Contacts of the helix formed by residues 564 - 592 (chain B) in PDB entry 3H3T
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 PRO 564 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TRP* 5.2 2.7 - - + +
562B TRP* 3.4 28.9 - - + -
563B ALA* 1.3 87.2 - - + +
565B ALA* 1.3 65.2 + - - +
566B SER* 4.6 5.8 - - - +
567B VAL* 3.1 31.8 + - + +
568B LEU* 3.0 21.0 + - - +
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Residues in contact with ALA 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B GLU* 5.1 3.4 - - - +
414B VAL* 3.6 17.9 - - + +
563B ALA 3.3 4.1 + - - -
564B PRO* 1.3 72.2 - - - +
566B SER* 1.3 63.7 - - - +
568B LEU* 3.2 6.7 + - - +
569B ARG* 3.0 51.1 + - - +
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Residues in contact with SER 566 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B PRO* 3.3 5.9 - - - +
565B ALA* 1.3 78.1 - - - +
567B VAL* 1.3 68.1 + - - +
569B ARG* 3.4 9.1 + - - +
570B ALA* 3.1 24.4 + - - +
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Residues in contact with VAL 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B TRP* 3.6 44.6 - - + +
474B PRO* 5.2 3.6 - - + -
564B PRO* 3.1 31.4 + - + +
566B SER* 1.3 83.1 + - - +
568B LEU* 1.3 67.3 + - + +
570B ALA* 3.1 11.1 + - - +
571B VAL* 3.0 22.5 + - + +
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Residues in contact with LEU 568 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B VAL* 4.7 24.9 - - + +
473B TRP* 3.3 44.0 - - + -
559B PRO* 4.0 28.5 - - + -
563B ALA* 3.5 36.1 - - + +
564B PRO 3.0 11.0 + - - +
565B ALA* 3.2 6.9 + - - +
567B VAL* 1.3 76.3 - - - +
569B ARG* 1.3 61.6 + - - +
571B VAL* 3.3 9.6 - - + +
572B ALA* 3.1 23.6 + - - +
600B 16H 4.8 5.8 - - + +
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Residues in contact with ARG 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ARG* 3.1 42.4 + - - +
407B GLU* 3.5 34.6 + - - +
408B VAL 4.0 4.8 + - - +
409B GLU* 3.6 19.8 + - - -
414B VAL* 3.5 28.3 - - + +
416B ASP* 2.6 43.6 + - - +
565B ALA* 3.0 30.2 + - - +
566B SER* 3.8 7.9 - - - +
567B VAL 3.1 0.2 - - - -
568B LEU* 1.3 78.9 - - - +
570B ALA* 1.3 61.6 + - - +
572B ALA* 3.7 2.2 + - - -
573B LYS* 3.2 14.2 + - - +
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Residues in contact with ALA 570 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B SER 3.1 16.7 + - - +
567B VAL* 3.1 6.7 + - - +
569B ARG* 1.3 79.1 - - - +
571B VAL* 1.3 58.5 + - + +
573B LYS* 3.5 9.3 + - - +
574B ARG* 3.0 30.2 + - - +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B VAL* 3.7 26.5 - - + +
473B TRP* 4.0 27.1 - - + -
567B VAL* 3.0 16.9 + - + +
568B LEU* 3.3 15.3 - - - +
570B ALA* 1.3 78.0 - - + +
572B ALA* 1.3 60.0 + - - +
574B ARG* 4.2 19.1 - - - +
575B GLU* 2.7 42.4 + - + +
600B 16H 3.8 24.0 - - + -
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Residues in contact with ALA 572 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ARG* 4.1 11.0 - - - +
416B ASP* 6.6 0.4 - - + -
418B LEU* 4.7 9.1 - - + +
568B LEU 3.1 17.0 + - - +
569B ARG* 3.7 7.0 - - - +
571B VAL* 1.3 80.8 - - - +
573B LYS* 1.3 62.6 + - - +
576B TYR* 3.1 49.1 + - + -
577B PRO* 3.6 1.9 - - - +
600B 16H 4.1 7.6 - - + -
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Residues in contact with LYS 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B VAL* 3.9 44.2 + - + +
396B VAL* 3.7 13.0 - - + +
403B VAL* 6.1 1.3 - - - -
405B ARG* 3.4 26.2 - - - +
569B ARG 3.2 14.5 + - - +
570B ALA* 3.7 8.1 - - - +
571B VAL 3.3 0.2 - - - -
572B ALA* 1.3 78.4 - - - +
574B ARG* 1.3 57.4 + - - +
577B PRO* 3.1 24.1 - - - +
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Residues in contact with ARG 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B VAL* 2.8 33.5 + - - +
570B ALA* 3.0 21.3 + - - +
571B VAL* 3.8 18.6 - - - +
572B ALA 3.2 0.2 - - - -
573B LYS* 1.3 79.8 - - - +
575B GLU* 1.3 93.9 + - - +
576B TYR 3.7 0.2 - - - -
577B PRO* 4.2 1.0 - - - +
578B LYS* 3.3 30.1 + - + +
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Residues in contact with GLU 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B THR* 4.7 1.7 + - - -
448B THR* 3.4 21.1 - - + +
472B VAL* 4.2 17.9 - - + +
571B VAL* 2.7 24.7 + - + +
574B ARG* 1.3 115.8 + - - +
576B TYR* 1.3 64.0 + - - +
578B LYS* 3.9 22.7 + - - +
579B PHE* 3.1 24.4 + - - +
600B 16H 3.8 29.4 - - + +
----------------------------------------------------------
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Residues in contact with TYR 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B VAL* 5.0 2.9 - - + -
418B LEU* 3.4 37.9 - - + -
553B TYR* 3.6 36.3 - + + -
555B ALA* 3.7 15.7 - - + +
557B VAL* 3.4 28.4 - - - +
572B ALA* 3.1 27.3 + - + +
575B GLU* 1.3 72.7 - - - +
577B PRO* 1.3 77.6 - - + +
579B PHE* 3.4 8.7 + + - -
580B LEU* 3.1 27.1 + - + +
600B 16H 3.5 52.5 - + + +
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Residues in contact with PRO 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396B VAL* 3.8 33.2 - - + -
398B GLU* 6.1 1.3 - - + -
401B MET* 4.0 24.4 - - + +
403B VAL* 4.2 11.0 - - + -
572B ALA 3.6 3.4 - - - +
573B LYS* 3.1 28.7 - - - +
574B ARG 3.7 2.0 - - - +
575B GLU 3.7 1.1 - - - -
576B TYR* 1.3 95.7 - - + +
578B LYS* 1.3 62.9 + - - +
580B LEU* 3.0 2.9 + - - +
581B LYS* 3.0 25.6 + - - +
----------------------------------------------------------
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Residues in contact with LYS 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B THR* 4.3 26.4 + - + +
574B ARG* 3.3 22.3 + - + +
575B GLU* 3.9 26.7 + - - +
576B TYR 3.3 0.4 - - - -
577B PRO* 1.3 79.9 - - - +
579B PHE* 1.3 62.5 + - - +
581B LYS* 3.7 4.7 + - - +
582B ARG* 3.3 28.5 + - + +
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Residues in contact with PHE 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B PHE* 3.8 10.3 - + - -
445B TRP* 3.3 41.8 - + - +
446B GLU* 5.6 4.5 - - - +
447B THR* 6.1 1.3 - - - -
527B MET* 3.8 23.6 - - + -
553B TYR* 3.6 28.5 - + - -
575B GLU 3.1 16.6 + - - +
576B TYR* 3.5 12.3 - - - -
578B LYS* 1.3 78.0 - - - +
580B LEU* 1.3 74.9 + - + +
582B ARG* 3.9 4.3 - - - +
583B PHE* 2.8 42.8 + + + +
600B 16H 3.8 27.1 - - + -
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401B MET* 3.8 24.0 - - + -
403B VAL* 4.7 2.0 - - + -
420B ALA* 3.6 31.2 - - + -
422B HIS* 4.8 10.5 - - + -
527B MET* 4.6 9.2 - - + -
551B ILE* 5.1 7.6 - - + -
553B TYR* 4.4 19.7 - - + -
576B TYR* 3.1 20.7 + - + +
577B PRO 3.0 5.1 + - - +
579B PHE* 1.3 98.3 - - + +
581B LYS* 1.3 55.1 + - - +
583B PHE* 4.7 1.6 - - + -
584B THR* 2.5 52.8 + - + +
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Residues in contact with LYS 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398B GLU* 2.9 40.9 + - - +
401B MET* 4.4 12.7 - - + -
422B HIS* 5.2 2.9 - - - -
577B PRO 3.0 15.6 + - - +
578B LYS* 4.0 5.6 - - - +
580B LEU* 1.3 77.4 - - - +
582B ARG* 1.3 57.0 + - - +
584B THR* 3.1 5.7 + - - -
585B SER* 3.0 37.9 + - - +
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Residues in contact with ARG 582 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ASN 5.5 0.8 + - - -
444B ASP 3.7 15.5 + - - -
445B TRP* 3.1 34.7 + - + +
447B THR* 3.6 27.0 - - - +
578B LYS* 3.3 21.1 + - + +
579B PHE* 3.9 4.3 - - - +
581B LYS* 1.3 78.8 - - - +
583B PHE* 1.3 60.1 + - - +
585B SER* 3.8 4.6 - - - -
586B TYR* 3.0 30.0 + - + +
----------------------------------------------------------
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Residues in contact with PHE 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B VAL* 3.5 37.2 - - + -
435B TYR* 3.9 5.2 - - + -
436B PHE* 3.6 28.0 - - + -
445B TRP* 3.5 39.3 - + + -
527B MET* 3.7 25.6 - - + -
579B PHE* 2.8 39.6 + + + +
580B LEU* 4.3 1.6 - - + +
582B ARG* 1.3 73.8 - - - +
584B THR* 1.3 75.5 + - + +
586B TYR* 3.3 6.2 - + - +
587B VAL* 3.2 43.8 + - + +
----------------------------------------------------------
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Residues in contact with THR 584 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422B HIS* 3.9 17.5 + - + -
424B VAL* 3.8 32.1 - - + +
432B VAL* 5.8 1.6 - - + -
551B ILE* 3.9 15.5 - - + -
580B LEU* 2.5 33.9 + - + +
581B LYS* 3.1 10.7 + - - -
583B PHE* 1.3 89.6 - - + +
585B SER* 1.3 63.8 + - - +
587B VAL* 3.4 6.6 + - - +
588B GLN* 3.1 27.1 + - - +
----------------------------------------------------------
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Residues in contact with SER 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
581B LYS* 3.0 28.0 + - - +
582B ARG* 3.8 5.8 - - - -
584B THR* 1.3 76.4 + - - +
586B TYR* 1.3 65.5 + - - +
588B GLN* 3.0 18.6 + - - +
589B GLU* 2.9 37.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 3.7 23.9 - + + -
441B VAL* 3.7 14.4 - - + +
444B ASP* 2.6 51.8 + - + +
445B TRP* 4.2 27.1 - + + -
582B ARG* 3.0 19.8 + - + +
583B PHE* 3.3 9.6 - - - +
585B SER* 1.3 77.0 - - - +
587B VAL* 1.3 70.4 + - + +
589B GLU* 3.0 26.4 + - - +
590B LYS* 3.0 45.8 + - + +
----------------------------------------------------------
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Residues in contact with VAL 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 6.3 0.2 - - + -
427B VAL* 4.0 14.4 - - + -
431B GLU 4.4 1.3 - - - +
432B VAL* 4.0 27.1 - - + +
435B TYR* 3.8 33.9 - - + -
583B PHE* 3.2 44.0 + - + +
584B THR* 3.8 6.7 - - - +
585B SER 3.2 0.4 - - - -
586B TYR* 1.3 77.0 - - + +
588B GLN* 1.3 57.7 + - - +
589B GLU 3.3 0.2 + - - -
590B LYS* 4.6 3.1 - - - +
591B THR* 2.6 39.5 + - + +
----------------------------------------------------------
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Residues in contact with GLN 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424B VAL* 3.3 26.5 - - + +
425B LYS* 2.8 35.8 + - - +
427B VAL* 4.0 7.2 - - + -
584B THR* 3.1 14.1 + - - +
585B SER* 3.0 17.4 + - - +
587B VAL* 1.3 77.9 - - - +
589B GLU* 1.3 61.0 + - + +
591B THR* 3.4 4.9 + - - -
592B ALA* 3.2 25.5 + - - +
----------------------------------------------------------
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Residues in contact with GLU 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B SER* 2.9 32.8 + - - +
586B TYR* 3.0 17.0 + - + +
588B GLN* 1.3 78.9 - - + +
590B LYS* 1.3 71.7 + - - +
591B THR 3.6 0.3 + - - -
592B ALA* 4.0 11.9 + - - +
----------------------------------------------------------
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Residues in contact with LYS 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 3.5 25.9 + - + +
441B VAL* 6.3 0.2 - - + -
444B ASP* 5.0 4.2 + - - +
586B TYR* 3.0 58.8 + - + +
587B VAL 4.2 1.8 - - - +
589B GLU* 1.3 88.4 + - - +
591B THR* 1.3 54.9 + - - +
592B ALA 5.3 0.4 - - - -
594B LYS* 2.8 43.9 + - - +
----------------------------------------------------------
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Residues in contact with THR 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B GLY 4.5 0.5 + - - -
427B VAL* 3.3 15.6 - - - +
431B GLU* 4.1 19.7 - - + +
435B TYR* 3.8 30.3 - - + +
544B ARG* 3.0 29.6 + - - +
587B VAL* 2.6 28.8 + - + +
588B GLN 3.4 2.6 + - - -
590B LYS* 1.3 79.8 - - - +
592B ALA* 1.3 67.3 + - - +
594B LYS* 2.9 23.3 + - + +
----------------------------------------------------------
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Residues in contact with ALA 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B ARG* 4.4 5.8 - - - +
588B GLN 3.2 19.2 + - - +
589B GLU* 4.2 10.2 - - - +
590B LYS 3.7 0.9 - - - +
591B THR* 1.3 75.0 + - - +
593B GLY* 1.3 63.5 + - - +
594B LYS* 3.1 7.4 + - - +
----------------------------------------------------------
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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