Contacts of the helix formed by residues 521 - 546 (chain D) in PDB entry 6T8B
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 MET 521 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617C GLN* 3.4 26.7 - - - +
618C LYS* 5.7 2.7 - - - +
499D PRO* 4.1 9.4 - - + -
520D ASP* 1.3 76.9 - - - +
522D LYS* 1.3 64.9 + - - +
523D GLU 3.4 1.1 + - - -
524D ALA* 3.6 13.3 + - - +
525D ALA* 4.3 2.3 + - - +
599D ASP* 3.3 27.4 - - + +
600D MET* 3.5 33.0 - - - +
603D ILE* 3.6 30.5 - - + -
604D VAL* 3.8 20.6 - - + +
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Residues in contact with LYS 522 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520D ASP* 4.0 7.5 - - + +
521D MET* 1.3 80.7 - - - +
523D GLU* 1.3 59.9 + - - +
524D ALA 3.6 0.2 + - - -
525D ALA* 4.1 8.5 + - - +
526D ASN* 3.1 22.8 + - - +
604D VAL* 5.7 2.0 - - - -
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Residues in contact with GLU 523 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515D CYS* 6.1 0.2 - - - +
518D VAL* 3.1 32.9 - - - +
520D ASP* 3.3 20.8 + - - +
521D MET 3.4 0.2 - - - -
522D LYS* 1.3 78.0 - - + +
524D ALA* 1.3 59.7 + - - +
525D ALA 3.4 0.7 - - - -
526D ASN* 3.2 14.8 + - + +
527D ALA* 2.9 35.5 + - - +
720D ILE* 5.0 0.7 - - - +
721D LEU* 3.1 53.7 + - + +
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Residues in contact with ALA 524 (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 24.5 - - + +
499D PRO* 6.2 0.2 - - + -
518D VAL* 4.0 9.0 - - - -
520D ASP* 3.9 13.8 + - - +
521D MET* 3.6 13.9 + - - +
522D LYS 3.4 1.0 - - - -
523D GLU* 1.3 78.0 - - - +
525D ALA* 1.3 63.5 + - - +
527D ALA* 3.3 3.5 + - - +
528D LEU* 3.0 28.9 + - - +
600D MET* 3.8 22.2 - - + -
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Residues in contact with ALA 525 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521D MET 4.3 3.9 + - - +
522D LYS 4.1 8.3 + - - +
523D GLU 3.4 0.2 - - - -
524D ALA* 1.3 79.0 - - - +
526D ASN* 1.3 56.4 + - - +
528D LEU* 4.4 9.2 - - - +
529D ARG* 2.9 56.7 + - - +
600D MET* 5.8 0.2 - - - +
604D VAL* 5.3 8.7 - - + -
607D LYS* 5.0 13.2 - - + -
608D VAL* 5.1 10.0 - - + +
611D LEU* 3.5 7.4 - - + +
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Residues in contact with ASN 526 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522D LYS* 3.1 30.2 + - - +
523D GLU* 3.2 23.7 + - + +
524D ALA 3.1 0.8 - - - -
525D ALA* 1.3 75.6 - - - +
527D ALA* 1.3 59.8 + - - +
529D ARG* 3.2 25.6 + - - +
530D TRP* 2.9 26.5 + - - +
720D ILE 4.0 7.8 - - - +
721D LEU 5.0 6.7 + - - +
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Residues in contact with ALA 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D ILE* 5.0 9.5 - - + +
497D ILE* 4.3 16.6 - - + -
518D VAL* 4.5 9.0 - - + -
523D GLU* 2.9 30.6 + - - +
524D ALA* 3.7 3.8 - - - +
526D ASN* 1.3 75.8 - - - +
528D LEU* 1.3 58.8 + - - +
530D TRP* 3.3 8.2 + - - +
531D SER* 2.9 25.8 + - - -
720D ILE* 4.1 19.5 - - + +
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Residues in contact with LEU 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D ILE* 4.3 9.0 - - + -
524D ALA 3.0 22.9 + - - +
525D ALA* 3.7 1.1 - - - +
527D ALA* 1.3 75.0 - - - +
529D ARG* 1.3 59.3 + - - +
531D SER* 2.4 32.0 + - - +
532D VAL* 2.9 18.2 + - - +
592D VAL* 4.0 27.4 - - + -
594D VAL* 5.3 1.8 - - + -
600D MET* 3.9 16.2 - - + -
608D VAL* 3.5 33.2 - - + -
611D LEU* 3.6 20.2 - - + -
612D ILE* 4.3 17.3 - - + -
615D ILE* 5.1 4.9 - - + -
626D LEU* 5.0 3.8 - - + -
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Residues in contact with ARG 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525D ALA* 2.9 48.8 + - - +
526D ASN* 3.2 25.6 + - - +
528D LEU* 1.3 75.4 - - - +
530D TRP* 1.3 63.8 + - - +
532D VAL* 3.2 8.8 + - - +
533D ALA* 2.9 22.0 + - - +
607D LYS* 4.0 37.2 - - - +
611D LEU* 3.5 24.2 - - + +
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Residues in contact with TRP 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D ILE* 4.0 22.2 - - + -
514D LEU* 4.3 15.7 - - + -
526D ASN 2.9 7.9 + - - +
527D ALA 3.5 7.4 - - - +
529D ARG* 1.3 78.1 - - - +
531D SER* 1.3 62.3 + - - +
533D ALA* 3.2 11.7 + - + +
534D GLU* 2.9 59.2 + - + +
537D ARG* 6.1 1.0 - - - +
590D ILE* 4.6 5.4 - - + -
717D ILE* 5.0 9.4 - - + -
719D ASP* 4.0 27.9 + - - +
720D ILE* 3.6 61.7 - - + +
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Residues in contact with SER 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495D ILE* 5.1 4.0 - - - -
527D ALA 2.9 12.4 + - - -
528D LEU* 2.4 37.2 + - - +
530D TRP* 1.3 82.4 - - - +
532D VAL* 1.3 58.0 + - - +
534D GLU* 3.3 4.7 + - - +
535D MET 2.9 24.1 + - - -
590D ILE* 6.1 0.9 - - - -
592D VAL* 4.7 18.8 - - - -
615D ILE* 3.2 19.2 - - - +
624D ILE* 3.4 18.5 - - - +
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Residues in contact with VAL 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528D LEU 2.9 22.0 + - - +
529D ARG* 3.4 10.5 - - - +
531D SER* 1.3 76.8 + - - +
533D ALA* 1.3 57.0 + - - +
535D MET* 3.2 15.7 + - + +
536D GLU* 2.9 36.3 + - + +
611D LEU* 4.4 15.3 - - + +
614D ARG* 3.3 37.5 - - - +
615D ILE* 3.5 26.9 - - + +
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Residues in contact with ALA 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529D ARG 2.9 12.5 + - - +
530D TRP* 3.2 17.0 + - + +
532D VAL* 1.3 77.1 - - - +
534D GLU* 1.3 57.5 + - - +
536D GLU* 3.2 9.3 + - - +
537D ARG* 2.9 32.1 + - - +
540D ARG* 5.0 0.3 + - - -
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Residues in contact with GLU 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D TRP* 2.9 44.6 + - + +
531D SER* 3.6 8.7 - - - +
533D ALA* 1.3 73.6 - - - +
535D MET* 1.3 60.6 + - - +
537D ARG* 2.6 45.3 + - - +
538D ARG* 2.8 59.5 + - - +
587D LEU* 5.6 0.5 - - - +
590D ILE* 3.8 25.1 - - + -
624D ILE* 4.6 2.0 - - + -
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Residues in contact with MET 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531D SER 2.9 6.8 + - - +
532D VAL* 3.3 21.5 - - + +
534D GLU* 1.3 76.6 - - - +
536D GLU* 1.3 78.9 + - - +
538D ARG* 3.2 7.5 + - - +
539D TYR* 2.9 52.0 + - + -
614D ARG* 3.2 32.8 - - + +
615D ILE* 4.3 3.6 - - - +
618D LYS* 3.7 13.7 - - - -
619D ALA* 3.6 33.4 - - + -
622D ALA* 4.2 2.7 - - + -
624D ILE* 3.5 23.2 - - + +
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Residues in contact with GLU 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532D VAL* 2.9 25.7 + - + +
533D ALA* 3.2 10.1 + - - +
535D MET* 1.3 89.6 - - - +
537D ARG* 1.3 58.5 + - - +
539D TYR* 3.2 8.7 + - - +
540D ARG* 2.9 58.0 + - - +
614D ARG* 4.0 14.9 + - - +
618D LYS* 3.2 28.6 + - - -
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Residues in contact with ARG 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D TRP* 6.1 1.1 - - - +
533D ALA 2.9 14.4 + - - +
534D GLU* 2.6 62.7 + - - +
536D GLU* 1.3 76.7 - - - +
538D ARG* 1.3 57.5 + - - +
540D ARG* 3.7 16.3 - - - +
541D LEU* 2.9 40.4 + - - +
587D LEU* 5.3 10.3 - - - +
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Residues in contact with ARG 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534D GLU* 2.8 49.0 + - - +
535D MET 3.5 4.9 - - - +
537D ARG* 1.3 76.0 - - - +
539D TYR* 1.3 62.3 + - - +
541D LEU* 4.4 5.6 - - - +
542D MET* 3.1 35.8 + - + +
550D LEU* 3.6 11.9 - - - +
587D LEU* 3.2 47.6 - - + +
588D PRO* 3.7 18.4 + - - +
590D ILE* 3.6 23.7 - - - +
622D ALA* 3.1 38.1 - - + +
623D GLY* 4.0 4.5 - - - +
624D ILE* 4.2 9.3 - - - +
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Residues in contact with TYR 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535D MET* 2.9 41.3 + - + -
536D GLU* 3.6 9.0 - - - +
538D ARG* 1.3 77.8 - - - +
540D ARG* 1.3 62.1 + - + +
541D LEU 3.3 0.2 - - - -
542D MET* 3.3 14.3 + - + +
543D ALA* 2.9 29.4 + - - +
548D ARG 5.7 2.2 - - - -
618D LYS* 3.1 29.1 - - + +
619D ALA* 2.8 26.3 + - - -
620D ARG* 3.8 3.1 + - - +
621D ALA* 4.0 8.2 + - + +
622D ALA* 3.4 29.7 + - + -
501E MET* 3.9 33.3 - - + +
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Residues in contact with ARG 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533D ALA 5.0 0.2 + - - -
536D GLU* 2.9 62.8 + - - +
537D ARG* 3.3 12.9 + - - +
539D TYR* 1.3 76.6 - - + +
541D LEU* 1.3 58.5 + - - +
543D ALA* 3.3 6.1 + - - +
544D ALA* 2.9 30.9 + - - +
570D PRO 6.0 0.4 - - - -
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Residues in contact with LEU 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537D ARG* 2.9 27.7 + - - +
538D ARG* 4.4 4.9 - - - +
539D TYR 3.3 0.2 - - - -
540D ARG* 1.3 74.5 - - - +
542D MET* 1.3 59.7 + - - +
544D ALA* 3.4 2.3 + - - -
545D MET* 2.9 48.0 + - + +
553D PHE* 3.5 31.4 - - + -
568D THR 5.7 0.4 - - - +
569D ASP* 5.0 8.3 - - + -
570D PRO* 4.3 28.7 - - + +
587D LEU* 4.1 20.0 - - + -
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Residues in contact with MET 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538D ARG* 3.1 21.9 + - + +
539D TYR* 3.3 17.6 + - + +
541D LEU* 1.3 77.4 - - + +
543D ALA* 1.3 52.9 + - - +
545D MET 3.2 0.3 + - - -
546D GLY 2.6 31.2 + - - -
547D VAL* 2.9 24.6 + - + +
548D ARG* 4.0 6.7 - - - +
549D ASN* 3.9 17.0 - - - -
550D LEU* 3.5 34.3 - - + +
553D PHE* 4.4 24.5 - - + -
587D LEU* 5.4 1.1 - - + -
621D ALA 3.5 5.8 - - - +
622D ALA* 3.3 32.8 - - - +
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Residues in contact with ALA 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539D TYR 2.9 17.1 + - - +
540D ARG* 3.6 7.9 - - - +
541D LEU 3.2 0.2 - - - -
542D MET* 1.3 76.4 - - - +
544D ALA* 1.3 62.9 + - - +
546D GLY* 3.2 14.2 + - - -
547D VAL 4.6 1.8 - - - -
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Residues in contact with ALA 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540D ARG 2.9 17.6 + - - +
541D LEU* 3.9 4.9 - - - +
543D ALA* 1.3 76.5 - - - +
545D MET* 1.3 63.4 + - - +
570D PRO* 3.7 36.4 - - + +
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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
----------------------------------------------------------
541D LEU* 2.9 29.5 + - + +
542D MET 3.8 2.0 - - - +
544D ALA* 1.3 83.0 - - + +
546D GLY* 1.3 56.2 + - - +
547D VAL* 3.6 7.3 + - + +
553D PHE* 3.4 31.6 - - + -
556D LYS* 3.5 45.7 - - + -
557D VAL* 5.2 3.1 - - + -
567D LEU* 3.6 37.2 - - + -
568D THR 4.7 2.7 - - - +
570D PRO* 4.6 17.5 - - - -
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Residues in contact with GLY 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542D MET 2.6 12.1 + - - -
543D ALA* 3.2 11.8 + - - -
545D MET* 1.3 73.8 - - - +
547D VAL* 1.3 65.7 + - - +
548D ARG* 5.0 1.9 - - - +
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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