Contacts of the helix formed by residues 588 - 614 (chain B) in PDB entry 3E7C
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 HIS 588 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B ASN 3.7 0.6 + - - -
587B LEU* 1.3 74.9 - - - +
589B LEU* 1.3 86.1 + - + +
590B ASP* 2.9 36.5 + - - +
591B ASP* 2.9 25.4 + - - +
592B GLN* 3.1 9.7 + - - +
681B LYS* 4.0 25.5 + - + +
682B SER* 3.0 23.0 + - - +
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Residues in contact with LEU 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU 3.5 2.2 + - - -
588B HIS* 1.3 83.6 + - + +
590B ASP* 1.3 66.8 + - - +
592B GLN* 3.4 19.8 + - - +
593B MET* 3.2 29.4 + - + +
746D ARG* 4.7 13.9 - - + +
749D LEU* 3.8 29.6 - - + +
750D ASP* 3.8 40.6 - - + +
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Residues in contact with ASP 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
588B HIS* 2.9 22.1 + - + +
589B LEU* 1.3 82.2 - - - +
591B ASP* 1.3 63.9 + - - +
593B MET* 3.3 16.9 + - - +
594B THR* 2.9 28.5 + - - +
681B LYS* 2.6 39.1 + - + +
746D ARG* 5.0 8.5 + - - -
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Residues in contact with ASP 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B LEU* 4.2 13.2 - - + +
588B HIS* 2.9 13.8 + - - +
590B ASP* 1.3 75.9 - - - +
592B GLN* 1.3 65.4 + - - +
594B THR* 3.0 5.6 + - - -
595B LEU* 2.9 26.5 + - - +
680B LEU* 3.6 29.0 - - + +
681B LYS* 2.9 28.8 + - - +
682B SER* 2.7 41.3 + - - -
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Residues in contact with GLN 592 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B LYS* 4.6 3.6 - - - +
584B PHE* 3.4 50.2 + - + +
585B ARG* 3.2 21.9 + - - +
587B LEU* 2.8 26.8 + - + +
588B HIS 3.1 6.9 + - - +
589B LEU* 3.6 23.5 - - - +
591B ASP* 1.3 75.8 - - - +
593B MET* 1.3 62.4 + - - +
595B LEU* 3.4 0.6 + - - -
596B LEU* 3.2 29.8 + - - +
749D LEU* 3.6 29.3 - - + +
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Residues in contact with MET 593 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B LEU* 3.2 17.1 + - + +
590B ASP* 3.6 15.9 - - - +
591B ASP 3.1 0.6 - - - -
592B GLN* 1.3 79.7 - - - +
594B THR* 1.3 63.9 + - - +
596B LEU* 3.9 0.5 - - - -
597B GLN* 3.0 52.4 + - - +
742D ASN* 4.0 16.2 - - + +
745D LEU* 4.0 12.7 - - + +
746D ARG* 3.2 61.9 - - - +
749D LEU* 3.5 22.4 - - + -
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Residues in contact with THR 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590B ASP* 2.9 15.7 + - - +
591B ASP* 3.0 12.9 + - - -
593B MET* 1.3 77.6 - - - +
595B LEU* 1.3 56.1 + - + +
597B GLN* 3.5 12.5 + - - +
598B TYR* 2.9 59.6 + - + -
676B PRO* 3.8 20.4 - - + +
680B LEU* 4.3 6.0 - - + +
763B LYS* 4.9 9.1 + - - +
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Residues in contact with LEU 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B PHE* 3.9 15.5 - - + -
587B LEU* 3.7 30.5 - - + -
591B ASP 2.9 19.3 + - - +
592B GLN 4.0 3.4 - - - +
593B MET 3.2 0.2 - - - -
594B THR* 1.3 75.6 - - - +
596B LEU* 1.3 62.9 + - - +
598B TYR* 3.5 4.0 + - + +
599B SER* 2.8 35.3 + - - -
671B LEU* 3.8 17.2 - - + +
672B LEU* 4.4 4.9 - - + -
674B SER 3.2 27.4 - - - +
675B VAL* 4.3 0.4 - - + -
680B LEU* 4.3 16.2 - - + -
686B PHE* 3.8 29.6 - - + -
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Residues in contact with LEU 596 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B VAL* 6.4 1.8 - - + -
574B ALA* 4.1 15.7 - - + +
575B VAL* 4.2 16.8 - - + -
578B ALA* 3.9 15.0 - - + -
584B PHE* 4.1 13.7 - - + -
592B GLN 3.2 17.8 + - - +
593B MET 4.1 2.5 - - - +
595B LEU* 1.3 73.6 - - - +
597B GLN* 1.3 66.1 + - - +
599B SER* 4.2 1.8 - - - -
600B TRP* 3.0 33.1 + - + +
603B LEU* 4.4 12.6 - - + -
671B LEU* 3.9 17.0 - - + -
756B ILE* 5.3 2.8 - - + +
745D LEU* 4.7 12.1 - - + -
749D LEU* 3.7 32.3 - - + -
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Residues in contact with GLN 597 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B MET* 3.0 45.8 + - - +
594B THR* 3.6 14.7 + - - +
596B LEU* 1.3 77.6 - - - +
598B TYR* 1.3 56.6 + - + +
600B TRP* 3.1 24.7 + - - -
756B ILE* 4.4 16.1 - - + +
759B ASN* 3.6 26.8 + - - +
760B GLN* 3.5 29.4 - - + +
763B LYS* 3.9 11.0 + - - +
764B TYR* 4.9 1.0 + - - -
742D ASN* 3.8 9.7 + - - +
745D LEU* 3.7 24.6 - - + +
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Residues in contact with TYR 598 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
594B THR* 2.9 42.1 + - + +
595B LEU* 3.5 5.6 + - + +
597B GLN* 1.3 77.2 - - - +
599B SER* 1.3 59.4 + - - +
600B TRP* 3.8 2.2 - - - -
601B MET* 5.2 0.5 + - - +
602B TYR* 3.4 19.3 - - - -
674B SER* 3.8 35.2 - - - +
675B VAL 3.7 2.5 - - - -
676B PRO* 3.5 36.6 - - + +
729B VAL* 5.4 0.9 - - - +
733B LEU* 5.5 1.4 - - - +
760B GLN* 3.8 13.9 - - - -
763B LYS* 4.1 27.5 + - + +
764B TYR* 4.3 11.7 + - - -
768B ASN* 3.8 10.7 + - - +
769B ILE* 3.7 35.2 - - + +
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Residues in contact with SER 599 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
595B LEU 2.8 21.1 + - - -
596B LEU* 4.2 0.7 - - - -
598B TYR* 1.3 81.2 - - - +
600B TRP* 1.3 66.7 + - - +
601B MET 3.0 3.8 - - - -
602B TYR* 2.9 23.1 + - - +
603B LEU* 2.9 16.6 + - - +
670B LEU 3.5 23.8 - - - -
671B LEU* 3.6 25.3 - - - +
673B SER* 4.9 1.3 - - - -
674B SER* 5.8 2.0 - - - -
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Residues in contact with TRP 600 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.6 31.9 - - - -
571B VAL* 3.8 36.1 - - + -
574B ALA* 6.0 3.3 - - + +
596B LEU* 3.0 17.7 + - + +
597B GLN 3.1 26.9 + - - -
598B TYR 4.7 1.8 + - - -
599B SER* 1.3 77.1 - - - +
601B MET* 1.3 84.7 + - + +
603B LEU* 3.3 13.8 + - - +
604B MET* 2.9 38.7 + - + +
733B LEU* 3.6 25.7 - - + +
736B CYS* 4.5 7.4 - - - -
737B PHE* 4.8 3.5 - + - -
753B LEU* 3.6 22.9 - - + -
756B ILE* 3.6 22.1 - - + +
757B ILE* 4.4 14.1 - - + -
760B GLN* 4.9 4.4 - - - +
764B TYR* 5.5 0.8 + - - -
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Residues in contact with MET 601 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.4 39.5 - - - +
598B TYR 5.2 0.4 + - - -
599B SER 3.0 1.0 - - - -
600B TRP* 1.3 94.7 - - + +
602B TYR* 1.3 61.0 + - - +
603B LEU 3.2 0.9 - - - -
604B MET* 3.7 17.7 - - - -
605B ALA* 2.9 26.3 + - - +
642B GLN* 5.0 0.4 - - - +
646B MET* 4.1 10.1 - - + -
729B VAL* 3.9 21.4 - - + +
732B LEU* 4.1 38.1 - - + +
733B LEU* 4.0 24.2 - - + -
736B CYS* 4.8 1.6 - - + -
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Residues in contact with TYR 602 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
598B TYR 3.4 16.2 - - - -
599B SER* 2.9 25.5 + - - +
601B MET* 1.3 76.2 - - - +
603B LEU* 1.3 57.9 + - - +
605B ALA* 3.9 1.0 - - - +
606B PHE* 2.9 31.7 + - - +
670B LEU* 4.0 23.6 - - + +
673B SER* 3.8 17.9 - - - -
674B SER* 3.9 11.5 + - - -
725B MET* 3.6 33.1 - - + +
726B HIS* 2.8 42.1 + + - +
729B VAL* 3.6 33.0 - - + +
764B TYR* 5.8 1.1 - - - -
771B LYS* 4.5 8.5 - - - -
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ALA* 4.2 17.5 - - + -
577B TRP* 3.8 28.9 - - + -
596B LEU* 4.4 7.2 - - + -
599B SER* 2.9 27.5 + - - +
600B TRP* 3.4 11.4 - - - +
602B TYR* 1.3 77.0 - - - +
604B MET* 1.3 63.9 + - - +
606B PHE* 4.2 3.1 - - - +
607B ALA* 3.0 28.4 + - - +
667B LYS* 3.7 28.7 - - + +
670B LEU* 4.2 4.9 - - + -
671B LEU* 3.8 22.4 - - + +
778B GOL 3.7 22.4 - - - +
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Residues in contact with MET 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.4 40.2 + - + +
567B GLY* 4.2 11.4 - - - +
570B GLN* 3.1 38.8 - - + +
571B VAL* 4.1 8.3 - - + +
574B ALA* 5.2 1.3 - - + -
600B TRP* 2.9 42.3 + - + +
601B MET* 3.7 16.8 - - - +
602B TYR 3.3 0.2 - - - -
603B LEU* 1.3 73.9 - - - +
605B ALA* 1.3 66.0 + - - +
608B LEU* 2.9 26.3 + - - +
778B GOL 3.1 28.7 - - - +
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Residues in contact with ALA 605 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B MET 2.9 19.4 + - - +
602B TYR 4.1 2.2 - - - +
604B MET* 1.3 76.4 - - - +
606B PHE* 1.3 58.2 + - - +
608B LEU* 3.8 1.1 - - - +
609B GLY* 2.7 26.7 + - - -
646B MET* 3.5 33.0 - - - +
649B VAL* 3.8 10.8 - - + +
725B MET* 4.1 15.3 - - + -
729B VAL* 4.9 0.2 - - + -
732B LEU* 3.6 15.5 - - + -
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Residues in contact with PHE 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B TYR 2.9 19.9 + - - +
603B LEU* 4.2 2.7 - - - +
605B ALA* 1.3 73.6 - - - +
607B ALA* 1.3 61.6 + - - +
609B GLY* 3.3 1.2 + - - -
610B TRP* 2.9 28.6 + - - +
649B VAL* 4.1 9.2 - - + -
653B LEU* 3.9 26.7 - - + +
663B TYR* 3.4 40.2 - + - -
666B MET* 3.8 46.9 - - + -
667B LYS* 3.9 12.1 - - + -
670B LEU* 3.3 25.4 - - + -
721B LEU* 4.6 7.0 - - + -
722B LEU* 4.9 1.1 - - + -
725B MET* 4.1 20.6 - - + +
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Residues in contact with ALA 607 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.6 21.8 - - + -
540B GLU* 5.4 0.4 - - - +
603B LEU 3.0 20.2 + - - +
606B PHE* 1.3 78.6 - - - +
608B LEU* 1.3 56.8 + - - +
610B TRP* 3.4 3.8 + - - +
611B ARG* 2.9 31.7 + - - +
663B TYR* 3.5 20.2 + - - +
667B LYS* 4.3 3.1 - - + +
778B GOL 3.6 22.2 - - - +
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.9 18.7 - - + +
604B MET 2.9 18.7 + - - +
605B ALA 3.8 1.8 - - - +
607B ALA* 1.3 73.5 - - - +
609B GLY* 1.3 69.1 + - - +
611B ARG* 3.1 2.9 + - + +
612B SER* 2.8 42.5 + - - +
621B LEU* 4.3 4.7 - - + -
622B CYS 3.6 8.7 - - - +
623B PHE* 3.5 64.4 - - + +
646B MET* 3.5 36.3 - - + -
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Residues in contact with GLY 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B ALA 2.7 22.1 + - - -
606B PHE 3.6 1.8 - - - -
608B LEU* 1.3 74.1 - - - +
610B TRP* 1.3 55.9 + - - +
612B SER* 3.6 2.5 - - - -
613B TYR* 2.8 30.7 + - - +
646B MET* 4.6 2.9 - - - -
649B VAL* 3.8 17.9 - - - -
650B SER* 3.9 14.5 - - - -
653B LEU* 3.6 7.2 - - - -
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Residues in contact with TRP 610 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B PHE 2.9 7.2 + - - +
607B ALA 3.5 7.0 - - - +
609B GLY* 1.3 75.1 - - - +
611B ARG* 1.3 67.3 + - + +
613B TYR* 3.2 29.9 + + - +
614B ARG* 3.1 48.6 + - + +
653B LEU* 3.3 21.0 - - + +
658B VAL* 3.3 35.4 - - + -
659B SER 3.6 18.6 - - - -
660B TYR* 3.2 43.3 - + + -
663B TYR* 3.4 47.6 - + + -
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Residues in contact with ARG 611 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.1 39.3 - - + -
541B PRO 4.7 3.8 + - - -
542B GLU 3.7 8.1 + - - -
543B VAL* 3.0 59.5 - - - +
544B LEU 4.3 2.4 - - - +
570B GLN* 4.8 4.9 + - - +
607B ALA 2.9 21.6 + - - +
608B LEU* 3.1 8.7 + - - +
610B TRP* 1.3 79.4 - - + +
612B SER* 1.3 62.0 + - - +
614B ARG* 3.4 9.7 + - - +
615B GLN* 3.5 26.5 + - - +
622B CYS* 4.1 22.8 + - + +
623B PHE 4.0 9.1 + - - -
624B ALA* 5.0 1.2 - - - +
625B PRO* 5.4 0.2 - - - +
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Residues in contact with SER 612 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
608B LEU* 2.8 26.0 + - - +
609B GLY 3.6 3.1 - - - -
611B ARG* 1.3 67.4 - - - +
613B TYR* 1.3 68.5 + - - +
614B ARG 3.1 1.6 - - - -
615B GLN 2.8 24.1 + - - +
618B ALA 4.4 3.5 - - - +
620B LEU 3.3 19.2 - - - +
621B LEU* 3.2 11.8 - - - +
622B CYS* 3.0 28.8 + - - -
650B SER* 4.1 16.8 + - - -
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Residues in contact with TYR 613 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLY 2.8 18.8 + - - +
610B TRP* 3.4 42.6 - + - +
612B SER* 1.3 75.6 - - - +
614B ARG* 1.3 67.1 - - - +
615B GLN* 2.7 15.4 + - - -
618B ALA 5.5 0.7 + - - +
650B SER* 3.7 18.5 + - - +
653B LEU* 4.0 17.5 - - + -
654B HIS* 3.3 51.4 - + + -
657B GLN* 3.2 30.0 + - - -
658B VAL 3.8 8.7 + - - -
----------------------------------------------------------
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Residues in contact with ARG 614 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B TRP* 3.1 40.1 + - + +
611B ARG* 3.6 10.3 - - - +
612B SER 3.1 1.4 - - - -
613B TYR* 1.3 97.6 - - - +
615B GLN* 1.3 76.3 + - - +
----------------------------------------------------------
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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