Contacts of the helix formed by residues 497 - 524 (chain C) in PDB entry 4P5O
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 GLY 497 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LYS* 3.1 26.0 + - - +
494C GLN 5.3 0.7 - - - -
495C ALA 3.1 4.6 + - - -
496C CYS* 1.3 82.6 - - - +
498C PHE* 1.3 66.8 + - - +
499C GLU 3.5 1.9 + - - -
500C TYR* 3.7 6.2 + - - +
501C THR* 3.7 9.9 + - - +
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Residues in contact with PHE 498 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493C LYS* 3.8 38.0 + - + +
497C GLY* 1.3 70.1 - - - -
499C GLU* 1.3 75.4 + - + +
501C THR* 2.9 19.7 + - - -
502C SER* 2.9 43.0 + - - -
506C ARG* 4.3 23.3 - - - -
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Residues in contact with GLU 499 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496C CYS 5.2 0.6 + - - +
497C GLY 3.5 1.0 - - - -
498C PHE* 1.3 86.2 - - + +
500C TYR* 1.3 63.9 + - - +
502C SER* 3.3 22.3 + - - -
503C LYS* 4.3 14.4 + - - +
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Residues in contact with TYR 500 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462C PHE* 6.2 0.4 - + - -
463C GLN* 2.3 76.0 + - + +
464C LYS* 6.5 0.4 - - + -
466C TYR* 3.9 5.2 - - + +
467C ALA* 3.6 19.7 + - + +
492C LEU* 4.1 13.9 - - + -
496C CYS* 3.7 33.2 + - + +
497C GLY 3.7 3.4 + - - +
498C PHE 3.2 1.0 - - - -
499C GLU* 1.3 80.5 - - - +
501C THR* 1.3 64.8 + - + +
502C SER 3.1 4.6 + - - -
503C LYS* 3.7 25.1 + - - +
504C LEU* 3.6 30.8 + - + +
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Residues in contact with THR 501 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ILE* 3.8 17.0 - - + +
492C LEU* 3.8 12.6 - - + -
493C LYS* 3.2 57.8 - - + +
497C GLY 4.1 2.2 - - - +
498C PHE* 2.9 16.7 + - - -
500C TYR* 1.3 78.7 - - + +
502C SER* 1.3 65.0 + - - +
503C LYS 3.4 0.4 - - - -
504C LEU* 3.8 15.7 - - + -
505C GLN* 2.9 27.6 + - - +
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Residues in contact with SER 502 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE* 2.9 43.2 + - - -
499C GLU* 3.3 22.8 + - - -
500C TYR 3.1 1.2 - - - -
501C THR* 1.3 79.6 - - - +
503C LYS* 1.3 65.5 + - - +
505C GLN 3.2 0.2 + - - -
506C ARG* 2.9 48.9 + - - +
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Residues in contact with LYS 503 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464C LYS* 4.2 22.6 - - - +
467C ALA* 5.3 9.0 - - - +
499C GLU* 4.5 14.1 - - - +
500C TYR* 3.7 25.3 + - + +
502C SER* 1.3 77.0 - - - +
504C LEU* 1.3 65.1 + - + +
506C ARG* 3.1 9.3 + - - +
507C MET* 2.9 29.9 + - + +
544C SER* 4.4 19.2 - - - +
546C PRO* 5.9 6.5 - - - +
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Residues in contact with LEU 504 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C TYR* 4.6 3.1 - - + -
467C ALA* 3.7 29.2 - - + -
470C LEU* 3.8 14.5 - - + +
489C ILE* 4.5 20.6 - - + -
492C LEU* 4.0 17.0 - - + -
500C TYR* 3.6 39.9 - - + +
501C THR* 3.6 20.2 - - + +
503C LYS* 1.3 79.0 - - + +
505C GLN* 1.3 64.5 + - - +
507C MET* 2.9 39.8 + - + +
508C PHE* 2.9 13.0 + - - +
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Residues in contact with GLN 505 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489C ILE* 4.4 19.1 - - + +
493C LYS* 6.0 4.6 - - - +
501C THR* 2.9 19.2 + - - +
502C SER 3.6 3.4 - - - +
504C LEU* 1.3 76.5 - - - +
506C ARG* 1.3 74.9 + - - +
508C PHE* 3.2 28.4 + - - +
509C GLN* 2.9 35.1 + - + +
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Residues in contact with ARG 506 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C PHE* 4.3 22.8 - - - -
502C SER* 2.9 47.9 + - - +
503C LYS* 3.1 7.8 + - - +
505C GLN* 1.3 91.3 - - - +
507C MET* 1.3 61.9 + - - +
509C GLN* 4.2 20.0 - - - +
510C ASP* 2.9 33.0 + - - +
544C SER* 3.5 24.7 - - - +
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Residues in contact with MET 507 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467C ALA* 3.8 10.5 - - + +
470C LEU* 3.7 11.7 - - + -
471C ALA* 3.6 19.7 - - - -
474C LEU* 4.2 4.7 - - + -
503C LYS* 2.9 9.6 + - + +
504C LEU* 2.9 41.3 + - + +
506C ARG* 1.3 76.5 - - - +
508C PHE* 1.3 63.6 + - - +
510C ASP 3.2 0.5 + - - -
511C ILE* 3.0 14.4 + - - +
544C SER 3.8 13.9 - - - +
545C TRP* 3.0 68.1 - - + +
546C PRO* 3.7 15.7 - - + -
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Residues in contact with PHE 508 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470C LEU* 6.1 0.2 - - + -
474C LEU* 4.0 29.1 - - + +
482C ASP* 4.4 19.7 - - + -
485C GLU* 4.7 12.3 - - + -
486C ALA* 4.2 30.7 - - + -
489C ILE* 4.5 16.8 - - + -
504C LEU 2.9 10.5 + - - +
505C GLN* 3.2 31.2 - - - +
507C MET* 1.3 77.8 - - - +
509C GLN* 1.3 58.1 + - + +
511C ILE* 3.2 24.4 - - + +
512C GLY* 3.7 2.6 + - - -
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Residues in contact with GLN 509 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505C GLN* 2.9 20.2 + - + +
506C ARG* 4.2 21.8 - - - +
508C PHE* 1.3 75.0 - - + +
510C ASP* 1.3 66.9 + - + +
511C ILE 3.2 0.2 - - - -
512C GLY* 2.9 17.7 + - - -
513C VAL* 3.0 27.3 + - + +
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Residues in contact with ASP 510 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506C ARG 2.9 20.6 + - - +
507C MET 3.2 0.6 + - - +
509C GLN* 1.3 79.5 - - + +
511C ILE* 1.3 57.4 + - - +
513C VAL* 3.5 9.4 + - - +
514C SER* 3.0 27.9 + - - -
539C VAL 4.1 3.5 - - - +
540C LEU* 3.2 6.3 - - - -
541C SER* 2.3 48.3 + - - -
545C TRP* 3.0 17.9 + - - +
33D TRP* 4.8 5.0 + - - -
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Residues in contact with ILE 511 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C LEU* 3.5 37.0 - - + +
475C VAL* 4.3 6.3 - - - -
507C MET 3.0 13.1 + - - +
508C PHE* 3.2 22.4 - - + +
510C ASP* 1.3 75.8 - - - +
512C GLY* 1.3 65.2 + - - +
514C SER* 3.2 4.5 + - - -
515C LYS* 2.9 27.0 + - - +
538C GLN* 3.0 36.9 + - + +
540C LEU* 3.7 24.0 - - + -
545C TRP* 4.1 6.0 - - + -
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Residues in contact with GLY 512 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508C PHE 3.7 2.0 + - - -
509C GLN* 2.9 9.6 + - - -
511C ILE* 1.3 82.3 - - - +
513C VAL* 1.3 64.3 + - - +
515C LYS* 3.0 17.9 + - - +
516C ASP* 3.0 20.5 + - - +
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Residues in contact with VAL 513 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509C GLN* 3.0 31.6 + - + +
510C ASP* 3.9 10.5 - - - +
512C GLY* 1.3 75.7 - - - +
514C SER* 1.3 57.8 + - - +
516C ASP* 3.4 9.4 + - + +
517C LEU* 2.9 36.6 + - + +
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Residues in contact with SER 514 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510C ASP 3.0 15.1 + - - -
511C ILE* 3.3 18.4 - - - -
512C GLY 3.1 0.2 - - - -
513C VAL* 1.3 75.1 - - - +
515C LYS* 1.3 60.1 + - - +
517C LEU* 3.4 6.1 + - - +
518C ASN* 2.9 30.1 + - - +
537C ILE 4.1 1.5 + - - +
538C GLN* 3.0 13.6 - - - -
539C VAL* 2.6 47.3 + - - +
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Residues in contact with LYS 515 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511C ILE 2.9 13.3 + - - +
512C GLY* 3.0 10.5 + - - +
514C SER* 1.3 75.4 - - - +
516C ASP* 1.3 65.3 + - - +
518C ASN* 3.3 8.6 + - - +
519C GLU* 3.0 22.0 + - - +
538C GLN* 4.8 14.3 - - - +
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Residues in contact with ASP 516 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512C GLY 3.0 18.9 + - - +
513C VAL* 3.8 12.0 - - + +
515C LYS* 1.3 78.0 - - - +
517C LEU* 1.3 57.0 + - - +
519C GLU* 3.1 14.2 + - - +
520C GLN* 2.9 26.2 + - - +
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Residues in contact with LEU 517 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513C VAL* 2.9 24.5 + - + +
514C SER* 3.7 6.3 - - - +
516C ASP* 1.3 77.2 - - - +
518C ASN* 1.3 64.6 + - - +
520C GLN* 3.0 17.1 + - + +
521C PHE* 2.9 21.5 + - + +
537C ILE* 6.5 0.4 - - + -
539C VAL* 4.6 21.1 - - + -
566C PHE* 5.2 13.2 - - + -
569C PHE* 4.9 17.4 - - + -
573C ARG* 5.1 19.7 - - + +
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Residues in contact with ASN 518 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514C SER 2.9 17.0 + - - +
515C LYS* 3.5 8.4 + - - +
517C LEU* 1.3 80.4 - - - +
519C GLU* 1.3 58.8 + - - +
521C PHE* 3.1 12.1 + - - +
522C LYS* 2.9 40.9 + - - +
535C PHE* 3.7 14.6 + - - +
536C SER* 3.5 10.2 - - - +
537C ILE* 2.8 50.8 + - - +
538C GLN* 6.0 1.3 - - + +
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Residues in contact with GLU 519 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515C LYS 3.0 12.8 + - - +
516C ASP* 3.5 16.1 - - - +
518C ASN* 1.3 78.8 - - - +
520C GLN* 1.3 58.7 + - - +
522C LYS* 2.8 35.2 + - + +
523C LYS* 3.0 13.0 + - + +
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Residues in contact with GLN 520 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516C ASP 2.9 12.3 + - - +
517C LEU* 3.0 18.8 + - + +
519C GLU* 1.3 75.1 - - - +
521C PHE* 1.3 57.9 + - - +
523C LYS* 3.3 8.6 + - + +
524C HIS* 2.9 28.8 + - + +
569C PHE* 4.5 22.5 - - + -
573C ARG* 4.8 16.6 + - - +
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Residues in contact with PHE 521 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517C LEU* 2.9 13.8 + - + +
518C ASN* 3.3 19.1 - - - +
520C GLN* 1.3 76.5 - - - +
522C LYS* 1.3 60.8 + - + +
524C HIS* 4.4 11.7 - - + -
525C LEU* 2.9 39.7 + - + +
535C PHE* 4.1 36.6 - + - -
562C SER* 5.7 1.3 - - - -
565C ARG* 5.2 6.7 - - + -
566C PHE* 4.2 38.1 - + + -
569C PHE* 4.4 35.5 - + + -
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Residues in contact with LYS 522 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518C ASN* 2.9 31.6 + - - +
519C GLU* 2.8 25.8 + - + +
521C PHE* 1.3 76.8 - - + +
523C LYS* 1.3 62.8 + - - +
525C LEU* 3.0 22.0 + - - +
526C THR* 3.9 5.7 + - - +
534C ASP* 5.0 9.0 - - - -
535C PHE 4.2 14.1 - - - +
536C SER* 4.8 8.0 + - - -
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Residues in contact with LYS 523 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519C GLU* 3.0 10.9 + - + +
520C GLN* 3.3 11.0 + - + +
522C LYS* 1.3 76.7 - - - +
524C HIS* 1.3 60.5 + - - +
525C LEU 3.3 0.9 + - - -
526C THR* 3.5 21.5 + - - +
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Residues in contact with HIS 524 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520C GLN* 2.9 18.5 + - + +
521C PHE* 3.7 13.4 - - + +
523C LYS* 1.3 73.4 - - - +
525C LEU* 1.3 64.9 + - - +
526C THR 3.1 4.8 + - - -
527C ASN* 3.8 23.6 + - + +
569C PHE* 4.2 37.8 - + + +
572C SER* 5.7 2.4 + - - -
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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