Contacts of the helix formed by residues 160 - 192 (chain H) in PDB entry 3GHG
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 ASN 160 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192G ASP* 3.1 30.7 + - + +
155H GLU* 3.0 26.2 + - - +
156H THR* 3.8 8.3 + - - +
159H SER* 1.3 99.1 + - - +
161H ILE* 1.3 58.3 + - + +
163H THR* 2.5 9.7 + - - -
164H ASN* 2.5 40.2 + - + +
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Residues in contact with ILE 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G VAL* 6.2 0.7 - - + -
129G LYS* 5.5 4.5 - - + -
130G VAL* 4.7 24.5 - - + +
133G ILE* 4.3 27.6 - - + -
156H THR* 3.1 31.7 + - + +
157H VAL* 4.6 4.9 - - + -
160H ASN* 1.3 78.9 - - + +
162H PRO* 1.4 57.5 - - + +
164H ASN* 3.1 8.8 + - + +
165H LEU* 2.5 46.8 + - + +
103I HIS* 3.6 25.6 - - + -
107I ILE* 5.9 3.8 - - + -
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Residues in contact with PRO 162 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H VAL 3.5 17.3 - - - +
158H ASN* 3.6 24.0 - - - +
159H SER 4.3 2.2 - - - +
160H ASN 3.6 2.0 - - - -
161H ILE* 1.4 94.8 - - + +
163H THR* 1.3 59.2 + - + +
165H LEU* 3.6 10.7 - - + +
166H ARG* 3.1 23.4 + - - +
103I HIS* 3.4 26.5 - - + +
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Residues in contact with THR 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158H ASN 5.5 0.7 - - - +
159H SER 2.9 23.9 + - - +
160H ASN* 2.5 22.9 + - - -
162H PRO* 1.3 78.4 - - + +
164H ASN* 1.3 64.2 + - - +
165H LEU 3.3 0.2 - - - -
166H ARG* 3.2 39.6 + - - +
167H VAL* 3.2 12.8 + - - +
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Residues in contact with ASN 164 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ILE* 2.8 40.4 - - + +
137G GLN* 3.7 7.8 + - - +
188G VAL* 2.9 36.5 - - - +
160H ASN* 2.5 24.1 + - + +
161H ILE* 3.2 18.0 - - + +
163H THR* 1.3 74.1 + - - +
165H LEU* 1.3 61.3 + - - +
167H VAL* 3.2 26.5 - - - +
168H LEU* 3.2 14.5 + - - +
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Residues in contact with LEU 165 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ILE* 5.0 9.4 - - + -
161H ILE* 2.5 29.5 + - + +
162H PRO* 3.6 10.1 - - + +
164H ASN* 1.3 72.6 - - - +
166H ARG* 1.3 57.1 + - - +
167H VAL 3.5 0.2 - - - -
168H LEU* 4.0 7.1 - - + +
169H ARG* 3.0 36.2 + - - +
103I HIS* 4.0 32.8 - - + +
106I SER* 3.8 27.8 - - - +
107I ILE* 4.1 24.7 - - + +
110I LEU* 4.0 22.0 - - + +
----------------------------------------------------------
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Residues in contact with ARG 166 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G GLN* 4.8 4.8 - - - +
162H PRO 3.1 17.1 + - - +
163H THR* 3.4 31.7 + - - +
164H ASN 3.1 0.8 - - - -
165H LEU* 1.3 76.3 - - - +
167H VAL* 1.3 94.2 + - - +
169H ARG* 3.6 7.7 - - - +
170H SER* 3.0 27.5 + - - -
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Residues in contact with VAL 167 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184G GLN* 3.1 44.0 - - + +
185G LEU* 5.0 13.2 - - + -
188G VAL* 5.0 13.7 - - + -
163H THR 3.2 3.0 + - - +
164H ASN* 3.2 21.5 - - - +
166H ARG* 1.3 91.5 - - - +
168H LEU* 1.3 85.7 + - + +
170H SER* 2.9 6.3 + - - -
171H ILE* 2.8 35.5 + - + +
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Residues in contact with LEU 168 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133G ILE* 5.1 13.5 - - + +
136G LEU* 4.2 25.8 - - + -
137G GLN* 4.8 15.0 - - + +
140G VAL* 4.9 16.4 - - + -
185G LEU* 4.7 16.6 - - + -
164H ASN* 3.2 19.1 + - - +
165H LEU* 4.0 3.8 - - + +
167H VAL* 1.3 94.6 - - + +
169H ARG* 1.3 63.7 + - - +
171H ILE* 3.3 10.1 - - + +
172H LEU* 3.2 27.1 + - + +
110I LEU* 3.8 25.2 - - + +
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Residues in contact with ARG 169 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165H LEU* 3.0 28.4 + - - +
166H ARG* 3.6 8.3 - - - +
168H LEU* 1.3 75.7 - - - +
170H SER* 1.3 65.1 + - - +
171H ILE 3.1 0.2 + - - -
172H LEU* 4.5 0.3 - - - +
173H GLU* 2.9 43.1 + - + +
106I SER* 3.6 34.4 + - - +
109I TYR* 4.6 24.7 - - + -
110I LEU* 3.9 20.2 - - + +
----------------------------------------------------------
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Residues in contact with SER 170 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181G GLN* 3.9 15.0 + - - -
184G GLN* 4.7 6.8 + - - -
166H ARG* 3.0 15.0 + - - -
167H VAL* 2.9 11.9 + - - -
169H ARG* 1.3 79.9 - - - +
171H ILE* 1.3 58.1 + - - +
173H GLU* 3.7 8.0 - - - +
174H ASN* 3.0 26.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE 171 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G VAL* 5.3 13.5 - - + +
144G LEU* 4.0 29.2 - - + -
181G GLN* 3.2 47.8 - - + +
185G LEU* 4.4 15.0 - - + -
167H VAL* 2.8 24.0 + - + +
168H LEU* 3.3 23.3 - - + +
170H SER* 1.3 70.8 + - - +
172H LEU* 1.3 74.0 + - + +
173H GLU 3.1 1.3 - - - -
174H ASN* 2.9 20.8 + - - +
175H LEU* 3.0 19.1 + - + +
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Residues in contact with LEU 172 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G VAL* 5.1 13.7 - - + -
143G GLN* 4.7 10.3 - - - +
168H LEU* 3.2 13.3 + - + +
171H ILE* 1.3 84.7 - - + +
173H GLU* 1.3 62.2 + - + +
175H LEU* 3.6 9.1 + - - -
176H ARG* 3.2 19.8 + - - +
110I LEU* 4.2 22.4 - - + +
113I ILE* 2.6 41.1 - - + -
114I TYR* 3.4 39.3 - - + +
117I ASN* 3.6 8.3 - - - +
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Residues in contact with GLU 173 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H ARG* 2.9 38.3 + - + +
170H SER* 3.7 6.4 - - - +
172H LEU* 1.3 78.3 - - + +
174H ASN* 1.3 66.7 + - - +
175H LEU 3.3 0.5 + - - -
176H ARG* 3.4 17.7 + - - +
177H SER* 3.5 10.0 + - - -
----------------------------------------------------------
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Residues in contact with ASN 174 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177G ASP* 3.1 26.3 + - - -
181G GLN* 4.3 13.6 + - + +
170H SER 3.0 16.5 + - - +
171H ILE* 2.9 15.4 + - - +
173H GLU* 1.3 74.3 - - - +
175H LEU* 1.3 64.9 + - + +
177H SER* 2.2 29.3 + - - -
178H LYS* 3.1 29.7 + - - +
----------------------------------------------------------
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G VAL 5.8 0.4 - - - +
143G GLN* 3.5 23.1 - - - +
144G LEU* 4.3 35.4 - - + +
147G MET* 4.2 22.9 - - + -
178G TYR* 4.9 10.1 - - + -
181G GLN* 6.2 1.1 - - + -
171H ILE* 3.0 23.7 + - + +
172H LEU* 3.7 9.4 - - + +
173H GLU 3.2 0.2 - - - -
174H ASN* 1.3 85.6 - - + +
176H ARG* 1.3 52.7 + - - +
177H SER 2.6 6.0 + - - -
178H LYS* 2.5 32.9 + - + -
179H ILE* 2.6 20.4 + - + -
117I ASN* 3.4 11.9 - - - +
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Residues in contact with ARG 176 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172H LEU 3.2 8.1 + - - +
173H GLU* 3.6 13.2 - - + +
175H LEU* 1.3 77.3 - - - +
177H SER* 1.3 56.2 + - - +
179H ILE* 3.1 21.9 - - - +
180H GLN* 3.1 18.0 + - - +
113I ILE* 3.1 40.4 - - - +
116I SER* 3.0 28.4 + - - -
117I ASN* 3.0 32.2 + - - +
120I LYS* 3.4 16.4 + - - +
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Residues in contact with SER 177 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173H GLU 3.5 5.6 + - - -
174H ASN* 2.2 33.3 + - - -
175H LEU 2.6 4.0 + - - -
176H ARG* 1.3 74.2 - - - +
178H LYS* 1.3 69.6 + - - +
180H GLN* 3.1 18.7 + - - +
181H LYS* 2.8 22.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 178 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G MET* 4.2 5.2 - - + -
151G GLU* 4.3 12.8 - - - +
174G ASP* 3.9 20.1 + - - -
177G ASP* 3.2 24.6 + - - -
178G TYR* 3.8 40.2 - - + +
174H ASN* 3.4 29.1 + - - +
175H LEU* 2.5 15.4 + - + +
177H SER* 1.3 78.5 + - - +
179H ILE* 1.3 57.5 + - - +
181H LYS* 2.9 40.1 + - + +
182H LEU* 3.1 8.8 + - - +
----------------------------------------------------------
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Residues in contact with ILE 179 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G MET* 3.7 28.2 - - + +
175H LEU* 2.6 19.8 + - + +
176H ARG* 3.1 28.5 - - - +
178H LYS* 1.3 74.8 - - - +
180H GLN* 1.3 58.4 + - - -
182H LEU* 4.1 5.2 + - - +
183H GLU* 3.7 21.3 + - - +
117I ASN* 3.9 11.2 - - - +
120I LYS* 3.3 49.4 - - + +
121I ILE* 4.2 17.3 - - + +
124I LEU* 4.5 11.1 - - + +
----------------------------------------------------------
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Residues in contact with GLN 180 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176H ARG 3.1 19.1 + - - +
177H SER* 3.1 24.7 + - - +
179H ILE* 1.3 78.2 - - - +
181H LYS* 1.3 91.8 + - - +
183H GLU* 3.2 24.5 - - + +
184H SER* 3.4 8.4 + - - -
120I LYS* 4.7 7.4 - - + +
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Residues in contact with LYS 181 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151G GLU* 4.5 3.8 - - - +
171G ARG* 4.7 7.6 - - - +
177H SER 2.8 11.6 + - - +
178H LYS* 2.9 29.6 + - + +
180H GLN* 1.3 92.5 - - - +
182H LEU* 1.3 98.1 + - + +
184H SER* 2.5 31.7 + - - +
185H ASP* 3.0 37.3 + - - +
----------------------------------------------------------
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Residues in contact with LEU 182 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G MET* 3.9 19.1 - - + -
150G LEU 4.9 2.5 - - - +
151G GLU* 3.1 53.2 - - + +
154G ILE* 4.7 16.8 - - + -
171G ARG* 4.0 11.0 - - - +
178H LYS 3.1 7.3 + - - +
179H ILE* 4.2 1.6 - - - +
181H LYS* 1.3 99.8 - - + +
183H GLU* 1.3 54.1 + - - +
184H SER 2.6 1.6 + - - -
185H ASP* 2.3 36.7 + - + +
186H VAL* 2.9 11.8 + - + -
124I LEU* 3.6 32.3 - - + -
----------------------------------------------------------
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Residues in contact with GLU 183 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179H ILE* 3.7 21.8 + - - +
180H GLN* 3.2 19.6 + - - +
182H LEU* 1.3 77.6 - - - +
184H SER* 1.3 54.7 + - - +
186H VAL* 4.8 1.8 - - - +
187H SER* 3.2 25.1 + - - -
120I LYS* 4.8 12.5 - - - +
123I ASN* 6.1 0.7 - - - +
124I LEU* 3.4 22.4 + - + +
127I LYS* 4.6 12.7 - - + -
----------------------------------------------------------
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Residues in contact with SER 184 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180H GLN* 3.4 7.6 + - - -
181H LYS* 2.5 28.1 + - - -
182H LEU 2.6 4.0 + - - -
183H GLU* 1.3 72.6 - - - +
185H ASP* 1.3 69.0 + - - -
187H SER* 3.6 5.3 + - - -
188H ALA* 2.8 27.9 + - - +
----------------------------------------------------------
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Residues in contact with ASP 185 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ILE* 5.7 1.3 - - + -
158G ILE* 4.4 7.7 - - + +
169G LEU* 4.1 18.1 - - + +
171G ARG* 3.0 39.8 + - - +
181H LYS* 3.0 25.4 + - - -
182H LEU* 2.3 25.9 + - - +
184H SER* 1.3 92.1 + - - +
186H VAL* 1.3 59.3 + - + +
187H SER 3.1 1.3 - - - -
188H ALA* 2.8 24.2 + - - +
189H GLN* 2.8 16.8 + - - +
----------------------------------------------------------
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Residues in contact with VAL 186 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154G ILE* 4.0 16.4 - - + -
158G ILE* 4.9 2.0 - - + +
182H LEU 2.9 12.2 + - - +
183H GLU 4.9 0.4 - - - +
185H ASP* 1.3 75.1 - - + +
187H SER* 1.3 60.9 + - - +
189H GLN* 3.5 2.7 + - - +
190H MET* 3.4 26.2 + - + +
124I LEU* 4.6 12.8 - - + -
127I LYS* 3.5 50.3 - - + +
128I VAL* 3.6 24.9 - - + +
131I LEU* 4.1 20.0 - - + +
----------------------------------------------------------
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Residues in contact with SER 187 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H GLU 3.2 20.9 + - - -
184H SER* 3.6 6.1 - - - -
185H ASP 3.1 0.2 - - - -
186H VAL* 1.3 78.1 - - - +
188H ALA* 1.3 60.0 + - - +
190H MET* 3.5 3.6 + - - +
191H GLU* 3.0 25.5 + - - +
127I LYS* 3.5 21.4 - - - +
----------------------------------------------------------
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Residues in contact with ALA 188 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169G LEU* 3.8 20.9 - - + -
184H SER 2.8 18.4 + - - +
185H ASP* 2.8 13.4 + - - +
187H SER* 1.3 75.1 - - - +
189H GLN* 1.3 54.3 + - - +
190H MET 3.2 0.4 - - - -
191H GLU* 3.1 20.3 + - - +
192H TYR* 3.1 27.7 + - + -
----------------------------------------------------------
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Residues in contact with GLN 189 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158G ILE* 4.5 14.0 - - + +
161G CYS* 4.2 11.5 - - - +
165G CYS* 4.5 0.5 - - - +
167G ARG 3.0 23.0 + - - +
168G ALA* 3.5 11.2 - - - +
169G LEU* 3.1 38.2 - - - +
185H ASP 2.8 16.8 + - - +
186H VAL 3.5 1.3 + - - +
187H SER 3.4 0.2 - - - -
188H ALA* 1.3 70.2 - - - +
190H MET* 1.3 63.0 + - - +
191H GLU 3.3 0.2 - - - -
192H TYR* 3.8 11.7 - - - +
193H CYS* 3.3 32.1 + - - +
131I LEU* 3.6 34.1 - - + +
----------------------------------------------------------
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Residues in contact with MET 190 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186H VAL 3.4 5.1 + - - +
187H SER 3.7 2.2 - - - +
188H ALA 3.2 1.0 - - - -
189H GLN* 1.3 77.4 - - - +
191H GLU* 1.3 76.7 + - - +
193H CYS* 3.2 6.6 + - - +
194H ARG* 3.2 21.5 + - - +
127I LYS* 3.4 44.6 - - + +
130I GLN* 3.8 14.6 - - + +
131I LEU* 3.5 47.3 - - + +
134I GLN* 4.9 8.7 - - - -
----------------------------------------------------------
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Residues in contact with GLU 191 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187H SER* 3.0 18.7 + - - +
188H ALA* 3.1 10.6 + - - +
190H MET* 1.3 86.8 - - - +
192H TYR* 1.3 68.1 + - + +
193H CYS 3.1 0.2 - - - -
194H ARG* 3.2 53.9 + - - +
195H THR* 4.5 2.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR 192 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165G CYS* 3.3 13.7 - - - +
166G SER* 2.5 28.2 + - - +
167G ARG* 3.0 65.1 + - + +
169G LEU* 5.2 6.3 - - + -
188H ALA* 3.1 39.0 + - + -
189H GLN* 3.8 15.0 + - - +
191H GLU* 1.3 84.7 - - + +
193H CYS* 1.3 58.6 + - - +
194H ARG 3.4 1.1 - - - -
195H THR 3.4 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