Contacts of the helix formed by residues 392 - 422 (chain A) in PDB entry 6R7X
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 392 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A PHE* 6.2 1.3 - - + -
282A GLU* 3.8 35.2 - - + +
283A GLU 4.4 4.9 - - - +
285A ARG* 3.5 15.9 - - - -
390A HIS* 4.1 2.3 - - - +
391A ARG* 1.3 112.4 - - + +
393A GLU* 1.3 62.4 + - - +
394A SER* 4.0 20.4 - - - +
395A ALA* 4.3 11.7 - - + +
396A TYR* 3.9 10.2 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 3.8 17.8 + - - +
283A GLU 5.1 1.2 + - - -
285A ARG* 3.4 30.0 + - + +
286A PRO* 4.5 7.6 - - - +
392A LEU* 1.3 74.0 - - - +
394A SER* 1.3 61.0 + - - +
395A ALA 3.3 0.7 - - - -
396A TYR* 3.4 28.5 + - - +
397A GLN* 2.9 43.4 + - + +
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 3.8 18.5 + - - -
392A LEU* 3.5 13.4 - - - +
393A GLU* 1.3 79.7 - - - +
395A ALA* 1.3 60.6 + - - +
397A GLN* 3.4 5.4 + - - +
398A ASN* 2.9 41.4 + - - +
704A PC1 5.4 0.7 + - - -
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 4.1 18.2 - - + +
391A ARG 5.4 0.7 - - - +
392A LEU* 4.3 18.6 + - + +
393A GLU 3.3 0.4 - - - -
394A SER* 1.3 80.4 + - - +
396A TYR* 1.3 59.5 + - - +
398A ASN* 3.3 0.7 + - - +
399A HIS* 2.7 42.1 + - + +
704A PC1 4.1 19.7 - - - +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 4.0 27.1 + - - -
382A GLU* 4.2 17.5 + - - +
385A THR* 3.6 44.1 - - + +
386A SER* 3.9 8.1 - - - -
390A HIS* 4.0 18.7 - - + +
392A LEU 3.9 13.4 + - - +
393A GLU* 3.4 32.2 + - - +
394A SER 3.4 0.2 - - - -
395A ALA* 1.3 79.4 - - - +
397A GLN* 1.3 72.9 + - - +
399A HIS 3.4 0.5 + - - -
400A LEU* 3.0 48.3 + - + +
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Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLU* 2.9 35.4 + - + +
394A SER* 3.8 6.5 - - - +
396A TYR* 1.3 99.9 - - - +
398A ASN* 1.3 59.6 + - - +
400A LEU* 3.5 13.8 + - - +
401A ILE* 2.9 51.4 + - + +
495A PHE* 4.9 12.0 - - - +
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER* 2.9 25.7 + - - +
395A ALA 3.7 4.5 - - - +
396A TYR 3.3 0.2 - - - -
397A GLN* 1.3 80.6 - - - +
399A HIS* 1.3 57.1 + - - +
401A ILE* 3.4 7.2 + - - +
402A LEU* 3.0 28.8 + - - +
554A VAL* 4.7 17.7 - - - +
704A PC1 3.2 62.2 + - - +
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Residues in contact with HIS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLN* 5.9 0.8 + - - -
314A ILE* 3.6 21.0 - - + +
385A THR* 3.8 18.2 - - + -
388A GLU* 4.1 2.9 - - - -
390A HIS* 3.3 31.5 - + - +
395A ALA* 2.7 30.8 + - + +
398A ASN* 1.3 74.4 - - - +
400A LEU* 1.3 62.8 + - - +
402A LEU* 3.3 3.1 + - - +
403A LYS* 3.0 39.9 + - - +
704A PC1 3.1 66.9 + - + +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 4.4 13.7 - - - +
381A ALA* 3.7 42.8 - - + +
382A GLU* 3.8 18.4 - - + +
385A THR* 4.0 10.2 - - + +
396A TYR* 3.0 41.9 + - + +
397A GLN* 3.9 15.0 - - - +
399A HIS* 1.3 74.8 - - - +
401A ILE* 1.3 58.9 + - + +
403A LYS* 3.4 1.5 + - - +
404A VAL* 3.0 44.5 + - + +
495A PHE* 4.8 8.1 - - + -
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLN* 2.9 39.6 + - + +
398A ASN* 3.8 4.7 - - - +
400A LEU* 1.3 75.7 - - + +
402A LEU* 1.3 57.3 + - - +
404A VAL* 4.3 0.2 - - - +
405A LEU* 2.9 55.8 + - + +
495A PHE* 3.5 31.9 - - + -
554A VAL* 3.7 34.1 - - + -
555A TRP* 4.5 15.3 - - + +
558A ALA* 6.2 0.2 - - + -
704A PC1 4.4 8.7 - - + -
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASN 3.0 17.2 + - - +
399A HIS* 3.7 6.1 - - - +
400A LEU 3.3 0.2 - - - -
401A ILE* 1.3 76.7 - - - +
403A LYS* 1.3 64.0 + - + +
405A LEU* 3.9 1.9 - - + +
406A VAL* 3.0 40.5 + - + +
704A PC1 3.7 101.4 - - + +
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Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 5.3 0.6 - - - +
318A SER* 3.9 20.2 + - - -
322A VAL* 4.2 10.3 - - + +
377A TYR* 3.5 29.2 + - + +
381A ALA* 4.5 14.4 - - + +
384A LEU* 5.1 6.5 - - + -
385A THR* 3.6 19.8 + - - +
388A GLU* 3.5 26.8 + - - -
399A HIS* 3.0 40.1 + - - +
400A LEU* 3.9 3.6 - - - +
402A LEU* 1.3 76.2 - - - +
404A VAL* 1.3 62.7 + - - +
406A VAL* 3.9 3.5 - - - +
407A PHE 3.1 19.4 + - - -
704A PC1 4.0 29.5 - - + +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A TYR* 4.1 11.9 - - + -
378A ARG* 4.1 22.2 - - + -
381A ALA* 4.3 11.2 - - + -
400A LEU* 3.0 35.7 + - + +
403A LYS* 1.3 74.7 - - - +
405A LEU* 1.3 58.4 + - - +
408A ASN* 2.9 55.0 + - - +
495A PHE* 3.6 26.5 - - + -
499A LEU* 3.8 8.7 - - + -
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE* 2.9 40.6 + - + +
402A LEU* 3.9 3.6 - - - +
404A VAL* 1.3 79.1 - - - +
406A VAL* 1.3 57.5 + - - +
408A ASN* 4.2 1.3 - - + +
409A PHE* 2.9 33.3 + - - +
495A PHE* 5.7 1.1 - - + -
499A LEU* 3.7 15.0 - - + -
502A PHE* 3.6 32.3 - - + -
555A TRP* 3.7 16.8 - - + -
558A ALA* 3.8 27.6 - - + -
704A PC1 4.0 32.2 - - + +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 4.7 7.9 - - + -
326A LEU* 4.2 16.6 - - + -
402A LEU* 3.0 36.7 + - + +
403A LYS* 3.9 3.6 - - - +
405A LEU* 1.3 77.6 - - + +
407A PHE* 1.3 63.1 + - - +
409A PHE* 3.8 1.7 - - - +
410A LEU* 3.0 22.7 + - - +
704A PC1 4.2 72.6 - - + +
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Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 5.8 0.2 - - + -
325A CYS* 3.3 36.6 - - + -
326A LEU* 3.6 23.6 - - + -
329A SER* 3.7 10.5 - - - -
373A MET* 3.9 19.3 - - + -
374A ASN* 3.7 17.5 - - - -
377A TYR* 3.5 57.7 - + + +
403A LYS 3.1 7.7 + - - +
404A VAL 4.3 0.4 - - - +
406A VAL* 1.3 78.5 - - - +
408A ASN* 1.3 67.5 + - - +
410A LEU 3.8 0.2 - - - -
411A ASN* 2.9 45.4 + - - +
712A UMQ 4.5 5.6 - - + -
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Residues in contact with ASN 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASN* 3.1 40.3 + - - +
377A TYR* 5.4 1.0 - - - -
404A VAL* 2.9 29.1 + - - +
405A LEU* 4.2 1.6 - - + +
407A PHE* 1.3 81.5 - - - +
409A PHE* 1.3 60.7 + - - +
411A ASN* 4.6 2.0 - - - -
412A CYS* 2.9 35.8 + - - +
499A LEU* 3.3 36.5 - - + +
503A LEU* 4.4 19.2 - - + +
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU 2.9 19.2 + - - +
406A VAL 3.8 2.7 - - - +
408A ASN* 1.3 76.6 - - - +
410A LEU* 1.3 61.8 + - + +
413A PHE* 3.0 55.0 + + + +
417A PHE* 4.0 30.7 - + - -
502A PHE* 4.7 4.7 - + + -
503A LEU* 4.8 2.8 - - - +
510A LEU* 4.1 4.9 - - + -
562A MET* 3.6 30.1 - - + -
565A ILE* 4.2 26.0 - - + -
704A PC1 3.6 52.0 - - + -
710A UMQ 4.1 7.6 - - + -
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.7 53.2 - - + +
329A SER* 4.5 6.1 - - - -
330A LEU* 3.9 19.1 - - + -
406A VAL 3.0 18.1 + - - +
407A PHE 4.0 2.2 - - - +
409A PHE* 1.3 78.7 - - + +
411A ASN* 1.3 57.6 + - - +
413A PHE 5.4 0.2 - - - -
414A ALA* 2.9 41.0 + - + +
704A PC1 3.8 25.6 - - + -
710A UMQ 4.0 22.9 - - + -
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Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 2.6 30.3 + - - +
332A VAL* 5.9 0.5 - - - +
366A TYR* 3.9 14.3 + - - -
370A ILE* 3.3 33.5 + - - +
373A MET* 3.9 22.1 - - - +
374A ASN* 2.9 27.2 + - - +
407A PHE* 2.9 39.9 + - + +
408A ASN 4.3 0.9 - - - +
410A LEU* 1.3 75.0 - - - +
412A CYS* 1.3 60.8 + - - +
414A ALA* 4.7 1.3 + - - -
415A SER 5.5 0.3 + - - -
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE* 4.2 12.5 - - - +
371A GLU* 6.0 0.4 - - - -
374A ASN* 3.9 18.6 - - - -
408A ASN 2.9 24.9 + - - +
409A PHE 4.3 0.9 - - - +
411A ASN* 1.3 81.9 - - - +
413A PHE* 1.3 73.6 + - + +
414A ALA 3.5 1.0 + - - -
415A SER* 4.7 2.6 + - - -
416A LEU* 4.3 2.6 - - - +
436A LEU* 4.1 14.6 - - - +
440A SER* 6.1 0.9 - - - -
503A LEU* 3.7 26.5 - - + -
507A TYR* 3.4 34.2 + - + +
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.0 55.6 + + - +
410A LEU* 3.9 0.7 - - - -
412A CYS* 1.3 78.1 - - + +
414A ALA* 1.3 59.7 + - - +
415A SER 3.4 2.0 - - - -
416A LEU* 3.9 11.3 - - + +
417A PHE* 2.9 49.1 + - + -
503A LEU* 4.0 28.9 - - + -
506A GLY* 3.6 32.3 - - - -
507A TYR* 3.5 39.9 - + - -
510A LEU* 3.9 12.6 - - + -
511A PHE* 4.3 5.2 - + + -
562A MET* 4.3 4.3 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 5.3 2.0 - - - +
330A LEU* 4.1 17.9 - - + -
333A MET* 3.4 26.3 - - + +
366A TYR* 5.2 2.0 - - - +
410A LEU* 2.9 26.9 + - + +
411A ASN* 4.5 4.0 - - - +
412A CYS 3.5 1.2 - - - -
413A PHE* 1.3 78.5 - - - +
415A SER* 1.3 58.4 + - - +
417A PHE* 3.4 6.4 + - - +
418A TYR* 2.9 23.6 + - - +
710A UMQ 4.7 11.0 - - + +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 3.7 13.3 - - - +
336A TYR* 4.3 4.9 - - - -
337A PHE* 3.6 19.1 - - - -
366A TYR* 3.6 27.2 + - - -
412A CYS 4.7 1.9 + - - -
413A PHE* 4.5 0.2 - - - +
414A ALA* 1.3 77.8 - - - +
416A LEU* 1.3 64.3 + - - +
418A TYR 3.4 0.3 + - - -
419A ILE* 2.9 33.4 + - - +
432A SER* 4.2 4.7 + - - -
436A LEU* 3.7 23.7 - - - +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A CYS 4.3 3.8 - - - +
413A PHE* 3.5 8.7 + - + +
414A ALA 3.3 0.4 - - - -
415A SER* 1.3 84.0 + - - +
417A PHE* 1.3 62.8 + - - +
419A ILE* 3.4 2.1 + - + +
420A ALA* 2.9 30.8 + - - +
429A LEU* 3.8 18.3 - - + +
432A SER* 3.6 26.5 - - - +
433A LEU* 3.8 29.6 - - + +
436A LEU* 4.1 6.7 - - + -
507A TYR* 3.6 31.0 - - + -
511A PHE* 3.6 33.5 - - + -
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Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 4.0 27.4 - + - -
413A PHE* 2.9 25.5 + - + +
414A ALA* 3.8 3.8 - - - +
416A LEU* 1.3 76.5 - - - +
418A TYR* 1.3 59.1 + - - +
420A ALA* 4.6 0.2 - - - -
421A PHE* 2.9 55.6 + + + +
422A VAL* 4.1 0.7 + - - +
510A LEU* 4.1 18.2 - - + -
511A PHE* 3.6 28.3 - + - -
565A ILE* 5.1 1.1 - - + -
569A THR* 3.8 25.1 - - + -
709A UMQ 5.5 2.4 - - + +
710A UMQ 3.7 45.3 - - + -
901B UMQ 4.9 5.4 - - + -
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 4.1 7.9 - - + -
334A MET* 4.3 21.7 - - + +
337A PHE* 3.5 40.2 - + + -
414A ALA 2.9 18.1 + - - +
415A SER 3.7 3.8 - - - +
416A LEU 3.3 0.2 - - - -
417A PHE* 1.3 75.8 - - - +
419A ILE* 1.3 62.3 + - - +
422A VAL* 3.3 38.8 + - + +
423A LEU* 3.2 42.3 + - + +
710A UMQ 3.9 32.7 - - - +
----------------------------------------------------------
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A TYR* 5.0 3.1 - - - +
337A PHE* 3.6 25.4 - - + -
415A SER* 2.9 23.4 + - - +
416A LEU* 3.9 6.1 - - + +
417A PHE 3.3 0.2 - - - -
418A TYR* 1.3 77.9 - - - +
420A ALA* 1.3 58.3 + - - +
423A LEU* 3.6 8.5 + - + +
424A LYS* 2.9 29.6 + - - -
425A ASP* 3.6 24.1 + - + +
428A LEU* 3.9 25.6 - - + +
429A LEU* 3.7 20.9 - - + +
432A SER* 3.8 31.2 - - - +
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU 2.9 18.2 + - - +
417A PHE* 4.2 1.6 - - - +
419A ILE* 1.3 78.9 - - - +
421A PHE* 1.3 76.5 + - + +
424A LYS* 3.8 11.2 - - - +
425A ASP 5.4 0.2 - - - +
426A MET* 4.7 4.9 - - - +
429A LEU* 3.7 26.7 - - + -
511A PHE* 4.7 4.9 - - + -
573A LEU* 3.9 18.9 - - + +
576A MET* 3.6 14.4 - - - +
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE* 2.9 50.2 + + - +
420A ALA* 1.3 88.1 - - + +
422A VAL* 1.3 64.6 + - + +
424A LYS* 4.1 16.7 + - - -
569A THR* 3.8 23.3 - - + -
572A ALA* 3.7 29.8 - - + -
573A LEU* 4.1 18.4 - - + -
576A MET* 3.8 17.7 - - + -
709A UMQ 3.9 44.5 - - + +
901B UMQ 4.0 25.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE 4.1 0.9 + - - +
418A TYR* 3.3 55.1 + - + +
420A ALA 3.7 0.4 - - - -
421A PHE* 1.3 84.2 - - + +
423A LEU* 1.3 71.8 + - + +
424A LYS* 3.4 6.3 + - - -
709A UMQ 3.5 53.8 - - + +
710A UMQ 5.6 4.9 - - - -
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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