Contacts of the helix formed by residues 171 - 204 (chain P) in PDB entry 1PP9
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 ASP 171 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E LYS* 5.7 2.8 + - - -
93E GLY* 5.5 5.0 - - - -
59P THR* 4.2 10.0 + - - +
135P TRP* 3.9 10.9 - - - -
165P TRP 5.2 0.6 + - - +
169P SER* 3.3 15.5 + - - +
170P VAL* 1.3 77.5 - - - +
172P LYS* 1.3 93.7 + - - +
173P ALA* 3.3 4.9 - - + +
174P THR* 2.9 15.8 + - - -
175P LEU 3.2 10.0 + - - -
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Residues in contact with LYS 172 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57P SER 4.8 0.4 - - - +
58P ASP* 2.8 36.7 + - - +
59P THR* 2.9 37.7 + - + +
60P THR* 3.6 14.5 - - - +
171P ASP* 1.3 92.4 + - - +
173P ALA* 1.3 62.1 + - - +
174P THR 3.2 0.3 + - - -
175P LEU* 3.2 2.8 + - - +
176P THR* 3.1 29.4 + - - +
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Residues in contact with ALA 173 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET 4.2 3.6 - - - +
54C HIS* 5.5 6.3 - - + +
65E SER* 6.1 0.9 - - - +
68E VAL* 5.9 4.5 - - + -
165P TRP 3.6 14.4 - - - +
166P GLY 4.0 12.6 - - - +
171P ASP* 3.3 3.2 + - + +
172P LYS* 1.3 77.9 - - - +
174P THR* 1.3 62.6 + - - +
176P THR* 3.7 4.6 + - - -
177P ARG* 3.1 45.2 + - - +
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Residues in contact with THR 174 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P VAL* 5.7 0.2 - - + -
135P TRP* 5.5 1.3 - - + -
143P ALA* 5.1 2.5 - - + -
164P ILE 4.9 0.2 - - - +
165P TRP* 2.8 38.2 + - + -
169P SER 4.1 0.2 + - - -
170P VAL* 3.6 20.7 - - + -
171P ASP 2.9 25.0 + - - -
173P ALA* 1.3 75.7 - - - +
175P LEU* 1.3 66.9 + - - +
177P ARG* 3.3 9.4 - - - +
178P PHE* 3.0 52.9 + - + -
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Residues in contact with LEU 175 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55P TYR* 3.6 17.0 - - - +
57P SER* 3.4 21.5 - - - +
59P THR* 3.9 14.1 - - + -
62P ALA* 3.7 25.8 - - + -
132P VAL* 3.9 5.6 - - + +
133P LEU* 3.8 22.4 - - + -
135P TRP* 3.7 44.8 - - + -
171P ASP 3.2 5.9 + - - +
172P LYS 3.2 4.7 + - - +
174P THR* 1.3 78.8 - - - +
176P THR* 1.3 61.5 + - - +
178P PHE* 3.4 3.5 + - - +
179P PHE* 3.1 21.7 + - - +
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Residues in contact with THR 176 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA 3.8 8.2 - - - +
53C MET 3.1 27.1 - - - +
54C HIS* 3.8 8.3 - - - +
55C TYR 3.5 23.6 - - - +
56C THR* 3.9 9.4 - - + +
57P SER* 3.4 26.3 + - - +
58P ASP* 4.9 0.9 - - - -
172P LYS* 3.1 19.2 + - - +
173P ALA* 4.1 2.9 - - - -
175P LEU* 1.3 76.9 - - - +
177P ARG* 1.3 61.0 + - - +
179P PHE* 3.4 6.1 + - - +
180P ALA 3.4 13.5 + - - -
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Residues in contact with ARG 177 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET* 3.6 30.7 + - + +
54C HIS* 3.9 16.9 - - - -
62E MET* 3.0 45.9 + - - +
63E SER 5.1 0.4 + - - -
163P TRP 2.9 28.1 + - - -
164P ILE 3.0 21.1 + - - -
166P GLY* 3.5 14.0 - - - +
173P ALA* 3.1 31.1 + - - +
174P THR* 3.3 7.6 - - - +
176P THR* 1.3 75.8 - - - +
178P PHE* 1.3 66.0 + - + +
180P ALA* 3.0 4.5 + - - +
181P PHE* 2.8 53.1 + - + -
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Residues in contact with PHE 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P PHE* 3.7 26.5 - + - -
129P MET* 3.4 32.8 - - + +
132P VAL* 4.0 28.9 - - + -
133P LEU* 4.0 11.7 - - + -
143P ALA* 4.5 4.7 - - + -
147P THR* 3.9 18.6 - - - -
164P ILE* 4.1 12.1 - - + -
174P THR* 3.0 39.9 + - + +
175P LEU* 3.7 7.0 - - - +
176P THR 3.3 0.2 - - - -
177P ARG* 1.3 82.5 - - + +
179P PHE* 1.3 59.3 + - - +
181P PHE* 3.9 3.2 - + - +
182P HIS* 2.8 33.6 + - - +
3001P SMA 3.9 20.2 - - + -
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Residues in contact with PHE 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA 6.1 0.7 - - - -
57C SER* 5.9 0.4 - - - -
179C PHE* 3.7 35.9 - + - -
180C ALA* 6.1 0.4 - - + -
183C PHE* 6.4 0.7 - + - -
52P ALA* 4.0 30.7 - - + -
55P TYR* 3.7 35.9 - + + -
57P SER* 3.9 23.8 - - - -
133P LEU* 3.7 22.8 - - + +
175P LEU 3.1 12.4 + - - +
176P THR* 3.7 9.4 - - + +
177P ARG 3.2 0.2 - - - -
178P PHE* 1.3 75.0 - - - +
180P ALA* 1.3 59.6 + - - +
182P HIS* 3.4 0.5 + - - +
183P PHE* 3.0 53.2 + + + +
501P HEM 4.2 11.0 - + + -
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Residues in contact with ALA 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 4.9 5.1 - - + +
52C ALA* 4.0 26.7 - - + +
53C MET* 4.6 8.5 - - + -
179C PHE* 6.2 0.7 - - + -
183C PHE* 3.7 26.0 - - + -
176P THR 3.4 3.6 + - - +
177P ARG* 3.0 11.8 + - - +
179P PHE* 1.3 81.7 - - - +
181P PHE* 1.3 65.2 + - + +
183P PHE* 3.3 3.3 + - - +
184P ILE* 3.2 23.8 + - - +
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Residues in contact with PHE 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C MET* 4.2 22.9 - - + -
62E MET* 4.1 22.9 - - + -
129P MET* 2.9 40.8 - - + -
164P ILE* 5.5 4.0 - - + -
177P ARG* 2.8 49.4 + - + -
178P PHE* 3.9 3.8 - + - +
180P ALA* 1.3 75.0 - - + +
182P HIS* 1.3 58.8 + - - +
183P PHE 3.3 0.2 + - - -
184P ILE* 3.4 8.7 + - + +
185P LEU* 3.0 36.9 + - + +
3001P SMA 4.3 13.2 - - + -
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Residues in contact with HIS 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126P THR* 2.9 30.9 + - + +
129P MET* 4.2 11.6 - - + -
130P GLY* 3.3 10.1 + - - -
133P LEU* 3.7 15.7 - - + -
178P PHE 2.8 22.0 + - - +
179P PHE* 3.9 3.8 - + - +
181P PHE* 1.3 72.8 - - - +
183P PHE* 1.3 56.9 + - - +
185P LEU* 4.9 2.2 - - - -
186P PRO* 2.9 28.3 - - - +
501P HEM 2.0 97.9 + + + -
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Residues in contact with PHE 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C PHE* 6.4 0.9 - + - -
180C ALA* 3.7 33.0 - - - -
183C PHE* 3.4 42.2 - + + -
184C ILE* 4.1 20.0 - - + -
49P LEU* 3.9 11.2 - - + -
52P ALA* 4.0 14.1 - - + -
179P PHE* 3.0 40.2 + + + +
180P ALA* 3.5 7.0 - - - +
181P PHE 3.2 0.2 - - - -
182P HIS* 1.3 79.4 - - - +
184P ILE* 1.3 59.3 + - - +
186P PRO* 3.5 3.3 - - - +
187P PHE* 3.4 20.4 - + - -
501P HEM 3.7 36.0 - - + +
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Residues in contact with ILE 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C LEU* 4.7 13.0 - - + -
183C PHE* 4.1 11.4 - - + -
184C ILE* 5.0 0.9 - - + -
187C PHE* 3.5 51.8 - - + -
180P ALA 3.2 11.3 + - - +
181P PHE* 3.7 13.9 - - + +
183P PHE* 1.3 78.6 - - - +
185P LEU* 1.3 70.1 + - + +
186P PRO* 3.3 2.7 - - - -
187P PHE* 3.0 30.3 + - + -
188P ILE* 3.3 26.9 + - + +
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Residues in contact with LEU 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P THR* 3.5 26.5 - - + +
125P ALA* 4.5 10.1 - - + -
126P THR* 3.0 39.5 - - + +
129P MET* 4.7 11.0 - - - -
181P PHE* 3.0 20.7 + - + +
182P HIS* 4.6 0.7 - - - +
184P ILE* 1.3 78.5 - - + +
186P PRO* 1.4 55.0 - - + +
188P ILE* 2.9 25.9 + - + +
189P ILE* 2.8 37.5 + - - +
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Residues in contact with PRO 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P LEU* 3.9 7.4 - - + +
45P ILE* 4.0 10.7 - - + +
126P THR* 3.9 12.6 - - + -
182P HIS 2.9 29.2 - - - +
183P PHE 3.5 3.4 - - - +
184P ILE 3.4 4.3 - - - -
185P LEU* 1.4 88.2 - - + +
187P PHE* 1.3 56.0 + - - +
189P ILE* 3.4 14.0 + - + +
190P MET* 3.0 24.3 + - - +
501P HEM 3.6 49.8 - - + -
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Residues in contact with PHE 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184C ILE* 3.5 39.9 - - + -
187C PHE* 6.0 3.1 - - + -
45P ILE* 3.8 32.8 - - + -
49P LEU* 4.3 12.1 - - + -
183P PHE* 3.4 34.1 - + - -
184P ILE* 3.0 19.5 + - + +
186P PRO* 1.3 74.8 - - + +
188P ILE* 1.3 65.4 + - + +
190P MET* 3.3 30.2 + - + +
191P ALA* 3.1 20.4 + - - +
501P HEM 4.0 10.5 - - + -
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Residues in contact with ILE 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122P THR* 5.3 0.9 - - + -
184P ILE* 3.3 31.2 + - + +
185P LEU* 2.9 30.2 + - + +
187P PHE* 1.3 77.1 - - - +
189P ILE* 1.3 59.1 + - - +
191P ALA* 3.1 7.7 + - + +
192P ILE* 2.9 46.5 + - + +
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Residues in contact with ILE 189 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P LEU* 4.1 15.5 - - + -
119P LEU* 3.7 15.4 - - + +
122P THR* 3.2 28.9 - - + +
123P VAL* 3.8 22.0 - - + -
126P THR* 3.4 25.4 - - - +
185P LEU 2.8 12.7 + - - +
186P PRO* 3.4 9.6 - - + +
188P ILE* 1.3 76.3 - - - +
190P MET* 1.3 57.2 + - - +
192P ILE* 3.2 9.0 + - - +
193P ALA* 2.8 28.1 + - - +
501P HEM 4.1 14.4 - - + -
502P HEM 4.0 17.9 - - + -
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Residues in contact with MET 190 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P LEU* 3.8 20.2 - - + -
42P ILE* 6.3 2.7 - - - -
45P ILE* 4.1 12.8 - - + -
186P PRO 3.0 11.1 + - - +
187P PHE* 3.4 44.0 - - + +
188P ILE 3.2 0.2 - - - -
189P ILE* 1.3 78.2 - - - +
191P ALA* 1.3 62.2 + - - +
193P ALA* 3.3 4.2 + - - +
194P MET* 3.1 38.1 + - + +
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Residues in contact with ALA 191 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187P PHE 3.1 12.1 + - - +
188P ILE* 3.1 11.7 + - + +
190P MET* 1.3 74.0 - - - +
192P ILE* 1.3 67.5 + - + +
194P MET* 3.3 23.7 + - + +
195P VAL* 3.2 25.1 + - - +
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Residues in contact with ILE 192 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P ILE* 3.7 20.9 - - + +
118P ILE* 4.4 22.4 - - + -
119P LEU* 3.5 20.0 - - + -
122P THR* 4.6 10.5 - - + +
188P ILE* 2.9 41.0 + - + +
189P ILE* 3.6 7.6 - - - +
191P ALA* 1.3 78.9 - - + +
193P ALA* 1.3 58.1 + - - +
195P VAL* 3.1 11.1 + - + +
196P HIS* 2.9 24.3 + - - +
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Residues in contact with ALA 193 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P LEU* 4.9 4.0 - - + -
119P LEU* 3.9 9.6 - - + +
189P ILE 2.8 17.4 + - - +
190P MET* 3.7 8.1 - - - +
192P ILE* 1.3 76.4 - - - +
194P MET* 1.3 64.2 + - + +
196P HIS* 3.0 11.2 - - + +
197P LEU* 3.0 27.4 + - + +
502P HEM 4.0 29.4 - - + -
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Residues in contact with MET 194 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190P MET* 3.1 24.4 + - + +
191P ALA* 3.4 32.3 - - + +
192P ILE 3.2 0.4 - - - -
193P ALA* 1.3 76.5 - - + +
195P VAL* 1.3 62.8 + - + +
197P LEU* 3.4 10.6 + - + +
198P LEU* 3.0 30.6 + - + +
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Residues in contact with VAL 195 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P ILE* 3.6 11.2 - - + -
191P ALA 3.2 14.7 + - - +
192P ILE* 3.1 12.0 + - + +
194P MET* 1.3 75.7 - - + +
196P HIS* 1.3 64.5 + - - +
198P LEU* 3.1 21.3 + - + +
199P PHE* 3.1 39.8 + - + -
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Residues in contact with HIS 196 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112P THR* 3.1 41.6 + - + +
115P ILE* 3.8 15.4 - - + +
116P GLY* 3.9 9.8 + - - -
119P LEU* 3.8 4.5 - - + -
192P ILE 2.9 12.1 + - - +
193P ALA* 3.0 18.2 - - - +
195P VAL* 1.3 77.6 - - - +
197P LEU* 1.3 59.9 + - + +
199P PHE* 3.5 2.4 + - - +
200P LEU* 3.2 18.9 + - + +
502P HEM 2.0 93.2 + + + -
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Residues in contact with LEU 197 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193P ALA* 3.0 15.0 + - + +
194P MET* 3.7 12.8 - - + +
196P HIS* 1.3 75.6 - - - +
198P LEU* 1.3 62.0 + - + +
200P LEU* 3.2 11.3 + - + +
201P HIS* 2.9 40.6 + - + +
502P HEM 3.7 44.0 - - + -
3002P UQ 3.8 45.3 - - + +
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Residues in contact with LEU 198 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194P MET* 3.0 22.5 + - + +
195P VAL* 3.1 16.5 + - + +
197P LEU* 1.3 78.1 - - + +
199P PHE* 1.3 64.2 + - + +
201P HIS* 3.3 26.1 + - + +
202P GLU* 3.5 17.5 + - - +
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Residues in contact with PHE 199 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111P GLU* 3.5 35.9 - - + -
112P THR* 3.5 17.6 + - - +
115P ILE* 3.3 24.0 - - + -
195P VAL* 3.1 35.4 + - + -
196P HIS 3.9 4.5 - - - +
198P LEU* 1.3 77.8 - - + +
200P LEU* 1.3 64.2 + - - +
202P GLU* 3.1 28.5 + - + +
203P THR* 3.9 5.7 + - - +
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Residues in contact with LEU 200 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109P PHE* 3.9 12.3 - - + -
112P THR* 3.2 12.0 + - + +
196P HIS* 3.2 11.7 + - + +
197P LEU* 3.2 17.8 + - + +
199P PHE* 1.3 79.8 - - - +
201P HIS* 1.3 54.6 + - + +
203P THR* 2.9 9.1 + - - -
204P GLY* 2.7 53.1 + - - +
205P SER* 4.4 4.9 - - - +
502P HEM 3.5 66.6 - - + +
3002P UQ 4.0 12.1 - - - +
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Residues in contact with HIS 201 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P ALA* 3.6 33.2 - - + +
21P LEU* 3.9 24.4 - - + +
197P LEU* 2.9 29.6 + - + +
198P LEU* 3.6 17.8 - - + +
199P PHE 3.2 0.6 - - - -
200P LEU* 1.3 83.4 - - + +
202P GLU* 1.3 67.6 + - - +
203P THR 3.1 0.4 + - - -
204P GLY* 3.9 7.3 + - - +
3002P UQ 2.3 40.1 + - + +
2T ARG* 3.7 19.9 + - - +
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Residues in contact with GLU 202 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198P LEU 3.5 15.6 + - - +
199P PHE* 3.1 20.4 + - + +
200P LEU 3.0 1.0 + - - -
201P HIS* 1.3 83.3 - - - +
203P THR* 1.3 64.2 + - + +
2T ARG* 3.5 16.4 + - - +
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Residues in contact with THR 203 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109P PHE* 3.3 42.6 - - + +
112P THR* 5.4 0.2 + - - -
199P PHE 4.3 4.1 + - - +
200P LEU* 2.9 8.9 + - - +
202P GLU* 1.3 88.1 - - + +
204P GLY* 1.3 70.9 + - - +
205P SER 4.9 1.0 - - - +
217P LYS* 5.2 1.6 + - - -
2T ARG* 3.5 23.8 + - - +
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Residues in contact with GLY 204 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21P LEU* 6.5 0.7 - - - -
22P PRO 5.2 8.3 - - - -
109P PHE* 3.4 12.0 - - - -
200P LEU* 2.7 23.9 + - - +
201P HIS* 3.9 8.5 + - - -
202P GLU 3.7 0.8 - - - -
203P THR* 1.3 90.5 + - - +
205P SER* 1.3 59.9 + - - -
217P LYS* 5.5 4.9 - - - -
3002P UQ 6.2 0.9 - - - -
2T ARG* 4.6 6.5 - - - -
----------------------------------------------------------
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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