Contacts of the helix formed by residues 531 - 559 (chain H) in PDB entry 2W3S
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 531 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457H ILE* 4.8 6.3 - - - -
458H SER* 5.1 6.3 - - - -
459H PHE* 3.2 23.4 - - - -
528H ALA 2.9 18.2 + - - -
529H ALA 2.8 12.7 + - - -
530H SER* 1.3 74.4 - - - +
532H GLY* 1.3 60.2 + - - +
533H ALA 3.3 2.9 - - - -
534H ASP* 3.2 9.7 + - - -
535H MET* 2.9 50.4 + - - +
1778H MTE 3.1 2.4 + - - -
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Residues in contact with GLY 532 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492H LEU* 3.5 6.5 - - - +
527H THR* 4.0 18.1 - - - +
528H ALA 4.5 1.6 + - - +
531H SER* 1.3 74.2 + - - +
533H ALA* 1.3 55.0 + - - +
535H MET* 5.5 1.8 - - - -
536H ASN* 2.6 46.8 + - - +
1778H MTE 2.6 21.8 + - - -
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Residues in contact with ALA 533 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492H LEU* 3.5 19.3 - - + +
495H LYS* 4.3 22.2 - - + +
496H MET* 3.9 13.5 - - + +
530H SER 5.6 0.2 - - - -
531H SER 3.3 0.4 - - - -
532H GLY* 1.3 74.7 - - - +
534H ASP* 1.3 67.8 + - - +
535H MET 3.3 0.2 - - - -
537H GLY* 2.9 22.3 + - - -
655H LEU* 4.5 7.4 - - + -
722H ILE* 3.6 6.9 - - - +
727H ALA* 6.3 2.0 - - - -
1778H MTE 3.7 9.6 + - - +
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Residues in contact with ASP 534 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457H ILE* 3.7 9.2 - - - +
530H SER 5.4 0.2 + - - -
531H SER* 3.3 15.6 - - - +
533H ALA* 1.3 80.3 - - - +
535H MET* 1.3 64.8 - - + +
538H MET* 3.5 22.3 + - - +
602H TYR* 5.3 1.3 - - - -
620H LEU* 5.7 1.0 - - - +
621H TYR* 2.8 41.1 + - - -
721H THR* 4.7 9.0 - - - +
722H ILE* 3.6 14.2 + - - +
725H SER* 5.0 4.5 + - - +
726H LYS* 4.1 2.1 - - - -
727H ALA* 3.1 26.4 + - - +
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Residues in contact with MET 535 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458H SER* 5.9 0.7 - - - -
459H PHE* 3.8 15.9 - - + -
464H LEU 3.9 3.4 - - - +
465H ASN* 3.3 37.5 - - - +
466H GLN 3.6 15.3 - - - +
467H ALA* 3.6 20.2 - - + +
525H SER* 5.2 2.7 - - - +
531H SER* 2.9 38.9 + - - +
532H GLY* 5.5 2.2 - - - -
534H ASP* 1.3 80.9 - - + +
536H ASN* 1.3 65.5 + - - +
537H GLY 3.2 1.3 - - - -
538H MET* 3.2 5.0 + - - +
539H ALA 3.1 17.5 + - - -
602H TYR* 3.7 18.8 - - + +
604H THR* 3.6 15.9 - - + +
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Residues in contact with ASN 536 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H ALA* 3.8 15.8 - - - +
468H GLY 3.7 6.1 - - - +
483H HIS* 3.7 14.2 - - + +
484H GLY* 3.3 25.0 + - - -
485H GLY* 3.3 27.5 + - - +
492H LEU* 4.8 0.4 - - - +
496H MET* 3.6 14.8 - - - -
532H GLY* 2.6 36.0 + - - +
535H MET* 1.3 74.0 - - - +
537H GLY* 1.3 57.3 + - - +
539H ALA* 3.0 4.4 + - - +
540H VAL* 2.7 37.4 + - - +
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Residues in contact with GLY 537 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496H MET* 3.4 17.5 - - - -
499H VAL* 3.8 6.4 - - - +
533H ALA 2.9 21.7 + - - -
534H ASP 4.1 0.7 - - - -
536H ASN* 1.3 76.5 - - - +
538H MET* 1.3 56.1 + - - +
540H VAL* 3.3 3.5 + - - +
541H LYS* 2.9 28.4 + - - +
722H ILE* 4.0 18.4 - - - -
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Residues in contact with MET 538 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534H ASP 3.5 15.8 + - - +
535H MET 3.2 2.8 + - - +
536H ASN 3.2 0.8 - - - -
537H GLY* 1.3 74.3 - - - +
539H ALA* 1.3 52.3 + - - +
541H LYS* 3.0 30.7 + - - +
542H ASP* 2.7 36.8 + - - +
602H TYR* 3.2 57.7 - - + +
720H GLU 4.4 10.5 - - - +
721H THR* 4.1 3.6 - - - -
722H ILE* 3.6 37.2 - - + +
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Residues in contact with ALA 539 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467H ALA 3.3 33.9 - - - +
468H GLY* 3.7 8.7 - - - -
469H ALA* 3.5 5.8 - - + +
535H MET 3.1 8.3 + - - +
536H ASN* 3.0 9.4 + - - +
538H MET* 1.3 74.7 - - - +
540H VAL* 1.3 61.5 + - - +
542H ASP* 3.4 0.6 - - - +
543H ALA* 3.2 16.1 + - - +
600H GLY* 3.3 25.4 - - - +
601H PHE 3.8 13.7 - - - +
602H TYR* 3.7 1.2 - - - +
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Residues in contact with VAL 540 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H ALA* 3.8 15.0 - - + -
471H VAL* 4.6 0.8 - - - +
481H LEU* 3.7 25.8 - - + -
483H HIS* 4.4 5.6 - - + -
496H MET* 4.0 24.0 - - + +
499H VAL* 3.8 18.6 - - + -
500H ALA* 3.9 27.1 - - + +
536H ASN 2.7 23.4 + - - +
537H GLY 3.5 3.8 - - - +
539H ALA* 1.3 69.3 - - - +
541H LYS* 1.3 66.1 - - - +
543H ALA* 3.0 5.6 + - - +
544H CYS* 2.9 24.9 + - - +
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Residues in contact with LYS 541 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499H VAL* 4.2 1.3 - - + -
503H VAL* 4.1 17.5 - - + -
537H GLY 2.9 13.8 + - - +
538H MET* 3.5 29.8 + - - +
540H VAL* 1.3 77.3 - - - +
542H ASP* 1.3 61.7 + - - +
544H CYS* 3.4 7.1 + - - +
545H GLU* 2.9 71.7 + - + +
722H ILE* 3.9 24.9 - - + -
723H PHE* 5.2 4.9 - - + -
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Residues in contact with ASP 542 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538H MET 2.7 16.3 + - - +
539H ALA 3.4 5.2 - - - +
540H VAL 3.1 0.2 - - - -
541H LYS* 1.3 83.7 - - - +
543H ALA* 1.3 56.7 + - - +
545H GLU* 3.4 9.2 + - - +
546H THR* 3.0 31.8 + - - -
599H THR 4.2 1.5 - - - +
600H GLY* 2.9 8.2 - - - -
601H PHE* 2.7 37.9 + - - +
----------------------------------------------------------
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Residues in contact with ALA 543 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H ALA 4.5 3.4 - - - +
471H VAL* 3.6 23.6 - - + -
539H ALA 3.2 3.7 + - - +
540H VAL* 3.0 5.4 + - - +
542H ASP* 1.3 79.0 - - - +
544H CYS* 1.3 57.6 + - - +
546H THR* 3.3 6.6 + - - -
547H LEU* 3.0 33.6 + - - +
598H ALA* 3.6 8.4 - - - +
599H THR 3.5 33.0 - - - +
600H GLY* 3.6 4.7 - - - +
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Residues in contact with CYS 544 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471H VAL* 4.2 14.4 - - - -
500H ALA* 3.7 38.1 - - - -
503H VAL* 3.4 25.6 - - + -
504H LEU* 3.4 21.1 - - + +
540H VAL* 2.9 21.6 + - - +
541H LYS* 3.5 1.6 - - - +
543H ALA* 1.3 77.4 - - - +
545H GLU* 1.3 50.3 + - - +
547H LEU* 3.2 7.0 + - - +
548H ARG* 2.6 34.7 + - - +
----------------------------------------------------------
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Residues in contact with GLU 545 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503H VAL* 3.5 13.6 - - + +
541H LYS* 2.9 56.6 + - - +
542H ASP* 3.7 5.8 - - - +
544H CYS* 1.3 69.7 - - - +
546H THR* 1.3 69.2 + - - +
548H ARG* 3.6 32.2 + - - +
549H GLY* 2.6 23.7 + - - -
----------------------------------------------------------
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Residues in contact with THR 546 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542H ASP* 3.0 19.8 + - - -
543H ALA* 3.3 10.5 + - - -
545H GLU* 1.3 76.8 - - - +
547H LEU* 1.3 63.0 + - - +
549H GLY* 3.3 1.8 + - - -
550H ARG* 3.1 50.9 + - + +
598H ALA* 4.1 9.9 - - + -
599H THR 4.4 5.6 + - - +
----------------------------------------------------------
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Residues in contact with LEU 547 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471H VAL* 3.7 37.7 - - + +
473H ILE* 4.0 30.1 - - + -
504H LEU* 4.3 6.3 - - + -
543H ALA 3.0 19.3 + - - +
544H CYS* 3.4 9.0 - - - +
546H THR* 1.3 75.0 - - - +
548H ARG* 1.3 63.9 + - - +
550H ARG* 2.9 44.4 + - - +
551H LEU* 3.0 16.8 + - - +
595H SER 4.1 1.1 - - - +
596H LEU* 3.4 26.7 - - + +
597H SER 3.6 1.3 - - - +
598H ALA* 3.7 7.4 - - + -
----------------------------------------------------------
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Residues in contact with ARG 548 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503H VAL* 3.3 33.1 + - - +
504H LEU* 4.2 7.7 - - + +
544H CYS 2.6 20.0 + - - +
545H GLU* 3.2 34.7 + - - +
547H LEU* 1.3 71.8 - - - +
549H GLY* 1.3 58.6 + - - +
551H LEU* 3.4 7.4 + - - +
552H ALA* 2.8 34.8 + - - +
566H VAL 5.5 2.0 - - - -
568H PHE* 3.6 39.9 - - + +
----------------------------------------------------------
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Residues in contact with GLY 549 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545H GLU 2.6 20.6 + - - -
546H THR 3.6 2.5 - - - -
548H ARG* 1.3 74.6 - - - +
550H ARG* 1.3 56.6 + - - +
552H ALA* 3.1 6.9 + - - +
553H GLY* 2.9 26.2 + - - -
563H ALA* 5.6 0.7 - - - +
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Residues in contact with ARG 550 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599F THR* 4.6 7.7 + - - -
546H THR* 3.1 36.5 + - + +
547H LEU* 2.9 21.4 + - - +
549H GLY* 1.3 71.9 - - - +
551H LEU* 1.3 69.3 + - + +
553H GLY* 3.4 1.7 + - - -
554H PHE* 3.2 23.4 + - - +
594H ILE* 4.0 21.8 - - + +
595H SER* 2.6 48.2 + - - +
596H LEU* 6.1 0.7 - - + -
597H SER 2.6 31.4 + - - -
598H ALA* 4.6 1.0 - - - +
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Residues in contact with LEU 551 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473H ILE* 4.5 8.3 - - + -
504H LEU* 6.2 0.4 - - + -
547H LEU 3.0 15.4 + - - +
548H ARG* 3.8 4.7 - - - +
550H ARG* 1.3 81.1 - - + +
552H ALA* 1.3 63.4 + - - +
554H PHE* 3.2 3.6 + - - +
555H VAL* 3.1 26.3 + - - +
568H PHE* 3.5 24.7 - - + -
582H PHE* 3.9 29.8 - - + -
585H ILE* 4.0 18.4 - - + +
586H VAL* 4.0 16.6 - - + -
589H ALA* 3.6 31.4 - - + -
594H ILE* 5.2 0.9 - - + -
596H LEU* 4.2 15.7 - - + -
----------------------------------------------------------
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Residues in contact with ALA 552 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548H ARG* 2.8 21.6 + - - +
549H GLY* 3.1 6.7 + - - +
551H LEU* 1.3 76.5 - - - +
553H GLY* 1.3 53.1 + - - +
556H ALA* 2.7 38.7 + - - +
563H ALA* 3.9 23.8 - - + +
566H VAL* 3.6 11.0 - - + +
568H PHE* 3.7 18.8 - - + -
----------------------------------------------------------
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Residues in contact with GLY 553 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549H GLY 2.9 15.3 + - - -
550H ARG* 3.9 2.0 - - - -
552H ALA* 1.3 76.2 - - - +
554H PHE* 1.3 55.3 + - - +
556H ALA* 3.4 1.3 - - - +
557H ALA* 2.9 31.5 + - - +
563H ALA* 4.0 15.6 - - - +
----------------------------------------------------------
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Residues in contact with PHE 554 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550H ARG 3.2 12.4 + - - +
551H LEU* 3.2 4.7 + - - +
553H GLY* 1.3 72.6 - - - +
555H VAL* 1.3 83.1 + - + +
557H ALA* 3.5 4.0 + - - +
558H ARG* 2.9 54.3 + - + +
585H ILE* 4.0 6.5 - - + -
588H ALA* 3.5 38.4 - - + -
589H ALA* 3.7 15.3 - - + -
592H ALA* 3.3 23.6 - - + -
594H ILE* 3.4 35.4 - - + +
----------------------------------------------------------
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Residues in contact with VAL 555 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551H LEU 3.1 14.1 + - - +
552H ALA 3.8 2.2 - - - +
554H PHE* 1.3 83.7 - - + +
556H ALA* 1.3 56.3 + - - +
558H ARG* 3.5 6.5 - - - +
559H GLU* 2.7 44.2 + - + +
566H VAL* 3.6 22.9 - - + -
573H VAL* 4.3 8.1 - - + -
575H ALA* 3.6 20.9 - - + -
580H TRP* 4.8 4.3 - - + -
585H ILE* 3.6 48.0 - - + -
----------------------------------------------------------
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Residues in contact with ALA 556 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552H ALA 2.7 23.0 + - - +
553H GLY 3.4 4.7 - - - +
555H VAL* 1.3 73.5 - - - +
557H ALA* 1.3 51.3 + - - +
559H GLU* 3.3 2.8 - - - -
560H GLY 2.8 29.1 + - - -
561H CYS* 3.0 33.5 + - - +
562H ALA 4.0 0.9 - - - -
563H ALA* 3.3 27.1 - - + +
566H VAL* 4.0 7.2 - - + +
----------------------------------------------------------
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Residues in contact with ALA 557 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553H GLY 2.9 20.3 + - - +
554H PHE* 3.7 4.9 - - + +
556H ALA* 1.3 68.0 - - - +
558H ARG* 1.3 55.0 + - - +
559H GLU 2.6 5.3 + - - -
560H GLY* 2.6 28.9 + - - -
561H CYS 5.2 0.2 - - - +
----------------------------------------------------------
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Residues in contact with ARG 558 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554H PHE* 2.9 41.8 + - + +
555H VAL* 3.5 5.9 - - - +
557H ALA* 1.3 74.0 - - - +
559H GLU* 1.3 97.6 + - - +
560H GLY 3.6 0.4 + - - -
580H TRP* 3.7 25.4 - - - +
584H GLU 5.1 1.0 + - - -
585H ILE* 3.7 26.8 - - - +
588H ALA* 4.1 18.2 - - - +
----------------------------------------------------------
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Residues in contact with GLU 559 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555H VAL* 2.7 29.6 + - + +
556H ALA* 3.3 2.5 - - - +
557H ALA 2.6 4.2 + - - -
558H ARG* 1.3 112.9 + - - +
560H GLY* 1.3 67.5 + - - +
561H CYS* 4.1 1.3 - - - -
575H ALA* 4.6 6.3 - - + -
576H SER* 3.2 24.5 + - - +
578H LYS* 2.9 31.2 + - - +
580H TRP* 3.6 17.3 - - + -
----------------------------------------------------------
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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