Contacts of the helix formed by residues 411 - 444 (chain A) in PDB entry 5BUO
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 ARG 411 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404A ALA 5.0 3.5 + - - +
407A ALA* 3.9 22.7 - - + +
409A PRO* 3.8 9.4 - - + +
410A PRO* 1.3 76.5 - - - +
412A PRO* 1.4 63.3 - - - +
414A HIS* 3.6 42.4 + - + +
415A VAL* 3.1 25.8 + - - +
479A VAL* 4.9 1.5 - - - +
1C SGN 3.1 41.9 + - - +
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Residues in contact with PRO 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A PRO* 3.6 9.9 - - + +
411A ARG* 1.4 86.9 - - - +
413A ARG* 1.4 56.9 + - - +
415A VAL* 3.3 2.6 + - - +
416A PHE* 3.0 28.1 + - - +
478A ALA 5.0 1.1 - - - +
479A VAL* 3.8 37.2 - - + +
482A GLU* 3.4 33.0 - - + +
483A ILE* 3.9 15.0 - - + +
1C SGN 4.1 5.4 - - - +
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Residues in contact with ARG 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PRO* 1.4 77.0 - - - +
414A HIS* 1.3 57.5 + - - +
416A PHE* 3.6 28.7 + - - +
417A ASN* 3.1 36.9 + - - +
482A GLU* 4.9 4.5 + - - +
483A ILE* 3.8 16.2 - - - +
486A GLU* 2.8 43.7 + - - +
1C SGN 3.1 67.3 + - - +
2C IDS 4.6 12.3 - - - +
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Residues in contact with HIS 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A ASN 5.5 0.4 + - - -
404A ALA* 3.6 31.5 - - + +
411A ARG* 3.6 44.5 + - + +
413A ARG* 1.3 75.0 - - - +
415A VAL* 1.4 57.0 + - - +
417A ASN* 3.5 10.5 + - - +
418A MET* 3.0 58.0 + - + +
1C SGN 3.0 27.0 + - - +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 4.0 12.9 - - + -
404A ALA* 3.4 37.9 - - + +
405A LEU* 3.8 22.0 - - + +
411A ARG 3.1 23.6 + - - +
412A PRO 3.3 5.1 + - - +
414A HIS* 1.4 73.7 - - - +
416A PHE* 1.4 53.4 + - - +
418A MET* 3.2 4.2 + - - +
419A LEU* 2.8 33.2 + - + +
473A LEU* 3.8 29.4 - - + -
479A VAL* 3.9 12.1 - - + -
483A ILE* 4.5 0.4 - - + -
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Residues in contact with PHE 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A PRO 3.0 11.6 + - - +
413A ARG* 3.8 34.5 - - - +
414A HIS 3.4 0.2 - - - -
415A VAL* 1.4 73.4 - - - +
417A ASN* 1.4 66.7 + - - +
419A LEU* 3.2 16.5 + - + +
420A LYS* 2.9 49.0 + - + +
483A ILE* 3.7 26.0 - - + +
486A GLU* 3.4 46.2 - - + -
487A VAL* 3.7 9.2 - - + -
490A LEU* 4.3 19.5 - - + -
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Residues in contact with ASN 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ARG* 3.1 25.5 + - - +
414A HIS* 3.6 12.5 + - - +
415A VAL 3.4 0.2 - - - -
416A PHE* 1.4 81.9 - - - +
418A MET* 1.3 73.6 + - + +
420A LYS* 3.7 9.4 + - - +
421A LYS* 3.4 30.8 + - - +
1C SGN 3.8 37.0 + - - -
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Residues in contact with MET 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA 3.8 7.8 - - - +
400A ASN* 3.8 31.4 - - - +
401A TYR* 3.8 21.6 - - - +
404A ALA* 4.1 8.5 - - + -
414A HIS* 3.0 46.8 + - + +
415A VAL 3.7 4.5 - - - +
417A ASN* 1.3 86.5 - - + +
419A LEU* 1.4 61.0 + - - +
421A LYS* 3.6 35.9 + - + +
422A TYR* 3.4 20.6 + - - +
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A TYR* 3.5 39.9 - - + +
415A VAL* 2.8 17.1 + - + +
416A PHE* 3.2 22.4 + - + +
418A MET* 1.4 75.7 - - - +
420A LYS* 1.4 52.8 + - - +
422A TYR* 2.9 12.3 + - + +
423A VAL* 2.7 43.6 + - + +
470A LEU* 3.7 25.4 - - + +
473A LEU* 4.4 9.6 - - + -
483A ILE* 5.3 0.9 - - + -
487A VAL* 3.7 30.1 - - + -
490A LEU* 5.0 3.1 - - + -
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Residues in contact with LYS 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A PHE* 2.9 34.6 + - + +
417A ASN* 3.8 10.3 - - - +
419A LEU* 1.4 75.6 - - - +
421A LYS* 1.4 59.0 + - + +
423A VAL* 3.3 5.5 + - - +
424A ARG* 3.0 77.4 + - - +
490A LEU* 4.2 25.5 - - + +
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Residues in contact with LYS 421 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A ALA* 3.7 12.4 - - + +
400A ASN* 6.0 1.8 - - - +
417A ASN* 3.4 17.8 + - - +
418A MET* 3.6 34.7 - - + +
419A LEU 3.3 0.4 - - - -
420A LYS* 1.4 80.4 - - + +
422A TYR* 1.3 60.9 + - - +
424A ARG* 4.1 6.8 - - - +
425A ALA* 3.3 21.8 + - - +
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Residues in contact with TYR 422 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ARG* 4.2 13.0 - - + -
397A ALA* 3.7 16.6 - - + +
398A LEU* 3.6 42.0 - - + -
401A TYR* 4.6 5.2 - + + -
418A MET 3.4 13.0 + - - +
419A LEU* 2.9 20.2 + - + +
421A LYS* 1.3 78.3 - - - +
423A VAL* 1.3 71.8 + - + +
425A ALA* 3.3 3.0 + - - +
426A GLU* 2.7 46.5 + - - +
465A ARG* 3.3 16.3 + - - +
466A MET* 3.4 19.9 - - + -
469A SER* 2.9 37.0 + - - -
470A LEU* 5.4 0.7 - - + -
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Residues in contact with VAL 423 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 2.7 39.7 + - + +
420A LYS 3.8 3.4 - - - +
422A TYR* 1.3 78.7 - - + +
424A ARG* 1.4 53.6 + - + +
426A GLU* 3.0 10.9 + - - +
427A GLN* 2.8 50.3 + - + +
466A MET* 4.4 14.8 - - + -
470A LEU* 4.4 13.5 - - + -
490A LEU* 3.7 28.9 - - + -
491A LEU* 5.3 4.5 - - + -
494A GLU* 4.6 9.2 - - + -
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Residues in contact with ARG 424 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LYS* 3.0 60.8 + - - +
421A LYS* 4.3 6.3 - - - +
423A VAL* 1.4 77.5 - - + +
425A ALA* 1.3 55.9 + - - +
427A GLN* 3.3 10.7 + - + +
428A LYS* 2.9 31.2 + - - +
490A LEU* 3.5 25.9 - - - +
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Residues in contact with ALA 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 4.7 6.4 - - - +
393A ARG* 4.5 9.0 - - + -
394A ARG* 4.0 35.6 - - + +
397A ALA* 4.4 3.6 - - + -
421A LYS 3.3 17.7 + - - +
422A TYR* 3.3 8.2 + - - +
423A VAL 3.3 0.4 - - - -
424A ARG* 1.3 76.3 - - - +
426A GLU* 1.3 60.7 + - - +
428A LYS* 4.0 7.4 - - - +
429A ASP* 3.5 18.7 + - - +
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Residues in contact with GLU 426 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ARG* 3.6 9.8 - - - +
422A TYR* 2.7 43.0 + - - +
423A VAL 3.0 10.9 + - - +
425A ALA* 1.3 75.8 - - - +
427A GLN* 1.3 59.3 + - - +
429A ASP* 3.2 8.5 + - - +
430A ARG* 3.0 27.4 + - - +
462A ILE* 3.5 27.2 - - + +
465A ARG* 2.5 41.9 + - - -
466A MET* 3.7 29.2 - - + -
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Residues in contact with GLN 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A VAL* 2.8 27.7 + - + +
424A ARG* 3.3 17.5 - - + +
426A GLU* 1.3 73.8 - - - +
428A LYS* 1.4 53.6 + - - +
430A ARG* 3.3 25.2 + - - +
431A GLN* 2.8 55.5 + - + +
466A MET* 4.0 15.0 - - - +
494A GLU* 3.5 46.8 + - + +
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Residues in contact with LYS 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.8 22.2 - - + -
424A ARG 2.9 19.1 + - - +
425A ALA* 4.1 5.6 - - - +
427A GLN* 1.4 68.9 - - - +
429A ASP* 1.3 60.1 + - - +
431A GLN* 3.8 10.8 - - - +
432A HIS* 2.9 33.6 + - - +
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Residues in contact with ASP 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A GLU* 3.6 7.3 - - - +
390A LEU* 3.7 26.3 - - + +
391A ASN* 4.7 2.2 - - - +
394A ARG* 5.3 3.1 + - + +
425A ALA 3.5 12.0 + - - +
426A GLU* 3.2 12.8 + - - +
428A LYS* 1.3 78.5 - - - +
430A ARG* 1.3 56.1 + - - +
432A HIS* 4.0 1.2 - - - +
433A THR* 2.6 35.6 + - - -
458A HIS* 3.3 9.7 + - - -
462A ILE* 3.4 14.3 - - + +
465A ARG* 4.0 5.9 + - - -
706A ZN 1.8 38.1 - - - -
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Residues in contact with ARG 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A GLU 3.0 13.9 + - - +
427A GLN* 3.5 29.3 - - - +
429A ASP* 1.3 75.2 - - - +
431A GLN* 1.4 56.3 + - + +
433A THR* 3.3 4.5 + - - -
434A LEU* 3.0 53.2 + - + +
459A LEU* 3.5 35.4 + - + +
462A ILE* 3.7 23.7 - - + +
463A TYR* 5.8 3.6 - - - +
----------------------------------------------------------
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Residues in contact with GLN 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A GLN* 2.8 43.5 + - - +
428A LYS* 3.8 9.2 - - - +
430A ARG* 1.4 74.3 - - + +
432A HIS* 1.3 57.5 + - - +
434A LEU* 3.2 11.5 + - + +
435A LYS* 2.9 29.2 + - - +
494A GLU 5.1 2.8 - - - +
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Residues in contact with HIS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 3.5 17.0 - + + -
382A HIS* 3.2 2.4 + - - -
383A MET* 3.6 23.4 - - - +
386A VAL* 3.2 42.6 - - + +
387A GLU* 5.8 1.6 - - - +
390A LEU* 4.1 12.7 - - + +
428A LYS 2.9 21.5 + - - +
429A ASP 4.1 1.1 - - - +
431A GLN* 1.3 74.3 - - - +
433A THR* 1.3 62.4 + - - +
435A LYS* 3.7 8.5 - - + +
436A HIS* 3.1 22.1 + - + +
704A ZN 2.1 36.8 - - - -
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Residues in contact with THR 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A MET* 5.6 2.9 - - - -
387A GLU* 4.9 1.0 + - - -
429A ASP* 2.6 24.7 + - - -
430A ARG* 3.4 5.4 - - - -
432A HIS* 1.3 77.9 + - - +
434A LEU* 1.4 58.0 + - - +
436A HIS* 3.6 7.3 + - - +
437A PHE* 3.0 28.8 + - - +
455A VAL* 4.1 22.4 - - + +
458A HIS* 3.2 39.9 - - + +
459A LEU* 4.1 16.2 - - + -
462A ILE* 4.2 1.0 - - - +
714A SCN 4.6 9.2 - - - -
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ARG* 3.0 52.7 + - + +
431A GLN* 3.2 11.6 + - + +
433A THR* 1.4 71.2 - - - +
435A LYS* 1.3 59.5 + - - +
437A PHE* 3.5 10.1 + - + +
438A GLU* 2.9 38.7 + - + +
455A VAL* 5.4 2.5 - - + -
459A LEU* 3.7 31.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 3.4 41.7 - - + +
431A GLN 2.9 17.4 + - - +
432A HIS* 3.7 12.1 - - + +
433A THR 3.3 0.2 - - - -
434A LEU* 1.3 76.1 - - - +
436A HIS* 1.3 61.4 + - - +
438A GLU* 3.5 6.4 + - - +
439A HIS* 3.2 22.2 + - - +
----------------------------------------------------------
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Residues in contact with HIS 436 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 5.9 1.1 - - - -
379A VAL* 4.1 12.5 - - + +
383A MET* 3.6 44.1 - - + +
432A HIS* 3.1 20.0 + - + +
433A THR* 3.9 5.4 - - - +
435A LYS* 1.3 74.3 - - - +
437A PHE* 1.3 69.2 + - + +
439A HIS* 3.4 3.7 + - - +
440A VAL* 3.2 41.6 + - + +
447A LYS* 5.4 2.5 - - - -
451A ILE* 4.2 4.1 - - + +
455A VAL* 5.4 0.4 - - + -
705A ZN 2.4 34.7 - - - -
714A SCN 4.7 9.0 - - - -
716A MG 3.4 24.0 - - - -
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Residues in contact with PHE 437 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A THR 3.0 19.1 + - - +
434A LEU* 3.9 10.1 - - + +
436A HIS* 1.3 80.1 - - + +
438A GLU* 1.3 62.1 + - - +
440A VAL* 3.4 4.2 + - - +
441A ARG* 3.0 54.3 + - + +
448A ALA* 3.4 33.2 - - + -
451A ILE* 3.7 9.2 - - + -
452A ARG* 3.8 33.9 - - + -
455A VAL* 3.7 37.2 - - + -
456A MET* 6.2 1.6 - - + -
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Residues in contact with GLU 438 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 2.9 24.1 + - + +
435A LYS* 3.7 7.2 - - - +
437A PHE* 1.3 78.1 - - - +
439A HIS* 1.3 64.0 + - - +
441A ARG* 2.8 48.4 + - - +
442A MET* 3.1 36.3 + - + +
----------------------------------------------------------
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Residues in contact with HIS 439 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS* 4.0 25.2 + - - -
379A VAL* 5.4 2.9 - - + -
435A LYS 3.2 13.6 + - - +
436A HIS* 3.5 8.7 - - - +
437A PHE 3.3 0.2 - - - -
438A GLU* 1.3 74.4 - - - +
440A VAL* 1.4 64.6 + - + +
442A MET* 3.0 7.3 + - - +
443A VAL* 3.0 54.1 + - + +
703A ZN 1.9 38.7 - - - -
713A SCN 3.3 1.9 + - - -
716A MG 3.9 21.1 - - - -
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A VAL* 6.1 0.9 - - + -
436A HIS* 3.2 38.5 + - + +
437A PHE 3.7 6.1 - - - +
439A HIS* 1.4 78.8 - - + +
441A ARG* 1.4 55.4 + - - +
443A VAL* 4.1 7.4 - - + -
444A ASP* 2.7 39.9 + - + +
447A LYS* 3.9 29.8 - - + +
448A ALA* 3.5 30.5 - - + +
451A ILE* 4.2 13.0 - - + -
----------------------------------------------------------
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Residues in contact with ARG 441 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A PHE* 3.0 40.9 + - + +
438A GLU* 2.8 51.0 + - - +
440A VAL* 1.4 75.7 - - - +
442A MET* 1.3 85.8 + - + +
444A ASP 4.8 0.2 - - - -
445A PRO* 4.0 19.1 - - - +
448A ALA* 3.6 22.8 - - + +
----------------------------------------------------------
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Residues in contact with MET 442 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A GLU* 3.1 18.6 + - + +
439A HIS* 3.0 10.8 + - - +
441A ARG* 1.3 118.3 - - + +
443A VAL* 1.3 65.1 + - + +
445A PRO* 5.0 3.2 - - - +
----------------------------------------------------------
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Residues in contact with VAL 443 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A HIS* 3.0 53.3 + - + +
440A VAL* 4.0 6.7 - - + +
442A MET* 1.3 81.6 - - + +
444A ASP* 1.3 70.0 + - + +
445A PRO* 4.1 4.1 - - - +
703A ZN 4.1 6.5 - - - -
----------------------------------------------------------
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440A VAL* 2.7 20.9 + - + +
443A VAL* 1.3 83.1 - - + +
445A PRO* 1.4 68.5 - - - +
446A LYS* 3.6 9.5 + - - +
447A LYS* 3.1 37.5 + - + +
448A ALA 3.1 17.3 + - - -
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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