Contacts of the helix formed by residues 555 - 581 (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 SER 555 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PRO 4.2 0.4 + - - -
554B ASP* 1.3 75.8 - - - +
556B THR* 1.3 64.8 + - - +
557B TRP* 3.0 22.1 + - - +
558B ARG* 3.1 25.6 + - - +
559B ILE* 3.2 14.2 + - - +
636B LEU* 4.3 10.8 - - - -
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Residues in contact with THR 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 5.3 0.9 - - + -
555B SER* 1.3 71.8 - - - +
557B TRP* 1.3 63.5 + - - +
559B ILE* 3.5 4.5 + - - +
560B MET* 2.9 55.4 + - + +
636B LEU* 3.7 13.6 - - - +
637B PRO* 2.5 50.6 + - - +
638B GLY* 4.9 4.5 - - - +
639B MET* 4.4 13.9 - - - -
735B TYR* 5.6 0.7 - - - +
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Residues in contact with TRP 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B SER* 3.0 10.4 + - - +
556B THR* 1.3 80.0 - - - +
558B ARG* 1.3 102.6 + - + +
560B MET* 3.7 14.0 - - + +
561B THR* 2.9 55.0 + - + -
745B MET 5.9 0.4 - - - -
746B SER* 2.6 33.6 + - - -
747B ILE* 4.0 5.8 - - + +
748B GLU* 5.9 1.6 - - + -
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Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TYR* 3.3 33.7 + - + +
549B ASP* 3.0 39.0 + - - +
552B VAL* 2.8 45.2 + - - +
553B PRO 2.9 18.2 + - - -
554B ASP* 3.8 0.2 + - - -
555B SER* 3.1 19.0 + - - +
557B TRP* 1.3 100.8 - - + +
559B ILE* 1.3 58.8 + - - +
561B THR* 3.4 2.1 + - - -
562B THR* 2.8 37.3 + - - +
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Residues in contact with ILE 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B TYR* 3.5 25.6 - - + +
554B ASP* 4.1 7.2 - - + -
555B SER 3.2 9.6 + - - +
556B THR* 4.1 4.3 - - - +
558B ARG* 1.3 74.1 - - - +
560B MET* 1.3 60.5 + - - +
562B THR* 3.2 3.0 + - - -
563B LEU* 2.8 55.7 + - + +
627B LEU* 4.3 9.0 - - + -
629B ILE* 3.8 19.1 - - + -
633B ARG* 4.0 21.5 - - + -
636B LEU* 3.5 32.1 - - + -
639B MET* 3.9 13.7 - - + -
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Residues in contact with MET 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 4.0 42.1 - - + -
556B THR* 2.9 46.8 + - + +
557B TRP* 3.7 19.7 - - + +
559B ILE* 1.3 76.8 - - - +
561B THR* 1.3 57.4 + - - +
563B LEU* 3.3 5.1 + - - +
564B ASN* 2.9 34.5 + - - +
639B MET* 5.3 1.8 - - - -
735B TYR* 5.7 1.3 - - - -
739B THR* 4.4 17.5 - - + -
745B MET* 4.8 17.9 - - + -
747B ILE* 3.9 20.0 - - + -
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Residues in contact with THR 561 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557B TRP* 2.9 39.3 + - + -
558B ARG* 3.8 5.6 - - - -
559B ILE 3.2 0.2 - - - -
560B MET* 1.3 75.1 - - - +
562B THR* 1.3 65.7 + - - +
564B ASN* 3.3 3.5 + - - +
565B MET* 3.1 30.5 + - + +
747B ILE* 2.8 27.6 - - - +
748B GLU* 4.3 26.0 + - + +
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Residues in contact with THR 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ALA* 3.3 39.3 - - + +
547B GLY 4.7 1.3 - - - +
548B TYR* 3.4 30.2 - - + -
558B ARG* 2.8 26.0 + - - +
559B ILE 3.8 2.7 - - - -
561B THR* 1.3 77.0 - - - +
563B LEU* 1.3 58.2 + - - +
565B MET* 3.6 6.9 + - + +
566B LEU* 3.0 26.0 + - - +
627B LEU* 4.4 3.4 - - + -
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Residues in contact with LEU 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.1 52.8 + - + +
546B ALA* 5.6 0.2 - - + -
559B ILE* 2.8 37.2 + - + +
560B MET* 3.8 4.0 - - - +
561B THR 3.2 0.2 - - - -
562B THR* 1.3 75.0 - - - +
564B ASN* 1.3 56.8 + - - +
566B LEU* 4.3 8.1 - - + -
567B GLY* 2.8 29.6 + - - -
623B PHE* 3.6 51.1 - - + -
627B LEU* 3.5 23.8 - - + -
629B ILE* 4.8 0.2 - - + -
639B MET* 4.3 2.5 - - + -
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Residues in contact with ASN 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 2.4 47.8 + - - +
560B MET 2.9 18.0 + - - +
561B THR 3.3 4.9 + - - +
563B LEU* 1.3 74.1 - - - +
565B MET* 1.3 60.3 + - - +
567B GLY* 3.7 0.3 - - - -
568B GLY 2.9 24.1 + - - -
747B ILE* 3.6 13.5 - - - +
748B GLU 3.0 28.7 + - - +
749B PHE* 3.3 31.6 - - + -
750B PRO* 3.1 19.1 - - + +
753B LEU* 4.2 1.9 - - - +
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Residues in contact with MET 565 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B ALA 6.1 0.7 - - - +
561B THR* 3.1 19.8 + - + +
562B THR* 3.9 8.1 - - + +
564B ASN* 1.3 74.8 - - - +
566B LEU* 1.3 64.7 + - - +
568B GLY* 3.3 2.8 + - - -
569B ARG* 3.3 29.7 + - - +
748B GLU* 3.4 43.3 - - + +
749B PHE 3.8 1.6 - - - +
750B PRO* 3.6 35.5 - - + +
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Residues in contact with LEU 566 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 4.0 8.1 - - + +
544B LEU* 3.8 23.8 - - + -
545B TYR 3.6 22.0 - - - +
546B ALA* 4.1 12.8 - - + -
562B THR 3.0 17.9 + - - +
563B LEU* 3.8 8.3 - - + +
565B MET* 1.3 75.7 - - - +
567B GLY* 1.3 58.7 + - - +
569B ARG* 3.1 15.2 + - - +
570B GLN* 2.9 43.1 + - - +
623B PHE* 3.6 31.0 - - + +
624B ALA* 3.9 15.3 - - + -
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Residues in contact with GLY 567 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.8 19.7 - - - -
563B LEU 2.8 19.4 + - - -
564B ASN 3.7 0.9 - - - -
566B LEU* 1.3 75.6 - - - +
568B GLY* 1.3 65.6 + - - +
570B GLN* 2.9 11.5 + - - +
571B VAL* 2.8 28.9 + - - +
604B MET* 4.5 2.5 - - - -
753B LEU* 3.4 6.1 - - - -
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Residues in contact with GLY 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B ASN 2.9 15.1 + - - -
565B MET 3.3 3.1 + - - -
567B GLY* 1.3 75.3 - - - +
569B ARG* 1.3 62.1 + - - +
571B VAL* 3.3 2.8 + - - +
572B ILE* 3.1 32.8 + - - +
750B PRO* 4.1 11.2 - - - -
752B MET* 4.5 4.0 - - - +
753B LEU* 2.8 23.2 - - - +
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Residues in contact with ARG 569 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 3.6 43.1 - - + +
545B TYR* 2.8 28.0 + - - +
546B ALA* 4.8 4.4 + - - +
565B MET* 3.3 17.9 + - - +
566B LEU* 3.1 15.8 + - - +
567B GLY 3.1 0.4 - - - -
568B GLY* 1.3 80.1 - - - +
570B GLN* 1.3 59.7 + - - +
572B ILE* 3.7 13.4 + - + +
573B ALA* 3.2 21.7 + - - +
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Residues in contact with GLN 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B 866 3.2 59.0 + - + +
541B PRO* 6.1 1.6 - - - +
542B GLU 5.0 3.6 - - - +
544B LEU* 4.0 19.0 + - - +
566B LEU* 2.9 46.0 + - - +
567B GLY* 2.9 4.7 + - - +
569B ARG* 1.3 75.6 - - - +
571B VAL* 1.3 58.8 + - - +
573B ALA* 3.2 8.2 + - - +
574B ALA* 2.8 27.0 + - - +
604B MET* 3.1 23.8 - - + -
611B ARG* 4.8 4.5 + - - +
623B PHE 4.0 1.8 + - - -
778B GOL 3.8 5.9 + - - +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B GLY 2.8 16.1 + - - +
568B GLY 3.7 6.7 - - - +
570B GLN* 1.3 74.7 - - - +
572B ILE* 1.3 65.5 + - - +
574B ALA* 2.9 20.0 + - + +
575B VAL* 3.1 15.3 + - + +
596B LEU* 6.4 1.6 - - + -
600B TRP* 3.8 39.9 - - + -
604B MET* 4.3 8.3 - - + -
752B MET* 3.7 24.5 - - + -
753B LEU* 4.0 14.4 - - + -
756B ILE* 3.8 18.2 - - + -
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Residues in contact with ILE 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B GLY 3.1 25.4 + - - +
569B ARG* 3.9 11.7 - - + +
571B VAL* 1.3 74.6 - - - +
573B ALA* 1.3 63.2 + - - +
575B VAL* 3.1 15.3 + - - +
576B LYS* 3.3 11.3 + - - +
752B MET* 3.9 21.5 - - + -
748D LEU* 3.9 36.5 - - + +
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Residues in contact with ALA 573 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PRO* 4.5 20.5 - - + +
544B LEU* 5.1 8.5 - - + -
569B ARG 3.2 11.6 + - - +
570B GLN* 3.2 13.0 + - - +
571B VAL 3.1 0.6 - - - -
572B ILE* 1.3 78.3 - - - +
574B ALA* 1.3 61.2 + - - +
576B LYS* 3.4 13.2 + - + +
577B TRP* 3.0 26.0 + - - +
778B GOL 5.8 0.4 - - - +
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Residues in contact with ALA 574 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570B GLN 2.8 13.8 + - - +
571B VAL* 2.9 16.8 + - + +
573B ALA* 1.3 77.3 - - - +
575B VAL* 1.3 56.8 + - - +
577B TRP* 3.2 10.9 + - - +
578B ALA* 2.8 30.7 + - - +
596B LEU* 4.1 5.9 - - + +
600B TRP* 6.0 3.4 - - + +
603B LEU* 4.2 17.7 - - + -
604B MET* 5.2 1.1 - - + -
778B GOL 3.9 24.9 + - - +
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Residues in contact with VAL 575 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B VAL* 3.1 17.4 + - + +
572B ILE 3.1 8.0 + - - +
574B ALA* 1.3 74.7 - - - +
576B LYS* 1.3 65.1 + - - +
578B ALA* 3.4 1.0 + - - +
579B LYS* 3.1 32.2 + - + +
596B LEU* 4.2 17.0 - - + -
752B MET* 4.0 12.6 - - + -
745D LEU* 3.8 22.2 - - + -
748D LEU* 3.8 31.4 - - + +
749D LEU* 3.8 25.6 - - + -
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Residues in contact with LYS 576 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A GLU* 5.8 2.0 + - - -
572B ILE* 3.3 8.4 + - + +
573B ALA* 3.6 13.7 - - + +
575B VAL* 1.3 80.1 - - - +
577B TRP* 1.3 63.7 + - - +
579B LYS* 3.8 11.2 + - - +
580B ALA* 3.5 19.3 + - + +
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Residues in contact with TRP 577 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.8 3.8 + - - +
539B ILE* 3.3 50.9 - - + +
540B GLU* 4.2 3.4 + - - -
541B PRO* 4.0 16.4 - - + -
573B ALA 3.0 14.1 + - - +
574B ALA* 3.4 14.1 - - - +
575B VAL 3.1 0.2 - - - -
576B LYS* 1.3 75.6 - - - +
578B ALA* 1.3 78.1 + - + +
580B ALA* 3.0 16.0 + - - +
581B ILE* 3.3 30.5 + - + +
603B LEU* 3.8 20.2 - - + -
664B LEU 5.3 0.7 - - - -
667B LYS* 3.9 28.3 - - + +
668B THR* 3.5 35.9 + - - -
671B LEU* 3.9 10.3 - - + -
778B GOL 3.1 30.5 - - - -
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Residues in contact with ALA 578 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B ALA 2.8 19.3 + - - +
575B VAL 3.9 3.8 - - - +
577B TRP* 1.3 75.2 - - + +
579B LYS* 1.3 58.6 + - - +
581B ILE* 2.9 31.0 + - - +
584B PHE* 3.2 39.0 - - + +
596B LEU* 3.9 19.5 - - + -
671B LEU* 4.0 12.1 - - + -
----------------------------------------------------------
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Residues in contact with LYS 579 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B VAL* 3.1 19.7 + - + +
576B LYS* 4.2 9.9 - - - +
578B ALA* 1.3 76.0 - - - +
580B ALA* 1.3 58.3 + - - +
581B ILE 3.6 3.0 + - - +
584B PHE* 4.1 7.0 - - - -
585B ARG* 2.9 63.8 + - + +
592B GLN* 4.6 4.5 - - - +
748D LEU 2.7 24.7 + - - +
749D LEU* 3.1 50.6 + - + +
751D LYS* 3.6 22.8 + - - +
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Residues in contact with ALA 580 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A VAL* 4.7 10.7 - - + +
535B LEU* 3.8 12.3 - - - +
539B ILE* 3.9 25.3 - - + +
576B LYS 3.5 11.3 + - - +
577B TRP 3.0 10.9 + - - +
579B LYS* 1.3 77.0 - - - +
581B ILE* 1.3 64.1 + - - +
582B PRO* 3.3 9.0 - - - +
585B ARG* 4.5 4.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 581 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B LEU* 4.4 5.2 - - + -
539B ILE* 3.9 14.6 - - + -
577B TRP* 3.3 39.2 + - + +
578B ALA* 2.9 13.5 + - - +
579B LYS 4.4 1.6 - - - +
580B ALA* 1.3 75.9 - - - +
582B PRO* 1.3 76.2 - - + +
583B GLY 3.1 0.5 + - - -
584B PHE* 2.9 27.2 + - + +
585B ARG 4.4 1.6 + - - -
668B THR* 3.9 11.0 - - + +
671B LEU* 3.5 30.3 - - + -
672B LEU* 6.4 0.2 - - + -
689B ILE* 5.8 2.2 - - + -
693B TYR* 3.4 27.8 - - + +
----------------------------------------------------------
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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