Contacts of the helix formed by residues 531 - 559 (chain F) 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 F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457F ILE* 5.1 6.3 - - - -
458F SER* 5.2 3.4 - - - -
459F PHE* 3.3 19.5 - - - -
465F ASN* 5.1 3.8 - - - -
526F ALA 5.0 0.2 + - - -
528F ALA 2.6 23.9 + - - -
529F ALA* 3.6 10.4 - - - +
530F SER* 1.3 79.1 - - - +
532F GLY* 1.3 59.0 + - - +
533F ALA 3.6 0.9 - - - -
534F ASP* 3.9 11.0 - - - -
535F MET* 2.9 52.3 + - - +
1778F MTE 3.2 1.0 + - - -
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Residues in contact with GLY 532 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492F LEU* 3.8 12.3 - - - -
527F THR* 4.7 7.9 - - - -
528F ALA 4.6 0.4 + - - -
530F SER 3.3 0.8 - - - -
531F SER* 1.3 74.6 + - - +
533F ALA* 1.3 60.5 + - - +
535F MET* 5.8 0.4 - - - -
536F ASN* 2.9 45.9 + - - +
1778F MTE 2.6 22.6 + - - -
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Residues in contact with ALA 533 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492F LEU* 3.5 20.3 - - + +
495F LYS* 4.3 16.8 - - + +
496F MET* 4.1 4.9 - - + +
530F SER 5.0 0.8 + - - +
532F GLY* 1.3 70.6 - - - +
534F ASP* 1.3 71.4 + - - +
537F GLY* 2.8 24.9 + - - -
655F LEU* 4.0 23.8 - - + -
722F ILE* 4.0 4.9 - - - +
727F ALA* 6.4 1.3 - - - -
1778F MTE 3.6 9.0 + - - +
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Residues in contact with ASP 534 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457F ILE* 3.9 5.7 - - + +
530F SER 4.4 0.6 + - - -
531F SER* 3.6 15.6 - - - +
533F ALA* 1.3 83.7 - - - +
535F MET* 1.3 63.1 + - + +
538F MET* 3.4 24.6 + - - +
602F TYR* 4.9 1.6 - - - -
620F LEU* 5.4 1.6 - - - +
621F TYR* 2.7 41.7 + - - -
721F THR* 4.2 12.2 - - - +
722F ILE* 3.8 13.7 + - - +
725F SER* 4.9 5.5 + - - +
726F LYS* 4.0 2.6 - - - -
727F ALA* 3.3 23.8 + - - +
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Residues in contact with MET 535 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459F PHE* 4.0 8.5 - - + -
464F LEU 3.8 9.4 - - - +
465F ASN* 3.5 16.4 - - - +
466F GLN* 3.4 39.5 - - - +
467F ALA* 3.2 21.3 - - + +
525F SER* 5.4 2.0 - - - -
526F ALA 5.7 0.9 - - - +
531F SER* 2.9 41.5 + - - +
534F ASP* 1.3 79.4 - - + +
536F ASN* 1.3 69.1 + - - +
537F GLY 3.4 0.2 - - - -
538F MET* 3.7 4.1 + - - +
539F ALA* 3.3 15.4 + - - +
602F TYR* 3.8 18.5 - - + +
604F THR* 3.6 17.9 - - - +
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Residues in contact with ASN 536 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467F ALA* 3.9 15.9 - - - +
468F GLY 3.5 9.1 - - - +
469F ALA* 5.1 0.2 - - - +
483F HIS* 3.6 10.5 + - + +
484F GLY* 3.2 15.4 + - - -
485F GLY* 3.2 35.1 + - - +
492F LEU* 5.0 0.4 - - + -
496F MET* 3.7 15.7 - - - -
527F THR* 5.4 0.6 + - - -
531F SER 4.8 1.0 + - - -
532F GLY* 2.9 31.4 + - - +
535F MET* 1.3 77.6 - - - +
537F GLY* 1.3 56.1 + - - +
539F ALA* 2.9 5.0 + - - +
540F VAL* 2.7 36.9 + - - +
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Residues in contact with GLY 537 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496F MET* 3.3 23.2 - - - -
499F VAL* 3.6 7.0 - - - +
533F ALA 2.8 18.8 + - - -
536F ASN* 1.3 77.7 - - - +
538F MET* 1.3 49.7 + - - +
540F VAL* 3.3 3.8 + - - +
541F LYS* 2.8 33.8 + - - +
722F ILE* 3.8 14.6 - - - -
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Residues in contact with MET 538 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534F ASP 3.4 17.8 + - - +
535F MET 3.7 3.8 - - - +
536F ASN 3.2 0.6 - - - -
537F GLY* 1.3 75.1 - - - +
539F ALA* 1.3 58.3 + - - +
541F LYS* 3.5 21.6 - - + +
542F ASP* 2.8 27.4 + - - +
602F TYR* 3.4 54.5 - - + +
720F GLU 4.0 14.6 - - - +
721F THR* 5.1 0.9 - - - -
722F ILE* 3.7 40.2 - - + +
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Residues in contact with ALA 539 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467F ALA* 3.7 17.3 - - + +
468F GLY* 3.8 12.3 - - - +
469F ALA* 3.8 3.1 - - - +
535F MET 3.3 10.9 + - - +
536F ASN 2.9 8.3 + - - +
538F MET* 1.3 76.5 - - - +
540F VAL* 1.3 64.9 + - - +
542F ASP* 3.4 6.7 + - - -
543F ALA* 3.1 18.9 + - - +
600F GLY* 3.5 29.3 - - - +
601F PHE 4.2 3.6 - - - -
602F TYR 3.9 5.8 - - - +
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Residues in contact with VAL 540 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F ALA* 3.8 15.5 - - + -
471F VAL* 5.3 0.4 - - + -
481F LEU* 3.8 25.1 - - + -
483F HIS* 4.2 7.9 - - + -
496F MET* 3.9 33.2 - - + +
499F VAL* 4.1 4.3 - - + -
500F ALA* 4.0 23.3 - - + +
536F ASN 2.7 25.9 + - - +
537F GLY* 3.5 6.1 - - - +
539F ALA* 1.3 70.5 - - - +
541F LYS* 1.3 60.0 + - - +
543F ALA* 3.3 4.0 + - - +
544F CYS* 2.9 31.9 + - - +
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Residues in contact with LYS 541 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499F VAL* 4.2 4.5 - - + +
503F VAL* 4.2 17.2 - - + +
537F GLY 2.8 20.5 + - - +
538F MET* 3.5 25.1 - - + +
540F VAL* 1.3 73.4 - - - +
542F ASP* 1.3 62.1 + - - +
544F CYS* 4.3 5.8 - - - -
545F GLU* 2.7 68.8 + - - +
722F ILE* 3.7 23.8 - - + +
723F PHE* 5.4 10.0 - - + +
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Residues in contact with ASP 542 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538F MET 2.8 20.8 + - - +
539F ALA 3.5 7.4 - - - +
540F VAL 3.3 0.2 - - - -
541F LYS* 1.3 76.9 - - - +
543F ALA* 1.3 59.0 + - - +
545F GLU* 4.0 9.1 - - - +
546F THR* 2.9 28.2 + - - -
599F THR 4.7 1.1 - - - +
600F GLY* 3.4 4.5 - - - -
601F PHE* 2.8 36.7 + - - +
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Residues in contact with ALA 543 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469F ALA* 4.6 2.9 - - + +
471F VAL* 3.7 17.5 - - + -
539F ALA 3.1 8.6 + - - +
540F VAL 3.8 0.9 - - - +
542F ASP* 1.3 78.2 - - - +
544F CYS* 1.3 64.1 + - - +
546F THR* 3.0 16.6 + - - -
547F LEU* 3.1 16.5 + - - +
598F ALA* 3.7 19.5 - - - +
599F THR 3.7 5.4 - - - -
600F GLY* 3.5 26.0 - - - +
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Residues in contact with CYS 544 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F VAL* 4.3 13.9 - - - -
500F ALA* 3.7 35.7 - - - -
503F VAL* 3.6 22.4 - - + +
504F LEU* 3.1 32.7 - - + +
540F VAL* 2.9 23.8 + - - +
541F LYS 3.7 0.7 - - - +
543F ALA* 1.3 73.1 - - - +
545F GLU* 1.3 60.6 + - - +
547F LEU* 3.5 5.7 + - - -
548F ARG* 3.0 22.3 + - - +
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Residues in contact with GLU 545 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F VAL* 3.6 8.5 - - + -
541F LYS* 2.7 55.8 + - - +
542F ASP* 4.0 7.2 - - - +
544F CYS* 1.3 73.9 - - - +
546F THR* 1.3 56.2 + - - +
548F ARG* 2.9 39.0 + - - +
549F GLY* 2.6 35.2 + - - -
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Residues in contact with THR 546 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542F ASP* 2.9 18.6 + - - -
543F ALA* 3.0 10.0 + - - -
545F GLU* 1.3 78.1 - - - +
547F LEU* 1.3 57.8 + - - +
549F GLY* 3.4 2.2 + - - +
550F ARG* 3.0 56.6 + - + +
598F ALA* 4.1 9.4 - - + -
599F THR 5.0 2.9 + - - +
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Residues in contact with LEU 547 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471F VAL* 3.8 39.3 - - + +
473F ILE* 3.7 30.1 - - + -
504F LEU* 4.4 4.5 - - + -
543F ALA 3.1 11.8 + - - +
544F CYS* 3.7 9.4 - - - +
545F GLU 3.1 0.4 - - - -
546F THR* 1.3 76.8 - - - +
548F ARG* 1.3 67.8 + - - +
550F ARG* 3.1 31.9 + - - +
551F LEU* 3.0 27.4 + - + +
595F SER 4.4 1.1 - - - +
596F LEU* 3.7 25.6 - - + +
598F ALA* 3.8 11.2 - - + +
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Residues in contact with ARG 548 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503F VAL* 2.8 46.9 + - - +
504F LEU* 4.1 9.7 - - + +
544F CYS 3.0 14.2 + - - +
545F GLU* 2.9 34.7 + - - +
547F LEU* 1.3 73.5 - - - +
549F GLY* 1.3 59.2 + - - +
551F LEU* 3.1 8.1 + - - +
552F ALA* 2.9 32.4 + - - +
566F VAL 5.7 0.4 - - - -
568F PHE* 3.5 42.8 - - + +
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Residues in contact with GLY 549 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545F GLU 2.6 19.1 + - - -
546F THR* 3.7 2.9 - - - -
548F ARG* 1.3 74.2 - - - +
550F ARG* 1.3 60.6 - - - +
552F ALA* 3.8 5.4 - - - +
553F GLY* 3.2 19.8 + - - -
563F ALA* 5.6 1.0 - - - +
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Residues in contact with ARG 550 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546F THR* 3.0 41.6 + - + +
547F LEU* 3.1 20.0 + - + +
549F GLY* 1.3 77.0 - - - +
551F LEU* 1.3 64.2 + - + +
553F GLY* 3.9 1.1 - - - -
554F PHE* 3.0 23.4 + - - +
594F ILE* 3.9 23.4 - - + +
595F SER* 2.7 50.1 + - - +
596F LEU* 6.2 1.3 - - + -
597F SER 3.0 28.5 + - - -
598F ALA* 4.1 4.2 - - - +
599H THR* 4.4 6.1 + - - -
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Residues in contact with LEU 551 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473F ILE* 4.9 9.4 - - + -
504F LEU* 6.0 1.1 - - + -
547F LEU* 3.0 16.6 + - + +
548F ARG* 3.1 8.5 + - - +
550F ARG* 1.3 77.1 - - + +
552F ALA* 1.3 57.5 + - - +
554F PHE* 3.2 7.0 - - - +
555F VAL* 2.9 30.7 + - - +
568F PHE* 3.6 19.3 - - + -
582F PHE* 3.9 35.0 - - + -
585F ILE* 4.4 15.0 - - + +
586F VAL* 4.3 11.7 - - + -
589F ALA* 3.5 30.7 - - + -
594F ILE* 5.9 1.1 - - + -
596F LEU* 4.2 16.4 - - + -
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Residues in contact with ALA 552 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548F ARG* 2.9 16.9 + - - +
549F GLY* 3.8 7.0 - - - +
551F LEU* 1.3 71.8 - - - +
553F GLY* 1.3 55.1 - - - +
555F VAL* 2.8 6.1 + - - +
556F ALA* 2.6 37.3 + - - +
563F ALA* 3.8 27.1 - - + +
566F VAL* 3.7 20.1 - - + +
568F PHE* 3.9 8.2 - - + -
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Residues in contact with GLY 553 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549F GLY 3.2 11.4 + - - -
550F ARG* 3.9 3.1 - - - -
552F ALA* 1.3 76.1 - - - +
554F PHE* 1.3 63.7 + - - +
556F ALA* 3.8 6.0 - - - +
557F ALA* 3.0 27.9 + - - +
563F ALA* 4.2 9.0 - - - +
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Residues in contact with PHE 554 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550F ARG 3.0 10.2 + - - +
551F LEU* 3.2 13.2 - - - +
553F GLY* 1.3 75.3 - - - +
555F VAL* 1.3 79.3 + - + +
557F ALA* 3.9 2.7 - - - +
558F ARG* 3.0 55.8 + - + +
585F ILE* 3.9 11.7 - - + -
588F ALA* 3.5 31.9 - - + -
589F ALA* 3.6 20.2 - - + -
592F ALA* 3.4 23.8 - - + -
594F ILE* 3.3 33.4 - - + +
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Residues in contact with VAL 555 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551F LEU 2.9 18.7 + - - +
552F ALA 2.8 9.3 + - - +
554F PHE* 1.3 78.7 - - + +
556F ALA* 1.3 57.1 + - - +
558F ARG* 3.9 8.3 - - - +
559F GLU* 2.8 43.5 + - + +
561F CYS* 5.3 0.2 - - - -
566F VAL* 4.0 27.8 - - + -
573F VAL* 4.5 1.6 - - + -
575F ALA* 4.3 9.0 - - + -
580F TRP* 4.1 15.5 - - + -
585F ILE* 3.6 35.0 - - + -
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Residues in contact with ALA 556 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552F ALA 2.6 17.5 + - - +
553F GLY* 3.8 4.3 - - - +
555F VAL* 1.3 71.9 - - - +
557F ALA* 1.3 68.5 + - - +
558F ARG 3.0 0.3 + - - -
559F GLU 3.1 0.9 + - - -
560F GLY 2.7 22.0 + - - -
561F CYS* 3.1 37.8 + - - +
562F ALA 3.7 19.5 - - - +
563F ALA* 3.8 9.9 - - + +
566F VAL* 4.6 1.6 - - + -
----------------------------------------------------------
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Residues in contact with ALA 557 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553F GLY 3.0 16.2 + - - +
554F PHE* 3.9 2.9 - - - +
556F ALA* 1.3 76.7 - - - +
558F ARG* 1.3 64.1 + - - +
560F GLY* 3.2 11.8 + - - -
561F CYS 5.2 0.4 - - - +
----------------------------------------------------------
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Residues in contact with ARG 558 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554F PHE* 3.0 44.0 + - + +
555F VAL* 3.7 8.7 - - - +
557F ALA* 1.3 78.5 - - - +
559F GLU* 1.3 89.0 + - - +
560F GLY 3.0 4.7 + - - -
580F TRP* 4.0 22.4 - - - +
584F GLU 5.2 0.8 + - - -
585F ILE* 5.2 8.8 - - - +
588F ALA* 3.6 26.7 - - - +
----------------------------------------------------------
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Residues in contact with GLU 559 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555F VAL* 2.8 29.4 + - + +
556F ALA* 3.2 2.5 - - - -
558F ARG* 1.3 101.6 + - + +
560F GLY* 1.3 67.5 + - - +
561F CYS* 3.3 4.1 + - - -
575F ALA* 5.4 1.6 - - + -
576F SER* 3.4 25.6 + - - +
578F LYS* 2.5 45.3 + - - +
580F TRP* 3.7 28.0 - - + -
----------------------------------------------------------
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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