Contacts of the helix formed by residues 553 - 581 (chain D) in PDB entry 3H52
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 PRO 553 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A ARG* 3.9 0.2 - - - -
550D SER 5.5 0.4 - - - +
551D SER 3.6 8.7 - - - +
552D VAL* 1.3 87.6 - - + +
554D ASP* 1.3 65.6 + - - +
555D SER* 4.1 11.7 - - - +
556D THR* 3.2 22.1 + - - +
557D TRP* 3.1 20.1 + - - +
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Residues in contact with ASP 554 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASP* 3.7 25.1 - - + +
555A SER* 3.2 35.1 + - - -
558A ARG* 3.0 37.5 + - - +
548D TYR* 4.7 5.2 + - - -
552D VAL 3.6 0.6 + - - +
553D PRO* 1.3 68.1 - - - +
555D SER* 1.3 68.6 + - - +
557D TRP* 3.9 0.7 - - - +
558D ARG* 3.1 24.8 + - - +
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Residues in contact with SER 555 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554A ASP* 3.0 18.2 + - - +
553D PRO* 4.1 11.0 - - - +
554D ASP* 1.3 80.5 - - - +
556D THR* 1.3 65.0 + - - -
558D ARG* 3.8 2.1 - - - +
559D ILE* 3.2 29.5 + - - +
636D LEU* 6.2 0.3 - - - +
638D ASP* 5.7 0.7 + - - -
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Residues in contact with THR 556 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552D VAL* 4.3 12.8 - - + -
553D PRO* 3.2 25.9 + - - +
555D SER* 1.3 76.7 + - - +
557D TRP* 1.3 58.4 + - - +
559D ILE* 3.3 4.4 + - + -
560D MET* 2.8 55.6 + - + +
638D ASP* 3.7 33.5 + - + +
639D MET* 6.2 0.2 - - + -
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Residues in contact with TRP 557 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 5.1 2.0 - + - -
558A ARG* 3.5 64.5 + - + +
561A THR* 4.9 6.6 - - + +
562A THR* 4.4 14.6 + - + -
565A MET* 5.2 16.8 - - + -
547D GLY 4.7 15.9 - - - -
548D TYR* 6.3 0.4 - - - -
549D ASP* 6.4 0.7 - - + -
552D VAL* 4.3 15.4 - - + +
553D PRO 3.1 15.9 + - - +
554D ASP 3.9 3.4 - - - +
555D SER 3.4 0.2 - - - -
556D THR* 1.3 76.2 - - - +
558D ARG* 1.3 57.4 + - - +
560D MET* 5.1 1.6 - - - -
561D THR* 2.7 67.7 + - + +
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Residues in contact with ARG 558 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 3.6 26.2 - - + -
549A ASP* 3.0 36.6 + - - +
552A VAL* 2.6 32.9 + - - +
553A PRO 3.5 16.2 + - - -
554A ASP* 3.3 24.5 + - + +
557A TRP* 3.6 55.6 - - + +
558A ARG* 5.9 0.4 - - + +
554D ASP 3.1 15.1 + - - +
555D SER 3.8 2.7 - - - +
557D TRP* 1.3 85.0 - - + +
559D ILE* 1.3 58.4 + - + +
561D THR* 4.5 0.2 - - - -
562D THR* 2.7 44.5 + - - +
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Residues in contact with ILE 559 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A TYR* 4.5 18.8 - - + +
554A ASP* 5.9 0.7 - - - +
555D SER* 3.2 21.9 + - - +
556D THR* 3.8 4.9 - - - +
558D ARG* 1.3 79.0 - - + +
560D MET* 1.3 61.8 + - + +
562D THR* 3.5 3.5 + - - -
563D LEU* 2.8 40.4 + - + +
627D LEU* 4.3 21.1 - - + +
629D ILE* 3.6 30.3 - - + -
639D MET* 4.2 25.1 - - - -
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Residues in contact with MET 560 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 3.9 20.0 - - + +
556D THR* 2.8 39.9 + - + +
557D TRP* 4.3 1.8 - - - +
559D ILE* 1.3 72.9 - - + +
561D THR* 1.3 60.1 + - - +
563D LEU* 3.7 21.5 - - + -
564D ASN* 2.9 46.9 + - - +
638D ASP 5.9 1.1 - - - +
639D MET* 4.3 17.0 - - + +
642D GLN* 5.0 1.3 - - - +
735D TYR* 3.6 24.0 - - + +
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Residues in contact with THR 561 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
557A TRP* 4.6 8.3 - - + +
561A THR* 4.5 17.3 - - + -
565A MET* 5.9 2.7 - - - -
557D TRP* 2.7 64.7 + - + +
558D ARG* 3.7 2.9 - - - -
560D MET* 1.3 72.4 - - - +
562D THR* 1.3 62.5 + - - +
564D ASN* 3.2 6.8 + - - +
565D MET* 3.0 37.8 + - + +
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Residues in contact with THR 562 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A ALA* 3.3 41.1 - - + +
547A GLY 4.8 2.5 - - - +
548A TYR* 4.5 13.0 - - + -
557A TRP* 4.0 17.4 + - + -
558D ARG* 2.7 35.9 + - - +
559D ILE* 3.8 4.7 - - - -
561D THR* 1.3 72.8 - - - +
563D LEU* 1.3 61.4 + - - +
565D MET* 3.6 7.1 + - - +
566D LEU* 3.1 22.9 + - - +
627D LEU* 4.4 11.7 - - + -
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Residues in contact with LEU 563 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 3.5 53.9 - - + -
559D ILE* 2.8 24.6 + - + +
560D MET* 3.6 24.2 - - - +
562D THR* 1.3 76.7 - - - +
564D ASN* 1.3 61.2 + - - +
566D LEU* 3.2 5.1 + - + +
567D GLY* 2.8 29.1 + - - -
623D PHE* 3.6 46.2 - - + -
627D LEU* 4.3 9.1 - - + +
639D MET* 4.1 5.2 - - + -
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Residues in contact with ASN 564 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 3.7 37.7 + - + +
560D MET* 2.9 39.4 + - - +
561D THR* 3.2 5.6 + - - +
563D LEU* 1.3 80.0 - - - +
565D MET* 1.3 57.3 + - - +
567D GLY* 3.5 1.0 + - - -
568D GLY* 2.9 25.6 + - - -
739D THR* 6.3 1.0 - - - +
752D MET* 6.1 2.0 - - + +
753D LEU* 4.7 12.1 - - - +
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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
----------------------------------------------------------
546A ALA 5.9 1.8 - - - +
557A TRP* 5.3 12.3 - - - -
561A THR* 6.0 3.4 - - - -
528B LEU* 4.2 26.2 - - + +
561D THR* 3.0 31.6 + - + +
562D THR* 3.9 5.8 - - - +
564D ASN* 1.3 72.5 - - + +
566D LEU* 1.3 65.7 + - - +
568D GLY* 3.2 3.6 + - - -
569D ARG* 3.1 39.1 + - - +
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Residues in contact with LEU 566 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.9 22.4 - - + +
545A TYR 3.6 21.8 - - - +
546A ALA* 4.0 10.5 - - + -
2D 486 4.3 3.6 - - + -
562D THR 3.1 18.5 + - - +
563D LEU* 3.2 5.1 + - + +
565D MET* 1.3 74.7 - - - +
567D GLY* 1.3 64.5 + - - +
569D ARG* 2.9 16.7 + - - +
570D GLN* 2.9 43.9 + - - +
623D PHE* 3.9 21.5 - - + +
624D ALA* 3.7 24.0 - - + -
627D LEU* 5.0 2.0 - - + -
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Residues in contact with GLY 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 3.7 39.0 - - - -
563D LEU 2.8 16.1 + - - -
564D ASN 3.8 0.2 - - - -
566D LEU* 1.3 77.6 - - - +
568D GLY* 1.3 59.6 + - - +
570D GLN* 3.2 6.6 + - - +
571D VAL* 3.0 27.9 + - - +
604D MET* 4.1 0.7 - - - +
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Residues in contact with GLY 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 4.1 15.1 + - - -
564D ASN 2.9 15.7 + - - -
565D MET* 3.5 5.6 - - - -
566D LEU 3.2 0.4 - - - -
567D GLY* 1.3 77.4 - - - +
569D ARG* 1.3 61.2 + - - +
571D VAL* 3.5 4.2 + - - +
572D ILE* 3.4 25.7 + - - +
752D MET* 6.5 0.2 - - - -
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Residues in contact with ARG 569 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.7 24.3 - - + +
545A TYR 2.6 33.3 + - - +
546A ALA* 4.0 11.7 + - - +
565D MET* 3.1 21.8 + - - +
566D LEU* 2.9 25.1 + - - +
568D GLY* 1.3 72.6 - - - +
570D GLN* 1.3 60.4 + - - +
572D ILE* 3.4 13.1 + - + +
573D ALA* 2.9 28.4 + - - +
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Residues in contact with GLN 570 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544A LEU* 3.7 28.1 - - + +
2D 486 2.7 47.6 + - - +
566D LEU* 2.9 32.0 + - + +
567D GLY 3.6 7.0 - - - +
569D ARG* 1.3 73.6 - - - +
571D VAL* 1.3 54.2 + - - +
573D ALA* 3.1 4.6 + - - +
574D ALA* 2.6 36.7 + - - +
604D MET* 3.1 27.6 + - + +
607D ALA* 6.3 0.2 - - - +
611D ARG* 3.3 17.0 + - - +
623D PHE 3.7 1.2 - - - +
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Residues in contact with VAL 571 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D 486 3.5 30.5 - - - -
567D GLY 3.0 7.4 + - - +
568D GLY 3.7 8.7 - - - +
569D ARG 3.4 0.2 - - - -
570D GLN* 1.3 74.1 - - - +
572D ILE* 1.3 69.3 + - + +
574D ALA* 3.0 5.0 + - - +
575D VAL* 2.9 33.1 + - + +
600D TRP* 3.5 34.1 - - + -
604D MET* 3.6 15.3 - - + -
756D ILE* 5.4 11.9 - - + -
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Residues in contact with ILE 572 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
568D GLY 3.4 14.8 + - - +
569D ARG* 3.5 12.1 - - + +
570D GLN 3.2 0.6 - - - -
571D VAL* 1.3 83.0 - - + +
573D ALA* 1.3 63.7 + - - +
575D VAL* 3.0 19.8 + - - +
576D LYS* 3.1 14.0 + - + +
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Residues in contact with ALA 573 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PRO* 4.9 17.4 - - + +
544A LEU* 4.3 17.0 - - + -
569D ARG 2.9 14.7 + - - +
570D GLN* 3.5 10.5 - - - +
572D ILE* 1.3 77.6 - - - +
574D ALA* 1.3 56.6 + - - +
576D LYS* 3.2 19.9 + - - +
577D TRP* 2.9 30.2 + - - +
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Residues in contact with ALA 574 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
570D GLN 2.6 16.3 + - - +
571D VAL 3.0 11.0 + - - +
573D ALA* 1.3 73.9 - - - +
575D VAL* 1.3 54.3 + - + +
577D TRP* 3.6 14.4 - - + -
578D ALA* 3.0 28.4 + - - +
596D LEU* 4.2 5.2 - - + +
600D TRP* 5.5 2.2 - - + -
603D LEU* 4.6 18.4 - - + -
604D MET* 4.0 20.2 - - + -
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Residues in contact with VAL 575 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
571D VAL* 2.9 28.8 + - + +
572D ILE* 3.0 9.4 + - - +
574D ALA* 1.3 78.0 - - + +
576D LYS* 1.3 60.5 + - - +
578D ALA* 3.4 3.6 + - - +
579D LYS* 3.1 33.9 + - + +
596D LEU* 3.7 32.3 - - + -
600D TRP* 6.5 0.9 - - + -
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Residues in contact with LYS 576 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A PRO* 5.1 9.9 - - - +
542A GLU* 5.6 6.1 + - - -
572D ILE* 3.1 13.6 + - + +
573D ALA* 3.2 19.3 + - - +
575D VAL* 1.3 74.5 - - - +
577D TRP* 1.3 68.5 + - - +
579D LYS* 3.5 18.3 + - - +
580D ALA* 3.5 16.1 + - - +
----------------------------------------------------------
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Residues in contact with TRP 577 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 4.8 1.6 + - - +
539A ILE* 3.6 35.0 - - + +
540A GLU* 3.6 18.4 + - - -
541A PRO* 4.6 11.4 - - + -
573D ALA 2.9 17.7 + - - +
574D ALA* 3.6 15.3 - - + +
576D LYS* 1.3 75.7 - - - +
578D ALA* 1.3 80.4 + - + +
580D ALA* 2.7 19.7 + - - +
581D ILE* 3.2 36.1 + - + +
603D LEU* 3.3 39.9 - - + -
664D LEU 5.5 0.4 - - - -
667D LYS* 3.6 32.1 - - + -
668D THR* 3.8 13.9 - - - -
671D LEU* 3.7 22.7 - - + -
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Residues in contact with ALA 578 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574D ALA 3.0 15.1 + - - +
575D VAL 3.5 6.5 - - - +
577D TRP* 1.3 87.1 - - + +
579D LYS* 1.3 62.4 + - - +
581D ILE* 3.0 16.5 + - - +
584D PHE* 3.1 28.8 - - + -
596D LEU* 3.7 23.3 - - + -
671D LEU* 3.8 20.2 - - + -
----------------------------------------------------------
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Residues in contact with LYS 579 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575D VAL* 3.1 25.9 + - + +
576D LYS* 3.5 18.6 - - - +
577D TRP 3.0 1.0 + - - -
578D ALA* 1.3 76.9 - - + +
580D ALA* 1.3 60.4 + - - +
584D PHE* 4.3 9.4 - - + -
585D ARG* 3.5 30.8 + - - +
592D GLN* 4.9 7.6 - - - +
596D LEU* 5.8 1.3 - - + -
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Residues in contact with ALA 580 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A LEU* 6.1 0.2 - - - +
539A ILE* 3.5 33.2 - - + +
576D LYS* 3.5 7.9 + - + +
577D TRP* 2.7 15.8 + - - +
579D LYS* 1.3 73.3 - - - +
581D ILE* 1.3 63.6 + - - +
582D PRO* 3.1 10.2 - - - +
585D ARG* 3.9 17.1 + - - +
----------------------------------------------------------
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Residues in contact with ILE 581 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A LEU* 3.1 31.0 - - + -
539A ILE* 3.5 3.3 - - + +
577D TRP* 3.2 51.0 + - + +
578D ALA* 3.0 21.0 + - - +
580D ALA* 1.3 73.9 - - - +
582D PRO* 1.3 72.4 - - - +
583D GLY 3.2 2.3 + - - -
584D PHE* 3.3 24.7 + - + +
585D ARG* 3.4 9.9 + - - +
668D THR* 3.7 15.7 - - + +
671D LEU* 4.4 4.7 - - + -
672D LEU* 6.3 1.1 - - + -
689D ILE* 5.9 0.2 - - + -
693D TYR* 3.3 19.7 - - + +
----------------------------------------------------------
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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