Contacts of the helix formed by residues 249 - 280 (chain B) in PDB entry 3X0Y
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 LEU 249 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 4.6 3.4 - - + -
246B ARG* 3.4 36.8 - - + +
247B GLY 3.1 2.4 - - - -
248B SER* 1.3 76.8 - - - +
250B PHE* 1.3 62.9 + - - +
251B ALA 3.5 0.7 - - - -
252B PRO* 3.3 6.0 - - + +
253B ILE* 3.1 39.5 + - + +
323B LEU* 5.1 3.1 - - + -
326B VAL* 3.7 30.3 - - + +
327B TRP* 4.1 25.4 - - + -
333B LEU* 3.9 18.6 - - + -
338B ARG* 4.2 11.4 - - + -
341B LEU* 4.0 17.5 - - + -
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 4.7 18.4 - + - -
99B THR* 4.9 22.1 - - - -
100B ASN* 5.8 3.6 - - - -
103B MET* 5.5 8.3 - - + -
106B LEU* 4.5 9.9 - - + +
131B SER* 4.8 12.1 - - - -
132B SER* 4.8 5.2 - - - -
174B PHE* 5.3 7.9 - + - -
237B PHE* 4.2 25.8 - + + -
241B PHE* 4.6 6.7 - - + -
247B GLY 3.3 14.6 + - - +
248B SER 3.2 1.4 - - - -
249B LEU* 1.3 78.2 - - - +
251B ALA* 1.3 65.5 + - - +
253B ILE* 3.7 5.3 - - - +
254B ALA* 3.1 34.2 + - + +
415B PHE* 3.9 44.9 - + + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER 4.4 1.0 + - - -
250B PHE* 1.3 80.8 - - - +
252B PRO* 1.3 65.8 - - + +
254B ALA* 3.0 3.4 + - - -
255B GLN* 2.7 36.3 + - + +
338B ARG* 4.0 0.9 - - - +
342B MET* 3.9 3.8 - - - -
414B GLY 3.6 9.3 + - - +
415B PHE 3.9 13.0 - - - +
416B THR 3.9 2.2 - - - -
417B SER* 3.2 41.7 - - - +
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Residues in contact with PRO 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B SER 3.5 9.4 - - - +
249B LEU* 3.3 29.8 - - + +
251B ALA* 1.3 94.9 - - + +
253B ILE* 1.3 59.5 + - + +
256B LEU* 3.0 28.9 + - - +
323B LEU* 5.1 2.7 - - + -
338B ARG* 4.0 6.7 - - + +
341B LEU* 4.0 34.1 - - + -
342B MET* 3.6 28.3 - - + -
345B VAL* 3.7 10.2 - - + +
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Residues in contact with ILE 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 3.5 35.7 - - + -
99B THR* 4.0 24.7 - - + +
102B PRO* 4.9 4.9 - - + -
106B LEU* 4.7 7.9 - - + -
249B LEU* 3.1 28.1 + - + +
250B PHE* 3.7 4.9 - - - +
251B ALA 3.2 0.6 - - - -
252B PRO* 1.3 77.3 - - - +
254B ALA* 1.3 64.2 + - - +
256B LEU* 3.9 1.6 - - - +
257B ILE* 3.1 24.5 + - + +
323B LEU* 4.0 26.8 - - + +
327B TRP* 3.8 30.1 - - + -
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Residues in contact with ALA 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B TYR* 5.7 4.5 - - + +
99B THR* 4.2 23.3 - - + +
250B PHE* 3.1 27.2 + - + +
251B ALA* 3.0 5.3 + - - +
253B ILE* 1.3 79.8 - - - +
255B GLN* 1.3 60.0 + - + +
257B ILE* 3.2 3.3 + - - +
258B PHE* 3.0 51.3 + - + -
415B PHE 5.5 2.0 - - - +
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Residues in contact with GLN 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ALA* 2.7 29.0 + - - +
254B ALA* 1.3 75.3 - - + +
256B LEU* 1.3 56.1 + - - +
258B PHE* 3.3 22.1 + - - +
259B ALA* 3.1 27.4 + - - +
342B MET* 4.1 6.3 - - + -
345B VAL* 3.6 19.3 - - + -
349B LYS* 2.8 36.1 + - + +
391B HIS* 4.3 1.6 + - - -
392B ASP* 2.9 25.0 + - - -
397B LYS* 3.2 26.0 - - - -
415B PHE 5.0 1.6 + - - -
416B THR* 4.2 19.2 + - - +
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Residues in contact with LEU 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ILE* 4.1 9.0 - - + -
252B PRO 3.0 19.1 + - - +
253B ILE* 3.9 3.1 - - - +
255B GLN* 1.3 76.4 - - - +
257B ILE* 1.3 58.5 + - + +
259B ALA* 3.6 2.9 + - - +
260B ASN* 2.7 48.7 + - - +
316B ALA 4.3 6.3 - - - +
319B ALA* 3.9 20.2 - - + +
320B ALA* 3.9 23.1 - - - -
323B LEU* 3.8 25.8 - - + -
345B VAL* 3.6 16.3 - - + +
348B VAL* 3.9 25.4 - - + -
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Residues in contact with ILE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B TRP* 4.2 13.5 - - + -
77B ILE* 4.6 17.9 - - + -
80B VAL* 4.5 10.2 - - + +
95B GLY* 3.7 35.2 - - - +
96B TYR* 4.4 1.1 - - - +
98B LEU* 4.7 10.5 - - + -
99B THR* 3.4 29.6 - - + -
253B ILE* 3.1 23.3 + - + +
254B ALA 3.2 8.5 + - - +
256B LEU* 1.3 75.6 - - + +
258B PHE* 1.3 69.9 + - + +
260B ASN* 3.4 6.6 + - - +
261B VAL* 3.0 28.5 + - + +
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Residues in contact with PHE 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B HIS* 4.3 8.1 - + - -
96B TYR* 3.7 40.8 - + + -
99B THR* 6.1 0.9 - - + -
254B ALA* 3.0 35.7 + - + -
255B GLN* 3.3 35.0 + - - +
257B ILE* 1.3 84.0 - - + +
259B ALA* 1.3 62.3 + - - +
261B VAL* 3.1 8.7 + - + +
262B TYR* 3.0 45.2 + - + +
349B LYS* 4.1 10.8 - - - -
388B HIS* 3.5 26.9 - + + -
391B HIS* 3.9 20.4 - + - -
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Residues in contact with ALA 259 (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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255B GLN 3.1 12.8 + - - +
256B LEU* 3.6 10.5 - - - +
257B ILE 3.3 0.2 - - - -
258B PHE* 1.3 75.6 - - - +
260B ASN* 1.3 57.5 + - - +
262B TYR* 3.2 7.1 + - - -
263B LEU* 3.0 24.3 + - - +
345B VAL 5.6 0.2 - - - +
348B VAL* 3.6 32.1 - - + +
349B LYS* 4.1 10.0 - - - +
352B ALA* 3.2 26.3 - - + +
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Residues in contact with ASN 260 (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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77B ILE* 3.3 32.3 - - + +
80B VAL* 4.9 5.6 - - + -
81B ARG* 3.1 41.0 + - + +
256B LEU* 2.7 44.1 + - - +
257B ILE* 3.9 4.7 - - - +
258B PHE 3.3 0.4 - - - -
259B ALA* 1.3 74.0 - - - +
261B VAL* 1.3 58.5 + - - +
263B LEU* 3.8 4.4 - - - +
264B GLY* 2.8 31.4 + - - -
316B ALA* 3.6 20.2 + - - +
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Residues in contact with VAL 261 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B VAL* 3.8 18.6 - - + -
84B ALA* 3.6 13.1 - - + +
88B GLY 4.1 2.9 - - - +
91B GLY 3.9 15.5 - - - +
92B HIS* 4.0 18.6 - - + +
210B MET* 3.9 27.8 - - + -
257B ILE* 3.0 26.8 + - + +
258B PHE* 3.3 13.5 - - + +
260B ASN* 1.3 76.5 - - - +
262B TYR* 1.3 60.9 + - + +
264B GLY 3.4 0.5 + - - -
265B ILE* 3.0 34.8 + - + +
388B HIS* 6.1 0.2 - - + -
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Residues in contact with TYR 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B PHE* 3.0 23.6 + - + -
259B ALA* 3.2 12.3 + - - +
261B VAL* 1.3 85.1 - - + +
263B LEU* 1.3 58.2 + - - +
265B ILE* 3.3 10.7 + - + +
266B ALA 2.9 23.0 + - - -
349B LYS* 3.5 34.7 + - + -
352B ALA 3.9 13.2 - - - +
353B THR* 3.7 28.5 - - - -
356B ALA* 3.3 18.9 - - + +
385B VAL* 4.1 14.1 - - + -
388B HIS* 2.8 54.7 + + + -
389B SER* 3.3 16.8 - - - -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.3 28.9 - - - +
259B ALA* 3.0 22.0 + - + +
260B ASN* 3.8 4.7 - - - +
261B VAL 3.3 0.2 - - - -
262B TYR* 1.3 72.5 - - - +
264B GLY* 1.3 66.6 + - - +
266B ALA* 3.2 5.1 + - + +
267B HIS* 2.9 31.6 + - - -
309B LEU* 3.7 18.6 - - + -
312B ALA* 3.5 31.2 - - + +
313B ASP* 3.5 9.9 - - - +
316B ALA* 3.8 22.9 - - + -
348B VAL* 5.1 0.9 - - + -
352B ALA* 3.7 22.4 - - + +
355B ALA* 4.8 2.0 - - + -
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Residues in contact with GLY 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.6 27.5 - - - +
84B ALA* 4.1 1.1 - - - -
85B ALA* 3.2 18.9 - - - +
260B ASN 2.8 20.1 + - - -
261B VAL 3.8 1.6 - - - -
263B LEU* 1.3 72.7 - - - +
265B ILE* 1.3 61.3 + - - +
267B HIS* 3.1 7.1 + - - +
268B GLY 2.9 18.0 + - - -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA 3.8 18.0 + - - +
85B ALA* 4.6 0.4 - - - +
88B GLY* 3.8 18.6 - - - +
210B MET* 4.2 7.2 - - + -
261B VAL* 3.0 37.5 + - + +
262B TYR* 3.4 12.8 - - + +
264B GLY* 1.3 74.1 - - - +
266B ALA* 1.3 58.8 + - - +
268B GLY* 2.9 4.3 + - - +
269B ALA* 2.9 25.8 + - - +
356B ALA* 5.5 0.7 - - + -
360B SER* 5.3 1.6 - - - -
381B PHE* 3.3 43.7 - - + +
384B ASN* 4.1 15.7 - - + +
385B VAL* 4.3 15.7 - - + +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR 2.9 13.4 + - - +
263B LEU* 3.5 9.2 - - - +
265B ILE* 1.3 76.6 - - - +
267B HIS* 1.3 58.6 + - - +
269B ALA* 3.4 7.6 + - - +
270B LEU* 2.9 29.8 + - - +
309B LEU* 3.8 22.7 - - + -
356B ALA* 3.7 25.8 - - + +
359B ILE* 3.9 12.2 - - + +
360B SER* 5.7 0.2 - - - -
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Residues in contact with HIS 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B ARG* 3.3 19.8 + - - -
85B ALA* 4.7 7.6 - - + -
263B LEU 2.9 25.9 + - - -
264B GLY* 3.5 9.4 - - - +
266B ALA* 1.3 75.2 - - - +
268B GLY* 1.3 56.3 + - - +
270B LEU* 3.8 6.9 - - + +
271B ASP* 3.0 46.1 + - - +
309B LEU* 3.8 24.8 - - + +
313B ASP* 2.7 27.4 + - - -
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Residues in contact with GLY 268 (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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32B ARG* 5.8 1.6 - - - -
85B ALA* 3.5 27.3 - - - +
264B GLY 2.9 10.3 + - - -
265B ILE 2.9 5.1 + - - -
267B HIS* 1.3 73.7 - - - +
269B ALA* 1.3 64.8 + - - +
271B ASP* 3.5 3.7 + - - +
272B ALA* 3.1 25.5 + - - +
381B PHE* 3.4 10.3 - - - -
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Residues in contact with ALA 269 (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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265B ILE 2.9 10.8 + - - +
266B ALA* 3.7 8.7 - - - +
268B GLY* 1.3 71.8 - - - +
270B LEU* 1.3 58.1 + - - +
272B ALA* 3.3 3.5 + - - +
273B ALA* 2.9 30.3 + - - +
359B ILE* 4.7 2.5 - - + -
360B SER* 4.1 22.4 - - - +
363B VAL* 4.1 11.7 - - + +
381B PHE* 3.4 38.7 - - + -
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Residues in contact with LEU 270 (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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266B ALA 2.9 17.9 + - - +
267B HIS* 3.8 9.9 - - + +
268B GLY 3.3 0.2 - - - -
269B ALA* 1.3 76.5 - - - +
271B ASP* 1.3 61.3 + - - +
273B ALA* 3.2 7.3 + - - +
274B ARG* 2.9 28.3 + - + +
302B TYR* 3.9 24.5 - - + -
305B PHE* 3.8 28.9 - - + -
306B THR* 4.2 23.3 - - + +
309B LEU* 4.0 21.5 - - + -
359B ILE* 4.4 4.5 - - + +
363B VAL* 4.3 6.3 - - + -
405C THR* 4.7 9.4 - - + -
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Residues in contact with ASP 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ARG* 5.7 2.6 + - - -
85B ALA* 6.0 0.7 - - - +
267B HIS* 3.0 33.0 + - - +
268B GLY* 4.0 4.1 - - - +
270B LEU* 1.3 79.5 - - - +
272B ALA* 1.3 58.1 + - - +
274B ARG* 2.8 44.8 + - - +
275B GLU* 2.9 31.1 + - - +
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B GLY 3.1 18.4 + - - +
269B ALA 3.6 3.8 - - - +
271B ASP* 1.3 76.1 - - - +
273B ALA* 1.3 62.6 + - - +
275B GLU* 3.5 13.5 + - - +
276B TYR* 3.0 24.3 + - - +
378B PHE* 4.3 20.4 - - + -
380B ARG* 5.7 1.3 - - - +
381B PHE* 4.1 20.6 - - + -
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Residues in contact with ALA 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ALA 2.9 8.4 + - - +
270B LEU 3.3 9.2 - - - +
272B ALA* 1.3 74.3 - - - +
274B ARG* 1.3 58.6 + - - +
276B TYR* 3.2 2.1 + - - +
277B THR* 2.8 28.9 + - - -
302B TYR* 2.9 21.4 + - + +
363B VAL* 3.3 39.0 - - + +
366B VAL* 4.6 1.3 - - + -
367B ILE* 4.3 16.0 - - + +
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Residues in contact with ARG 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B LEU* 2.9 14.2 + - + +
271B ASP* 2.8 41.1 + - - +
273B ALA* 1.3 76.2 - - - +
275B GLU* 1.3 63.0 + - - +
277B THR* 3.4 0.7 + - - -
278B ARG* 3.1 46.3 + - - +
302B TYR* 3.4 16.7 + - + -
405C THR* 3.0 36.9 + - + +
406C LEU* 3.9 11.7 - - + +
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ASP 2.9 15.7 + - - +
272B ALA* 3.6 16.9 - - - +
274B ARG* 1.3 79.1 - - - +
276B TYR* 1.3 67.5 + - - +
278B ARG* 3.6 6.8 + - - +
279B THR* 3.2 40.1 + - + +
280B GLN* 5.1 2.8 - - - +
378B PHE* 5.2 5.9 - - - -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272B ALA 3.0 18.9 + - - +
273B ALA* 3.7 5.2 - - - +
275B GLU* 1.3 83.9 - - - +
277B THR* 1.3 62.6 + - - +
279B THR* 4.1 1.6 - - - -
280B GLN* 2.7 64.6 + - + +
281B ALA* 3.3 9.2 + - + -
367B ILE* 3.2 39.6 + - + -
370B ARG* 3.8 22.2 + - - +
371B GLY* 3.5 21.1 + - - -
376B TYR* 3.7 26.8 + + - -
378B PHE* 3.6 29.2 - + + -
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Residues in contact with THR 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B ALA 2.8 12.6 + - - -
276B TYR* 1.3 74.9 - - - +
278B ARG* 1.3 62.0 + - - +
279B THR 3.4 0.3 + - - -
281B ALA* 3.6 31.9 + - + +
292B ALA* 4.5 10.4 - - + +
293B THR* 4.0 8.9 - - + +
298B THR* 4.2 20.4 - - + -
302B TYR* 2.5 28.7 + - - +
366B VAL* 4.1 15.6 + - - +
367B ILE* 4.6 1.9 + - - -
406C LEU* 3.8 24.9 - - + -
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Residues in contact with ARG 278 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.1 33.2 + - - +
275B GLU* 3.9 7.9 - - - +
277B THR* 1.3 77.8 - - - +
279B THR* 1.3 64.0 + - + +
293B THR* 4.0 17.7 - - + +
406C LEU* 3.1 36.2 + - + +
407C ASN* 3.7 23.0 + - - +
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Residues in contact with THR 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 3.2 30.7 + - + +
276B TYR 3.3 0.6 + - - -
277B THR 4.6 0.2 - - - -
278B ARG* 1.3 85.5 - - + +
280B GLN* 1.3 90.6 + - - +
281B ALA 3.8 2.0 - - - +
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Residues in contact with GLN 280 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 5.1 2.7 - - - +
276B TYR* 2.7 52.8 + - + +
279B THR* 1.3 94.9 + - - +
281B ALA* 1.3 64.3 + - - +
282B ARG* 4.3 2.6 - - - +
370B ARG* 2.8 32.1 + - - +
375B ARG* 5.6 1.0 - - - +
376B TYR* 4.3 15.3 + - + +
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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) + - + + + + + -
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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