Contacts of the helix formed by residues 315 - 343 (chain A) in PDB entry 5Y36
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 ALA 315 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 4.1 17.5 - - + -
143A VAL* 3.9 18.8 - - + -
313A THR* 3.2 13.3 + - - +
314A LYS* 1.4 78.3 - - - +
316A PRO* 1.3 62.7 - - - +
317A LEU 3.3 0.3 + - - -
318A SER* 4.2 4.0 - - - -
319A ALA* 3.1 22.3 + - - +
418A GLU* 3.2 27.1 - - - +
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Residues in contact with PRO 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A LEU* 4.2 20.0 - - + +
308A VAL* 3.8 32.1 - - + +
309A ASN 4.6 5.6 - - - +
310A THR* 4.3 18.2 - - + -
313A THR* 4.0 6.5 - - + +
314A LYS* 3.4 10.8 - - - +
315A ALA* 1.3 89.1 - - - +
317A LEU* 1.3 57.7 + - - +
319A ALA* 3.7 7.6 - - + +
320A SER* 3.0 28.9 + - - -
414A ILE* 4.6 9.6 - - + -
418A GLU* 4.3 3.4 - - + +
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Residues in contact with LEU 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 5.7 2.7 - - + -
139A ARG* 3.5 14.1 - - - +
164A PHE* 5.7 0.9 - - + -
306A LEU* 3.5 25.1 - - + +
316A PRO* 1.3 76.6 - - - +
318A SER* 1.3 66.8 + - - +
320A SER* 3.4 13.7 + - - -
321A MET* 3.5 18.7 + - + +
410A ILE* 3.9 22.4 - - + -
414A ILE* 3.7 32.8 - - + +
415A HIS* 3.4 37.0 - - + +
418A GLU* 3.2 8.8 + - - +
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Residues in contact with SER 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A TYR* 3.5 32.3 - - - +
139A ARG* 2.8 26.8 + - - +
140A LYS* 4.4 1.8 - - - -
315A ALA* 4.0 9.6 - - - -
317A LEU* 1.3 74.7 - - - +
319A ALA* 1.4 59.8 + - - +
321A MET* 3.4 5.9 + - - +
322A ILE* 3.3 27.6 + - - +
418A GLU* 2.7 32.0 + - - -
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A LYS* 5.4 9.6 - - + +
308A VAL* 4.3 10.9 - - + +
312A ILE* 6.2 0.4 - - + -
313A THR* 4.1 15.7 - - + +
315A ALA 3.1 18.9 + - - +
316A PRO* 3.7 9.2 - - + +
318A SER* 1.4 73.1 - - - +
320A SER* 1.3 63.3 + - - +
322A ILE* 3.2 22.6 + - + +
323A LYS* 3.2 15.6 + - - +
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Residues in contact with SER 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ILE 4.7 2.4 + - - -
306A LEU* 2.9 27.5 + - - -
308A VAL* 3.6 18.7 - - - +
316A PRO 3.0 18.5 + - - -
317A LEU* 3.4 11.2 + - - -
319A ALA* 1.3 76.3 - - - +
321A MET* 1.3 62.2 + - - +
323A LYS* 4.0 9.4 + - - +
324A ARG* 4.1 21.9 + - - -
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Residues in contact with MET 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A THR* 6.4 0.2 - - - -
136A TYR* 3.7 49.8 - - + +
317A LEU* 3.5 16.1 + - + +
318A SER 3.4 9.1 + - - +
319A ALA 3.3 0.4 - - - -
320A SER* 1.3 77.7 - - - +
322A ILE* 1.4 61.5 + - - +
324A ARG* 3.7 13.7 + - - +
325A TYR* 3.1 23.5 + - - +
402A GLN* 4.3 17.0 - - + +
407A ASN* 3.8 39.9 - - + +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 6.1 4.3 - - + -
134A THR* 4.7 7.2 - - + -
136A TYR* 3.8 34.1 - - + +
137A HIS* 3.9 17.5 - - + +
140A LYS* 4.4 17.7 - - + +
318A SER 3.3 19.7 - - - +
319A ALA* 3.2 12.2 + - - +
321A MET* 1.4 73.6 - - - +
323A LYS* 1.4 66.3 + - - +
325A TYR* 3.2 10.1 + - + +
326A ASP* 3.0 39.8 + - - +
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Residues in contact with LYS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A VAL* 5.9 7.0 - - + -
319A ALA 3.2 12.4 + - - +
320A SER* 4.1 6.7 - - - +
321A MET 3.5 0.2 - - - -
322A ILE* 1.4 80.1 - - - +
324A ARG* 1.3 62.9 + - - +
326A ASP* 3.4 5.5 + - - +
327A GLU* 2.7 55.3 + - + +
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Residues in contact with ARG 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A ARG* 5.3 9.5 - - - +
320A SER* 4.1 18.7 + - - +
321A MET* 3.7 16.6 + - - +
322A ILE 3.5 0.2 - - - -
323A LYS* 1.3 77.7 - - - +
325A TYR* 1.3 63.8 + - - +
327A GLU* 3.2 15.4 + - - +
328A HIS* 3.0 58.7 + - + +
396A GLU 4.9 1.2 + - - -
397A ASP* 2.9 37.6 + - + +
400A ARG* 4.6 11.9 - - - -
407A ASN* 5.6 3.2 + - - -
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Residues in contact with TYR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 3.2 32.1 + - + +
134A THR* 4.8 12.8 - - + -
136A TYR* 6.6 0.2 - - + -
321A MET 3.1 20.6 + - - +
322A ILE* 3.2 10.5 + - + +
324A ARG* 1.3 76.7 - - - +
326A ASP* 1.4 76.0 + - - +
328A HIS* 3.4 20.2 - - - +
329A HIS* 3.3 44.1 + + - -
402A GLN* 4.6 21.1 - - + +
44B U 2.8 13.9 + - - -
45B U 2.1 34.9 + - - -
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Residues in contact with ASP 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PRO* 5.3 5.5 - - - +
322A ILE* 3.0 31.1 + - - +
323A LYS* 3.8 5.9 - - - +
325A TYR* 1.4 93.6 - - - +
327A GLU* 1.3 62.1 + - + +
329A HIS* 3.4 17.3 + - - +
330A GLN* 3.4 23.6 + - - +
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Residues in contact with GLU 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LYS* 2.7 52.7 + - + +
324A ARG* 3.2 18.7 + - - +
326A ASP* 1.3 74.6 - - + +
328A HIS* 1.4 59.5 + - + +
330A GLN* 3.3 16.9 + - - +
331A ASP* 2.9 42.5 + - - +
392A LYS* 4.8 15.2 + - - +
397A ASP* 5.4 8.4 - - - +
----------------------------------------------------------
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Residues in contact with HIS 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ARG* 3.0 42.5 + - + +
325A TYR* 3.4 17.5 - - + +
327A GLU* 1.4 76.7 - - + +
329A HIS* 1.4 60.3 + - + +
331A ASP* 4.0 3.8 - - - -
332A LEU* 3.0 31.1 + - - +
397A ASP 3.2 19.1 + - - -
398A LEU* 4.6 0.4 - - + -
399A LEU* 3.2 37.2 - - + +
400A ARG* 3.0 44.2 + - - -
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Residues in contact with HIS 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A TYR* 3.3 63.0 + + - -
326A ASP* 3.4 10.1 + - - +
328A HIS* 1.4 75.5 - - + +
330A GLN* 1.3 58.8 + - + +
332A LEU* 3.9 12.0 - - - +
333A THR* 2.7 38.4 + - - +
44B U 4.8 17.4 - - - -
45B U 5.3 2.5 - - - -
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Residues in contact with GLN 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A ASP* 3.4 16.4 + - - +
327A GLU* 3.3 22.6 + - - +
329A HIS* 1.3 76.2 - - + +
331A ASP* 1.4 61.7 + - - +
333A THR* 3.8 4.9 - - - -
334A LEU* 3.0 29.5 + - - +
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Residues in contact with ASP 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A GLU* 2.9 25.4 + - - +
328A HIS* 4.1 4.5 - - - +
330A GLN* 1.4 72.7 - - - +
332A LEU* 1.3 60.8 + - - +
334A LEU* 3.5 11.3 + - - +
335A LEU* 3.0 28.8 + - - +
388A GLU* 5.6 3.5 - - - +
389A LEU* 3.8 24.6 - - + +
392A LYS* 2.7 40.2 + - - +
397A ASP 4.9 3.8 - - - +
398A LEU* 4.2 15.0 - - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS 3.0 20.0 + - - +
329A HIS* 3.9 12.3 - - - +
331A ASP* 1.3 73.7 - - - +
333A THR* 1.3 59.6 + - - +
335A LEU* 3.3 7.2 + - + +
336A LYS* 2.8 65.0 + - - +
351A PHE* 4.1 4.5 - - + -
359A TYR* 3.7 35.4 - - + -
363A ILE* 5.5 11.0 - - + -
399A LEU* 4.0 18.7 - - + +
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Residues in contact with THR 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A HIS* 2.7 24.2 + - - +
330A GLN* 3.8 6.1 - - - -
332A LEU* 1.3 74.8 - - - +
334A LEU* 1.4 61.8 + - - +
336A LYS* 3.5 10.7 + - + +
337A ALA* 3.0 25.5 + - + +
----------------------------------------------------------
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Residues in contact with LEU 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A GLN 3.0 19.2 + - - +
331A ASP* 3.5 9.2 - - - +
332A LEU 3.4 0.2 - - - -
333A THR* 1.4 75.0 - - - +
335A LEU* 1.3 57.1 + - - +
337A ALA* 3.3 9.8 + - + +
338A LEU* 3.0 50.5 + - + +
385A GLY 4.9 7.0 - - - +
388A GLU* 4.9 14.1 - - + +
389A LEU* 4.3 23.1 - - + -
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Residues in contact with LEU 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASP 3.0 18.3 + - - +
332A LEU* 3.7 8.1 - - + +
334A LEU* 1.3 74.3 - - - +
336A LYS* 1.4 53.8 + - - +
338A LEU* 3.2 8.7 + - + +
339A VAL* 2.8 54.9 + - + +
351A PHE* 5.1 3.1 - - + -
359A TYR* 3.0 34.1 - - + +
376A ILE* 5.5 3.4 - - + -
379A ILE* 5.9 1.6 - - + -
380A LEU* 3.6 35.2 - - + -
383A MET* 4.5 11.9 - - + -
389A LEU* 4.0 12.8 - - + -
398A LEU* 6.0 4.7 - - + -
399A LEU* 5.9 2.2 - - + -
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A LEU* 2.8 55.0 + - + +
333A THR* 3.6 9.4 - - - +
335A LEU* 1.4 71.5 - - - +
337A ALA* 1.3 55.4 + - - +
339A VAL* 3.5 2.2 + - - +
340A ARG* 3.0 52.9 + - - +
347A TYR* 4.5 5.6 - - + +
351A PHE* 3.6 38.6 - - + -
43B G 5.9 3.8 + - - -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 3.0 15.0 + - + +
334A LEU* 3.5 12.6 - - + +
336A LYS* 1.3 76.3 - - - +
338A LEU* 1.3 59.8 + - + +
340A ARG* 3.6 11.9 + - - +
341A GLN* 3.2 30.9 + - + +
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Residues in contact with LEU 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LEU* 3.0 32.9 + - + +
335A LEU* 3.4 7.6 - - + +
337A ALA* 1.3 76.8 - - + +
339A VAL* 1.4 55.1 + - - +
341A GLN* 3.5 3.8 + - + -
342A GLN* 2.9 52.3 + - - +
383A MET* 3.6 13.9 - - + -
384A ASP 3.6 6.7 - - - +
385A GLY* 3.6 24.9 - - - +
386A THR* 4.1 10.3 - - + -
389A LEU* 4.0 22.2 - - + -
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Residues in contact with VAL 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A LEU* 2.8 37.1 + - + +
336A LYS 3.9 3.6 - - - +
338A LEU* 1.4 68.2 - - - +
340A ARG* 1.3 62.5 + - - +
343A LEU* 2.8 45.9 + - + +
347A TYR* 3.9 20.2 - - + -
350A ILE* 3.9 31.0 - - + -
351A PHE* 4.3 13.9 - - + -
379A ILE* 5.5 1.6 - - + -
383A MET* 3.9 20.4 - - + -
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Residues in contact with ARG 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A LYS* 3.0 36.3 + - - +
337A ALA* 3.7 10.1 - - - +
338A LEU 3.5 0.2 - - - -
339A VAL* 1.3 75.0 - - - +
341A GLN* 1.3 69.5 + - + +
344A PRO* 3.5 21.9 - - - +
347A TYR* 3.1 46.0 + - + -
41B A 5.9 2.9 + - - -
43B G 5.8 2.4 + - - -
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Residues in contact with GLN 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA* 3.2 20.6 + - + +
338A LEU* 3.9 4.9 - - + +
339A VAL 3.3 0.2 - - - -
340A ARG* 1.3 84.1 + - - +
342A GLN* 1.4 64.5 + - + +
344A PRO* 4.4 5.7 - - - +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A LEU* 2.9 34.1 + - - +
341A GLN* 1.4 80.9 - - + +
343A LEU* 1.3 69.9 + - + +
344A PRO* 3.4 9.8 - - - +
383A MET* 3.3 26.5 - - + +
384A ASP* 2.8 55.7 + - - +
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A VAL* 2.8 29.0 + - + +
342A GLN* 1.3 85.8 - - + +
344A PRO* 1.3 64.4 - - - +
345A GLU* 3.3 4.2 + - - +
346A LYS* 3.5 16.7 + - + +
347A TYR* 3.4 13.9 + - - +
350A ILE* 4.2 14.6 - - + -
379A ILE* 4.2 15.0 - - + -
383A MET* 3.9 29.4 - - + -
----------------------------------------------------------
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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