Contacts of the helix formed by residues 231 - 264 (chain B) in PDB entry 1O69
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 231 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 2.5 38.0 - - - -
190A GLY* 4.6 2.0 - - - -
234A LEU* 4.0 11.6 - - - +
34B VAL* 3.7 2.2 - - - +
54B ASN* 5.8 0.2 - - - +
229B ARG 3.7 2.2 + - - -
230B LEU* 1.3 83.2 - - - +
232B ASN* 1.3 57.9 + - - +
233B VAL* 3.4 4.7 + - - +
234B LEU* 3.1 26.7 + - - +
235B GLY 2.8 23.7 + - - -
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Residues in contact with ASN 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.7 8.7 + - - +
21B VAL* 3.7 29.7 + - + +
31B GLY* 3.4 20.2 - - - +
32B GLU* 4.1 10.1 - - - +
33B PHE* 2.9 29.6 + - - +
34B VAL* 3.2 14.2 + - + +
230B LEU 3.8 1.8 + - - -
231B SER* 1.3 72.7 - - - +
233B VAL* 1.3 57.5 + - - +
235B GLY* 3.3 0.5 + - - -
236B ALA* 3.0 26.7 + - - +
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Residues in contact with VAL 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189A SER* 3.5 23.5 + - - +
233A VAL* 4.0 26.0 - - + -
234A LEU* 4.1 7.4 - - + -
237A ILE* 4.0 9.2 - - + -
18B ILE* 4.1 20.4 - - + +
21B VAL* 3.9 12.6 - - + -
22B PHE* 3.6 28.0 - - + -
231B SER* 3.2 7.7 + - - +
232B ASN* 1.3 77.8 - - - +
234B LEU* 1.3 63.1 + - + +
236B ALA* 3.2 15.8 + - - +
237B ILE* 3.3 13.2 + - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A SER* 4.0 15.3 - - - +
233A VAL* 4.4 3.8 - - + -
234A LEU* 3.8 34.3 - - + -
37B PHE* 4.9 0.3 - - - -
54B ASN* 6.0 2.0 - - + +
189B SER* 3.5 19.4 + - - +
190B GLY* 3.7 29.7 - - - +
230B LEU* 3.7 29.7 - - + +
231B SER* 3.1 14.6 + - - +
233B VAL* 1.3 74.2 - - - +
235B GLY* 1.3 60.2 + - - +
237B ILE* 3.3 17.8 + - + +
238B GLY* 2.8 24.9 + - - -
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Residues in contact with GLY 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PHE* 3.7 19.9 - - - +
34B VAL* 4.4 3.1 - - - -
37B PHE* 3.8 6.6 - - - +
230B LEU* 3.7 14.7 - - - +
231B SER 2.8 14.5 + - - -
232B ASN 3.7 4.0 - - - -
233B VAL 3.2 0.4 - - - -
234B LEU* 1.3 77.9 - - - +
236B ALA* 1.3 55.2 + - - +
238B GLY* 3.1 2.6 + - - -
239B VAL* 2.9 32.2 + - - +
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Residues in contact with ALA 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU 5.3 1.1 - - - -
17B TYR* 3.6 44.7 - - + +
18B ILE* 4.1 6.5 - - + -
21B VAL* 4.0 5.4 - - + -
33B PHE* 3.5 21.0 - - + +
232B ASN 3.0 12.2 + - - +
233B VAL 3.4 10.5 - - - +
234B LEU 3.2 0.2 - - - -
235B GLY* 1.3 76.8 - - - +
237B ILE* 1.3 62.1 + - - +
239B VAL* 3.4 1.6 + - - +
240B ALA* 3.2 18.0 + - - +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A PHE* 3.7 26.9 - - + -
233A VAL* 4.0 10.5 - - + -
14B GLU* 4.1 21.3 - - + +
18B ILE* 3.7 20.9 - - + -
189B SER* 3.7 32.5 - - - +
233B VAL 3.3 7.9 + - - +
234B LEU* 3.6 23.8 - - + +
235B GLY 3.3 0.4 - - - -
236B ALA* 1.3 74.9 - - - +
238B GLY* 1.3 60.6 + - - +
240B ALA* 3.2 3.1 + - - +
241B GLN* 2.9 47.0 + - - +
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Residues in contact with GLY 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.5 29.9 - - - -
180B TYR* 5.9 0.2 - - - -
234B LEU 2.8 14.4 + - - -
235B GLY 3.1 4.4 + - - -
237B ILE* 1.3 77.4 - - - +
239B VAL* 1.3 55.9 + - - +
241B GLN* 3.2 13.4 + - - +
242B MET* 2.9 33.6 + - - +
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Residues in contact with VAL 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B TYR* 3.6 22.4 - - + -
33B PHE* 3.6 12.6 - - + +
36B ARG* 3.7 27.6 - - + +
37B PHE* 3.3 34.7 - - - +
40B SER* 4.6 6.6 - - - -
235B GLY 2.9 17.0 + - - +
236B ALA 3.7 6.5 - - - +
238B GLY* 1.3 74.0 - - - +
240B ALA* 1.3 64.0 + - - +
242B MET* 3.2 7.0 + - - +
243B GLU* 3.1 36.4 + - + +
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Residues in contact with ALA 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B GLY 4.9 3.0 + - - -
13B ASN* 3.9 11.2 - - + +
14B GLU* 3.6 42.8 - - + +
17B TYR* 4.1 3.8 - - + -
236B ALA 3.2 10.4 + - - +
237B ILE 3.5 7.9 - - - +
239B VAL* 1.3 78.6 - - - +
241B GLN* 1.3 61.5 + - - +
243B GLU* 3.3 22.8 + - - +
244B VAL* 3.6 16.9 + - - +
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Residues in contact with GLN 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLU* 4.3 10.3 - - - +
180B TYR* 3.6 42.7 - - + +
181B ASN* 2.9 26.0 + - - +
189B SER* 4.6 1.6 + - - -
237B ILE* 2.9 35.5 + - + +
238B GLY* 3.6 15.6 - - - +
240B ALA* 1.3 71.9 - - - +
242B MET* 1.3 63.8 + - - +
244B VAL* 3.3 11.9 + - - +
245B LEU* 3.1 21.4 + - - +
248B ARG* 4.4 20.6 + - - +
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Residues in contact with MET 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B PHE* 3.7 11.0 - - + -
40B SER* 3.3 37.7 - - - +
41B VAL* 3.9 8.7 - - + -
44B TYR* 3.6 35.5 - - + -
160B LEU* 3.8 27.6 - - + -
180B TYR* 3.8 14.6 - - + -
238B GLY 2.9 19.6 + - - +
239B VAL 3.2 4.2 + - - +
241B GLN* 1.3 76.3 - - - +
243B GLU* 1.3 63.8 + - + +
244B VAL 3.2 0.5 + - - -
245B LEU* 3.3 31.9 + - + +
246B GLU 4.8 0.7 + - - -
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Residues in contact with GLU 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 5.9 0.2 + - - -
13B ASN* 2.8 30.2 + - - +
17B TYR* 2.5 31.5 + - - -
36B ARG* 4.5 2.3 + - - -
40B SER* 6.4 1.1 - - - -
239B VAL* 3.1 27.3 + - + +
240B ALA* 3.6 8.6 - - - +
241B GLN 3.2 0.4 - - - -
242B MET* 1.3 77.7 - - + +
244B VAL* 1.3 63.5 + - + +
245B LEU 3.6 0.2 - - - -
246B GLU 5.3 0.7 + - - -
247B GLN* 3.5 11.8 - - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 4.3 18.8 - - - +
240B ALA 3.6 12.1 + - - +
241B GLN 3.4 11.0 - - - +
243B GLU* 1.3 86.5 - - + +
245B LEU* 1.3 63.3 + - - +
246B GLU 3.3 2.9 + - - -
247B GLN* 3.4 26.0 + - + +
248B ARG* 3.1 59.3 + - + +
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 3.7 32.8 - - + +
160B LEU* 3.5 50.5 - - + +
161B GLY 4.4 1.1 - - - +
241B GLN 3.1 12.6 + - - +
242B MET* 3.3 29.5 + - + +
243B GLU 3.6 0.2 - - - -
244B VAL* 1.3 77.2 - - - +
246B GLU* 1.3 58.7 + - - +
248B ARG* 3.1 8.6 + - - +
249B VAL* 2.8 38.2 + - + +
281B TRP* 4.2 17.0 - - + -
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Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B TYR* 2.7 40.1 + - + -
242B MET 4.8 0.8 + - - -
243B GLU 5.3 0.4 + - - -
244B VAL 3.3 0.6 - - - -
245B LEU* 1.3 80.3 - - - +
247B GLN* 1.3 65.3 + - + +
249B VAL* 3.2 4.1 + - - +
250B LEU* 3.0 39.5 + - + +
277B ARG* 2.6 35.0 + - - -
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Residues in contact with GLN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLU 3.5 20.8 - - - +
244B VAL* 3.4 22.3 + - + +
246B GLU* 1.3 79.2 - - + +
248B ARG* 1.3 62.3 + - + +
250B LEU* 3.5 11.9 + - + +
251B LYS* 3.1 22.5 + - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY 5.9 1.4 - - - +
14B GLU* 4.4 15.0 + - - -
241B GLN* 4.4 23.8 + - - +
244B VAL* 3.1 45.9 + - + +
245B LEU* 3.5 10.2 - - - +
247B GLN* 1.3 75.5 - - + +
249B VAL* 1.3 59.1 + - - +
251B LYS* 3.2 4.7 + - - +
252B LYS* 2.8 34.8 + - - +
281B TRP* 4.1 28.9 - - + -
366B THR* 3.9 30.0 + - + +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B GLY* 3.9 18.4 - - - +
245B LEU* 2.8 38.0 + - + +
246B GLU* 3.6 7.9 - - - +
248B ARG* 1.3 76.5 - - - +
250B LEU* 1.3 62.1 + - - +
252B LYS* 3.3 9.2 + - - +
253B ARG* 2.9 35.8 + - - +
277B ARG* 3.7 33.0 - - - +
279B ASN* 4.0 23.1 - - + -
281B TRP* 4.1 5.4 - - + -
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Residues in contact with LEU 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B GLU* 3.0 42.3 + - + +
247B GLN* 3.8 10.5 - - + +
249B VAL* 1.3 75.8 - - + +
251B LYS* 1.3 58.6 + - - +
253B ARG* 3.3 12.7 + - - +
254B GLU* 3.0 33.1 + - + +
277B ARG* 3.9 11.7 - - - +
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Residues in contact with LYS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B GLN 3.1 14.3 + - - +
248B ARG* 3.2 8.5 + - - +
250B LEU* 1.3 74.1 - - - +
252B LYS* 1.3 59.0 + - - +
254B GLU* 3.1 21.8 + - - +
255B ILE* 2.9 34.0 + - + +
258B TRP* 3.8 25.4 - - - -
366B THR* 2.6 51.5 + - - +
367B ALA 4.2 1.4 - - - -
368B MET 2.6 26.9 + - - -
369B SER* 4.8 1.6 - - - +
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Residues in contact with LYS 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B ARG 2.8 22.1 + - - +
249B VAL 3.3 4.5 + - - +
251B LYS* 1.3 72.6 - - - +
253B ARG* 1.3 57.9 + - - +
255B ILE* 3.4 8.4 + - - +
256B TYR* 3.0 26.9 + - - +
279B ASN 3.2 22.9 - - - +
280B ARG* 3.5 10.3 - - - +
281B TRP* 2.8 66.9 + - + +
282B LEU* 5.0 2.2 - - - +
283B SER* 4.5 1.2 + - - -
364B SER* 2.8 35.6 + - - +
365B GLY* 4.7 2.0 - - - -
366B THR* 3.8 17.4 - - + +
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Residues in contact with ARG 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B VAL* 2.9 35.5 + - - +
250B LEU* 3.7 11.8 - - + +
252B LYS* 1.3 73.2 - - - +
254B GLU* 1.3 64.6 + - - +
256B TYR* 3.4 8.2 + - - +
257B GLU* 3.1 30.3 + - + +
272B GLU* 2.9 35.0 + - - -
276B SER 5.6 0.2 + - - -
277B ARG* 3.7 19.9 - - - +
278B SER* 2.8 42.5 + - - +
279B ASN 4.3 2.5 - - - +
280B ARG* 4.0 12.6 - - + +
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Residues in contact with GLU 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B LEU* 3.0 17.1 + - + +
251B LYS* 3.1 28.6 + - - +
253B ARG* 1.3 77.2 - - - +
255B ILE* 1.3 62.2 + - - +
257B GLU* 3.2 8.4 + - - +
258B TRP* 3.0 55.3 + - + +
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Residues in contact with ILE 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 2.9 27.6 + - + +
252B LYS* 3.6 8.7 - - - +
254B GLU* 1.3 75.0 - - - +
256B TYR* 1.3 62.9 + - - +
258B TRP* 3.3 28.6 + - + +
259B TYR* 2.9 49.1 + - + -
283B SER* 4.1 5.6 - - - +
363B PRO 4.5 1.3 - - - +
364B SER* 4.0 15.0 - - - +
365B GLY 3.4 25.8 - - - +
366B THR* 4.0 11.0 - - - -
368B MET* 3.8 18.8 - - + +
373B VAL* 4.1 3.8 - - + -
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Residues in contact with TYR 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252B LYS 3.0 14.1 + - - +
253B ARG 3.5 8.1 - - - +
254B GLU 3.2 0.2 - - - -
255B ILE* 1.3 76.5 - - - +
257B GLU* 1.3 75.1 + - - +
259B TYR* 3.3 5.5 + - - +
260B LYS* 2.9 43.7 + - + +
269B PHE* 3.3 45.9 + + - +
270B LEU 3.5 1.4 + - - -
280B ARG* 3.2 67.5 + - + -
282B LEU 5.5 0.2 - - - -
283B SER* 3.4 26.7 - - - +
284B THR 4.0 14.7 + - - -
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Residues in contact with GLU 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B ARG* 3.1 20.1 + - + +
254B GLU* 3.5 10.5 - - - +
256B TYR* 1.3 94.8 - - - +
258B TRP* 1.3 61.6 + - + +
260B LYS* 3.4 25.8 + - - +
261B GLU* 2.9 28.8 + - - +
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Residues in contact with TRP 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B LYS* 3.8 29.8 - - - -
254B GLU* 3.0 42.1 + - + +
255B ILE* 3.3 24.7 + - + +
257B GLU* 1.3 76.0 - - + +
259B TYR* 1.3 66.2 + - - +
261B GLU* 3.2 9.1 + - - +
262B PHE* 2.9 39.3 + - + -
369B SER* 3.7 7.0 - - - -
370B LYS* 3.4 72.6 - - + +
373B VAL* 3.8 19.1 - - + -
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Residues in contact with TYR 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B ILE* 2.9 39.0 + - + -
256B TYR* 3.6 6.1 - - - +
258B TRP* 1.3 72.0 - - - +
260B LYS* 1.3 53.9 + - - +
262B PHE 3.2 0.3 + - - -
263B LEU* 2.8 51.4 + - + +
269B PHE* 3.7 17.3 - - + -
283B SER* 3.8 18.6 - - - -
362B LEU* 3.9 20.6 - - + -
363B PRO* 2.7 45.5 + - - +
368B MET* 4.1 1.7 - - - +
373B VAL* 3.5 17.6 - - + +
376B ILE* 3.9 24.6 - - + +
377B SER* 3.4 20.9 - - - -
380B ILE* 4.5 4.0 - - + -
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Residues in contact with LYS 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 2.9 27.1 + - + +
257B GLU* 3.4 31.4 + - - +
259B TYR* 1.3 75.6 - - - +
261B GLU* 1.3 58.1 + - - +
264B GLY* 2.9 31.0 + - - -
269B PHE* 3.7 42.6 + - + -
271B ASP* 3.9 19.6 + - - -
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Residues in contact with GLU 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B GLU 2.9 14.6 + - - +
258B TRP* 3.2 12.6 + - - +
260B LYS* 1.3 77.8 - - - +
262B PHE* 1.3 82.2 + - + +
263B LEU 3.6 0.2 + - - -
264B GLY* 4.2 2.3 + - - -
370B LYS* 3.9 20.7 + - - -
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Residues in contact with PHE 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B TRP* 2.9 29.5 + - + +
259B TYR 4.0 0.4 - - - +
261B GLU* 1.3 105.8 - - + +
263B LEU* 1.3 60.4 + - - +
264B GLY 3.7 0.2 - - - -
265B GLU* 6.0 1.0 - - - +
370B LYS* 3.7 33.2 - - + -
373B VAL* 3.8 3.1 - - + -
374B TYR* 3.3 63.7 - + + -
377B SER* 3.6 24.9 - - - +
381B LEU* 3.6 24.1 - - + +
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B TYR* 2.8 41.5 + - + +
262B PHE* 1.3 72.4 - - - +
264B GLY* 1.3 57.6 + - - +
265B GLU* 3.0 12.0 + - - -
266B TYR* 3.2 4.2 + - - +
267B PHE* 3.0 34.9 + - + +
269B PHE* 3.9 17.7 - - + -
362B LEU* 4.3 7.6 - - + -
377B SER* 3.7 30.7 - - - +
380B ILE* 3.5 39.9 - - + -
381B LEU* 3.8 18.6 - - + -
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Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260B LYS* 2.9 21.7 + - - -
261B GLU 4.2 2.2 + - - -
262B PHE 3.7 1.0 - - - -
263B LEU* 1.3 76.2 - - - +
265B GLU* 1.3 59.3 + - - +
266B TYR 3.4 0.4 - - - -
267B PHE 3.5 17.0 - - - +
269B PHE* 4.0 7.2 - - - -
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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