASN* 3.2 7.2 + - - +
190A ASP* 2.9 38.5 + - - +
326A SER* 5.4 5.6 - - - +
327A GLU* 5.1 23.6 - - + +
184B LEU* 6.2 2.9 - - + -
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Residues in contact with ARG 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A LYS 3.2 12.2 + - - +
184A LEU* 3.7 20.2 - - + +
185A LEU 3.3 0.2 - - - -
186A LYS* 1.3 72.7 - - - +
188A GLN* 1.3 71.7 + - + +
190A ASP* 3.2 3.2 + - - +
191A ILE* 3.1 35.0 + - + +
201A TYR* 2.9 30.5 + - - -
204A GLY* 6.0 0.6 - - - -
323A TYR* 3.5 41.2 - - + +
325A PRO* 5.7 2.0 - - + +
189C ASN* 5.5 2.2 + - - -
193C GLN* 4.6 11.9 - - - +
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Residues in contact with GLN 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A LEU* 3.0 20.8 + - + +
185A LEU* 3.3 4.9 - - - +
187A ARG* 1.3 82.0 - - + +
189A ASN* 1.3 57.1 + - - +
191A ILE* 3.4 3.9 + - - +
192A LEU* 2.8 32.4 + - - +
188B GLN* 3.2 20.2 - - - +
192B LEU* 5.9 0.2 - - - +
185C LEU* 3.5 28.0 - - + +
188C GLN* 4.1 10.7 - - - +
189C ASN* 3.0 51.7 + - - +
192C LEU* 4.1 19.5 - - + +
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Residues in contact with ASN 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185A LEU 2.8 17.0 + - - +
186A LYS* 3.6 7.9 - - - +
187A ARG 3.2 0.2 - - - -
188A GLN* 1.3 75.1 - - - +
190A ASP* 1.3 65.7 + - - +
192A LEU* 4.3 5.1 - - - +
193A GLN* 2.9 61.9 + - - +
184B LEU* 5.6 2.9 - - - +
188B GLN* 3.5 24.7 + - - +
191B ILE* 5.5 1.4 - - - +
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Residues in contact with ASP 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A LYS* 2.9 21.2 + - - +
187A ARG* 3.2 3.0 + - - +
189A ASN* 1.3 79.3 + - - +
191A ILE* 1.3 63.9 + - - +
193A GLN* 3.4 5.3 + - - +
194A VAL* 3.4 24.6 + - - +
206A PHE* 4.7 2.9 - - + -
323A TYR* 2.6 41.7 + - + +
324A VAL 5.7 0.2 - - - -
325A PRO* 3.7 0.9 - - - +
326A SER* 3.1 39.2 + - - -
327A GLU 5.0 0.3 + - - -
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Residues in contact with ILE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A ARG* 3.1 41.1 + - + +
188A GLN* 3.9 4.5 - - - +
190A ASP* 1.3 79.1 - - - +
192A LEU* 1.3 57.9 + - - +
194A VAL* 3.3 3.3 + - - +
195A VAL* 2.9 28.8 + - + +
201A TYR* 3.7 61.9 - - + +
206A PHE* 4.0 10.3 - - + -
323A TYR* 4.2 10.3 - - + -
192C LEU* 3.9 21.5 - - + -
193C GLN* 5.3 4.7 - - - +
196C SER* 4.0 7.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A GLN 2.8 19.7 + - - +
189A ASN* 3.8 4.9 - - - +
190A ASP 3.3 0.4 - - - -
191A ILE* 1.3 77.6 - - - +
193A GLN* 1.3 62.4 + - - +
195A VAL* 3.6 3.3 - - + -
196A SER* 2.6 52.2 + - - +
188B GLN* 3.6 41.5 - - + +
191B ILE* 3.7 22.4 - - + -
192B LEU* 4.2 17.9 - - + -
195B VAL* 5.0 7.0 - - + -
192C LEU* 4.2 24.2 - - + +
----------------------------------------------------------
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A ASN* 2.9 55.3 + - - +
190A ASP* 3.8 6.3 - - - +
192A LEU* 1.3 89.7 - - - +
194A VAL* 1.3 61.7 + - + +
196A SER* 3.5 7.9 + - - -
197A GLN* 3.0 38.2 + - - +
191B ILE* 4.6 4.6 - - - +
201B TYR* 4.0 29.4 - - - +
202B PHE* 5.8 0.5 - - - -
203B LYS 5.6 1.2 + - - -
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A ASP 3.4 11.8 + - - +
191A ILE 3.3 1.9 + - - +
192A LEU 3.2 0.6 - - - -
193A GLN* 1.3 77.2 - - + +
195A VAL* 1.3 60.4 + - - +
197A GLN* 2.9 32.0 + - - +
199A TRP* 3.4 35.1 + - + +
206A PHE* 3.4 40.4 - - + -
321A ARG* 3.7 23.6 - - - +
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Residues in contact with VAL 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 2.9 28.3 + - + +
192A LEU* 3.8 5.6 - - + +
194A VAL* 1.3 69.7 - - - +
196A SER* 1.3 57.9 + - - +
197A GLN 2.9 9.9 + - - -
198A GLY* 3.2 11.1 + - - -
199A TRP 3.4 21.3 - - - +
200A LYS 4.6 0.7 - - - -
201A TYR* 4.1 10.1 - - + -
206A PHE* 5.2 1.6 - - + -
195B VAL* 4.3 17.7 - - + +
199B TRP 5.6 0.2 - - - +
200B LYS* 5.0 1.6 - - - +
192C LEU* 4.7 6.5 - - + -
195C VAL* 4.5 17.0 - - + +
196C SER* 3.3 33.0 - - - +
----------------------------------------------------------
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Residues in contact with SER 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192A LEU* 2.6 29.8 + - - +
193A GLN* 3.7 7.8 - - - -
194A VAL 3.2 0.4 - - - -
195A VAL* 1.3 70.8 - - - +
197A GLN* 1.3 57.5 + - - +
198A GLY 3.6 1.1 - - - -
191B ILE* 3.7 13.5 - - - +
195B VAL* 3.3 27.1 - - - +
200B LYS* 3.2 13.3 - - - +
201B TYR* 2.9 53.4 + - - +
241B PHE* 4.4 0.3 - - - -
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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