Contacts of the helix formed by residues 531 - 560 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 5.2 1.8 - - - -
458B SER* 5.1 7.9 - - - -
459B PHE* 3.0 21.8 - - - -
526B ALA 4.9 1.2 + - - -
528B ALA 2.6 23.8 + - - -
529B ALA* 2.7 9.4 + - - -
530B SER* 1.3 75.6 - - - +
532B GLY* 1.3 67.2 + - - +
533B ALA 3.5 1.6 - - - -
534B ASP* 3.1 9.9 + - - +
535B MET* 2.9 48.0 + - - +
1778B MTE 3.3 0.2 + - - -
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Residues in contact with GLY 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 4.0 6.1 - - - -
527B THR* 4.3 13.2 - - - +
528B ALA 4.4 0.8 + - - +
531B SER* 1.3 78.7 + - - +
533B ALA* 1.3 56.7 + - - +
535B MET* 5.9 0.7 - - - -
536B ASN* 2.9 47.2 + - - +
1778B MTE 2.7 20.4 + - - -
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Residues in contact with ALA 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 3.6 24.2 - - + +
495B LYS* 4.3 22.4 - - + +
496B MET* 3.9 11.5 - - + +
530B SER 5.3 0.2 + - - -
531B SER 3.5 0.2 - - - -
532B GLY* 1.3 70.6 - - - +
534B ASP* 1.3 68.5 + - - +
537B GLY* 2.9 21.7 + - - -
655B LEU* 4.6 6.7 - - + -
722B ILE* 3.6 7.1 - - - +
727B ALA* 6.4 1.8 - - - -
1778B MTE 3.8 11.7 + - - +
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Residues in contact with ASP 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ILE* 3.6 9.9 - - - +
530B SER 4.4 1.9 + - - -
531B SER* 3.1 13.8 + - - +
533B ALA* 1.3 82.3 - - - +
535B MET* 1.3 63.5 + - + +
538B MET* 3.3 27.8 + - - +
602B TYR* 5.1 1.6 - - + -
620B LEU* 5.8 0.2 - - - +
621B TYR* 2.5 38.5 + - - -
721B THR* 4.8 9.6 - - - +
722B ILE* 3.7 15.7 + - - +
725B SER* 4.8 2.9 + - - -
726B LYS* 4.2 2.9 - - - -
727B ALA* 3.6 20.6 + - - -
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Residues in contact with MET 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B SER* 6.0 0.2 - - - -
459B PHE* 3.7 7.0 - - + -
464B LEU 3.6 14.6 - - - +
465B ASN* 3.3 33.4 - - - +
466B GLN 3.5 18.4 - - - +
467B ALA* 3.4 23.0 - - + +
525B SER* 4.8 2.9 - - - +
526B ALA 5.8 0.4 - - - +
531B SER* 2.9 40.1 + - - +
532B GLY* 4.6 0.9 - - - +
534B ASP* 1.3 75.9 - - + +
536B ASN* 1.3 63.7 + - - +
538B MET* 3.1 4.3 + - - +
539B ALA* 2.8 23.2 + - - +
602B TYR* 3.7 17.8 - - + +
604B THR* 3.4 17.3 - - + +
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Residues in contact with ASN 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ALA* 3.7 15.8 - - - +
468B GLY 3.4 11.1 + - - +
483B HIS* 3.5 15.4 - - + +
484B GLY* 3.1 25.2 + - - -
485B GLY* 3.3 28.6 + - - +
492B LEU* 4.9 0.4 - - + -
496B MET* 3.5 10.1 - - + -
532B GLY* 2.9 30.4 + - - +
535B MET* 1.3 74.7 - - - +
537B GLY* 1.3 57.6 - - - +
539B ALA* 3.0 3.5 + - - +
540B VAL* 2.7 38.1 + - - +
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Residues in contact with GLY 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B MET* 3.2 22.0 - - - -
499B VAL* 3.8 5.5 - - - +
533B ALA 2.9 22.5 + - - -
534B ASP 4.0 0.4 - - - -
536B ASN* 1.3 74.1 - - - +
538B MET* 1.3 60.4 + - - +
540B VAL* 3.9 0.4 - - - +
541B LYS* 3.1 25.1 + - - +
722B ILE* 3.4 19.1 - - - +
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Residues in contact with MET 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ASP 3.3 16.0 + - - +
535B MET 3.1 4.2 + - - +
537B GLY* 1.3 74.4 - - - +
539B ALA* 1.3 57.7 + - - +
541B LYS* 3.4 26.5 + - + +
542B ASP* 2.9 29.6 + - - +
602B TYR* 3.2 54.7 - - + -
720B GLU* 4.3 13.7 - - + +
721B THR* 4.3 2.0 - - - -
722B ILE* 3.8 37.2 - - + +
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Residues in contact with ALA 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B ALA 3.5 26.5 - - - +
468B GLY 3.6 22.2 - - - -
469B ALA* 3.6 5.2 - - + +
535B MET 2.8 15.2 + - - +
536B ASN* 3.5 9.9 - - - +
538B MET* 1.3 72.7 - - - +
540B VAL* 1.3 61.7 + - - +
542B ASP* 3.3 8.2 + - - -
543B ALA 3.3 10.0 + - - -
600B GLY* 3.4 14.7 - - - +
601B PHE 4.1 11.4 - - - +
602B TYR* 3.8 0.8 - - - +
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Residues in contact with VAL 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ALA* 3.6 19.1 - - + -
471B VAL* 4.4 0.6 - - - +
481B LEU* 3.8 23.1 - - + -
483B HIS* 4.2 10.1 - - + -
496B MET* 3.9 25.8 - - + +
499B VAL* 4.1 4.7 - - + -
500B ALA* 3.7 34.8 - - + +
536B ASN 2.7 22.8 + - - +
537B GLY 3.9 3.1 - - - +
539B ALA* 1.3 68.7 - - - +
541B LYS* 1.3 60.2 - - - +
542B ASP 3.3 0.2 + - - -
543B ALA* 3.3 3.7 + - - +
544B CYS* 2.9 29.4 + - - -
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499B VAL* 3.8 17.3 - - + -
503B VAL* 4.1 12.5 - - + +
537B GLY 3.1 14.2 + - - +
538B MET* 3.7 27.2 - - + +
540B VAL* 1.3 80.5 - - - +
542B ASP* 1.3 57.3 + - - +
544B CYS* 3.7 6.7 - - - +
545B GLU* 2.9 66.2 + - - +
722B ILE* 3.7 18.2 - - + -
723B PHE* 5.1 7.9 - - + +
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Residues in contact with ASP 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B MET 2.9 16.9 + - - +
539B ALA 3.5 5.8 - - - +
540B VAL 3.1 0.4 - - - -
541B LYS* 1.3 77.0 - - - +
543B ALA* 1.3 63.0 + - - +
545B GLU* 3.6 10.0 + - - +
546B THR* 3.1 26.1 + - - -
599B THR 4.1 2.1 - - - +
600B GLY* 3.1 9.4 - - - -
601B PHE* 3.0 34.7 + - - +
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Residues in contact with ALA 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ALA* 4.5 2.9 - - + +
471B VAL* 3.6 24.5 - - + -
539B ALA 3.3 5.2 + - - +
540B VAL 3.3 3.6 + - - +
542B ASP* 1.3 75.8 + - - +
544B CYS* 1.3 61.1 + - - +
546B THR* 3.1 5.0 + - - -
547B LEU* 2.8 28.9 + - - +
598B ALA* 3.7 15.3 - - + +
599B THR 3.6 32.1 - - - +
600B GLY* 3.7 4.9 - - - +
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Residues in contact with CYS 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 4.2 14.4 - - - -
500B ALA* 3.6 36.8 - - - -
503B VAL* 3.6 23.3 - - + -
504B LEU* 3.8 18.4 - - + +
540B VAL* 2.9 22.1 + - - +
541B LYS* 3.7 3.8 - - - +
543B ALA* 1.3 74.6 - - - +
545B GLU* 1.3 60.1 + - - +
547B LEU* 3.2 7.7 + - - +
548B ARG* 2.8 28.6 + - - +
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Residues in contact with GLU 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503B VAL* 3.6 18.8 - - + +
541B LYS* 2.9 60.0 + - - +
542B ASP* 4.0 8.6 - - - +
544B CYS* 1.3 71.5 - - - +
546B THR* 1.3 61.1 + - - +
548B ARG* 3.6 22.0 + - - +
549B GLY* 2.7 30.5 + - - -
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Residues in contact with THR 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B ASP* 3.1 18.9 + - - -
543B ALA* 3.1 10.7 + - - -
545B GLU* 1.3 78.2 - - - +
547B LEU* 1.3 63.5 + - - +
549B GLY* 3.3 1.5 + - - -
550B ARG* 3.1 50.5 + - + +
598B ALA* 3.9 11.4 - - + -
599B THR 4.7 4.0 + - - +
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Residues in contact with LEU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B VAL* 3.6 45.5 - - + +
473B ILE* 4.0 27.1 - - + -
504B LEU* 4.3 5.6 - - + -
543B ALA 2.8 13.9 + - - +
544B CYS* 3.6 7.4 - - - +
546B THR* 1.3 76.1 - - - +
548B ARG* 1.3 62.6 + - - +
550B ARG* 3.1 30.9 + - + +
551B LEU* 3.2 17.7 + - - +
595B SER 4.1 1.3 - - - +
596B LEU* 3.5 36.8 - - + +
597B SER 3.7 6.5 - - - +
598B ALA* 3.6 8.7 - - + -
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Residues in contact with ARG 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502B ALA 5.3 0.4 + - - -
503B VAL* 3.1 45.0 + - - +
504B LEU* 4.2 11.7 - - + +
544B CYS 2.8 20.1 + - - +
545B GLU* 3.7 23.2 + - - +
547B LEU* 1.3 69.5 - - - +
549B GLY* 1.3 66.9 + - - +
551B LEU* 3.0 8.1 + - - +
552B ALA* 2.8 26.6 + - - +
566B VAL 5.7 1.1 - - - -
568B PHE* 3.6 42.4 - - + +
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Residues in contact with GLY 549 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B GLU 2.7 20.3 + - - -
546B THR 3.7 2.0 - - - -
548B ARG* 1.3 74.4 - - - +
550B ARG* 1.3 61.1 + - - +
552B ALA* 3.5 6.3 + - - +
553B GLY* 3.1 20.6 + - - -
563B ALA* 5.3 0.9 - - - +
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Residues in contact with ARG 550 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B THR* 3.1 35.2 + - + +
547B LEU* 3.1 18.8 + - + +
549B GLY* 1.3 76.9 - - - +
551B LEU* 1.3 63.3 + - + +
553B GLY* 4.0 1.3 - - - -
554B PHE* 3.1 23.6 + - - +
594B ILE* 4.2 20.3 - - + +
595B SER* 2.6 51.0 + - - +
596B LEU* 6.2 0.4 - - + -
597B SER 2.6 32.3 + - - -
598B ALA* 4.3 2.8 - - - +
599D THR* 4.6 6.9 + - - -
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Residues in contact with LEU 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ILE* 4.7 9.0 - - + -
504B LEU* 5.6 0.7 - - + -
547B LEU 3.2 13.9 + - - +
548B ARG* 3.0 5.4 + - - +
550B ARG* 1.3 75.8 - - + +
552B ALA* 1.3 65.6 + - - +
554B PHE* 3.4 3.8 + - - +
555B VAL* 3.0 29.5 + - - +
568B PHE* 3.5 24.7 - - + -
582B PHE* 3.9 29.6 - - + -
585B ILE* 4.4 13.5 - - + -
586B VAL* 4.2 15.5 - - + -
589B ALA* 3.7 28.3 - - + -
594B ILE* 4.9 1.6 - - + -
596B LEU* 4.0 17.5 - - + -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ARG* 2.8 18.4 + - - +
549B GLY* 3.9 6.1 - - - +
551B LEU* 1.3 76.8 - - - +
553B GLY* 1.3 55.0 + - - +
554B PHE 3.2 0.3 + - - -
555B VAL 3.2 0.9 + - - -
556B ALA* 2.7 37.1 + - - +
563B ALA* 3.5 32.1 - - + +
566B VAL* 3.7 17.5 - - + +
568B PHE* 4.0 9.8 - - + -
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Residues in contact with GLY 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLY 3.1 13.8 + - - -
550B ARG 4.0 1.6 - - - -
552B ALA* 1.3 78.6 - - - +
554B PHE* 1.3 60.0 + - - +
556B ALA* 4.0 2.2 - - - +
557B ALA* 3.4 21.8 + - - +
563B ALA* 4.0 13.0 - - - -
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Residues in contact with PHE 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B ARG 3.1 13.0 + - - +
551B LEU* 3.6 4.5 - - - +
552B ALA 3.1 0.6 - - - -
553B GLY* 1.3 75.2 - - - +
555B VAL* 1.3 80.7 + - + +
557B ALA* 3.4 6.1 + - - +
558B ARG* 3.1 44.7 + - + +
585B ILE* 4.0 7.2 - - + -
588B ALA* 3.6 32.5 - - + -
589B ALA* 3.6 21.5 - - + -
592B ALA* 3.4 23.6 - - + -
594B ILE* 3.3 35.7 - - + -
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Residues in contact with VAL 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B LEU* 3.0 21.1 + - + +
552B ALA 3.7 3.1 - - - +
554B PHE* 1.3 79.5 - - + +
556B ALA* 1.3 57.9 + - - +
558B ARG* 2.9 7.1 + - - +
559B GLU* 2.7 42.7 + - + +
566B VAL* 3.7 15.0 - - + -
573B VAL* 4.7 2.5 - - + -
575B ALA* 3.5 32.3 - - + -
580B TRP* 4.6 7.2 - - + -
585B ILE* 3.6 37.7 - - + -
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Residues in contact with ALA 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552B ALA 2.7 21.2 + - - +
553B GLY* 4.1 4.9 - - - +
555B VAL* 1.3 73.4 - - - +
557B ALA* 1.3 53.0 + - - +
560B GLY* 2.7 30.7 + - - -
561B CYS* 2.9 43.4 + - - +
562B ALA 3.8 2.0 - - - +
563B ALA* 3.7 22.7 - - + +
566B VAL* 4.1 2.4 - - + +
----------------------------------------------------------
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Residues in contact with ALA 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B GLY 3.4 15.7 + - - +
554B PHE* 3.4 5.8 + - - +
555B VAL 3.2 0.8 - - - -
556B ALA* 1.3 80.3 - - - +
558B ARG* 1.3 61.6 + - - +
560B GLY* 4.0 5.6 + - - -
561B CYS 5.2 0.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B PHE* 3.1 35.3 + - + +
555B VAL* 2.9 10.0 + - - +
557B ALA* 1.3 77.9 - - - +
559B GLU* 1.3 91.5 + - - +
560B GLY 3.3 1.6 + - - -
580B TRP* 3.4 31.3 - - - +
585B ILE* 4.2 12.1 - - - +
588B ALA* 4.1 19.8 - - - +
----------------------------------------------------------
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Residues in contact with GLU 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B VAL* 2.7 26.4 + - + +
556B ALA 3.5 0.7 - - - +
558B ARG* 1.3 115.9 + - - +
560B GLY* 1.3 67.0 + - - +
561B CYS* 4.9 2.0 - - - -
575B ALA* 4.4 6.3 - - + -
576B SER* 2.8 29.8 + - - +
578B LYS* 2.9 35.4 + - - +
580B TRP* 3.6 25.0 - - + -
----------------------------------------------------------
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Residues in contact with GLY 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556B ALA 2.7 7.2 + - - -
557B ALA* 4.0 4.8 + - - -
558B ARG 3.3 5.1 + - - -
559B GLU* 1.3 83.2 - - - +
561B CYS* 1.3 69.3 + - - +
576B SER* 3.8 2.6 + - - -
----------------------------------------------------------
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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