Contacts of the helix formed by residues 563 - 594 (chain D) in PDB entry 7CR3
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 563 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B VAL* 4.7 10.7 - - + +
568B ILE* 4.0 7.3 - - - +
322D GLU* 4.5 16.2 - - - +
325D ARG* 3.6 42.0 + - + +
326D GLN* 4.9 5.7 - - - +
329D PHE* 4.6 14.6 - - + -
562D TYR* 1.3 80.7 - - - +
564D VAL* 1.3 81.9 + - - +
566D ASP* 3.5 15.1 + - - +
567D VAL* 3.7 8.5 + - - +
325G ARG* 3.8 19.0 + - - -
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Residues in contact with VAL 564 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562D TYR* 5.1 3.8 - - + -
563D ASP* 1.3 89.1 + - - +
565D MET* 1.3 66.3 + - + +
566D ASP 3.1 0.2 - - - -
567D VAL* 3.2 11.5 - - + +
568D ILE* 2.9 43.5 + - + +
325G ARG* 4.1 31.4 - - + +
329G PHE* 3.8 30.1 - - + -
563G ASP* 4.7 16.4 - - + +
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Residues in contact with MET 565 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560D ARG 5.5 4.0 - - - +
562D TYR* 3.5 42.7 - - + +
563D ASP 3.4 0.4 - - - -
564D VAL* 1.3 79.0 - - + +
566D ASP* 1.3 58.8 + - - +
569D GLU* 2.7 53.9 + - - +
328G HIS* 3.9 30.7 - - + +
329G PHE* 3.5 34.3 - - + -
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Residues in contact with ASP 566 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ILE* 3.7 25.9 - - + +
329D PHE* 4.9 10.0 - - - +
331D LYS* 5.2 7.4 - - - +
561D PRO* 4.8 11.6 - - - +
562D TYR 3.2 24.8 + - - +
563D ASP 3.5 6.7 - - - +
564D VAL 3.1 0.6 - - - -
565D MET* 1.3 76.6 - - - +
567D VAL* 1.3 58.0 + - - +
570D GLN* 2.9 52.5 + - - +
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Residues in contact with VAL 567 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B VAL* 4.1 24.5 - - + -
568B ILE* 4.2 12.7 - - + +
571B TYR* 4.4 10.7 - - + -
563D ASP 3.7 9.3 + - - +
564D VAL* 3.2 23.8 - - + +
566D ASP* 1.3 76.4 - - - +
568D ILE* 1.3 63.7 + - + +
570D GLN* 4.8 2.2 - - - -
571D TYR* 2.9 39.7 + - + +
567G VAL* 4.1 27.8 - - + -
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Residues in contact with ILE 568 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D VAL* 2.9 35.9 + - + +
565D MET* 4.3 1.1 - - - -
567D VAL* 1.3 79.6 - - + +
569D GLU* 1.3 80.0 + - - +
571D TYR* 3.8 2.6 - - + +
572D SER* 3.0 25.9 + - - +
329G PHE* 4.1 22.9 - - + -
331G LYS* 5.3 10.3 - - + -
563G ASP 4.0 10.8 - - - +
566G ASP* 3.7 40.4 - - + +
567G VAL* 4.2 15.7 - - + +
570G GLN* 5.0 3.1 - - - +
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Residues in contact with GLU 569 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565D MET* 2.7 61.7 + - - +
566D ASP* 4.5 0.4 - - - +
568D ILE* 1.3 83.7 - - - +
570D GLN* 1.3 57.5 + - - +
572D SER* 2.6 21.9 + - - +
573D ALA* 2.9 18.6 + - - +
329G PHE* 4.4 8.0 - - - -
331G LYS* 4.9 14.4 + - - +
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Residues in contact with GLN 570 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568B ILE* 5.0 2.6 - - - +
571B TYR* 2.9 39.9 + - + +
572B SER* 3.9 29.4 + - - +
575B HIS* 4.1 19.4 + - + +
566D ASP* 2.9 33.1 + - - +
567D VAL* 5.4 0.2 - - - -
569D GLU* 1.3 77.9 - - - +
571D TYR* 1.3 57.9 + - - +
573D ALA* 4.2 6.3 - - + -
574D GLY* 2.7 21.4 + - - -
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Residues in contact with TYR 571 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 3.1 26.9 - + + -
567D VAL* 2.9 25.5 + - + +
568D ILE* 3.9 3.1 - - + +
570D GLN* 1.3 75.5 - - - +
572D SER* 1.3 59.9 + - - +
575D HIS* 2.8 40.4 + - + +
578D MET* 4.5 12.1 - - + -
567G VAL* 4.7 14.4 - - + -
570G GLN* 2.9 59.9 + - + +
571G TYR* 3.1 37.4 - + + -
574G GLY* 3.3 14.2 - - - -
578G MET* 4.9 1.3 - - + +
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Residues in contact with SER 572 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D ILE* 3.0 16.5 + - - +
569D GLU* 2.6 28.2 + - - +
571D TYR* 1.3 75.1 - - - +
573D ALA* 1.3 59.7 + - - -
575D HIS* 3.9 1.0 - - - +
576D LEU* 3.0 32.8 + - - +
331G LYS* 4.6 16.7 + - - -
570G GLN* 3.9 18.5 + - - +
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Residues in contact with ALA 573 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B HIS* 5.5 1.8 - - + -
569D GLU 2.9 18.4 + - - +
570D GLN* 4.0 8.7 - - + +
572D SER* 1.3 77.2 + - - +
574D GLY* 1.3 53.9 + - - +
576D LEU* 3.2 15.1 - - + +
577D ASP* 2.6 45.8 + - - +
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Residues in contact with GLY 574 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 3.3 17.5 - - - -
575B HIS* 3.4 25.0 + - - -
570D GLN 2.7 16.0 + - - -
572D SER 3.4 0.2 - - - -
573D ALA* 1.3 74.5 - - - +
575D HIS* 1.3 56.7 + - - +
577D ASP* 3.5 2.6 + - - +
578D MET* 2.9 35.9 + - - +
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Residues in contact with HIS 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 4.3 0.4 + - - -
571D TYR* 2.8 28.8 + + + +
572D SER 4.2 0.2 - - - +
574D GLY* 1.3 70.6 - - - -
576D LEU* 1.3 61.7 + - - +
578D MET* 3.1 17.9 + - + +
579D LEU* 2.8 42.6 + - + +
570G GLN* 4.1 24.3 + - + +
573G ALA* 4.6 1.8 - - + -
574G GLY* 3.4 30.0 + - - -
577G ASP* 3.4 27.4 + - - +
581G ARG* 3.6 21.6 + - - -
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Residues in contact with LEU 576 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
572D SER* 3.0 26.1 + - - +
573D ALA* 3.2 24.0 - - + +
575D HIS* 1.3 73.7 - - - +
577D ASP* 1.3 88.9 + - - +
579D LEU* 3.0 20.7 + - + +
580D SER* 3.0 19.9 + - - -
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Residues in contact with ASP 577 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B HIS* 3.4 23.6 - - - +
579B LEU* 6.1 1.3 - - + -
573D ALA* 2.6 32.7 + - - +
574D GLY 3.7 4.0 - - - +
576D LEU* 1.3 88.0 - - - +
578D MET* 1.3 58.0 + - - +
580D SER* 2.3 26.8 + - - +
581D ARG* 2.8 26.8 + - - +
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Residues in contact with MET 578 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571B TYR* 4.9 1.6 - - + +
578B MET* 3.8 37.2 - - + +
571D TYR* 4.5 12.3 - - + -
574D GLY* 2.9 26.8 + - - +
575D HIS* 3.1 31.4 + - + +
577D ASP* 1.3 76.6 - - - +
579D LEU* 1.3 53.9 + - - +
581D ARG* 3.0 16.0 + - - +
582D ILE 2.9 16.8 + - - -
578G MET* 3.8 42.8 - - + +
581G ARG* 2.3 36.5 + - - +
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Residues in contact with LEU 579 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D HIS* 2.8 41.3 + - + +
576D LEU* 3.0 18.6 + - + +
578D MET* 1.3 72.1 - - - +
580D SER* 1.3 62.6 + - - +
582D ILE* 3.1 9.2 - - + +
583D LYS* 3.0 27.1 + - - +
577G ASP* 6.1 1.3 - - + -
581G ARG* 3.2 20.8 - - - +
----------------------------------------------------------
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Residues in contact with SER 580 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576D LEU 3.0 7.6 + - - -
577D ASP* 2.3 38.8 + - - +
579D LEU* 1.3 74.0 - - - +
581D ARG* 1.3 49.5 + - - +
583D LYS* 3.2 24.0 - - - +
584D SER* 2.5 37.8 + - - -
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Residues in contact with ARG 581 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B HIS* 3.6 9.0 + - - -
578B MET* 2.3 64.2 + - - +
579B LEU* 3.2 26.1 - - - +
581B ARG* 4.4 3.2 - - - +
582B ILE* 3.5 39.5 - - + +
585B LEU* 5.1 2.9 - - + +
577D ASP* 2.8 27.9 + - - +
578D MET* 3.0 24.8 + - - +
580D SER* 1.3 77.9 - - - +
582D ILE* 1.3 57.9 + - - +
584D SER* 2.6 19.4 + - - -
585D LEU* 2.8 19.5 + - - +
581G ARG* 4.4 2.9 - - - +
----------------------------------------------------------
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Residues in contact with ILE 582 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578D MET 2.9 16.8 + - - +
579D LEU* 3.1 23.3 - - + +
581D ARG* 1.3 73.2 - - - +
583D LYS* 1.3 58.5 + - + +
585D LEU* 3.2 19.1 + - + +
586D GLN* 2.9 61.3 + - + +
581G ARG* 3.5 57.9 - - + +
584G SER* 4.1 1.8 - - - +
----------------------------------------------------------
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Residues in contact with LYS 583 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579D LEU 3.0 21.7 + - - +
580D SER* 3.2 30.1 - - - +
582D ILE* 1.3 77.2 - - + +
584D SER* 1.3 69.2 + - - +
586D GLN* 3.4 5.9 + - - +
587D SER* 2.6 39.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 584 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B ILE* 4.1 1.4 - - - +
586B GLN* 3.5 31.4 + - - -
580D SER 2.5 26.1 + - - -
581D ARG* 2.6 19.1 + - - -
583D LYS* 1.3 80.8 - - - +
585D LEU* 1.3 58.2 + - - +
587D SER* 2.9 7.9 + - - -
588D ARG* 2.9 39.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 585 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 3.9 34.0 - - + +
581D ARG 2.8 18.9 + - - +
582D ILE* 3.3 22.4 - - + +
583D LYS 3.2 0.2 - - - -
584D SER* 1.3 73.2 + - - +
586D GLN* 1.3 79.3 + - - +
588D ARG* 4.1 0.6 - - - +
589D VAL* 2.9 50.0 + - + +
581G ARG* 5.1 2.2 - - + +
584G SER 5.3 0.4 - - - +
585G LEU* 3.9 45.8 - - + +
588G ARG* 5.6 0.9 - - + -
589G VAL* 6.4 0.7 - - + -
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Residues in contact with GLN 586 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582D ILE* 2.9 30.9 + - + +
583D LYS* 4.0 5.6 - - - +
585D LEU* 1.3 87.6 - - - +
587D SER* 1.3 57.9 + - - +
589D VAL* 3.2 3.0 - - - +
590D ASP* 2.9 36.4 + - - +
584G SER* 3.5 29.1 + - - -
588G ARG* 3.2 39.2 - - - +
----------------------------------------------------------
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Residues in contact with SER 587 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
583D LYS* 2.6 26.0 + - - +
584D SER* 2.9 17.8 + - - -
586D GLN* 1.3 76.4 - - - +
588D ARG* 1.3 59.2 + - - +
590D ASP* 3.2 8.1 + - - +
591D GLN* 2.9 31.0 + - - +
----------------------------------------------------------
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Residues in contact with ARG 588 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 5.7 1.1 - - + -
586B GLN* 3.2 41.5 + - - +
589B VAL* 3.8 20.4 - - + -
590B ASP* 2.4 39.5 + - - -
593B VAL* 5.5 2.5 - - - +
584D SER* 2.9 24.1 + - - +
585D LEU* 4.1 2.5 - - - +
587D SER* 1.3 75.7 + - - +
589D VAL* 1.3 62.0 + - + +
591D GLN* 3.1 23.8 + - - +
592D ILE* 2.9 30.5 + - - +
----------------------------------------------------------
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Residues in contact with VAL 589 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B LEU* 6.4 0.4 - - + -
589B VAL* 5.2 12.3 - - + -
585D LEU* 2.9 39.9 + - + +
586D GLN* 3.2 18.2 - - - +
588D ARG* 1.3 76.9 - - + +
590D ASP* 1.3 58.5 + - - +
592D ILE* 3.2 15.8 + - + +
593D VAL* 2.9 29.5 + - + +
588G ARG* 3.8 32.1 - - + -
589G VAL* 5.2 13.7 - - + -
592G ILE* 4.0 9.3 - - + +
----------------------------------------------------------
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Residues in contact with ASP 590 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586D GLN 2.9 15.3 + - - +
587D SER* 3.4 7.9 - - - +
588D ARG 3.2 0.2 - - - -
589D VAL* 1.3 77.2 - - - +
591D GLN* 1.3 53.9 + - - +
592D ILE 3.1 0.2 - - - -
593D VAL* 2.9 13.5 + - - +
594D GLY* 2.4 34.7 + - - -
588G ARG* 2.4 39.3 + - - -
----------------------------------------------------------
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Residues in contact with GLN 591 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
593B VAL* 5.1 12.1 - - + +
587D SER* 2.9 18.9 + - - +
588D ARG* 3.1 27.8 + - - +
590D ASP* 1.3 75.7 - - - +
592D ILE* 1.3 63.3 + - + +
594D GLY* 3.9 3.8 - - - +
595D ARG* 3.5 24.9 + - - +
----------------------------------------------------------
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Residues in contact with ILE 592 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589B VAL* 4.0 11.2 - - + +
592B ILE* 3.9 31.2 - - + +
593B VAL* 3.7 31.0 - - + +
588D ARG* 2.9 15.9 + - + +
589D VAL* 3.3 15.9 - - + +
590D ASP 3.1 0.2 - - - -
591D GLN* 1.3 78.4 - - - +
593D VAL* 1.3 60.6 + - - +
595D ARG* 3.6 18.5 + - + +
592G ILE* 3.9 32.7 - - + +
595G ARG* 3.2 12.0 + - - -
----------------------------------------------------------
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Residues in contact with VAL 593 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
589D VAL* 2.9 20.3 + - + +
590D ASP* 2.9 19.5 + - + +
592D ILE* 1.3 75.5 - - - +
594D GLY* 1.3 62.7 + - - +
595D ARG 3.1 0.9 - - - -
588G ARG* 5.5 4.0 - - + +
591G GLN* 5.1 14.8 - - + +
592G ILE* 3.7 18.6 - - + -
595G ARG* 2.6 46.6 + - - +
----------------------------------------------------------
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Residues in contact with GLY 594 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
590D ASP 2.4 24.1 + - - -
591D GLN* 3.5 6.5 + - - -
592D ILE 3.3 0.6 - - - -
593D VAL* 1.3 70.4 - - - +
595D ARG* 1.3 58.6 + - - +
----------------------------------------------------------
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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