Contacts of the helix formed by residues 664 - 701 (chain D) in PDB entry 3A8P
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 664 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D VAL* 5.1 0.3 - - - +
663D SER* 1.3 88.5 - - - +
665D PRO* 1.3 70.7 - - + +
666D LYS* 3.3 16.6 + - - +
667D ASN* 2.5 43.2 + - - +
668D ARG* 3.4 16.1 + - - +
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Residues in contact with PRO 665 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664D ASP* 1.3 81.0 - - + +
666D LYS* 1.3 54.3 + - + +
667D ASN 2.5 18.9 + - - -
668D ARG* 3.0 27.2 + - + +
669D LYS* 3.2 16.1 + - - +
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Residues in contact with LYS 666 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664D ASP* 3.3 10.7 + - - +
665D PRO* 1.3 75.1 - - + +
667D ASN* 1.3 70.2 + - - +
669D LYS* 2.7 34.0 + - - +
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Residues in contact with ASN 667 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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662D VAL* 4.8 9.6 - - + +
663D SER 4.4 1.6 - - - +
664D ASP* 2.5 38.9 + - - +
665D PRO 2.5 7.9 + - - -
666D LYS* 1.3 94.4 + - - +
668D ARG* 1.3 59.3 + - - +
669D LYS* 3.1 11.0 + - - +
670D ALA* 3.3 18.4 + - - +
671D ILE* 3.6 6.8 + - - +
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Residues in contact with ARG 668 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D LEU* 3.4 40.8 + - + +
660D SER* 5.6 0.2 - - - +
662D VAL* 3.3 26.2 + - + -
663D SER* 5.2 0.4 - - - +
664D ASP 3.4 9.1 + - - +
665D PRO* 3.0 35.9 + - + +
667D ASN* 1.3 78.3 - - - +
669D LYS* 1.3 59.9 + - - +
671D ILE* 2.9 25.5 - - - +
672D GLU* 3.3 40.3 + - - +
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Residues in contact with LYS 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665D PRO 3.2 8.9 + - - +
666D LYS* 2.7 34.0 + - - +
667D ASN* 3.1 16.1 - - - +
668D ARG* 1.3 79.5 - - + +
670D ALA* 1.3 78.6 + - - +
671D ILE 3.3 0.2 - - - -
672D GLU* 3.1 15.4 + - - +
673D ASN* 2.6 35.2 + - - +
676D ARG* 5.4 0.3 + - - -
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Residues in contact with ALA 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667D ASN* 3.3 11.2 + - - +
669D LYS* 1.3 97.8 - - - +
671D ILE* 1.3 60.5 + - - +
673D ASN* 3.1 8.8 + - - +
674D GLN* 2.8 28.6 + - - +
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Residues in contact with ILE 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D ALA* 2.9 40.6 - - + +
658D GLN* 4.5 6.3 - - + -
659D LEU* 3.3 29.6 - - + +
662D VAL* 4.5 5.6 - - + -
667D ASN 3.6 3.4 + - - +
668D ARG* 2.9 37.9 - - - +
670D ALA* 1.3 78.6 - - - +
672D GLU* 1.3 57.0 + - - +
674D GLN* 3.2 7.7 + - + +
675D ILE* 2.9 42.1 + - + +
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Residues in contact with GLU 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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659D LEU* 3.9 20.3 - - + +
668D ARG* 3.3 34.3 + - - +
669D LYS* 3.2 17.8 - - - +
670D ALA 3.1 0.4 - - - -
671D ILE* 1.3 80.3 - - - +
673D ASN* 1.3 64.5 + - - +
675D ILE* 3.2 10.3 + - + +
676D ARG* 3.1 36.7 + - - +
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Residues in contact with ASN 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D LYS* 2.6 20.2 + - + +
670D ALA* 3.5 8.6 - - - +
672D GLU* 1.3 73.7 - - - +
674D GLN* 1.3 65.9 + - - +
676D ARG* 3.1 35.9 - - - +
677D GLN* 3.2 10.2 + - - +
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Residues in contact with GLN 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655D ALA* 5.5 0.2 - - + -
670D ALA 2.8 13.2 + - - +
671D ILE* 3.4 13.9 - - + +
672D GLU 3.1 0.2 - - - -
673D ASN* 1.3 79.6 + - - +
675D ILE* 1.3 64.5 + - - +
677D GLN* 3.3 19.7 + - - +
678D TRP* 3.1 70.5 + - + +
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Residues in contact with ILE 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652D LYS* 3.5 19.1 - - + +
655D ALA* 3.2 34.1 - - + -
656D GLU* 3.4 40.8 - - + +
659D LEU* 5.5 3.4 - - + -
671D ILE* 2.9 29.7 + - + +
672D GLU* 3.2 9.6 + - + +
674D GLN* 1.3 75.2 - - - +
676D ARG* 1.3 58.2 + - - +
678D TRP* 3.2 10.6 + - + +
679D GLU* 2.9 40.8 + - + +
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Residues in contact with ARG 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669D LYS 5.4 0.2 + - - -
672D GLU* 3.1 30.6 + - - +
673D ASN* 3.1 25.6 - - - +
675D ILE* 1.3 76.6 - - - +
677D GLN* 1.3 66.5 + - - +
679D GLU* 3.1 21.6 + - - +
680D GLN* 3.1 26.1 + - - +
717D PRO* 4.5 19.3 - - + -
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Residues in contact with GLN 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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673D ASN* 3.2 11.6 + - - +
674D GLN* 3.3 25.3 + - - +
676D ARG* 1.3 78.6 - - - +
678D TRP* 1.3 63.5 + - - +
680D GLN* 3.1 23.7 + - - +
681D ASN* 3.0 41.7 + - - +
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Residues in contact with TRP 678 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648D ASP* 3.8 37.2 + - + +
651D MET* 3.5 51.0 - - + +
652D LYS* 3.9 28.5 - - + -
655D ALA* 3.4 26.0 - - + -
674D GLN* 3.1 61.0 + - + +
675D ILE* 3.4 10.3 - - + +
676D ARG 3.2 0.2 - - - -
677D GLN* 1.3 74.6 - - - +
679D GLU* 1.3 65.9 + - - +
681D ASN* 3.1 12.3 + - - +
682D LEU* 2.9 28.8 + - + +
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Residues in contact with GLU 679 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652D LYS* 3.4 28.7 + - - +
656D GLU* 5.2 0.5 - - - +
675D ILE* 2.9 28.4 + - - +
676D ARG* 3.1 24.4 + - - +
678D TRP* 1.3 76.4 - - - +
680D GLN* 1.3 57.9 + - - +
682D LEU* 3.4 7.0 + - - +
683D GLU* 3.0 34.2 + - - +
713D ALA 5.0 0.5 - - - +
715D SER* 3.7 30.3 - - - -
716D ARG 5.5 0.3 + - - -
717D PRO* 4.5 5.1 - - - +
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Residues in contact with GLN 680 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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676D ARG* 3.1 13.9 + - - +
677D GLN* 3.4 25.3 - - - +
679D GLU* 1.3 76.0 - - - +
681D ASN* 1.3 65.4 + - - +
683D GLU* 3.4 11.0 + - - +
684D LYS* 3.3 19.8 + - - +
740D ARG* 3.2 47.7 + - - +
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Residues in contact with ASN 681 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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648D ASP* 3.8 24.0 + - - +
674D GLN* 5.9 0.2 - - - +
677D GLN* 3.0 34.1 + - - +
678D TRP* 3.1 17.7 + - - +
680D GLN* 1.3 77.5 - - - +
682D LEU* 1.3 58.2 + - - +
684D LYS* 3.2 9.0 + - - +
685D PHE* 3.0 42.0 + - + -
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Residues in contact with LEU 682 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D ILE* 3.7 47.3 - - + +
648D ASP* 3.8 17.9 - - + +
649D SER* 3.8 25.4 - - - +
652D LYS* 4.0 20.4 - - + -
678D TRP 2.9 19.1 + - - +
679D GLU* 3.7 6.1 - - - +
681D ASN* 1.3 75.5 - - - +
683D GLU* 1.3 59.8 + - - +
685D PHE* 3.8 4.7 - - + +
686D HIS* 2.8 45.5 + - + +
713D ALA* 5.4 1.8 - - + +
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Residues in contact with GLU 683 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679D GLU 3.0 23.0 + - - +
680D GLN* 3.6 14.8 - - - +
681D ASN 3.2 0.2 - - - -
682D LEU* 1.3 75.5 - - - +
684D LYS* 1.3 58.7 + - - +
686D HIS* 3.4 4.7 + - - +
687D MET* 2.9 31.3 + - - +
713D ALA* 3.5 18.6 - - - +
715D SER* 2.9 28.6 + - - +
718D SER* 2.6 27.0 + - - -
733D PHE* 3.7 24.3 - - + -
737D VAL* 4.5 4.5 - - + +
740D ARG* 2.6 33.7 + - - +
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Residues in contact with LYS 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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680D GLN 3.3 9.4 + - - +
681D ASN* 3.2 12.1 + - - +
683D GLU* 1.3 79.0 - - - +
685D PHE* 1.3 71.3 + - + +
687D MET* 3.2 3.8 + - - +
688D ASP* 2.9 62.1 + - - +
737D VAL* 3.4 33.1 - - + +
740D ARG* 5.6 0.2 - - - +
741D ASP* 4.9 14.1 - - - -
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Residues in contact with PHE 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D LEU* 4.1 22.4 - - + +
644D LYS* 3.8 46.7 - - + -
645D ILE* 3.6 21.6 - - + +
648D ASP* 3.8 23.1 - - - -
681D ASN* 3.0 33.7 + - + +
682D LEU* 3.8 12.6 - - + +
684D LYS* 1.3 83.4 - - + +
686D HIS* 1.3 56.4 + - - +
688D ASP* 3.3 7.5 + - - +
689D LEU* 2.9 29.3 + - - +
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Residues in contact with HIS 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645D ILE* 3.4 41.4 - - + +
649D SER* 6.3 0.2 - - - -
682D LEU* 2.8 44.6 + - + +
683D GLU 3.8 2.5 - - - +
685D PHE* 1.3 72.5 - - - +
687D MET* 1.3 58.6 + - - +
689D LEU* 3.3 11.1 + - + +
690D PHE* 2.9 30.5 + - - +
709D SER 5.4 4.9 + - - -
710D LEU* 3.6 19.6 - - + +
713D ALA* 3.6 26.1 - - + +
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Residues in contact with MET 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ILE* 3.9 13.5 - - + -
683D GLU 2.9 16.6 + - - +
684D LYS* 3.2 6.9 + - - +
686D HIS* 1.3 78.1 - - - +
688D ASP* 1.3 64.6 + - - +
690D PHE* 3.3 3.3 + - - +
691D ARG* 3.1 22.7 + - + +
710D LEU* 3.9 19.7 - - + +
730D VAL 4.2 1.1 - - - +
733D PHE* 3.4 36.1 - - + +
734D HIS* 3.3 59.0 - - + +
737D VAL* 4.1 17.9 - - + -
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Residues in contact with ASP 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641D LEU* 3.7 23.8 - - + +
684D LYS* 2.9 50.7 + - - +
685D PHE* 3.7 8.8 - - - +
687D MET* 1.3 76.3 - - - +
689D LEU* 1.3 60.4 + - - +
691D ARG* 3.2 25.5 + - - +
692D MET* 2.9 34.8 + - + +
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Residues in contact with LEU 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D THR* 3.9 37.0 - - - +
641D LEU* 3.5 13.6 - - + +
642D LEU* 3.6 25.4 - - + -
645D ILE* 3.7 16.4 - - + -
685D PHE 2.9 17.9 + - - +
686D HIS* 3.6 12.1 - - + +
688D ASP* 1.3 74.9 - - - +
690D PHE* 1.3 64.0 - - - +
692D MET* 3.1 3.8 + - - +
693D ARG* 2.9 60.7 + - - +
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Residues in contact with PHE 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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572D ILE* 4.3 11.2 - - + -
574D GLN* 3.5 25.8 - - - -
686D HIS 2.9 17.0 + - - +
687D MET 3.5 4.7 - - - +
689D LEU* 1.3 77.2 - - - +
691D ARG* 1.3 58.4 + - - +
693D ARG* 3.3 9.3 + - - +
694D CYS* 2.9 50.3 + - - -
705D PRO* 3.6 32.3 - - + +
706D ASN 3.6 22.4 - - - -
707D PRO* 3.8 9.6 - - + -
709D SER* 6.3 0.2 - - - -
710D LEU* 3.7 31.9 - - + -
730D VAL* 3.8 19.7 - - + -
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Residues in contact with ARG 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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570D ASP* 3.0 52.3 + - - +
572D ILE* 3.8 26.0 - - + -
621D PHE* 4.1 13.1 - - - -
687D MET* 3.1 14.2 + - - +
688D ASP* 3.5 27.0 + - - +
689D LEU 3.2 0.2 - - - -
690D PHE* 1.3 74.7 - - - +
692D MET* 1.3 76.6 + - + +
694D CYS* 3.1 6.5 + - - +
695D TYR* 3.0 72.2 + - + -
734D HIS* 4.7 6.3 + - - -
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Residues in contact with MET 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D PHE* 3.7 45.1 - - + -
634D LEU* 3.8 11.6 - - + +
637D GLN* 3.7 19.1 - - + +
638D THR* 3.5 21.3 - - + -
641D LEU* 3.9 16.6 - - + -
688D ASP* 2.9 20.6 + - + +
689D LEU* 3.5 5.8 - - - +
691D ARG* 1.3 98.8 - - - +
693D ARG* 1.3 57.3 + - - +
695D TYR* 3.3 19.4 + - + +
696D LEU* 3.0 32.8 + - - +
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Residues in contact with ARG 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703C GLU* 4.8 11.3 + - - -
638D THR* 4.8 8.3 - - + -
642D LEU* 4.1 21.6 - - - +
689D LEU* 2.9 57.0 + - + +
690D PHE* 3.6 6.5 - - - +
692D MET* 1.3 74.5 - - - +
694D CYS* 1.3 65.9 + - - +
696D LEU* 3.8 11.4 - - + +
697D ALA* 3.1 26.0 + - - +
705D PRO* 3.8 26.9 - - + +
709D SER* 6.2 1.2 - - - -
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Residues in contact with CYS 694 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D ILE* 4.5 6.5 - - + -
574D GLN* 4.1 8.5 - - - -
614D HIS* 3.5 28.6 + - + +
690D PHE* 2.9 47.7 + - - +
691D ARG* 3.1 11.0 + - - +
693D ARG* 1.3 76.8 - - - +
695D TYR* 1.3 67.0 + - + +
697D ALA* 3.6 2.4 + - - +
698D SER* 3.1 28.6 + - - -
704D LEU* 4.7 4.6 - - - +
705D PRO* 3.7 16.6 - - - -
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Residues in contact with TYR 695 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D ASP* 3.3 15.0 - - - -
571D SER 2.7 28.6 + - - -
614D HIS* 3.9 28.0 - + - +
617D CYS* 3.3 30.9 - - + +
618D ALA* 3.7 24.7 - - + -
621D PHE* 4.6 3.8 - - + -
634D LEU* 3.7 19.1 - - + -
691D ARG* 3.0 46.3 + - + -
692D MET* 3.7 20.0 - - + +
694D CYS* 1.3 79.5 - - + +
696D LEU* 1.3 64.0 + - - +
698D SER* 3.4 1.7 + - - -
699D LEU* 3.0 28.6 + - - +
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Residues in contact with LEU 696 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D VAL* 3.9 14.8 - - + +
634D LEU* 3.4 29.4 - - + +
635D LYS* 3.9 27.1 - - + -
638D THR* 3.9 24.5 - - + +
692D MET 3.0 21.4 + - - +
693D ARG* 3.8 12.3 - - + +
695D TYR* 1.3 75.9 - - - +
697D ALA* 1.3 56.8 + - - +
699D LEU* 3.4 3.0 + - - -
700D GLN* 2.9 50.5 + - - +
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Residues in contact with ALA 697 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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693D ARG 3.1 14.1 + - - +
694D CYS 3.9 4.0 - - - +
695D TYR 3.3 0.2 - - - -
696D LEU* 1.3 78.3 - - - +
698D SER* 1.3 60.0 + - - +
700D GLN* 4.8 2.0 - - - -
701D GLY* 2.7 28.1 + - - -
702D GLY* 3.0 24.1 + - - +
703D GLU 3.5 27.8 - - - +
704D LEU* 4.0 9.9 - - + -
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Residues in contact with SER 698 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610D VAL* 4.3 4.2 - - - +
611D THR* 3.8 41.5 + - - +
614D HIS* 2.9 45.9 + - - +
615D SER* 4.3 4.3 + - - -
694D CYS 3.1 6.9 + - - -
695D TYR 4.0 2.0 - - - -
697D ALA* 1.3 79.4 - - - +
699D LEU* 1.3 61.4 + - - +
700D GLN 3.6 0.2 + - - -
701D GLY* 3.8 5.8 + - - -
702D GLY 5.3 0.2 - - - -
704D LEU* 4.4 8.5 - - - +
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Residues in contact with LEU 699 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615D SER* 3.4 37.7 - - - +
618D ALA* 3.9 11.9 - - + -
630D THR* 3.7 33.4 - - + -
631D VAL* 4.4 14.4 - - + -
634D LEU* 3.9 11.7 - - + -
695D TYR 3.0 16.6 + - - +
696D LEU 3.9 3.4 - - - +
698D SER* 1.3 76.6 - - - +
700D GLN* 1.3 63.1 + - + +
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Residues in contact with GLN 700 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D VAL* 3.9 19.0 - - + +
635D LYS* 3.8 28.1 - - - +
696D LEU* 2.9 38.2 + - - +
697D ALA* 4.3 2.3 - - - +
699D LEU* 1.3 81.3 - - + +
701D GLY* 1.3 59.0 + - - +
702D GLY* 3.2 7.1 + - - +
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Residues in contact with GLY 701 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697D ALA 2.7 11.0 + - - -
698D SER* 3.8 5.1 + - - -
699D LEU 3.5 2.6 - - - -
700D GLN* 1.3 74.3 - - - +
702D GLY* 1.3 64.8 + - - +
703D GLU* 5.0 0.2 - - - +
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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) + - + + + + + -
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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