Contacts of the helix formed by residues 305 - 339 (chain B) in PDB entry 3QMK
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 305 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B MET* 4.4 1.6 - - - +
302B GLY 5.4 0.2 - - - -
303B GLU 3.8 2.4 + - - -
304B ILE* 1.3 76.4 - - - +
306B GLU* 1.3 53.1 + - - +
307B HIS* 3.7 8.4 + - - +
308B GLU* 3.1 33.1 + - - +
309B GLY* 2.7 32.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 306 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SO4 4.5 6.5 - - - +
300B MET* 4.0 11.2 - - - +
304B ILE 4.0 0.2 + - - -
305B SER* 1.3 72.7 - - - +
307B HIS* 1.3 54.4 + - - +
309B GLY 3.2 0.5 + - - -
310B PHE* 2.7 41.4 + - - +
375B THR* 4.9 0.9 - - - +
376B HIS* 2.7 45.7 + - + +
379B ARG* 3.0 51.8 + - + -
380B VAL* 5.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SO4 3.4 37.1 + - - +
305B SER* 3.3 8.6 + - - +
306B GLU* 1.3 80.7 - - - +
308B GLU* 1.3 64.8 + - + +
310B PHE* 3.3 5.8 + + - +
311B LEU* 3.1 58.0 + - + +
376B HIS* 4.3 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU 3.8 5.7 - - - +
304B ILE* 3.4 29.7 - - + +
305B SER* 3.1 31.0 + - - +
307B HIS* 1.3 85.2 - - + +
309B GLY* 1.3 61.2 + - - +
311B LEU* 3.3 8.6 + - - +
312B ARG* 3.1 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 309 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B MET* 3.7 28.2 - - - +
304B ILE* 3.8 6.3 - - - -
305B SER 2.7 20.8 + - - -
306B GLU 3.6 1.1 - - - -
308B GLU* 1.3 73.5 - - - +
310B PHE* 1.3 61.7 + - - +
312B ARG* 4.0 5.5 - - - +
313B ALA* 3.1 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLU* 2.7 24.5 + - - +
307B HIS* 3.4 8.1 - + - +
309B GLY* 1.3 73.8 - - - +
311B LEU* 1.3 68.3 + - + +
313B ALA* 3.3 5.2 + - - +
314B LYS* 2.9 54.8 + - + +
369B ARG* 5.9 0.2 - - - -
372B LEU* 3.6 38.4 - - + -
373B VAL* 4.4 14.8 - - + -
376B HIS* 3.5 55.2 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B HIS* 3.1 48.6 + - + +
308B GLU* 3.3 7.8 + - - +
310B PHE* 1.3 82.4 - - + +
312B ARG* 1.3 53.0 + - - +
314B LYS* 3.1 28.1 + - - +
315B MET* 2.7 37.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B GLU* 3.1 16.3 + - + +
309B GLY* 4.0 6.1 - - - +
311B LEU* 1.3 77.9 - - - +
313B ALA* 1.3 58.8 + - - +
315B MET* 3.9 5.9 - - - +
316B ASP* 3.0 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B GLY 3.1 18.6 + - - +
310B PHE* 3.6 5.2 - - - +
312B ARG* 1.3 75.1 - - - +
314B LYS* 1.3 65.9 + - - +
316B ASP* 3.3 8.1 + - - +
317B LEU* 3.1 30.1 + - + +
372B LEU* 4.0 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B PHE* 2.9 35.9 + - + +
311B LEU* 3.3 31.7 + - - +
313B ALA* 1.3 78.1 - - - +
315B MET* 1.3 67.3 + - - +
317B LEU* 3.5 3.5 + - - +
318B GLU* 3.0 32.3 + - + +
369B ARG* 3.8 26.7 + - - +
372B LEU* 3.6 19.7 - - + +
2C IDS 5.0 4.9 + - - -
3C SGN 2.7 35.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B LEU 2.7 20.2 + - - +
312B ARG* 3.9 7.2 - - - +
314B LYS* 1.3 83.9 - - - +
316B ASP* 1.3 68.8 + - - +
318B GLU* 3.1 32.7 + - - +
319B GLU* 3.0 49.6 + - + +
2C IDS 5.4 12.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ARG* 3.0 30.5 + - - +
313B ALA* 3.7 7.4 - - - +
315B MET* 1.3 79.3 - - - +
317B LEU* 1.3 64.9 + - + +
319B GLU* 3.4 5.8 + - - +
320B ARG* 3.0 34.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 317 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ALA* 3.1 20.6 + - + +
314B LYS* 3.8 4.3 - - - +
316B ASP* 1.3 76.4 - - + +
318B GLU* 1.3 59.9 + - - +
320B ARG* 3.3 33.0 + - - +
321B ARG* 2.9 36.4 + - + +
368B GLU* 3.3 51.6 - - + +
369B ARG* 6.1 0.2 - - - -
372B LEU* 4.4 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 318 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A ARG* 3.2 38.4 + - - +
432A GLN* 3.9 30.6 + - - +
433A HIS* 6.0 1.2 - - - -
314B LYS* 3.0 21.3 + - + +
315B MET* 3.1 38.6 + - - +
317B LEU* 1.3 76.2 - - - +
319B GLU* 1.3 61.2 + - - +
321B ARG* 3.4 2.0 + - - +
322B MET* 2.9 41.1 + - - +
369B ARG* 5.3 5.8 + - - +
2C IDS 4.7 1.9 + - - -
3C SGN 4.9 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 319 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ARG* 3.0 39.1 + - - -
429A ARG* 4.6 0.3 + - - -
315B MET* 3.0 40.4 + - + +
316B ASP* 3.8 5.8 - - - +
318B GLU* 1.3 81.5 - - - +
320B ARG* 1.3 62.9 + - - +
322B MET* 3.2 12.4 + - - +
323B ARG* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 320 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B ASP* 3.0 25.8 + - - +
317B LEU* 3.3 32.9 + - - +
319B GLU* 1.3 77.2 - - - +
321B ARG* 1.3 67.8 + - - +
323B ARG* 3.4 6.6 + - - +
324B GLN* 3.1 45.7 + - + +
368B GLU* 4.7 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A GLN* 4.1 16.8 - - + +
317B LEU 2.9 22.3 + - - +
318B GLU* 3.9 3.4 - - - +
320B ARG* 1.3 77.9 - - + +
322B MET* 1.3 61.5 + - - +
324B GLN* 3.1 34.3 + - - +
325B ILE* 2.9 38.1 + - + +
361B LEU* 3.8 9.3 - - + +
364B GLN* 3.1 49.6 + - - +
365B VAL* 3.7 23.0 - - + +
368B GLU* 2.9 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 322 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A ARG* 3.7 61.5 - - + +
428A LEU* 3.9 18.4 - - + +
429A ARG* 3.8 33.7 - - - +
432A GLN* 4.5 6.1 - - + -
318B GLU* 2.9 38.9 + - + +
319B GLU* 3.2 14.5 + - - +
321B ARG* 1.3 76.0 - - - +
323B ARG* 1.3 58.8 + - - +
325B ILE* 3.5 7.3 + - - +
326B ASN* 2.9 29.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 323 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLU 3.1 11.8 + - - +
320B ARG* 3.6 10.1 - - - +
322B MET* 1.3 73.8 - - - +
324B GLN* 1.3 66.0 + - + +
326B ASN* 3.2 7.1 + - - +
327B GLU* 3.0 23.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 324 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320B ARG* 3.1 35.5 + - + +
321B ARG* 3.1 54.0 + - - +
323B ARG* 1.3 77.3 - - + +
325B ILE* 1.3 64.7 + - - +
327B GLU* 3.2 7.3 + - - +
328B VAL* 3.0 26.3 + - + +
361B LEU* 4.0 17.8 - - + +
364B GLN* 4.6 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A LEU* 3.8 19.3 - - + +
431A TYR* 3.6 44.9 - - + -
432A GLN* 4.0 26.5 - - + +
435A ALA* 6.1 0.9 - - + -
449A VAL* 5.3 0.2 - - + -
321B ARG* 2.9 24.1 + - + +
322B MET* 3.8 4.3 - - - +
324B GLN* 1.3 77.6 - - - +
326B ASN* 1.3 63.0 + - - +
328B VAL* 3.2 4.0 + - - +
329B MET* 2.9 32.7 + - + +
358B LEU* 4.9 2.9 - - + -
361B LEU* 3.9 29.4 - - + -
365B VAL* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 326 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 3.3 28.4 + - - +
428A LEU* 3.8 23.9 - - + +
453A LEU* 4.4 8.7 - - - +
322B MET 2.9 18.9 + - - +
323B ARG* 3.2 7.4 + - - +
325B ILE* 1.3 76.2 - - - +
327B GLU* 1.3 57.8 + - - +
329B MET* 3.2 4.8 + - - +
330B ARG* 2.8 56.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 327 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ARG 3.0 13.3 + - - +
324B GLN* 3.2 10.7 + - - +
326B ASN* 1.3 76.3 - - - +
328B VAL* 1.3 64.7 + - + +
330B ARG* 3.2 9.7 + - - +
331B GLU* 3.1 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B GLN* 3.0 14.7 + - + +
325B ILE 3.7 5.8 - - - +
327B GLU* 1.3 75.1 - - + +
329B MET* 1.3 64.2 + - - +
331B GLU* 3.1 12.8 + - - +
332B TRP* 2.9 22.0 + - + +
354B PHE* 4.3 17.2 - - + -
357B ILE* 4.0 29.6 - - + -
358B LEU* 3.8 28.9 - - + -
361B LEU* 4.2 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 329 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A TYR* 3.9 16.8 - - + -
446A ARG 4.0 10.1 - - - +
449A VAL* 3.8 19.7 - - + -
450A HIS* 3.7 35.2 + - - +
453A LEU* 3.6 28.7 - - + -
325B ILE* 2.9 23.6 + - + +
326B ASN* 3.5 4.0 - - - +
328B VAL* 1.3 76.9 - - - +
330B ARG* 1.3 63.4 + - + +
332B TRP* 3.5 15.4 + - - +
333B ALA* 3.1 22.7 + - - +
358B LEU* 3.6 32.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLN* 5.9 2.8 - - - +
457A GLU* 2.8 34.2 + - - +
326B ASN* 2.8 48.2 + - - +
327B GLU* 3.2 7.2 + - - +
329B MET* 1.3 71.8 - - + +
331B GLU* 1.3 65.2 + - - +
333B ALA* 3.3 6.5 + - - +
334B MET* 3.0 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 331 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B GLU 3.1 13.0 + - - +
328B VAL* 3.1 13.9 + - - +
330B ARG* 1.3 75.4 - - - +
332B TRP* 1.3 54.2 + - - +
334B MET* 3.1 8.2 + - - +
335B ALA* 2.8 34.7 + - - +
353B HIS* 5.6 2.4 - - - -
354B PHE* 3.7 22.9 - - + -
357B ILE* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 332 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A ARG* 4.3 4.3 - - + -
447A PHE* 4.2 25.8 - + - -
450A HIS* 3.4 48.7 + + + -
328B VAL* 2.9 15.5 + - + +
329B MET* 3.7 9.4 - - - +
331B GLU* 1.3 76.0 - - - +
333B ALA* 1.3 58.5 + - - +
335B ALA* 3.2 2.7 + - + +
336B ASP* 2.9 39.2 + - - -
350B LEU 5.9 0.2 - - - -
351B ASN* 3.7 28.4 + - - +
354B PHE* 3.6 44.2 - + + +
355B GLN* 4.3 20.6 - - + -
358B LEU* 3.5 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 333 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450A HIS* 3.3 9.3 - - + -
454A GLN* 3.4 36.6 + - + +
329B MET 3.1 15.3 + - - +
330B ARG* 3.6 10.5 - - - +
331B GLU 3.2 0.2 - - - -
332B TRP* 1.3 71.4 - - - +
334B MET* 1.3 66.1 + - - +
336B ASP* 3.0 7.1 + - - +
337B ASN* 3.0 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 334 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330B ARG 3.0 13.4 + - - +
331B GLU* 3.4 11.0 - - - +
333B ALA* 1.3 76.4 - - - +
335B ALA* 1.3 64.1 + - - +
337B ASN* 3.0 14.2 + - - +
338B GLN* 2.9 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B GLU 2.8 13.3 + - - +
332B TRP* 3.5 9.6 - - + +
333B ALA 3.2 0.2 - - - -
334B MET* 1.3 77.3 - - - +
336B ASP* 1.3 52.1 + - - +
338B GLN* 3.3 9.8 + - - +
339B SER* 2.7 40.8 + - - -
350B LEU* 4.2 17.7 - - + +
354B PHE* 3.6 25.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 336 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A PHE* 6.1 0.5 - - - -
450A HIS* 2.6 33.5 + - - -
454A GLN* 4.5 7.8 + - - +
332B TRP* 2.9 26.8 + - - +
333B ALA* 3.0 9.5 + - - +
335B ALA* 1.3 77.7 - - - +
337B ASN* 1.3 65.1 + - - +
339B SER* 3.7 9.6 + - - -
340B LYS* 3.7 11.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 337 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A GLN* 5.0 5.0 - - - +
333B ALA* 3.0 30.5 + - - +
334B MET* 3.0 12.4 + - - +
336B ASP* 1.3 80.8 - - - +
338B GLN* 1.3 65.0 + - + +
339B SER 3.2 0.5 + - - -
340B LYS* 3.5 13.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 338 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334B MET* 2.9 14.8 + - + +
335B ALA* 3.8 9.3 - - - +
337B ASN* 1.3 79.8 - - + +
339B SER* 1.3 59.2 + - - +
340B LYS 3.5 0.7 + - - -
341B ASN* 4.4 8.8 + - - +
342B LEU* 5.0 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 339 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B ALA 2.7 30.1 + - - -
336B ASP* 3.7 7.4 + - - -
337B ASN 3.2 0.6 + - - -
338B GLN* 1.3 72.2 - - - +
340B LYS* 1.3 67.3 + - - +
341B ASN* 2.8 5.1 + - - +
342B LEU* 3.3 38.0 + - - -
347B ARG* 3.6 19.4 - - - +
350B LEU* 3.4 17.7 - - - +
----------------------------------------------------------
Back to top of page
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