Contacts of the helix formed by residues 525 - 553 (chain D) in PDB entry 5DO7
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 LEU 525 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523D PRO 3.3 4.6 + - - -
524D GLY* 1.3 76.5 - - - +
526D GLN* 1.3 85.5 + - + +
527D PRO* 3.2 4.0 - - - +
528D PHE* 2.8 30.8 + - - +
529D LEU* 3.2 38.9 + - + +
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Residues in contact with GLN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LEU* 1.3 88.6 - - + +
527D PRO* 1.3 72.0 - - + +
529D LEU* 3.5 5.1 + - - +
530D LEU* 3.3 19.8 + - + +
610D ARG* 3.1 29.5 + - - +
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Residues in contact with PRO 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516D TYR* 3.5 10.3 - - - +
522D ARG* 3.5 36.6 - - + +
523D PRO 3.6 14.6 - - - +
525D LEU 3.2 5.4 - - - +
526D GLN* 1.3 92.5 - - + +
528D PHE* 1.3 66.6 + - - +
529D LEU 2.8 1.9 + - - -
530D LEU* 2.8 4.4 + - + +
531D HIS* 2.8 24.2 + - - +
606D ILE* 3.9 23.2 - - + +
607D GLN* 4.6 3.6 - - - +
610D ARG* 4.8 10.0 - - - +
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Residues in contact with PHE 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509D ILE* 4.7 3.6 - - + -
512D GLY 5.6 0.7 - - - -
513D MET* 3.5 42.4 - - + -
516D TYR* 3.1 39.4 + + + +
517D TRP* 3.6 39.3 - + - -
523D PRO 5.9 0.4 - - - +
524D GLY 5.4 1.8 - - - +
525D LEU* 2.8 22.6 + - + +
527D PRO* 1.3 73.6 - - - +
529D LEU* 1.3 78.2 + - + +
531D HIS* 3.2 3.4 - - - +
532D PHE* 2.8 43.5 + + + -
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Residues in contact with LEU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D LEU* 3.2 43.2 + - + +
526D GLN* 4.1 4.7 - - - +
527D PRO 2.8 2.4 + - - -
528D PHE* 1.3 94.0 - - + +
530D LEU* 1.3 63.2 + - - +
532D PHE* 3.8 9.3 - - + +
533D LEU* 2.8 34.2 + - - +
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Residues in contact with LEU 530 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526D GLN* 3.3 12.0 + - + +
527D PRO 2.8 7.1 + - - +
529D LEU* 1.3 77.6 - - - +
531D HIS* 1.3 67.8 + - - +
533D LEU* 3.6 10.6 - - + +
534D LEU* 3.0 11.3 + - - +
606D ILE* 3.4 35.7 - - + -
610D ARG* 4.3 25.4 - - - +
640D LEU* 5.4 5.4 - - + +
644D TYR* 2.6 55.1 + - + +
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Residues in contact with HIS 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D ILE* 3.5 33.8 - - + +
512D GLY* 4.1 13.0 + - - -
516D TYR* 3.5 36.7 - + + +
521D LEU* 3.9 11.0 - - + +
527D PRO 2.8 11.0 + - - +
528D PHE* 3.2 10.8 + - - +
530D LEU* 1.3 73.4 - - - +
532D PHE* 1.3 83.5 + - - +
534D LEU* 2.8 17.6 + - - +
535D VAL* 3.0 21.2 + - + +
603D LEU* 3.1 34.6 - - + +
606D ILE* 4.2 7.8 - - + +
607D GLN* 3.8 11.2 - - - +
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Residues in contact with PHE 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D CYS* 4.8 2.9 - - + -
508D ILE* 3.5 24.9 - - + -
509D ILE* 3.5 43.3 - - + -
512D GLY* 5.0 9.9 - - - -
528D PHE* 2.8 36.7 + + + +
529D LEU* 3.8 10.3 - - + +
531D HIS* 1.3 80.6 + - - +
533D LEU* 1.3 82.6 + - + +
535D VAL* 2.8 10.1 + - + +
536D TRP* 2.8 46.7 + + - +
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Residues in contact with LEU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D LEU 2.8 23.6 + - - +
530D LEU* 3.6 10.5 - - + +
532D PHE* 1.3 81.1 - - + +
534D LEU* 1.3 58.6 + - - +
536D TRP* 3.1 29.0 - - + +
537D LEU* 3.2 22.5 + - + +
644D TYR* 4.0 22.4 - - + -
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Residues in contact with LEU 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530D LEU 3.0 7.3 + - - +
531D HIS* 2.8 13.9 + - - +
533D LEU* 1.3 68.3 - - - +
535D VAL* 1.3 69.4 + - - +
536D TRP 2.9 1.1 - - - -
537D LEU* 2.8 3.7 + - - +
538D VAL* 2.8 43.6 + - + +
598D TRP 4.0 3.1 - - - +
599D CYS* 3.6 12.3 - - - +
602D GLY* 3.5 15.5 - - - -
603D LEU* 3.5 35.2 - - + +
606D ILE* 5.2 0.4 - - + -
643D ILE* 4.8 6.3 - - + -
644D TYR* 3.5 34.5 - - + +
647D VAL* 4.3 21.5 - - + -
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Residues in contact with VAL 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D ILE* 4.6 11.2 - - + +
456D GLY* 6.1 0.9 - - - -
508D ILE* 4.2 15.3 - - + -
511D TYR* 4.7 19.1 - - + -
512D GLY* 5.2 4.5 - - - -
531D HIS* 3.0 37.6 + - + +
532D PHE* 2.8 9.8 + - - +
534D LEU* 1.3 77.1 - - - +
536D TRP* 1.3 55.2 + - - +
538D VAL* 3.2 8.0 + - - +
539D VAL* 2.8 49.2 + - + +
599D CYS* 4.9 6.3 - - - -
603D LEU* 4.3 17.5 - - + -
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Residues in contact with TRP 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501D LEU* 4.1 26.0 - - + -
504D HIS* 3.5 19.9 + + - -
505D CYS* 3.7 31.2 - - - +
508D ILE* 3.2 27.3 - - + +
532D PHE* 2.8 36.2 + + - +
533D LEU* 3.1 26.2 - - + +
535D VAL* 1.3 77.3 - - - +
537D LEU* 1.3 72.4 + - + -
540D PHE* 2.8 56.0 + + + +
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Residues in contact with LEU 537 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D LEU* 3.2 26.6 + - + +
534D LEU* 2.8 9.0 + - - +
536D TRP* 1.3 94.2 - - + +
538D VAL* 1.3 57.7 + - - +
540D PHE* 3.9 9.0 - - + +
541D CYS* 2.8 31.5 + - - +
644D TYR* 3.8 30.7 - - + +
647D VAL* 3.3 21.3 - - + +
648D ILE* 4.1 35.2 - - + -
651D SER* 4.4 2.2 + - - +
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Residues in contact with VAL 538 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D GLY* 5.1 6.5 - - - +
460D PRO* 6.3 0.9 - - + -
534D LEU* 2.8 37.2 + - + +
535D VAL* 3.5 7.2 - - - +
537D LEU* 1.3 74.1 - - - +
539D VAL* 1.3 64.2 + - + +
540D PHE 3.2 0.2 + - - -
541D CYS* 3.3 7.1 + - - +
542D CYS* 2.8 28.5 + - - +
595D PHE* 3.6 39.4 - - + +
596D LEU* 4.8 4.7 - - + +
599D CYS* 3.5 34.1 - - + +
647D VAL* 4.9 6.5 - - + -
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Residues in contact with VAL 539 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456D GLY* 6.4 0.7 - - - -
459D ILE* 3.4 37.2 - - + -
460D PRO* 6.2 1.1 - - - -
463D VAL* 4.5 12.5 - - + +
504D HIS* 3.9 17.7 - - + +
507D TYR* 5.4 2.7 - - + -
508D ILE* 3.8 17.0 - - + -
511D TYR* 5.8 1.1 - - + -
535D VAL* 2.8 36.6 + - + +
538D VAL* 1.3 78.1 - - + +
540D PHE* 1.3 57.0 + - - +
542D CYS* 3.0 9.8 + - - +
543D ARG* 2.8 35.7 + - - +
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Residues in contact with PHE 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D ILE* 3.8 28.9 - - + -
501D LEU* 4.1 19.3 - - + -
504D HIS* 3.5 23.8 + + - +
536D TRP* 2.8 46.6 + + + +
537D LEU* 3.9 9.0 - - + +
539D VAL* 1.3 74.8 - - - +
541D CYS* 1.3 68.8 + - - +
543D ARG* 3.1 10.7 + - + +
544D ILE* 3.0 48.8 + - + +
651D SER* 4.2 10.5 - - - -
655D MET* 4.7 6.3 - - + -
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Residues in contact with CYS 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537D LEU 2.8 19.8 + - - +
538D VAL* 3.4 6.5 - - - +
540D PHE* 1.3 75.4 - - - +
542D CYS* 1.3 60.9 + - - +
544D ILE* 3.1 8.6 + - - +
545D MET* 2.8 25.1 + - - +
595D PHE* 4.0 24.2 - - + -
647D VAL* 4.3 4.3 - - + +
650D LEU* 4.0 5.6 - - - -
651D SER* 3.3 32.1 - - - +
654D PHE* 3.7 29.8 - - - -
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Residues in contact with CYS 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460D PRO* 4.2 11.4 - - + -
463D VAL* 4.2 13.5 - - + -
464D ILE* 3.2 35.0 - - - -
538D VAL 2.8 14.7 + - - +
539D VAL* 3.2 15.0 - - - +
541D CYS* 1.3 77.2 - - - +
543D ARG* 1.3 60.4 + - - +
545D MET* 3.1 12.0 + - - +
546D ALA* 3.0 21.1 + - - +
567D TYR* 5.8 0.4 - - - -
595D PHE* 3.5 33.6 - - + -
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Residues in contact with ARG 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463D VAL* 3.0 40.9 - - + +
466D ASP* 3.9 14.9 + - - -
467D VAL* 4.2 18.6 - - + +
470D LYS* 4.5 3.6 - - - +
500D GLU* 3.9 28.8 - - - +
503D GLU* 3.1 30.7 + - - -
504D HIS* 3.5 47.2 - - + +
507D TYR* 4.0 16.8 - - - -
539D VAL* 2.8 17.5 + - - +
540D PHE* 3.1 15.2 + - + +
542D CYS* 1.3 69.5 - - - +
544D ILE* 1.3 65.8 + - + +
546D ALA* 2.8 15.6 + - - +
547D LEU* 2.9 18.2 + - + +
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Residues in contact with ILE 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D ILE* 4.7 13.2 - - + -
540D PHE* 3.0 51.5 + - + +
541D CYS* 3.1 5.5 + - - +
543D ARG* 1.3 75.2 - - + +
545D MET* 1.3 67.0 + - - +
547D LEU* 2.8 20.8 + - + +
548D ALA* 2.8 12.8 + - - +
651D SER* 4.0 10.8 - - - +
654D PHE* 3.6 9.2 - - + +
655D MET* 3.3 59.2 - - + +
658D TYR* 4.9 6.1 - - + -
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Residues in contact with MET 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 4.5 9.9 - - + -
541D CYS 2.8 13.2 + - - +
542D CYS* 3.1 16.8 + - - +
544D ILE* 1.3 76.5 - - - +
546D ALA* 1.3 63.4 + - - +
548D ALA* 3.4 2.6 + - - +
549D ALA* 2.8 23.7 + - + +
563D SER* 3.5 48.7 - - - +
566D LEU* 3.7 31.9 - - + -
567D TYR* 4.9 4.5 - - + +
570D PHE* 5.2 0.2 - - - -
595D PHE* 4.2 20.2 - - + -
654D PHE* 3.5 38.7 - - + +
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Residues in contact with ALA 546 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464D ILE* 4.3 13.7 - - + +
467D VAL* 3.3 26.0 - - + -
468D ILE* 3.4 23.7 - - + +
542D CYS 3.0 9.9 + - - +
543D ARG 2.8 10.9 + - - +
545D MET* 1.3 78.3 - - - +
547D LEU* 1.3 64.7 + - - +
549D ALA* 2.8 7.6 + - - +
550D ALA 2.8 20.6 + - - -
563D SER* 4.7 2.7 - - - -
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Residues in contact with LEU 547 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467D VAL* 3.6 28.3 - - + +
471D CYS* 4.1 16.3 - - + -
496D LYS* 3.9 24.2 - - + -
497D ILE* 4.2 27.6 - - + -
500D GLU* 4.2 13.0 - - - +
543D ARG* 2.9 17.5 + - + +
544D ILE* 2.8 21.1 + - + +
546D ALA* 1.3 72.0 - - - +
548D ALA* 1.3 63.4 + - - +
550D ALA* 3.2 3.9 + - - +
551D ALA 2.8 21.1 + - - -
658D TYR* 3.2 30.8 - - + +
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Residues in contact with ALA 548 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544D ILE 2.8 14.9 + - - +
545D MET* 3.5 9.6 - - - +
547D LEU* 1.3 71.9 - - - +
549D ALA* 1.3 65.8 + - - +
550D ALA 2.9 0.5 + - - -
551D ALA* 3.1 0.5 + - - +
552D LEU* 2.8 29.1 + - - +
654D PHE* 3.7 28.0 - - + +
657D LEU* 3.9 16.8 - - + -
658D TYR* 3.5 21.4 - - + +
661D SER* 4.5 0.3 + - - -
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Residues in contact with ALA 549 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 4.5 0.7 - - + -
545D MET* 2.8 20.4 + - + +
546D ALA* 2.8 10.1 + - - +
548D ALA* 1.3 71.6 - - - +
550D ALA* 1.3 56.1 + - - +
552D LEU* 3.8 4.7 - - - +
553D LEU* 3.1 36.2 + - - +
559D ALA* 3.7 4.8 - - - +
562D PHE* 4.0 27.1 - - + -
563D SER* 3.3 25.8 - - - +
657D LEU* 5.0 0.6 - - - +
----------------------------------------------------------
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Residues in contact with ALA 550 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D ILE* 3.4 23.1 - - + -
471D CYS* 4.1 18.4 - - + -
472D TYR* 2.9 42.2 + - + -
546D ALA 2.8 12.0 + - - +
547D LEU 3.6 4.0 - - - +
549D ALA* 1.3 72.5 - - - +
551D ALA* 1.3 65.5 + - - +
552D LEU 3.2 0.4 - - - -
553D LEU 3.3 7.6 - - - +
559D ALA* 3.7 4.5 - - - -
667D GLN* 3.2 6.7 + - - -
----------------------------------------------------------
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Residues in contact with ALA 551 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471D CYS* 4.5 4.0 - - - -
547D LEU 2.8 10.9 + - - +
548D ALA 4.0 0.4 - - - +
550D ALA* 1.3 73.7 - - - +
552D LEU* 1.3 61.0 + - - +
553D LEU 3.8 3.2 - - - +
658D TYR* 3.4 35.2 - - + -
661D SER* 3.9 9.9 - - - +
662D LEU* 3.7 16.8 - - + +
665D ILE* 3.9 7.1 - - - +
666D LYS 3.8 11.4 - - - +
667D GLN* 3.1 22.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 552 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548D ALA 2.8 15.5 + - - +
549D ALA 3.8 2.9 - - - +
551D ALA* 1.3 75.5 - - - +
553D LEU* 1.3 88.2 + - + +
554D PRO* 4.8 0.2 - - - +
562D PHE* 4.9 14.1 - - + -
657D LEU* 3.1 35.9 - - + -
661D SER* 3.2 20.3 - - - +
665D ILE* 4.2 12.3 - - - +
----------------------------------------------------------
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Residues in contact with LEU 553 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472D TYR* 3.0 8.2 + - - +
549D ALA 3.1 18.3 + - - +
550D ALA 3.3 6.4 - - - +
551D ALA 3.8 4.5 - - - +
552D LEU* 1.3 107.6 - - + +
554D PRO* 1.4 68.5 - - + +
558D MET* 3.2 53.6 - - + +
559D ALA* 3.3 13.0 - - + +
561D PHE* 5.7 0.7 - - + -
562D PHE* 3.7 34.3 - - + -
666D LYS 5.6 0.5 - - - +
667D GLN* 4.3 3.5 + - - -
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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