Contacts of the helix formed by residues 172 - 203 (chain N) in PDB entry 1KYO
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 172 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88E VAL* 6.0 0.5 - - - +
58N ILE* 3.5 14.6 - - - -
166N TRP 5.4 0.2 + - - -
168N GLY* 5.2 4.9 - - - -
169N PHE 5.7 0.2 + - - -
170N SER* 3.0 14.1 + - - -
171N VAL* 1.3 74.6 - - - +
173N ASN* 1.3 67.4 + - - +
174N PRO* 3.0 19.3 - - - +
175N THR* 2.8 22.3 + - - -
176N ILE* 3.3 6.8 + - - +
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Residues in contact with ASN 173 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56N SER 4.0 0.2 + - - -
57N ASN* 3.3 22.1 + - - +
58N ILE* 2.5 59.4 - - + +
59N GLU* 5.0 1.3 - - - +
172N SER* 1.3 78.0 - - - +
174N PRO* 1.3 67.9 - - + +
175N THR 3.2 0.3 + - - -
176N ILE* 3.2 1.0 + - - -
177N GLN* 3.0 41.0 + - - +
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Residues in contact with PRO 174 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C MET 4.5 4.9 - - - +
53C HIS* 6.0 4.0 - - + +
85E THR* 5.0 4.7 - - - +
88E VAL* 4.7 17.5 - - + -
166N TRP 3.6 13.5 - - - +
167N GLY 3.6 19.3 - - - +
168N GLY* 5.5 0.2 - - - -
172N SER* 3.0 17.5 - - - +
173N ASN* 1.3 95.2 - - + +
175N THR* 1.3 60.2 + - - +
177N GLN* 3.7 6.0 + - + +
178N ARG* 3.1 41.8 + - - +
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Residues in contact with THR 175 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165N LEU 4.3 0.4 - - - +
166N TRP* 3.2 44.2 + - + -
170N SER 3.7 2.1 + - - -
171N VAL* 3.4 16.8 - - + -
172N SER* 2.8 29.6 + - - -
174N PRO* 1.3 76.1 - - - +
176N ILE* 1.3 57.8 + - - +
178N ARG* 3.3 5.6 - - - +
179N PHE* 3.0 62.9 + - + -
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Residues in contact with ILE 176 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54N TYR* 4.0 15.5 - - - +
56N SER* 3.5 18.0 - - - +
58N ILE* 3.9 13.9 - - + -
61N ALA* 4.5 9.6 - - + -
133N CYS* 4.3 27.8 - - + +
134N CYS* 4.7 4.0 - - - -
136N TYR* 3.7 32.3 - - + -
141N HIS* 6.0 0.2 - - - -
144N ALA* 5.1 2.9 - - + -
171N VAL* 4.3 13.7 - - + -
172N SER 3.8 11.2 - - - +
173N ASN 3.2 5.3 + - - +
175N THR* 1.3 77.1 - - - +
177N GLN* 1.3 57.1 + - - +
179N PHE* 3.5 7.3 + - + +
180N PHE* 3.1 26.5 + - - +
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Residues in contact with GLN 177 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C ALA 4.0 6.8 - - - +
52C MET 4.0 13.3 - - - +
53C HIS* 4.0 16.5 + - - +
54C TYR 3.5 9.1 + - - +
55C SER* 3.0 27.5 + - - -
56N SER* 3.3 39.2 + - - +
57N ASN* 3.7 16.6 + - - +
173N ASN* 3.0 34.8 + - - +
174N PRO* 4.2 2.9 - - + +
176N ILE* 1.3 75.1 - - - +
178N ARG* 1.3 63.1 + - - +
180N PHE* 3.7 3.5 + - - +
181N ALA* 3.4 20.1 + - - +
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Residues in contact with ARG 178 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C MET* 3.7 35.5 + - + +
53C HIS* 4.7 12.2 - - - -
82E MET* 3.0 59.4 + - - +
164N TRP 3.2 14.3 + - - -
165N LEU* 3.1 30.9 + - - +
166N TRP 3.8 3.2 + - - -
167N GLY* 3.4 13.7 - - - -
174N PRO* 3.1 28.9 + - - +
175N THR* 3.3 11.2 - - - +
177N GLN* 1.3 74.6 - - - +
179N PHE* 1.3 75.4 + - + +
181N ALA* 3.4 3.5 - - - +
182N LEU* 3.0 36.4 + - + +
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Residues in contact with PHE 179 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129N PHE* 4.6 10.5 - + - -
130N LEU* 3.5 35.6 - - + +
133N CYS* 4.2 20.9 - - + -
134N CYS* 4.5 2.9 - - - -
144N ALA* 4.5 13.9 - - + -
148N THR* 3.8 28.0 - - + -
165N LEU* 5.0 7.4 - - + -
175N THR* 3.0 44.1 + - + +
176N ILE* 3.8 11.0 - - + +
177N GLN 3.2 0.2 - - - -
178N ARG* 1.3 93.3 - - + +
180N PHE* 1.3 60.5 + - - +
182N LEU* 3.4 3.8 + - + +
183N HIS* 2.8 28.8 + - - +
525N SMA 4.1 20.2 - - + -
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Residues in contact with PHE 180 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE* 4.7 19.7 - + - -
184C TYR* 6.2 0.7 - + - -
51N ALA* 4.0 24.2 - - + -
54N TYR* 3.7 35.2 - + + -
56N SER* 3.9 22.0 - - - -
134N CYS* 3.7 23.0 - - - -
176N ILE 3.1 16.8 + - - +
177N GLN 4.0 2.5 - - - +
178N ARG 3.3 0.2 - - - -
179N PHE* 1.3 74.4 - - - +
181N ALA* 1.3 67.9 + - - +
183N HIS* 2.8 17.8 + + + +
184N TYR* 3.0 28.6 + + - +
521N HEC 4.0 32.1 - + + -
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Residues in contact with ALA 181 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 4.6 2.5 - - + +
51C ALA* 4.1 20.4 - - + -
52C MET* 4.0 17.3 - - + +
184C TYR* 2.8 31.6 + - - +
177N GLN 3.4 13.6 + - - +
178N ARG* 3.4 13.7 - - - +
180N PHE* 1.3 85.3 - - - +
182N LEU* 1.3 63.1 + - + +
184N TYR* 3.4 2.6 + - - +
185N LEU* 3.3 7.3 + - - +
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Residues in contact with LEU 182 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 4.5 12.6 - - + -
52C MET* 4.0 28.0 - - + -
82E MET* 5.5 5.4 - - + -
130N LEU* 3.9 18.2 - - + -
165N LEU* 6.5 0.2 - - + -
178N ARG* 3.0 28.4 + - + +
179N PHE* 3.9 7.2 - - + +
181N ALA* 1.3 75.1 - - + +
183N HIS* 1.3 66.4 + - - +
184N TYR 3.0 2.0 + - - -
185N LEU* 4.3 11.7 - - + -
186N VAL* 3.1 34.9 + - + +
525N SMA 4.2 21.1 - - + -
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Residues in contact with HIS 183 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127N THR* 2.8 31.7 + - + +
130N LEU* 3.8 13.7 - - + +
131N GLY* 3.2 19.6 + - - +
134N CYS* 4.5 4.7 - - - -
179N PHE 2.8 18.0 + - - +
180N PHE* 2.8 12.1 + + - +
182N LEU* 1.3 76.9 - - - +
184N TYR* 1.3 56.2 + - - +
186N VAL* 5.0 0.4 - - - -
187N PRO* 3.0 25.9 - - - +
521N HEC 2.0 92.5 + + + -
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Residues in contact with TYR 184 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C PHE* 5.8 1.6 - + - -
181C ALA* 2.7 36.3 + - - +
184C TYR* 3.7 44.0 - + + -
185C LEU* 3.6 13.5 + - - +
48N ILE* 4.2 12.7 - - + +
51N ALA* 4.5 6.1 - - + -
180N PHE* 3.0 23.8 + + + +
181N ALA* 3.4 11.2 - - - +
182N LEU 3.0 0.2 - - - -
183N HIS* 1.3 80.1 - - - +
185N LEU* 1.3 61.9 + - - +
187N PRO* 3.3 10.0 - - - +
188N PHE* 3.3 37.7 - + - -
521N HEC 3.4 40.4 - - + +
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Residues in contact with LEU 185 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE* 3.7 30.7 - - + -
184C TYR* 3.5 13.0 + - - +
188C PHE* 3.5 31.4 - - + -
181N ALA 3.3 4.4 + - - +
182N LEU* 3.2 18.3 + - + +
184N TYR* 1.3 78.7 - - - +
186N VAL* 1.3 70.1 + - + +
188N PHE* 3.1 16.2 + - - +
189N ILE* 3.5 30.8 + - + +
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Residues in contact with VAL 186 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123N LEU* 3.8 31.4 - - + +
126N ALA* 5.5 2.5 - - + -
127N THR* 3.3 23.6 - - + +
130N LEU* 4.0 19.1 - - + -
182N LEU* 3.1 20.9 - - + +
185N LEU* 1.3 77.5 - - + +
187N PRO* 1.3 60.9 - - + +
189N ILE* 2.6 38.7 + - + +
190N ILE* 2.8 14.5 + - + -
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Residues in contact with PRO 187 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N LEU* 4.9 1.1 - - + +
44N ILE* 4.2 19.3 - - + +
127N THR* 3.6 17.0 - - + -
183N HIS 3.0 27.4 - - - +
184N TYR 3.3 7.4 - - - +
186N VAL* 1.3 91.8 - - + +
188N PHE* 1.3 58.5 + - + +
190N ILE* 3.2 15.9 + - + +
191N ALA* 2.9 28.3 + - - +
521N HEC 3.7 37.2 - - + -
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Residues in contact with PHE 188 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 3.7 28.3 - - + -
188C PHE* 3.8 50.0 - + + -
44N ILE* 4.7 20.6 - - + -
48N ILE* 4.6 9.2 - - + -
184N TYR* 3.3 49.6 - + - -
185N LEU* 3.1 8.6 + - + +
186N VAL 3.1 0.8 - - - -
187N PRO* 1.3 74.8 - - + +
189N ILE* 1.3 65.3 + - + +
191N ALA* 3.4 10.7 - - + +
192N ALA* 3.1 19.2 + - - +
521N HEC 4.9 4.9 - - + -
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Residues in contact with ILE 189 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123N LEU* 4.4 15.5 - - + -
185N LEU* 3.9 33.9 - - + +
186N VAL* 2.6 26.5 + - + +
188N PHE* 1.3 71.7 - - + +
190N ILE* 1.3 53.0 + - - +
192N ALA* 2.9 10.7 + - + +
193N MET* 2.8 47.4 + - + +
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Residues in contact with ILE 190 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N LEU* 3.8 22.7 - - + -
89N PHE* 5.5 0.4 - - + -
120N ILE* 4.2 19.7 - - + -
123N LEU* 4.1 18.6 - - + -
124N THR* 3.9 24.5 - - - +
127N THR* 3.2 30.7 - - + +
186N VAL* 2.8 13.4 + - + +
187N PRO* 3.3 14.8 - - + +
189N ILE* 1.3 74.3 - - - +
191N ALA* 1.3 53.3 + - - +
193N MET* 3.0 12.0 + - - +
194N VAL* 2.7 38.2 + - + +
521N HEC 4.7 9.6 - - + -
522N HEC 4.6 2.7 - - + -
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Residues in contact with ALA 191 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N LEU* 3.9 20.6 - - + -
44N ILE* 5.1 5.8 - - + -
187N PRO 2.9 13.4 + - - +
188N PHE* 3.4 17.5 - - + +
189N ILE 3.1 0.2 - - - -
190N ILE* 1.3 77.2 - - - +
192N ALA* 1.3 61.0 + - - +
194N VAL* 3.1 13.7 + - - +
195N ILE* 3.2 20.7 + - + +
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Residues in contact with ALA 192 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188N PHE 3.1 9.0 + - - +
189N ILE* 2.9 14.2 + - + +
191N ALA* 1.3 77.1 - - - +
193N MET* 1.3 69.5 + - + +
195N ILE* 3.1 25.0 + - - +
196N MET* 3.3 17.5 + - - +
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Residues in contact with MET 193 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116N VAL* 3.6 23.7 - - - +
119N ILE* 4.3 22.4 - - + -
120N ILE* 3.6 17.7 - - + +
123N LEU* 3.8 24.2 - - + -
189N ILE* 2.8 23.6 + - + +
190N ILE* 3.2 13.0 - - - +
192N ALA* 1.3 76.8 - - + +
194N VAL* 1.3 58.6 - - - +
196N MET* 3.1 37.2 + - - +
197N HIS 3.2 15.8 + - - -
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Residues in contact with VAL 194 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N GLY* 6.3 0.4 - - - -
40N LEU* 4.5 10.5 - - + -
120N ILE* 4.0 9.6 - - + -
190N ILE* 2.7 22.1 + - + +
191N ALA* 3.3 12.1 - - - +
192N ALA 3.0 0.2 - - - -
193N MET* 1.3 71.0 - - - +
195N ILE* 1.3 63.3 + - + +
196N MET 3.0 1.8 - - - -
197N HIS* 2.8 11.7 + - + +
198N LEU* 2.8 41.3 + - + +
522N HEC 3.6 49.6 - - + -
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Residues in contact with ILE 195 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191N ALA 3.2 15.4 + - - +
192N ALA* 3.1 14.3 + - - +
194N VAL* 1.3 78.8 - - + +
196N MET* 1.3 58.7 + - + +
198N LEU* 3.4 12.2 + - + +
199N MET* 2.9 39.3 + - + +
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Residues in contact with MET 196 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C TYR* 2.6 72.8 + - + +
116N VAL* 4.4 6.7 - - + -
192N ALA* 3.4 13.7 - - - +
193N MET* 3.1 38.1 - - + +
194N VAL 3.0 0.6 - - - -
195N ILE* 1.3 74.1 - - + +
197N HIS* 1.3 61.2 - - - +
198N LEU 3.1 1.6 - - - -
199N MET* 3.2 7.0 + - - +
200N ALA* 2.9 19.4 + - - +
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Residues in contact with HIS 197 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113N LEU* 3.2 42.5 + - + +
116N VAL* 3.9 10.0 - - + +
117N GLY* 3.9 8.9 + - - -
120N ILE* 4.0 5.2 - - + -
193N MET 3.2 11.8 + - - +
194N VAL* 2.8 15.5 + - - +
196N MET* 1.3 77.7 - - - +
198N LEU* 1.3 58.4 + - + +
200N ALA* 4.6 1.1 - - - -
201N LEU* 3.0 22.6 + - + +
522N HEC 2.0 100.4 + + + -
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Residues in contact with LEU 198 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16N TYR* 4.0 25.7 - - + -
194N VAL* 2.8 26.0 + - + +
195N ILE* 3.6 13.9 - - + +
197N HIS* 1.3 79.9 - - + +
199N MET* 1.3 59.9 + - - +
201N LEU* 3.0 14.0 + - + +
202N HIS* 2.8 31.2 + - - +
522N HEC 3.9 40.4 - - + -
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Residues in contact with MET 199 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.1 29.0 - - + +
9C TYR* 4.1 25.4 - - + -
12C LEU* 4.2 24.9 - - + -
16N TYR* 3.8 18.8 + - + +
195N ILE* 2.9 33.3 + - + +
196N MET* 3.2 10.5 + - - +
198N LEU* 1.3 75.5 - - - +
200N ALA* 1.3 60.9 + - - +
201N LEU 3.4 0.2 + - - -
202N HIS* 3.5 9.2 + - - +
203N ILE* 3.5 21.3 + - - +
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Residues in contact with ALA 200 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.8 8.0 - - + +
9C TYR* 3.3 21.5 + - + +
110N ARG* 5.5 2.1 - - - +
112N THR* 4.1 13.8 - - + +
113N LEU* 4.0 31.5 - - - +
116N VAL* 5.1 0.4 - - + -
196N MET 2.9 8.2 + - - +
197N HIS* 3.7 5.4 - - - +
199N MET* 1.3 74.6 - - - +
201N LEU* 1.3 66.0 + - - +
203N ILE* 3.9 17.9 - - - +
204N HIS* 4.5 6.1 + - - +
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Residues in contact with LEU 201 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110N ARG* 6.3 0.2 - - - -
113N LEU* 3.9 25.8 - - + -
197N HIS 3.0 15.0 + - - +
198N LEU* 3.3 20.6 - - + +
200N ALA* 1.3 78.2 - - - +
202N HIS* 1.3 58.9 + - - +
203N ILE 3.0 3.6 + - - -
204N HIS* 3.1 4.0 + - - +
205N GLY* 2.9 40.6 + - - +
206N SER* 4.0 20.6 - - - +
522N HEC 3.6 41.7 - - + -
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Residues in contact with HIS 202 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H GLY* 4.7 12.4 + - - -
15N SER* 2.9 43.0 + - - -
16N TYR* 3.6 39.3 - + + +
20N SER* 4.8 6.0 + - - -
198N LEU 2.8 15.6 + - - +
199N MET 3.8 4.7 - - - +
200N ALA 3.4 0.4 - - - -
201N LEU* 1.3 79.2 - - - +
203N ILE* 1.3 63.0 + - + +
204N HIS 3.4 0.2 - - - -
205N GLY* 4.1 3.3 + - - +
10S MET* 3.9 15.2 - - + +
12S TRP* 3.7 23.4 - + - -
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Residues in contact with ILE 203 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C VAL* 4.2 28.0 - - + -
112N THR* 6.1 4.9 - - + -
199N MET 3.5 14.1 + - - +
200N ALA* 3.9 12.6 - - - +
201N LEU 3.0 1.0 + - - -
202N HIS* 1.3 81.6 - - + +
204N HIS* 1.3 89.6 + - + +
8S THR* 3.3 39.4 + - + +
10S MET* 3.8 11.5 - - - +
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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