Contacts of the helix formed by residues 579 - 609 (chain B) in PDB entry 3RMD
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 ASP 579 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386B HIS* 5.8 1.6 - - - -
427B PRO* 5.0 6.9 - - + +
430B ILE* 3.5 14.4 - - - +
570B LEU* 4.6 2.4 + - - +
577B TYR 3.6 4.0 + - - +
578B TYR* 1.3 83.7 - - - +
580B LEU* 1.3 70.3 + - - +
581B ARG* 2.9 46.6 + - - -
582B ASN* 2.9 33.5 + - - +
583B ALA* 2.9 12.3 + - - +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389B GLN* 4.1 39.9 - - + +
390B PRO 4.9 1.6 - - - +
391B TYR* 3.9 33.2 - - + -
578B TYR* 3.6 32.4 - - + +
579B ASP* 1.3 73.9 + - - +
581B ARG* 1.3 64.6 + - - +
583B ALA* 3.2 3.8 + - + +
584B THR* 2.9 33.4 + - - +
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Residues in contact with ARG 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B ILE* 3.9 14.5 - - - +
433B THR* 5.3 4.4 - - - +
459B ASN* 3.4 9.4 + - - +
461B MET* 3.3 43.4 - - + +
579B ASP* 2.9 30.8 + - - +
580B LEU* 1.3 80.3 - - - +
582B ASN* 1.3 61.6 + - - +
584B THR* 3.7 2.4 - - - -
585B ALA* 2.8 27.9 + - - +
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Residues in contact with ASN 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 3.4 18.9 - - + +
426B SER* 3.4 6.5 + - - +
427B PRO* 3.4 36.8 - - - +
430B ILE* 3.3 21.6 - - - +
461B MET* 4.9 0.2 - - - +
463B TYR* 3.1 19.3 + - - -
570B LEU* 6.1 4.7 - - + -
577B TYR 5.1 1.4 + - - +
579B ASP* 2.9 20.5 + - + +
581B ARG* 1.3 74.8 - - - +
583B ALA* 1.3 66.9 + - - +
585B ALA* 3.4 0.9 - - - +
586B ILE* 3.0 31.8 + - + +
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Residues in contact with ALA 583 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B TYR* 3.8 34.4 - - + +
567B TYR* 4.7 4.0 - - + -
570B LEU* 4.5 16.4 - - - +
571B GLY* 4.6 2.9 - - - -
578B TYR* 5.0 2.7 - - + -
579B ASP 2.9 13.1 + - - +
580B LEU* 3.2 12.3 + - + +
582B ASN* 1.3 76.7 - - - +
584B THR* 1.3 63.2 + - - +
586B ILE* 3.5 11.0 + - - +
587B THR* 3.2 21.9 + - - +
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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
----------------------------------------------------------
391B TYR* 4.0 19.2 - - - +
392B PRO* 4.1 20.3 - - + +
459B ASN* 4.0 15.3 - - + +
580B LEU* 2.9 22.8 + - - +
581B ARG* 3.7 4.3 - - - -
583B ALA* 1.3 75.7 - - - +
585B ALA* 1.3 65.3 + - - +
587B THR* 3.2 6.4 + - - -
588B THR* 2.5 48.1 + - - +
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Residues in contact with ALA 585 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ILE* 3.9 10.1 - - + -
457B SER* 2.8 22.3 + - - +
459B ASN* 3.3 25.3 - - - +
463B TYR* 3.0 28.5 - - + +
581B ARG 2.8 14.0 + - - +
582B ASN 3.4 5.6 - - - +
584B THR* 1.3 75.5 - - - +
586B ILE* 1.3 63.0 + - - +
588B THR* 3.8 0.2 - - - -
589B PHE* 2.9 14.6 + - - +
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Residues in contact with ILE 586 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B TYR* 3.3 42.3 - - + +
419B ILE* 3.7 14.9 - - + +
420B ILE* 3.8 26.9 - - + -
425B ILE* 3.7 25.1 - - + -
567B TYR* 4.5 15.7 - - + -
570B LEU* 4.2 16.2 - - + -
582B ASN* 3.0 19.8 + - + +
583B ALA* 3.5 11.4 - - - +
585B ALA* 1.3 76.5 - - - +
587B THR* 1.3 63.8 + - - +
589B PHE* 3.8 0.7 - - - +
590B GLY 3.1 17.3 + - - -
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Residues in contact with THR 587 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B TYR* 4.1 0.7 - - + -
392B PRO* 2.8 29.2 + - - +
393B GLY* 3.9 16.2 - - - +
394B ALA* 5.4 0.9 - - - -
416B TYR* 3.6 32.0 + - + +
567B TYR* 3.3 27.8 - - + +
583B ALA 3.2 9.1 + - - +
584B THR* 3.2 14.7 + - - -
586B ILE* 1.3 75.7 - - - +
588B THR* 1.3 64.9 + - - +
590B GLY* 3.2 1.9 + - - -
591B GLN* 2.9 22.2 + - - +
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Residues in contact with THR 588 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO* 4.7 7.1 - - - +
439B LEU* 4.2 13.6 - - + +
458B PRO* 3.7 24.2 - - + +
459B ASN* 3.7 19.6 - - + +
584B THR* 2.5 43.8 + - - +
585B ALA 3.8 2.0 - - - -
587B THR* 1.3 70.7 + - - +
589B PHE* 1.3 66.3 + - - +
591B GLN* 2.9 23.4 + - - +
592B MET* 3.1 11.6 + - - +
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Residues in contact with PHE 589 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ILE* 3.5 27.1 - - + -
422B GLN* 3.2 28.3 - - + -
423B VAL* 3.6 20.2 - - + -
456B CYS 3.9 7.6 - - - -
457B SER* 3.2 14.4 + - - +
458B PRO* 3.7 25.4 - - + -
585B ALA 2.9 11.8 + - - +
586B ILE 3.8 3.4 - - - +
588B THR* 1.3 75.9 - - - +
590B GLY* 1.3 64.1 + - - +
592B MET* 3.1 6.7 + - + +
593B ALA* 2.9 20.3 + - + -
670B MET* 3.7 23.1 - - + -
674B MET* 4.3 10.5 - - + -
676B ASN* 3.1 19.1 - - - -
681B MET* 4.1 15.3 - - + -
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Residues in contact with GLY 590 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B LEU* 4.4 13.2 - - - +
416B TYR* 5.0 3.4 - - - -
419B ILE* 3.4 21.7 - - - +
586B ILE 3.1 11.8 + - - -
587B THR* 3.2 3.8 + - - -
588B THR 3.1 0.2 - - - -
589B PHE* 1.3 76.5 - - - +
591B GLN* 1.3 63.2 + - - +
593B ALA* 3.0 7.6 + - - +
594B LEU* 3.0 24.9 + - - +
622B THR 5.3 1.8 - - - -
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Residues in contact with GLN 591 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO* 5.0 7.3 - - - +
393B GLY 2.6 30.4 + - - +
394B ALA* 3.8 5.1 - - - +
395B PHE* 3.4 37.2 - - + +
439B LEU* 3.5 24.2 - - + +
587B THR 2.9 9.8 + - - +
588B THR* 2.9 15.3 + - - +
590B GLY* 1.3 75.6 - - - +
592B MET* 1.3 62.4 + - - +
594B LEU* 3.7 3.4 + - - +
595B GLN* 3.4 32.6 + - - +
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Residues in contact with MET 592 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B LEU* 4.2 8.9 - - + +
442B TYR* 4.0 21.3 - - + +
443B ILE* 4.3 29.2 - - + +
458B PRO* 3.2 34.3 - - + -
588B THR 3.1 6.3 + - - +
589B PHE* 3.4 15.3 - - + +
590B GLY 3.1 0.2 - - - -
591B GLN* 1.3 74.7 - - - +
593B ALA* 1.3 55.8 + - - +
595B GLN* 3.0 2.8 + - - +
596B TRP* 2.7 41.7 + - + +
670B MET* 3.5 38.1 - - + +
673B TYR* 5.7 0.2 - - - -
674B MET* 4.0 22.2 - - + -
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Residues in contact with ALA 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.8 3.6 - - + -
415B LEU* 4.8 5.6 - - + -
589B PHE* 2.9 13.7 + - + +
590B GLY* 3.4 12.8 - - - +
592B MET* 1.3 77.2 - - - +
594B LEU* 1.3 62.8 + - - +
596B TRP* 3.6 0.7 - - - +
597B ILE* 3.1 27.7 + - - +
667B PHE* 3.8 7.8 - - + -
670B MET* 3.8 29.6 - - + -
681B MET* 4.3 17.3 - - - -
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Residues in contact with LEU 594 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.6 28.3 - - + +
412B LEU* 4.6 10.0 - - + +
590B GLY 3.0 14.2 + - - +
591B GLN* 4.1 4.5 - - - +
593B ALA* 1.3 77.5 - - - +
595B GLN* 1.3 58.2 + - - +
597B ILE* 3.6 9.5 - - + +
598B GLU* 3.2 24.7 + - + +
620B GLY* 4.0 5.4 - - - -
621B ASP 3.4 26.0 - - - +
622B THR* 3.8 18.4 - - - +
623B ASP* 4.1 9.2 - - - -
624B SER 3.7 18.8 - - - +
625B ILE* 3.5 26.3 - - + +
683B MET* 4.7 0.4 - - + -
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Residues in contact with GLN 595 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.4 57.7 - - + +
439B LEU* 4.6 3.6 - - - +
440B HIS* 6.1 1.0 - - - -
443B ILE* 3.5 39.0 - - + +
591B GLN* 3.4 20.2 + - - +
592B MET 3.0 2.2 + - - +
594B LEU* 1.3 78.2 - - - +
596B TRP* 1.3 64.0 + - - +
598B GLU* 3.2 16.5 + - - +
599B ARG* 3.0 22.9 + - - +
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Residues in contact with TRP 596 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B TYR 3.0 28.5 - - - -
443B ILE* 3.2 25.7 - - + +
445B ALA* 3.6 21.1 - - + -
592B MET* 2.7 25.8 + - + +
593B ALA 3.6 3.8 - - - +
595B GLN* 1.3 72.2 - - - +
597B ILE* 1.3 69.4 + - + +
599B ARG* 3.0 15.8 + - - +
600B LYS* 2.9 35.5 + - + +
666B GLY 3.2 20.5 + - - -
667B PHE* 4.8 0.4 - + - -
669B GLU* 3.4 22.7 - - + -
670B MET* 3.6 46.5 - - + +
673B TYR* 3.3 32.8 - + + -
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Residues in contact with ILE 597 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 5.0 0.7 - - + -
593B ALA 3.1 15.1 + - - +
594B LEU* 3.6 11.0 - - + +
596B TRP* 1.3 80.7 - - + +
598B GLU* 1.3 61.2 + - - +
600B LYS* 3.5 11.4 - - + +
601B VAL* 2.6 38.2 + - + +
625B ILE* 4.3 12.6 - - + -
663B ILE* 4.1 15.0 - - + +
666B GLY 5.1 0.2 - - - -
667B PHE* 3.1 48.9 - - + +
683B MET* 3.0 47.1 - - + -
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Residues in contact with GLU 598 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 4.9 8.1 - - + -
397B LYS* 2.8 33.4 + - - -
594B LEU* 3.2 18.4 + - + +
595B GLN* 3.2 26.0 + - - +
596B TRP 3.1 0.6 - - - -
597B ILE* 1.3 76.5 - - - +
599B ARG* 1.3 63.6 + - - +
601B VAL* 3.4 1.1 + - - -
602B ASN* 3.0 40.4 + - - +
617B VAL* 3.6 34.4 - - + +
625B ILE* 5.0 5.6 - - + -
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Residues in contact with ARG 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B ILE* 2.7 28.2 + - + +
444B ASN* 3.1 44.3 + - - +
445B ALA* 4.0 9.9 - - - +
595B GLN 3.0 12.2 + - - +
596B TRP* 3.2 20.8 - - - +
598B GLU* 1.3 80.5 - - - +
600B LYS* 1.3 93.0 + - - +
602B ASN* 3.4 6.2 + - - +
603B GLU* 3.0 64.9 + - + +
669B GLU* 4.5 0.4 + - - -
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Residues in contact with LYS 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B TRP* 2.9 35.8 + - + +
597B ILE* 3.3 11.4 + - + +
599B ARG* 1.3 103.4 - - - +
601B VAL* 1.3 64.6 + - - +
603B GLU* 3.0 16.5 + - + +
604B TYR* 2.8 23.0 + - - +
662B ALA 5.6 2.9 - - - +
663B ILE* 6.1 2.5 - - - -
666B GLY* 4.4 17.0 - - - -
669B GLU* 3.1 37.7 + - - -
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Residues in contact with VAL 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410B PHE* 6.3 0.4 - - + -
597B ILE* 2.6 27.8 + - + +
598B GLU 3.8 2.9 - - - +
600B LYS* 1.3 71.1 - - + +
602B ASN* 1.3 64.9 + - - +
604B TYR* 3.0 8.5 + - + +
605B LEU* 2.9 47.0 + - + +
617B VAL* 4.0 17.0 - - + -
625B ILE* 3.8 21.3 - - + -
627B VAL* 4.0 10.5 - - + -
659B MET* 5.1 7.0 - - - -
663B ILE* 4.2 26.9 - - + -
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Residues in contact with ASN 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B GLU* 3.0 31.9 + - - +
599B ARG* 3.7 6.4 - - - +
601B VAL* 1.3 78.9 - - - +
603B GLU* 1.3 62.7 + - + +
606B ASN* 3.1 33.8 + - - +
614B GLU 3.4 8.1 - - - +
615B ALA* 3.4 6.8 - - - +
616B PHE* 2.5 39.1 + - - +
617B VAL* 3.3 25.2 + - - +
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Residues in contact with GLU 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B ARG* 3.0 54.5 + - + +
600B LYS* 3.0 20.8 + - + +
602B ASN* 1.3 76.8 - - + +
604B TYR* 1.3 64.4 + - - +
606B ASN* 3.9 4.8 - - - +
607B GLU* 3.3 21.8 + - - +
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Residues in contact with TYR 604 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600B LYS 2.8 12.4 + - - +
601B VAL* 3.0 10.7 + - + +
603B GLU* 1.3 73.6 - - - +
605B LEU* 1.3 79.2 + - + +
607B GLU* 3.0 11.8 + - - +
608B VAL* 2.9 53.6 + - + +
654B PHE* 4.4 9.9 - + - -
658B ARG* 3.3 61.6 + - + +
659B MET* 4.6 5.6 - - + -
662B ALA* 3.6 27.4 - - + -
665B ARG* 4.0 17.6 + - - -
897D LEU* 4.8 1.0 - - - +
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Residues in contact with LEU 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B VAL* 2.9 27.9 + - + +
604B TYR* 1.3 85.6 - - + +
606B ASN* 1.3 57.8 + - - +
608B VAL* 3.6 3.3 - - + -
609B CYS* 2.8 36.8 + - - +
616B PHE* 3.5 35.4 - - + -
627B VAL* 3.5 32.1 - - + -
632B ILE* 4.7 11.7 - - + -
654B PHE* 3.9 32.5 - - + -
659B MET* 3.9 13.9 - - + -
----------------------------------------------------------
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Residues in contact with ASN 606 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B ASN* 3.1 26.5 + - - +
603B GLU* 3.9 5.6 - - - +
605B LEU* 1.3 76.1 - - - +
607B GLU* 1.3 59.6 + - + +
609B CYS 3.4 0.2 + - - -
610B GLY 2.9 7.3 + - - -
611B THR* 2.5 60.9 + - - +
612B GLU* 3.3 7.8 + - - -
613B GLY* 3.7 11.0 - - - +
614B GLU* 2.6 50.1 + - - +
616B PHE* 3.6 3.5 - - - -
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Residues in contact with GLU 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
603B GLU 3.3 13.1 + - - +
604B TYR* 3.0 10.4 + - - +
606B ASN* 1.3 80.2 - - - +
608B VAL* 1.3 79.2 + - - +
610B GLY* 3.3 12.1 + - - +
611B THR 5.0 2.0 - - - -
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Residues in contact with VAL 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604B TYR* 2.9 55.4 + - + +
605B LEU* 3.9 5.2 - - + +
607B GLU* 1.3 88.0 - - - +
609B CYS* 1.3 61.5 + - - +
610B GLY 3.3 0.4 - - - -
632B ILE* 5.6 1.6 - - + -
635B LYS* 3.3 15.9 + - - +
654B PHE* 4.6 17.3 - - + -
896D SER 4.6 5.7 - - - +
897D LEU* 3.5 40.6 - - + +
----------------------------------------------------------
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Residues in contact with CYS 609 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LEU* 2.8 20.2 + - - +
606B ASN 4.1 1.8 - - - +
608B VAL* 1.3 79.2 - - - +
610B GLY* 1.3 64.1 + - - +
611B THR* 3.4 9.6 + - - +
616B PHE* 4.2 12.3 - - + -
631B LYS* 3.9 37.7 - - + -
632B ILE* 3.9 28.3 - - - -
635B LYS* 3.7 29.5 - - + +
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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