Contacts of the helix formed by residues 695 - 718 (chain B) in PDB entry 1OFD
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 695 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677B TRP* 3.4 13.6 + - + +
693B ARG 4.1 2.2 + - - -
694B ILE* 1.3 78.0 - - - +
696B LEU* 1.3 64.2 + - - +
697B PRO* 3.4 16.9 - - + +
698B THR* 2.8 35.3 + - - -
699B ALA 3.2 15.6 + - - -
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Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B GLU* 3.6 44.0 - - + +
673B VAL 4.6 0.9 - - - +
674B ARG* 4.0 23.6 - - + +
677B TRP* 3.4 57.5 - - + +
678B LEU* 5.0 6.7 - - + -
695B ASP* 1.3 71.7 - - - +
697B PRO* 1.3 72.4 - - + +
699B ALA* 3.1 13.8 + - + +
700B LEU* 3.1 29.4 + - + +
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Residues in contact with PRO 697 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 4.5 10.3 - - + +
433B GLU* 3.6 28.7 - - + +
695B ASP* 3.4 19.3 - - + +
696B LEU* 1.3 95.1 - - + +
698B THR* 1.3 55.7 + - - +
700B LEU* 3.5 9.2 + - + +
701B LYS* 3.0 30.6 + - - +
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Residues in contact with THR 698 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693B ARG 4.4 7.2 + - - +
694B ILE* 4.2 14.4 - - + -
695B ASP* 2.8 34.5 + - - -
697B PRO* 1.3 73.0 - - - +
699B ALA* 1.3 56.7 + - - +
701B LYS* 3.7 20.0 + - - +
702B ASN* 2.8 57.2 + - - +
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Residues in contact with ALA 699 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465B ALA* 3.5 26.1 - - - +
673B VAL* 4.0 16.8 - - + -
676B TRP* 4.1 13.7 - - + -
677B TRP* 4.4 7.0 - - + -
694B ILE* 3.9 12.3 - - + +
695B ASP 3.2 11.1 + - - +
696B LEU* 3.1 11.7 + - + +
698B THR* 1.3 77.0 - - - +
700B LEU* 1.3 56.1 + - - +
702B ASN* 3.4 1.2 + - - +
703B TYR* 3.0 23.0 + - - +
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Residues in contact with LEU 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B PHE* 3.7 48.9 - - + -
432B ALA 4.0 13.9 - - - +
433B GLU* 5.0 1.8 - - + -
670B LEU* 3.6 43.5 - - + +
673B VAL* 3.8 18.2 - - + -
674B ARG* 4.3 8.3 - - + +
696B LEU* 3.1 36.0 + - + +
697B PRO* 4.0 2.9 - - + +
699B ALA* 1.3 75.2 - - - +
701B LYS* 1.3 58.2 + - - +
703B TYR* 3.1 7.4 + - - +
704B ARG* 3.0 23.2 + - - +
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Residues in contact with LYS 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B ASP 5.8 2.0 - - - +
431B PHE* 3.7 17.5 - - + -
697B PRO 3.0 17.5 + - - +
698B THR* 3.7 24.6 + - - +
700B LEU* 1.3 74.0 - - - +
702B ASN* 1.3 65.2 + - - +
704B ARG* 3.3 6.2 + - - +
705B GLN* 2.9 46.2 + - + +
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Residues in contact with ASN 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464B MET 3.3 8.5 - - - +
465B ALA 3.0 30.2 + - - +
466B SER 3.6 15.0 + - - -
467B GLN 4.3 1.6 - - - -
468B GLY* 3.7 15.3 - - - +
694B ILE* 3.9 11.7 - - - +
698B THR* 2.8 33.1 + - - +
699B ALA 3.6 0.4 - - - +
701B LYS* 1.3 77.3 + - - +
703B TYR* 1.3 56.1 + - - +
705B GLN* 3.3 15.3 + - - +
706B SER* 2.9 32.6 + - - -
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Residues in contact with TYR 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461B VAL* 4.4 13.0 - - + -
464B MET* 3.7 37.2 + - + -
465B ALA* 4.3 2.2 - - + -
545B LEU* 4.3 8.3 - - + -
648B TRP* 2.6 42.1 + - - -
653B PHE* 3.6 10.2 - + - -
666B PRO* 4.5 0.9 - - + -
669B ALA* 3.3 20.4 - - + +
670B LEU* 3.9 24.9 - - + -
673B VAL* 4.1 23.3 - - + -
699B ALA 3.0 14.0 + - - +
700B LEU* 3.1 10.0 + - - +
702B ASN* 1.3 78.0 - - - +
704B ARG* 1.3 66.3 + - - +
706B SER* 3.2 5.2 + - - -
707B VAL* 3.1 34.9 + - + +
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Residues in contact with ARG 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B SER 3.2 23.4 + - - -
429B ASP* 5.0 1.4 - - - +
431B PHE* 3.6 26.0 - - + -
542B ARG* 4.4 9.1 - - - +
543B SER* 4.7 3.0 + - - -
545B LEU* 3.1 42.7 + - + +
547B ASN* 3.6 18.0 - - - +
550B GLU* 2.3 38.4 + - - -
700B LEU 3.0 11.8 + - - +
701B LYS* 3.7 10.3 - - - +
703B TYR* 1.3 77.4 - - + +
705B GLN* 1.3 58.6 + - - +
707B VAL* 3.2 3.3 + - - +
708B GLU* 2.9 53.3 + - - +
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Residues in contact with GLN 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B GLN 5.2 0.6 + - - -
468B GLY* 3.3 26.3 + - - +
469B LYS* 5.7 0.4 - - - +
701B LYS* 2.9 32.1 + - + +
702B ASN* 3.4 17.0 + - - +
704B ARG* 1.3 77.4 - - - +
706B SER* 1.3 55.7 + - - +
708B GLU* 3.3 11.4 + - - +
709B ALA* 2.9 33.7 + - + +
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Residues in contact with SER 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B MET* 3.1 37.4 + - - -
468B GLY 2.9 31.8 - - - -
469B LYS* 3.0 5.2 + - - +
470B GLU* 4.1 13.5 + - - +
650B THR* 3.9 4.1 + - - -
702B ASN 2.9 7.3 + - - -
703B TYR 3.2 9.4 + - - -
705B GLN* 1.3 76.0 - - - +
707B VAL* 1.3 58.7 + - - +
709B ALA* 4.0 3.7 - - - +
710B GLY* 3.0 25.6 + - - -
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Residues in contact with VAL 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B MET* 5.0 4.5 - - - -
544B PRO* 6.0 0.4 - - + -
545B LEU* 3.8 18.2 - - + -
648B TRP 4.6 2.7 - - - +
650B THR* 4.3 11.3 + - - +
653B PHE* 3.6 48.9 - - + -
703B TYR* 3.1 34.7 + - + +
704B ARG 3.2 6.9 + - - +
706B SER* 1.3 75.8 - - - +
708B GLU* 1.3 60.0 + - + +
710B GLY* 3.2 1.4 + - - -
711B LEU* 2.9 40.3 + - + +
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Residues in contact with GLU 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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518B LEU* 3.6 27.9 - - + +
543B SER* 2.6 35.0 + - - +
544B PRO* 5.3 1.3 - - + -
545B LEU* 5.6 1.3 - - + -
704B ARG* 2.9 43.2 + - + +
705B GLN* 3.7 9.5 - - - +
707B VAL* 1.3 79.5 - - + +
709B ALA* 1.3 62.7 + - - +
711B LEU* 3.3 2.9 + - + -
712B PHE* 3.1 32.8 + - + -
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Residues in contact with ALA 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468B GLY 5.6 2.7 - - - +
469B LYS* 6.4 1.1 - - - -
470B GLU* 4.9 0.4 - - - -
509B PRO* 5.3 0.9 - - - +
510B LEU* 6.1 4.9 - - + -
705B GLN* 2.9 19.5 + - + +
706B SER* 4.0 5.4 - - - +
708B GLU* 1.3 75.8 - - - +
710B GLY* 1.3 57.5 + - - +
712B PHE* 3.4 13.2 + - - +
713B LYS* 3.0 27.9 + - - +
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Residues in contact with GLY 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU* 3.4 18.3 + - - -
650B THR* 3.4 27.8 - - - +
706B SER 3.0 11.4 + - - -
707B VAL 3.6 0.4 - - - -
708B GLU 3.2 0.2 - - - -
709B ALA* 1.3 75.6 - - - +
711B LEU* 1.3 59.3 + - - +
713B LYS* 3.5 2.8 + - - +
714B ILE* 3.0 33.3 + - - +
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Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LEU* 4.2 19.3 - - + -
544B PRO* 3.5 31.2 - - + -
650B THR 4.2 5.4 - - - +
653B PHE* 4.1 11.9 - - + +
654B ALA* 3.7 40.4 - - + +
657B VAL* 5.6 1.3 - - + -
707B VAL* 2.9 31.5 + - + +
708B GLU* 3.3 5.8 + - + +
710B GLY* 1.3 74.6 - - - +
712B PHE* 1.3 66.3 + - - +
713B LYS 3.2 0.2 - - - -
714B ILE* 3.3 1.5 + - - +
715B LEU* 2.9 36.7 + - + +
723B LEU* 4.7 14.1 - - + -
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Residues in contact with PHE 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B PRO* 3.7 16.2 - - + +
513B ASN* 3.4 31.9 - - - +
516B MET* 3.6 35.7 - - + +
517B SER* 3.9 9.4 - - - -
518B LEU* 3.6 41.5 - - + -
708B GLU* 3.1 27.1 + - + -
709B ALA* 3.5 11.7 - - - +
711B LEU* 1.3 74.6 - - - +
713B LYS* 1.3 63.0 + - - +
715B LEU* 3.9 5.9 - - + +
716B SER* 2.9 25.6 + - - -
721B SER 5.2 0.7 - - - -
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Residues in contact with LYS 713 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B GLU* 3.3 27.8 - - - +
509B PRO* 4.0 15.0 - - + +
650B THR* 6.1 0.2 - - + -
709B ALA 3.0 15.0 + - - +
710B GLY 3.5 8.1 - - - +
711B LEU 3.2 0.2 - - - -
712B PHE* 1.3 77.0 - - - +
714B ILE* 1.3 63.9 - - + +
716B SER* 2.7 23.7 + - - +
717B LYS* 3.1 25.2 + - - +
975B GLU* 3.0 41.5 + - + +
978B GLN* 5.9 0.2 - - - +
1069B PRO* 3.7 19.5 - - + +
1071B SER* 4.9 1.8 - - - +
1072B SER* 4.4 2.5 - - - +
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Residues in contact with ILE 714 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B GLN* 3.5 42.4 - - + +
498B ARG 5.3 1.7 - - - +
650B THR* 3.3 36.6 - - + +
651B HIS 4.0 0.2 - - - +
654B ALA* 3.7 20.6 - - + -
710B GLY 3.0 13.3 + - - +
711B LEU* 3.3 6.0 + - - +
713B LYS* 1.3 77.1 - - + +
715B LEU* 1.3 64.7 + - + +
717B LYS* 3.2 29.2 + - - +
718B MET* 4.0 3.1 + - - +
726B TYR* 3.4 31.7 - - + +
731B ILE* 6.1 0.5 - - - +
1071B SER* 5.9 0.7 - - - +
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Residues in contact with LEU 715 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516B MET* 5.8 0.9 - - - -
518B LEU* 4.9 4.7 - - + -
711B LEU* 2.9 28.8 + - + +
712B PHE* 3.9 6.7 - - + +
714B ILE* 1.3 77.9 - - + +
716B SER* 1.3 60.9 + - - +
718B MET* 3.2 9.4 + - - +
720B ILE* 3.0 44.1 + - + +
721B SER 4.4 4.5 - - - +
722B LEU 3.6 11.9 - - - +
723B LEU* 3.5 44.6 - - + +
726B TYR* 3.4 48.7 - - + -
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Residues in contact with SER 716 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506B PRO* 3.2 3.9 - - - +
507B ILE* 3.0 54.7 + - - -
509B PRO* 3.4 25.0 - - - +
516B MET* 4.6 2.2 - - - -
712B PHE 2.9 16.7 + - - -
713B LYS* 2.7 19.9 + - - +
715B LEU* 1.3 73.1 - - - +
717B LYS* 1.3 60.4 + - - +
719B GLY 2.9 14.8 + - - +
720B ILE 4.0 1.3 + - - -
974B GLY 4.8 2.0 + - - -
975B GLU* 6.1 0.7 - - - +
1004B PRO* 5.4 0.7 - - - +
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Residues in contact with LYS 717 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497B GLN* 2.6 36.0 + - + +
498B ARG 4.5 4.0 - - - +
499B PHE* 3.6 10.1 - - + +
500B ALA* 2.8 25.7 + - - +
506B PRO* 3.7 6.6 - - - +
713B LYS* 3.1 22.5 + - - +
714B ILE* 3.3 22.0 - - - +
715B LEU 3.2 0.2 - - - -
716B SER* 1.3 78.3 + - - +
718B MET* 1.3 56.1 + - - +
974B GLY* 3.3 40.0 - - - +
975B GLU* 3.7 17.2 + - + -
1071B SER* 5.0 1.8 + - - -
1072B SER* 3.2 24.4 + - - +
1076B ALA* 3.8 15.7 - - + +
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Residues in contact with MET 718 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASN* 2.9 35.6 + - + +
498B ARG* 3.5 36.1 - - + +
499B PHE 3.4 34.3 - - - +
500B ALA* 3.8 18.2 - - - +
504B ASN* 3.0 23.1 + - - +
714B ILE 4.0 2.2 + - - +
715B LEU 3.2 4.4 + - - +
716B SER 3.2 0.4 - - - -
717B LYS* 1.3 76.6 - - - +
719B GLY* 1.3 57.9 + - - +
720B ILE* 3.7 29.6 - - + -
726B TYR* 6.0 0.4 - - + -
731B ILE* 3.8 18.4 - - + -
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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