Contacts of the helix formed by residues 680 - 714 (chain B) in PDB entry 5EP6
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 SER 680 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B SER* 1.3 73.9 + - - +
681B ASN* 1.3 60.5 + - - +
683B LEU* 3.8 12.8 - - - +
684B VAL* 3.1 32.9 + - - +
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Residues in contact with ASN 681 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B SER* 2.9 3.5 + - - +
680B SER* 1.3 77.2 + - - +
682B THR* 1.3 65.1 + - - +
684B VAL* 4.2 5.4 - - - +
685B GLU* 3.6 21.4 + - - +
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Residues in contact with THR 682 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B SER* 2.8 10.8 + - - -
681B ASN* 1.3 78.2 + - - +
683B LEU* 1.3 59.9 + - - +
685B GLU* 3.3 11.5 - - - +
686B MET* 3.1 36.5 + - + +
216C SER* 3.3 35.1 + - - +
220C GLN* 3.2 31.1 + - + +
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Residues in contact with LEU 683 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.0 32.3 - - + +
679B SER* 2.9 37.3 + - - +
680B SER* 4.1 10.3 - - - +
682B THR* 1.3 75.8 - - - +
684B VAL* 1.3 65.1 + - - +
685B GLU 3.2 1.3 - - - -
686B MET* 3.0 3.7 + - + -
687B THR* 3.0 20.5 + - - -
216C SER* 4.7 11.2 - - - -
219C MET* 3.9 12.1 - - - -
683D LEU* 3.7 34.5 - - + -
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Residues in contact with VAL 684 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680B SER* 3.1 21.4 + - - +
681B ASN* 4.2 5.8 - - - +
682B THR 3.5 0.2 - - - -
683B LEU* 1.3 74.6 - - - +
685B GLU* 1.3 60.7 + - - +
687B THR* 3.2 8.1 + - - -
688B LEU* 3.0 46.3 + - + +
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Residues in contact with GLU 685 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B ASN 3.6 10.5 + - - +
682B THR* 3.3 18.3 + - - +
683B LEU 3.2 0.6 - - - -
684B VAL* 1.3 81.8 - - + +
686B MET* 1.3 69.1 + - + +
688B LEU* 4.2 7.5 - - - +
689B GLY* 2.8 26.0 + - - -
220C GLN* 2.8 33.6 + - - +
223C TYR* 5.0 5.7 - - + -
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Residues in contact with MET 686 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 4.0 3.6 - - + -
682B THR* 3.1 26.2 + - + +
683B LEU* 3.0 12.4 + - + +
685B GLU* 1.3 97.6 - - + +
687B THR* 1.3 60.5 + - - +
689B GLY* 3.2 1.5 + - - -
690B MET* 2.9 36.2 + - + +
216C SER* 6.0 0.2 - - - -
219C MET* 3.8 52.0 - - + +
220C GLN* 3.3 34.1 - - - +
223C TYR* 3.7 37.4 - - + -
690D MET* 4.7 2.0 - - - +
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Residues in contact with THR 687 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A SER 5.1 1.9 + - - -
218A ASN* 3.9 27.4 - - + +
219A MET* 3.2 31.2 + - - +
222A ALA* 3.9 4.3 - - + +
683B LEU 3.0 6.1 + - - -
684B VAL* 3.5 10.5 - - - -
686B MET* 1.3 76.7 - - - +
688B LEU* 1.3 59.4 + - + +
690B MET* 3.3 13.0 + - - +
691B LYS* 3.0 47.1 + - - +
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Residues in contact with LEU 688 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684B VAL* 3.0 36.8 + - + +
685B GLU* 4.2 5.8 - - - +
687B THR* 1.3 77.9 - - + +
689B GLY* 1.3 56.6 + - - +
691B LYS* 3.3 34.1 + - + +
692B LYS* 2.9 29.1 + - - +
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Residues in contact with GLY 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
685B GLU 2.8 20.1 + - - -
686B MET 3.2 0.9 + - - -
688B LEU* 1.3 78.0 - - - +
690B MET* 1.3 55.8 + - - +
692B LYS* 3.3 5.5 + - - +
693B LEU* 2.9 32.9 + - - +
223C TYR* 3.6 31.8 + - - -
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Residues in contact with MET 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A MET* 3.4 46.0 - - + +
222A ALA* 3.8 16.5 - - + +
223A TYR* 3.7 32.8 - - + +
226A LEU* 3.9 27.0 - - + +
686B MET* 2.9 22.5 + - + +
687B THR* 3.3 4.5 + - - +
689B GLY* 1.3 73.6 - - - +
691B LYS* 1.3 65.5 + - - +
693B LEU* 3.5 5.9 + - + +
694B LYS* 3.1 23.9 + - - +
219C MET* 4.7 4.7 - - + -
223C TYR* 5.4 1.3 - - + -
686D MET* 4.4 4.7 - - - +
690D MET* 4.5 21.1 - - - +
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Residues in contact with LYS 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ASN* 5.7 2.2 - - - -
222A ALA* 4.2 14.4 - - + -
687B THR* 3.0 31.0 + - - +
688B LEU* 3.4 34.8 - - + +
689B GLY 3.2 0.2 - - - -
690B MET* 1.3 76.8 - - - +
692B LYS* 1.3 62.2 + - - +
694B LYS* 3.3 12.6 + - - +
695B GLU* 3.1 36.2 + - - +
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Residues in contact with LYS 692 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B LEU 2.9 17.1 + - - +
689B GLY* 3.3 5.6 + - - +
691B LYS* 1.3 74.3 - - - +
693B LEU* 1.3 65.5 + - + +
695B GLU* 3.2 16.0 + - + +
696B GLU* 2.9 51.7 + - - +
223C TYR* 5.4 6.5 - - - +
227C LYS* 6.4 1.8 - - + -
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Residues in contact with LEU 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 4.0 16.4 - - + -
689B GLY 2.9 22.1 + - - +
690B MET* 3.8 5.8 - - + +
692B LYS* 1.3 76.3 - - + +
694B LYS* 1.3 57.2 + - - +
696B GLU* 3.3 10.9 + - - +
697B MET* 2.9 36.9 + - - +
223C TYR* 3.7 26.0 - - + +
226C LEU* 3.9 33.0 - - + +
227C LYS* 4.0 17.5 - - + +
230C MET* 3.8 35.6 - - + +
690D MET* 5.6 0.2 - - - -
697D MET* 6.0 0.7 - - + -
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Residues in contact with LYS 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A ALA 5.6 0.4 - - - +
225A GLU* 3.7 37.2 - - + +
226A LEU* 3.8 14.1 - - + +
228A ARG* 5.0 7.6 - - - +
229A GLU* 3.8 12.4 - - + +
690B MET 3.1 15.0 + - - +
691B LYS* 3.5 15.5 - - - +
693B LEU* 1.3 75.4 - - - +
695B GLU* 1.3 77.7 + - - +
697B MET* 3.3 5.5 + - - +
698B GLU* 2.9 63.2 + - + +
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Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B LYS* 3.1 25.8 + - - +
692B LYS* 3.2 15.8 + - + +
694B LYS* 1.3 95.1 + - - +
696B GLU* 1.3 61.6 + - + +
698B GLU* 3.3 13.7 + - - +
699B GLY* 3.1 17.8 + - - -
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Residues in contact with GLU 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692B LYS* 2.9 54.2 + - - +
693B LEU* 3.7 13.9 - - - +
695B GLU* 1.3 75.5 - - + +
697B MET* 1.3 63.3 + - - +
699B GLY* 3.1 4.0 + - - -
700B VAL* 3.0 25.5 + - - +
227C LYS* 5.6 3.1 - - - +
230C MET* 3.8 28.1 - - - +
234C HIS* 2.9 33.0 + - + +
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Residues in contact with MET 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 3.4 33.2 - - - +
229A GLU* 3.6 13.2 - - + +
230A MET* 3.4 52.0 - - + +
233A LEU* 4.1 12.7 - - + +
693B LEU* 2.9 20.7 + - - +
694B LYS 3.5 4.9 - - - +
696B GLU* 1.3 77.2 - - - +
698B GLU* 1.3 57.4 + - - +
700B VAL* 3.2 7.4 + - - +
701B VAL* 2.9 33.6 + - + +
230C MET* 3.4 23.6 - - + -
233C LEU* 5.1 2.2 - - + -
693D LEU* 6.2 0.9 - - - -
697D MET* 4.2 10.3 - - + -
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Residues in contact with GLU 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 3.5 29.6 - - - +
694B LYS* 2.9 50.5 + - + +
695B GLU* 3.3 13.6 - - - +
697B MET* 1.3 76.1 - - - +
699B GLY* 1.3 60.7 + - - +
701B VAL* 3.3 3.9 + - - +
702B LYS* 3.0 23.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B GLU 3.1 10.2 + - - -
696B GLU* 3.1 4.6 + - - -
698B GLU* 1.3 79.0 - - - +
700B VAL* 1.3 62.5 + - - +
702B LYS* 3.4 9.1 + - - +
703B GLU* 3.1 23.7 + - - +
234C HIS* 6.1 0.7 - - - -
----------------------------------------------------------
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Residues in contact with VAL 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.1 4.9 - - + -
696B GLU 3.0 16.7 + - - +
697B MET 3.2 7.6 + - - +
699B GLY* 1.3 74.3 - - - +
701B VAL* 1.3 60.9 + - - +
703B GLU* 3.2 6.9 + - - +
704B LEU* 2.9 43.3 + - + +
230C MET* 4.8 1.1 - - - -
233C LEU* 3.9 33.7 - - + -
234C HIS* 3.7 29.2 - - + +
237C THR* 3.6 27.6 - - + +
----------------------------------------------------------
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Residues in contact with VAL 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A GLU* 3.8 16.4 - - - +
232A ASN* 4.1 12.3 - - + +
233A LEU* 3.8 38.8 - - + +
236A VAL* 4.0 22.8 - - + +
697B MET 2.9 21.1 + - - +
698B GLU* 3.7 4.5 - - - +
699B GLY 3.3 0.2 - - - -
700B VAL* 1.3 74.5 - - - +
702B LYS* 1.3 59.0 + - - +
704B LEU* 3.3 2.3 + - - +
705B ALA* 2.9 29.7 + - + +
801B GOL 6.0 1.8 - - - +
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Residues in contact with LYS 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698B GLU 3.0 14.3 + - - +
699B GLY* 3.6 11.4 - - - +
700B VAL 3.2 0.2 - - - -
701B VAL* 1.3 76.2 - - - +
703B GLU* 1.3 58.6 + - - +
705B ALA* 3.3 7.7 + - - +
706B GLU* 3.0 51.7 + - + +
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Residues in contact with GLU 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
699B GLY 3.1 16.8 + - - +
700B VAL* 3.2 4.8 + - - +
702B LYS* 1.3 75.6 - - - +
704B LEU* 1.3 60.2 + - - +
706B GLU* 3.1 17.5 + - + +
707B ASN* 2.9 36.1 + - - +
237C THR* 4.1 14.1 - - + +
238C GLN* 3.0 32.5 + - - +
241C ALA* 3.4 23.7 - - - +
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 4.0 7.2 - - + -
236A VAL* 4.0 28.9 - - + +
237A THR* 4.5 1.8 - - - +
240A GLN* 4.3 3.9 + - - +
700B VAL* 2.9 36.7 + - + +
701B VAL 3.8 4.0 - - - +
703B GLU* 1.3 76.1 - - - +
705B ALA* 1.3 56.9 + - - +
707B ASN* 3.2 6.4 + - - +
708B ASN* 2.9 32.2 + - - +
237C THR* 4.0 21.3 - - + +
240C GLN* 3.6 24.0 - - - +
704D LEU* 3.9 37.0 - - + -
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Residues in contact with ALA 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.8 14.1 - - + +
701B VAL* 2.9 20.3 + - + +
702B LYS* 3.6 7.6 - - - +
704B LEU* 1.3 75.5 - - - +
706B GLU* 1.3 62.3 + - + +
708B ASN* 3.3 8.0 + - - +
709B HIS* 3.0 26.2 + - - +
801B GOL 4.7 16.2 - - - +
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Residues in contact with GLU 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702B LYS* 3.0 48.0 + - + +
703B GLU* 3.1 20.2 + - + +
705B ALA* 1.3 73.9 - - + +
707B ASN* 1.3 68.0 + - - +
709B HIS* 3.2 8.8 + - - +
710B ILE* 3.2 27.3 + - + +
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Residues in contact with ASN 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 4.4 2.0 - - - +
703B GLU* 2.9 28.8 + - - +
704B LEU* 3.2 15.3 + - - +
706B GLU* 1.3 79.4 - - - +
708B ASN* 1.3 62.1 + - - +
710B ILE* 3.2 12.7 + - - +
711B LEU* 3.0 26.3 + - - +
237C THR 4.4 3.2 + - - -
240C GLN* 2.8 43.6 + - - +
241C ALA* 4.1 13.6 - - - +
244C LEU* 3.6 22.6 - - + +
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Residues in contact with ASN 708 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A VAL* 3.4 40.8 + - - +
239A VAL* 3.7 16.9 - - + +
240A GLN* 3.0 37.6 + - - +
243A LEU* 3.1 25.0 - - + +
704B LEU 2.9 11.5 + - - -
705B ALA* 3.5 10.0 - - - +
706B GLU 3.3 0.2 - - - -
707B ASN* 1.3 77.2 - - - +
709B HIS* 1.3 57.0 + - - +
711B LEU* 3.2 2.4 + - - +
712B GLU* 2.8 28.3 + - - +
----------------------------------------------------------
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Residues in contact with HIS 709 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
705B ALA 3.0 13.4 + - - +
706B GLU* 3.5 11.9 - - - +
707B ASN 3.2 0.4 - - - -
708B ASN* 1.3 74.3 - - - +
710B ILE* 1.3 68.0 + - + +
712B GLU* 3.4 22.2 + - - +
713B ARG* 3.2 51.3 + - + +
714B PHE* 6.5 0.7 - + - -
----------------------------------------------------------
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Residues in contact with ILE 710 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706B GLU* 3.2 16.5 + - + +
707B ASN* 3.2 17.0 + - - +
709B HIS* 1.3 79.2 - - + +
711B LEU* 1.3 59.1 + - - +
713B ARG 3.4 0.7 + - - -
714B PHE* 2.9 47.7 + - + +
715B GLY 3.8 0.2 + - - -
244C LEU* 4.8 18.8 - - + +
717D LEU* 3.9 31.6 - - + -
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Residues in contact with LEU 711 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A GLN* 4.6 11.7 - - + +
243A LEU* 3.9 12.3 - - + -
244A LEU* 4.5 15.5 - - + -
247A LEU* 3.3 28.8 - - + +
707B ASN 3.0 21.5 + - - +
708B ASN* 3.6 17.5 - - - +
710B ILE* 1.3 78.1 - - - +
712B GLU* 1.3 58.6 + - - +
715B GLY* 2.8 26.5 + - - +
240C GLN* 5.6 0.2 - - - +
244C LEU* 4.0 21.3 - - + -
711D LEU* 3.8 35.2 - - + -
716D SER 5.6 0.2 - - - +
717D LEU* 4.4 10.5 - - + -
----------------------------------------------------------
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Residues in contact with GLU 712 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LEU* 3.9 19.0 - - + +
247A LEU* 4.8 0.2 - - - -
708B ASN 2.8 17.0 + - - +
709B HIS* 3.6 28.9 + - - +
711B LEU* 1.3 75.7 - - - +
713B ARG* 1.3 63.0 + - - +
722D GLY* 3.1 17.0 - - - -
723D LEU* 3.1 37.2 + - + +
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Residues in contact with ARG 713 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B HIS* 3.2 43.2 + - + +
712B GLU* 1.3 89.0 - - - +
714B PHE* 1.3 104.4 + - + +
719D MET* 4.5 6.8 - - - +
721D GLY* 3.2 18.5 + - - +
722D GLY* 3.5 2.6 - - - -
----------------------------------------------------------
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Residues in contact with PHE 714 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709B HIS* 6.5 0.7 - + - -
710B ILE* 2.9 35.6 + - + +
713B ARG* 1.3 126.6 - - + +
715B GLY* 1.3 65.9 + - - +
716B SER* 5.0 0.2 + - - -
716D SER 3.5 0.2 - - - +
717D LEU* 3.3 15.8 - - + -
718D THR* 2.9 52.2 + - - +
719D MET* 4.1 31.6 - - + -
721D GLY* 3.6 2.9 - - - -
722D GLY 3.5 5.4 - - - +
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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