Contacts of the helix formed by residues 335 - 359 (chain A) in PDB entry 5W97
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 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A TYR* 3.2 39.5 - - - -
333A LYS* 3.0 20.7 + - - +
334A TRP* 1.3 80.3 - - - +
336A PRO* 1.3 74.8 - - - +
337A ALA* 3.5 3.7 + - - -
338A MET* 3.1 24.3 + - - +
339A MET* 3.2 13.5 + - - +
407A ASP* 5.2 0.7 - - - -
411A LYS* 5.0 0.4 - - - +
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Residues in contact with PRO 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A SER* 1.3 88.9 - - - +
337A ALA* 1.3 57.4 + - - +
339A MET* 2.9 30.2 + - + +
340A TRP* 3.1 23.6 + - + +
394A VAL* 3.7 20.0 - - + -
407A ASP* 3.8 37.0 - - - +
410A ALA* 3.6 33.7 - - + +
411A LYS* 4.2 10.0 - - + -
414A PHE* 6.0 1.1 - - + -
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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
----------------------------------------------------------
257A ILE* 3.6 8.0 - - + +
261A TYR* 3.6 27.1 - - + +
335A SER* 3.2 3.0 + - - +
336A PRO* 1.3 78.9 - - - +
338A MET* 1.3 64.1 + - - +
340A TRP* 3.3 12.7 + - - +
341A ALA* 3.0 22.9 + - - +
391A GLY* 3.6 23.6 - - - +
394A VAL* 4.2 4.2 - - + +
395A HIS* 3.8 13.0 - - + +
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Residues in contact with MET 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A ILE* 4.2 3.5 - - - +
258A VAL* 4.2 20.6 - - - +
261A TYR* 3.9 27.1 - - + +
262A SER* 3.7 13.7 - - - +
327A LEU* 3.3 33.0 - - + -
332A ILE* 4.0 15.0 - - + -
333A LYS 3.5 17.0 - - - +
334A TRP* 4.6 4.7 - - + -
335A SER* 3.1 23.5 + - - +
337A ALA* 1.3 77.1 - - - +
339A MET* 1.3 57.7 + - + +
341A ALA* 3.3 3.3 + - - +
342A LEU* 3.0 46.3 + - + +
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Residues in contact with MET 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A TRP* 3.4 47.6 - - + +
335A SER 3.2 7.3 + - - +
336A PRO* 2.9 11.0 + - - +
338A MET* 1.3 75.0 - - - +
340A TRP* 1.3 65.6 + - - +
342A LEU* 3.3 8.1 + - - +
343A GLY 3.0 19.9 + - - -
411A LYS* 3.7 37.5 - - + -
414A PHE* 3.5 44.4 - - + -
201D TGL 3.8 36.2 - - + +
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Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A PRO* 3.1 27.5 + - - +
337A ALA* 3.5 7.0 - - - +
339A MET* 1.3 77.6 - - - +
341A ALA* 1.3 57.3 + - - +
343A GLY* 3.4 1.4 + - - -
344A PHE* 2.9 28.2 + - - +
387A PHE* 3.6 54.2 - + - +
390A MET* 3.5 30.0 - - + +
391A GLY* 3.6 28.7 - - - -
394A VAL* 4.3 14.0 - - + +
410A ALA 4.8 4.4 + - - -
413A HIS* 3.6 31.3 + + - -
414A PHE* 3.7 33.0 - + - +
417A MET* 3.8 27.4 - - + -
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Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 3.8 22.9 - - + +
257A ILE* 3.7 20.2 - - + -
258A VAL* 4.0 17.5 - - + -
337A ALA 3.0 16.7 + - - +
338A MET* 3.6 6.5 - - - +
339A MET 3.2 0.2 - - - -
340A TRP* 1.3 78.0 - - - +
342A LEU* 1.3 57.6 + - - +
344A PHE* 3.3 4.0 + - - +
345A ILE* 3.1 32.6 + - - +
391A GLY* 5.3 0.2 - - - -
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A VAL* 5.9 0.4 - - + -
327A LEU* 3.9 33.7 - - + -
334A TRP* 3.7 30.3 - - + -
338A MET* 3.0 35.7 + - + +
339A MET* 3.8 5.6 - - - +
341A ALA* 1.3 72.5 - - - +
343A GLY* 1.3 66.3 + - - +
345A ILE* 3.1 20.8 + - + +
346A PHE* 3.2 14.6 + - - +
42B ILE* 4.4 13.0 - - + +
46B LEU* 3.8 26.0 - - + -
201D TGL 4.2 19.7 - - + +
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Residues in contact with GLY 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET 3.0 14.1 + - - -
340A TRP 3.7 3.6 - - - -
342A LEU* 1.3 77.9 - - - +
344A PHE* 1.3 60.9 + - - +
346A PHE* 3.4 1.1 + - - +
347A LEU* 3.0 33.7 + - - +
387A PHE* 3.9 18.2 - - - -
414A PHE* 4.9 1.1 - - - -
418A PHE* 4.8 3.1 - - - -
201D TGL 4.1 15.9 - - - +
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Residues in contact with PHE 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.0 7.6 - - + -
250A GLY 4.8 1.8 - - - -
251A PHE* 3.8 25.8 - + - -
254A ILE* 3.8 37.2 - - + -
323A TRP* 3.8 26.5 - + - -
340A TRP 2.9 13.4 + - - +
341A ALA 3.3 8.7 - - - +
343A GLY* 1.3 71.2 - - - +
345A ILE* 1.3 75.4 + - + +
348A PHE* 2.9 47.6 + + + +
383A MET 3.9 10.3 - - - -
384A GLY* 3.2 44.0 - - - -
387A PHE* 3.8 5.2 - - + -
388A ALA* 4.1 7.0 - - + -
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Residues in contact with ILE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ILE* 4.4 2.9 - - + -
258A VAL* 4.1 18.2 - - + -
320A VAL* 4.2 18.6 - - + +
323A TRP* 3.8 40.2 - - + -
324A LEU* 4.1 21.3 - - + -
327A LEU* 4.7 15.9 - - + -
341A ALA 3.1 17.0 + - - +
342A LEU* 3.1 14.7 + - + +
344A PHE* 1.3 88.8 - - + +
346A PHE* 1.3 61.0 + - - +
348A PHE* 4.4 1.8 - - - +
349A THR* 2.7 27.5 + - - -
38B VAL* 4.8 1.7 - - + +
42B ILE* 4.1 11.0 - - + -
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Residues in contact with PHE 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A LEU 3.2 11.2 + - - +
343A GLY 4.1 1.6 - - - +
344A PHE 3.1 0.4 - - - -
345A ILE* 1.3 79.2 - - - +
347A LEU* 1.3 85.2 + - + +
349A THR* 3.2 7.7 + - - -
350A VAL* 3.1 38.2 + - + +
418A PHE* 5.7 3.6 - + - -
608A TGL 4.1 29.6 - - + -
35B SER* 3.7 24.9 - - - -
38B VAL* 4.4 13.2 - - + -
39B LEU* 3.9 35.2 - - + -
42B ILE* 4.0 12.1 - - + -
201D TGL 4.7 13.9 - - + -
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A GLY* 3.0 18.7 + - - +
346A PHE* 1.3 96.9 - - + +
348A PHE* 1.3 66.0 + - - +
350A VAL* 3.3 6.4 + - + +
351A GLY* 3.1 18.7 + - - -
379A TYR* 3.6 21.0 - - + +
383A MET* 3.7 32.8 - - + +
387A PHE* 3.6 26.5 - - + -
418A PHE* 3.7 22.9 - - + -
422A ASN* 3.9 23.8 - - - +
608A TGL 5.2 2.7 - - + -
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Residues in contact with PHE 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ILE* 4.0 8.1 - - + -
251A PHE* 3.6 31.0 - + - -
316A THR* 3.7 25.8 - - + -
320A VAL* 4.7 9.4 - - + -
323A TRP* 5.3 0.4 - + - -
344A PHE* 2.9 46.8 + + + +
345A ILE 4.4 1.1 - - - +
347A LEU* 1.3 78.0 - - - +
349A THR* 1.3 65.0 + - - +
351A GLY 3.3 1.4 + - - +
352A GLY* 2.8 26.2 + - - -
379A TYR 4.8 6.5 - - - -
380A VAL* 4.0 17.7 - - + +
383A MET 4.4 2.6 + - - -
384A GLY* 4.8 2.0 - - - -
602A HEA 3.7 48.9 - - + -
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Residues in contact with THR 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.8 23.6 - - - +
345A ILE 2.7 17.9 + - - -
346A PHE* 3.2 13.1 + - + -
348A PHE* 1.3 79.1 - - - +
350A VAL* 1.3 56.4 + - + +
352A GLY* 3.3 1.4 + - - -
353A LEU* 2.9 48.0 + - + +
602A HEA 3.8 32.9 - - + +
34B ILE* 4.7 0.9 - - + -
35B SER* 5.1 4.7 - - - -
38B VAL* 4.3 20.0 - - + +
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 3.1 42.5 + - + +
347A LEU* 3.6 8.5 - - + +
348A PHE 3.3 0.2 - - - -
349A THR* 1.3 74.9 - - - +
351A GLY* 1.3 63.0 + - - +
353A LEU* 3.2 10.9 + - - +
354A THR* 3.1 25.2 + - + +
379A TYR* 3.9 24.9 - - + -
426A PHE* 5.8 0.4 - - + -
429A HIS* 5.1 4.0 - - + +
608A TGL 3.6 42.3 - - + +
35B SER* 4.6 6.3 - - - -
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Residues in contact with GLY 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU 3.1 11.5 + - - -
348A PHE 3.7 2.9 - - - -
350A VAL* 1.3 77.3 - - - +
352A GLY* 1.3 60.2 + - - +
354A THR* 3.0 13.8 + - - -
355A GLY 3.2 0.5 + - - -
376A HIS* 2.8 27.6 + - - -
379A TYR* 3.6 24.6 - - - +
380A VAL* 3.7 12.1 - - - -
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Residues in contact with GLY 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A PHE* 2.8 18.8 + - - -
349A THR 3.7 1.1 - - - -
351A GLY* 1.3 69.6 - - - +
353A LEU* 1.3 63.8 + - - +
355A GLY* 3.2 10.0 + - - -
356A ILE 3.2 9.4 + - - -
376A HIS* 5.0 0.7 - - - -
380A VAL* 3.9 4.2 - - - +
602A HEA 3.6 50.0 - - - +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 2.9 27.1 + - + +
350A VAL* 3.2 6.5 + - - +
352A GLY* 1.3 76.8 - - - +
354A THR* 1.3 63.3 + - - +
356A ILE* 3.3 7.8 + - + +
357A VAL* 3.3 23.0 + - - +
602A HEA 4.0 36.8 - - + -
608A TGL 6.1 0.2 - - + -
31B VAL* 3.7 48.2 - - + +
34B ILE* 3.9 30.7 - - + -
35B SER* 4.0 15.0 - - - -
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Residues in contact with THR 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A VAL* 3.1 11.9 + - + +
351A GLY* 3.0 18.9 + - - -
352A GLY 3.3 0.2 - - - -
353A LEU* 1.3 76.1 - - + +
355A GLY* 1.3 62.3 + - - +
356A ILE 3.3 0.2 - - - -
357A VAL* 3.4 7.0 + - + +
358A LEU* 3.2 25.7 + - - +
372A TYR* 3.6 32.0 - - + +
376A HIS* 3.4 22.6 - - - -
429A HIS* 4.0 23.7 + - + +
608A TGL 4.8 15.7 - - + -
31B VAL* 5.6 2.5 - - + -
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Residues in contact with GLY 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLY 3.2 6.9 + - - -
352A GLY 3.2 7.9 + - - -
353A LEU 3.2 0.8 - - - -
354A THR* 1.3 77.3 + - - +
356A ILE* 1.3 59.8 + - - +
358A LEU* 3.3 3.8 + - - +
359A ALA 3.0 21.7 + - - -
376A HIS* 3.6 11.2 + - - -
602A HEA 3.2 41.5 - - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A THR 4.6 0.4 - - - +
310A MET* 4.3 28.7 - - + +
313A ALA* 4.0 20.9 - - + +
352A GLY 3.2 11.7 + - - +
353A LEU* 3.5 11.2 - - + +
354A THR 3.3 0.2 - - - -
355A GLY* 1.3 74.9 - - - +
357A VAL* 1.3 66.3 + - + +
359A ALA* 3.3 11.8 + - - +
360A ASN* 3.0 16.5 + - - +
602A HEA 3.8 49.1 - - + -
27B THR* 5.3 4.3 - - + -
31B VAL* 6.0 2.2 - - + -
73B LEU* 4.5 5.4 - - + -
76B ILE* 4.2 25.1 - - + -
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Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A LEU 3.3 13.9 + - - +
354A THR* 3.5 9.6 - - + +
355A GLY 3.2 0.6 - - - -
356A ILE* 1.3 77.3 - - - +
358A LEU* 1.3 58.9 + - - +
360A ASN* 2.8 30.1 + - - +
363A LEU* 3.7 28.1 - - + +
367A LEU* 4.0 14.1 - - + -
372A TYR* 3.8 24.0 - - + +
24B HIS* 4.4 10.3 - - + +
27B THR* 3.8 22.2 - - + -
28B LEU* 5.6 2.7 - - + +
31B VAL* 4.0 13.7 - - + -
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.9 2.1 - - - -
354A THR 3.2 15.3 + - - +
355A GLY* 3.5 8.1 - - - +
356A ILE 3.2 0.2 - - - -
357A VAL* 1.3 71.7 - - - +
359A ALA* 1.3 62.1 + - - +
360A ASN 3.0 7.9 + - - -
364A ASP* 3.4 42.5 - - + +
367A LEU* 3.9 24.5 - - + -
372A TYR* 4.1 12.3 - - + -
373A VAL* 3.9 21.3 - - + -
376A HIS* 3.8 35.7 - - + -
602A HEA 3.6 31.0 - - + +
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Residues in contact with ALA 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PHE* 3.4 6.4 - - - -
306A THR* 2.8 36.8 + - - +
309A THR* 3.6 26.9 - - + -
310A MET* 4.1 17.5 - - + -
355A GLY 3.0 12.5 + - - +
356A ILE* 3.4 15.0 - - - +
357A VAL 3.2 0.8 - - - -
358A LEU* 1.3 76.6 - - - +
360A ASN* 1.3 52.2 + - - +
361A SER 3.4 0.3 + - - -
602A HEA 3.1 11.7 - - + -
----------------------------------------------------------
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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