Contacts of the strand formed by residues 501 - 525 (chain A) in PDB entry 5C58
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 501 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A TYR* 3.5 12.2 - - + +
496A ASP* 3.2 4.0 - - - -
497A TYR* 2.8 60.3 + - + +
500A TRP* 1.3 97.0 - - + +
502A THR* 1.3 68.3 + - - +
503A LEU* 4.6 17.0 - - + -
569A VAL* 5.5 3.1 - - + -
570A ALA 3.7 1.1 - - - +
571A VAL* 3.6 23.3 - - + -
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Residues in contact with THR 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A PRO* 4.6 12.5 - - + +
494A THR* 5.9 3.6 - - - -
495A TYR 3.2 7.2 - - - -
496A ASP* 3.4 20.9 - - - +
499A GLY 6.3 0.2 - - - -
500A TRP* 5.2 2.2 - - - -
501A LEU* 1.3 79.5 - - - +
503A LEU* 1.3 70.5 + - - +
504A GLU* 5.2 2.3 + - - +
568A ALA* 4.5 2.0 + - - +
569A VAL* 3.8 2.8 - - - +
570A ALA* 2.9 45.0 + - - +
579A GLU* 4.1 17.9 - - - +
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Residues in contact with LEU 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A LEU 3.7 2.8 - - - +
494A THR* 3.7 1.5 - - - +
495A TYR* 2.7 62.1 + - + +
501A LEU* 4.6 16.6 - - + -
502A THR* 1.3 80.1 - - - +
504A GLU* 1.3 61.4 + - - +
505A GLY 4.1 0.2 + - - -
568A ALA 3.7 1.3 - - - +
569A VAL* 3.9 27.6 - - + -
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Residues in contact with GLU 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A GLU* 5.3 3.8 - - - +
120A PRO* 4.7 11.8 - - + +
121A ARG* 5.5 6.6 - - - +
454A ARG* 5.5 2.8 + - - -
492A ASN* 4.7 17.9 + - + +
493A LEU 3.3 5.2 - - - +
494A THR* 3.6 28.6 + - + +
502A THR* 5.2 2.2 + - - +
503A LEU* 1.3 75.8 - - - +
505A GLY* 1.3 63.5 + - - +
506A GLY 5.3 0.2 - - - +
566A THR* 5.5 4.5 - - + -
567A LEU* 3.6 5.6 - - - +
568A ALA* 2.8 53.0 + - + +
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Residues in contact with GLY 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A ALA 4.5 0.5 - - - +
492A ASN* 3.7 1.5 - - - -
493A LEU* 2.8 37.6 + - - +
503A LEU 4.1 0.4 + - - -
504A GLU* 1.3 78.0 - - - +
506A GLY* 1.3 58.6 + - - -
566A THR 3.3 10.8 - - - -
567A LEU* 3.7 12.3 - - - -
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Residues in contact with GLY 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY* 6.5 0.7 - - - -
491A ALA 3.5 2.0 - - - -
492A ASN* 3.5 26.3 - - - +
504A GLU* 5.3 0.6 - - - +
505A GLY* 1.3 75.2 - - - -
507A LEU* 1.3 58.8 + - - -
565A PRO* 3.5 1.2 - - - +
566A THR* 2.7 46.6 + - - +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A GLY* 5.6 1.1 - - - +
489A LEU 5.4 2.2 - - - +
490A PHE* 3.4 2.9 - - - +
491A ALA* 3.1 42.5 + - + +
506A GLY* 1.3 74.8 - - - +
508A ARG* 1.3 62.8 + - - +
509A TYR 5.5 0.2 - - - +
563A LEU* 3.9 34.3 - - + -
564A SER 3.3 9.6 - - - +
565A PRO* 4.4 7.9 - - + -
566A THR* 5.5 0.2 - - - -
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Residues in contact with ARG 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A THR 3.0 24.2 + - - -
214A GLY* 4.3 8.6 - - - +
215A GLY 5.3 0.7 - - - -
216A MET 5.8 1.3 - - - -
218A SER* 3.0 41.8 + - - -
219A ALA 3.3 3.8 + - - -
221A THR* 5.7 1.0 - - - -
488A SER* 4.7 7.2 - - - -
489A LEU 3.6 10.8 - - - +
490A PHE* 3.9 17.3 - - + -
507A LEU* 1.3 76.3 - - - +
509A TYR* 1.3 62.0 + - - +
510A ASP* 2.6 50.8 + - - +
562A LYS 3.7 2.4 - - - +
563A LEU* 3.3 4.9 - - - +
564A SER* 2.8 50.1 + - - +
566A THR* 5.3 2.0 + - - -
586A LYS 4.1 17.8 + - - -
587A SER* 4.5 9.1 - - - +
588A TRP 5.0 4.0 - - - +
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Residues in contact with TYR 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487A ALA 3.6 1.7 - - - +
488A SER* 3.3 3.1 - - - -
489A LEU* 2.9 48.7 + - + +
507A LEU* 5.5 0.6 - - + +
508A ARG* 1.3 71.6 - - - +
510A ASP* 1.3 78.6 + - - +
511A ARG* 3.9 28.6 + - + +
561A GLY* 3.7 13.6 + - - -
562A LYS 3.9 15.5 - - - -
563A LEU* 3.9 22.2 - - + +
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Residues in contact with ASP 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A ALA* 3.2 14.7 - - - +
486A VAL* 4.5 5.4 - - + -
487A ALA 3.4 4.3 - - - +
488A SER* 3.2 17.9 + - - +
508A ARG* 2.6 48.6 + - - +
509A TYR* 1.3 76.6 - - - +
511A ARG* 1.3 63.1 + - - +
561A GLY* 3.1 22.5 - - - -
562A LYS 3.1 13.8 + - - +
564A SER* 4.6 0.5 + - - -
588A TRP* 3.5 35.2 - - + +
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Residues in contact with ARG 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A VAL* 3.2 2.3 - - - +
487A ALA* 2.7 47.7 + - + +
509A TYR* 3.9 28.9 + - + +
510A ASP* 1.3 78.5 - - - +
512A TYR* 1.3 62.5 + - - +
513A ARG* 5.4 6.7 - - + +
559A ASP* 2.6 32.9 + - - +
560A GLN* 3.5 18.8 - - - +
561A GLY 5.2 0.4 - - - +
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Residues in contact with TYR 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ARG* 4.1 13.0 - - + +
485A SER 3.1 11.9 - - - +
486A VAL* 3.6 13.6 - - + +
511A ARG* 1.3 77.5 - - - +
513A ARG* 1.3 65.3 + - - +
514A LEU* 3.8 27.1 - - + -
558A ARG* 2.7 33.2 + - + +
559A ASP* 3.1 25.6 - - - +
560A GLN* 3.3 44.9 + - + -
588A TRP* 3.4 23.9 - + - -
590A PRO* 3.4 31.0 - - + -
591A PRO* 3.4 20.5 - - + +
616A PRO* 5.1 0.2 - - + -
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Residues in contact with ARG 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN* 3.6 5.0 - - - +
484A ARG* 3.4 2.3 - - - -
485A SER* 2.8 44.6 + - - +
511A ARG* 5.4 5.2 - - + +
512A TYR* 1.3 77.9 - - - +
514A LEU* 1.3 58.9 + - - +
515A ARG* 3.1 50.6 + - + +
557A ASP* 3.5 27.8 + - - +
558A ARG 3.2 12.6 - - - +
559A ASP* 3.8 19.5 + - + +
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Residues in contact with LEU 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN 3.2 17.5 - - - +
484A ARG* 3.7 14.6 - - + -
512A TYR* 3.8 11.5 - - + -
513A ARG* 1.3 72.8 - - - +
515A ARG* 1.3 70.7 + - - +
556A VAL* 3.8 7.4 - - + +
557A ASP* 3.6 2.6 - - - -
558A ARG* 2.8 53.3 + - + +
591A PRO* 3.7 13.0 - - + +
592A ALA 3.5 11.7 - - - +
593A ILE* 3.8 20.4 - - + -
596A THR* 3.4 37.2 - - + +
597A LEU* 4.7 2.7 - - + -
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Residues in contact with ARG 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TYR* 2.9 39.4 + - - -
482A GLY* 3.5 3.1 - - - -
483A ASN* 2.9 57.7 + - - +
485A SER* 5.6 1.2 + - - -
513A ARG* 3.1 44.8 + - + +
514A LEU* 1.3 80.4 - - - +
516A GLY* 1.3 58.5 + - - +
517A GLN* 6.2 0.4 - - - +
556A VAL* 3.3 7.6 - - - +
557A ASP* 3.4 22.7 - - + +
597A LEU* 4.1 3.0 - - - +
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Residues in contact with GLY 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A ALA 4.5 5.2 - - - -
482A GLY* 4.6 2.0 - - - -
483A ASN* 5.4 0.2 - - - -
515A ARG* 1.3 76.0 - - - +
517A GLN* 1.3 77.1 + - - +
555A ASP* 3.8 0.9 - - - +
556A VAL* 2.8 36.2 + - - +
597A LEU* 3.7 18.8 - - - -
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Residues in contact with GLN 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480A PRO* 5.3 3.3 - - - +
481A ALA 4.8 7.0 + - - +
515A ARG* 6.2 0.2 - - - +
516A GLY* 1.3 83.6 - - - +
518A THR* 1.3 64.8 + - - +
554A TRP 3.5 8.5 - - - +
555A ASP* 3.4 26.1 + - + +
597A LEU* 4.4 6.5 - - - +
599A ASN* 5.5 0.5 - - - +
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Residues in contact with THR 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A GLN* 1.3 75.8 - - - +
519A GLY* 1.3 60.9 + - - +
551A ARG* 4.8 1.8 - - - -
553A ASP* 3.7 2.9 - - - +
554A TRP* 2.7 53.0 + - + +
556A VAL* 4.5 0.7 - - + -
597A LEU* 2.8 44.7 + - + -
599A ASN* 3.7 10.6 - - - +
610A PRO* 3.1 30.1 - - + +
612A PRO* 4.3 5.8 - - + -
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Residues in contact with GLY 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A THR* 1.3 79.5 + - - +
520A LEU* 1.3 65.1 + - - +
551A ARG* 3.2 28.5 - - - +
552A GLU 3.5 5.2 - - - -
554A TRP* 4.3 4.0 - - - -
599A ASN* 4.0 15.7 + - - +
609A TYR* 5.2 1.2 - - - -
610A PRO* 3.4 16.4 - - - +
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Residues in contact with LEU 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A GLY* 1.3 76.3 - - - +
521A SER* 1.3 84.4 + - - +
522A TYR* 4.3 10.0 - - + -
550A THR 3.8 0.7 - - - +
551A ARG* 3.3 10.6 - - - +
552A GLU* 3.2 30.4 + - + +
554A TRP* 5.1 7.4 - - - +
609A TYR* 3.5 35.7 - - + -
610A PRO* 4.5 8.5 - - + -
663A LYS* 4.2 9.6 - - + -
664A PRO* 3.7 22.2 - - + -
720A TRP* 4.5 8.7 - - + -
721A LEU* 3.7 29.4 - - + -
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Residues in contact with SER 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 1.3 78.6 - - - +
522A TYR* 1.3 66.2 + - - +
549A THR* 4.4 11.2 + - - -
550A THR 3.3 9.0 - - - -
551A ARG* 3.2 24.4 + - - +
609A TYR* 5.5 1.0 - - - -
663A LYS* 3.3 24.2 + - - +
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Residues in contact with TYR 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A LEU* 4.3 17.9 - - + -
521A SER* 1.3 82.0 - - - +
523A PRO* 1.3 81.9 - - + +
524A ASP* 4.1 7.2 - - + -
531A ARG* 4.5 15.8 + - - -
549A THR* 4.7 4.4 + - - -
550A THR* 3.0 62.8 + - + +
552A GLU* 3.5 26.6 + - + +
663A LYS* 3.9 11.7 - - + +
664A PRO* 3.2 45.2 - - + +
665A GLY* 4.0 12.3 - - - -
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Residues in contact with PRO 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A TYR* 1.3 96.2 - - + +
524A ASP* 1.3 62.6 + - - +
548A THR 4.1 4.5 - - - +
549A THR* 4.9 0.7 - - - -
663A LYS* 5.2 0.9 - - + -
664A PRO 4.7 0.4 - - - +
666A LEU* 2.9 43.4 + - + +
667A VAL 5.3 1.1 - - - +
668A GLN* 3.5 47.6 - - + +
58B SER* 6.2 0.9 - - - -
63B GLN* 4.0 34.3 - - + +
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Residues in contact with ASP 524 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A TYR* 4.1 4.0 - - + -
523A PRO* 1.3 78.2 - - - +
525A LEU* 1.3 81.6 + - - +
526A ALA* 3.3 13.9 + - - +
531A ARG* 3.2 33.8 + - - +
548A THR* 2.7 36.9 + - - +
550A THR* 2.9 32.4 + - - +
666A LEU* 3.6 14.8 - - - +
725A LEU* 3.2 20.9 - - + +
738A VAL* 5.5 0.2 - - - +
63B GLN* 5.0 0.4 - - - +
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Residues in contact with LEU 525 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A ASP* 1.3 79.3 + - - +
526A ALA* 1.3 61.2 + - - +
531A ARG* 4.2 3.1 - - - +
532A TYR* 3.2 31.9 + - + +
543A LEU* 4.0 17.5 - - + +
546A CYS* 3.4 27.8 - - + +
547A SER* 3.6 18.4 - - - +
666A LEU* 3.8 23.7 - - + +
725A LEU* 5.1 0.2 - - - +
727A TYR* 3.6 29.2 - - + +
737A TYR 5.3 6.1 - - - +
738A VAL* 3.6 24.7 - - + +
64B VAL* 5.1 4.0 - - + -
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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