Contacts of the helix formed by residues 500 - 523 (chain A) in PDB entry 2IUK
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 VAL 500 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A GLY* 1.3 70.9 - - - -
501A ASP* 1.3 63.5 + - - +
502A SER 3.2 2.5 - - - -
503A THR* 2.9 24.3 + - - +
504A ILE* 3.0 14.9 + - + +
749A TYR* 3.9 23.1 - - + +
752A MET* 3.5 27.8 - - + -
753A VAL* 3.7 38.8 - - + +
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Residues in contact with ASP 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 5.3 0.7 - - - +
494A LEU 4.5 4.6 - - - +
496A ALA* 3.4 22.9 - - + +
498A GLU 4.6 6.5 - - - +
499A GLY 3.4 0.2 - - - -
500A VAL* 1.3 81.1 - - - +
502A SER* 1.3 55.5 + - - +
503A THR 3.3 0.2 - - - -
504A ILE* 3.9 17.3 - - - +
505A TRP* 3.1 21.3 + - - +
749A TYR* 5.4 1.9 + - - -
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Residues in contact with SER 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365A MET* 5.9 1.2 - - - +
496A ALA* 3.2 32.5 - - - +
497A THR 3.7 19.3 + - - -
498A GLU 4.2 1.1 + - - -
499A GLY 2.8 23.4 + - - -
501A ASP* 1.3 76.3 - - - +
503A THR* 1.3 59.6 + - - +
505A TRP* 3.7 4.8 - - - +
506A LEU* 3.1 25.5 + - - +
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Residues in contact with THR 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
499A GLY 3.4 12.6 + - - -
500A VAL* 2.9 13.3 + - - -
502A SER* 1.3 79.2 + - - +
504A ILE* 1.3 60.2 + - - +
505A TRP 3.2 0.2 - - - -
506A LEU* 3.5 11.8 + - + +
507A LEU* 3.0 38.3 + - + +
752A MET* 3.6 29.9 + - + +
756A PRO* 3.5 39.9 - - + +
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Residues in contact with ILE 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A VAL* 3.5 24.0 - - + +
500A VAL* 3.0 10.4 + - + +
501A ASP* 4.1 18.4 - - - +
503A THR* 1.3 77.3 - - - +
505A TRP* 1.3 61.3 + - - +
507A LEU* 3.5 7.6 + - - +
508A ALA* 3.1 20.8 + - - +
741A ILE* 3.9 27.2 - - + +
742A PRO 5.5 0.2 - - - +
749A TYR* 4.2 19.7 - - + +
752A MET* 3.6 29.2 - - + -
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Residues in contact with TRP 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A ASP* 3.2 43.1 - - - -
471A PRO* 3.2 31.9 - - + -
473A ALA* 4.1 2.5 - - - -
474A ILE* 3.6 32.9 - - + +
493A VAL* 2.7 40.2 + - + +
494A LEU 3.1 18.8 - - - +
495A PRO* 3.7 30.1 - - + -
496A ALA 4.5 7.4 - - - +
501A ASP 3.1 16.9 + - - +
502A SER* 3.9 7.6 - - - +
503A THR 3.2 0.4 - - - -
504A ILE* 1.3 75.3 - - - +
506A LEU* 1.3 60.5 + - - +
508A ALA* 2.9 3.9 + - + +
509A LYS* 2.9 49.6 + - + +
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Residues in contact with LEU 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A PHE* 4.8 9.9 - - + -
364A VAL 4.0 17.0 - - - +
365A MET* 4.0 30.7 - - + -
502A SER 3.1 17.2 + - - +
503A THR* 3.8 13.7 - - + +
504A ILE 3.3 0.2 - - - -
505A TRP* 1.3 79.9 - - - +
507A LEU* 1.3 56.2 + - + +
509A LYS* 3.7 30.3 + - + +
510A ALA* 3.0 26.3 + - - +
756A PRO* 5.6 3.6 - - + +
760A TYR* 3.7 31.4 - - + +
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Residues in contact with LEU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A THR* 3.0 29.4 + - + +
504A ILE* 3.9 4.5 - - - +
505A TRP 3.2 0.2 - - - -
506A LEU* 1.3 77.8 - - + +
508A ALA* 1.3 54.9 + - - +
510A ALA* 3.6 6.7 - - + +
511A HIS* 3.2 31.9 + - - -
739A ARG* 3.4 19.1 - - - +
741A ILE* 3.7 15.9 - - + -
742A PRO* 4.1 3.6 - - + -
752A MET* 3.5 32.5 - - + -
756A PRO 5.5 1.1 - - - +
759A ALA* 3.5 11.4 - - + +
760A TYR* 3.8 21.3 - - + -
763A THR* 3.3 27.6 - - - +
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Residues in contact with ALA 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A ILE* 3.8 21.6 - - + +
476A LEU* 4.3 12.1 - - + +
493A VAL* 3.9 27.4 - - + -
504A ILE 3.1 13.7 + - - +
505A TRP* 2.9 11.0 + - + +
507A LEU* 1.3 71.1 - - - +
509A LYS* 1.3 66.7 + - - +
510A ALA 3.2 1.1 - - - -
511A HIS* 3.1 4.7 + - - +
512A VAL* 3.0 26.2 + - - +
741A ILE* 4.2 0.9 - - - +
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Residues in contact with LYS 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A VAL 5.9 0.2 - - - -
365A MET* 2.8 31.9 + - - +
366A THR 4.5 0.2 - - - -
367A ASP* 3.2 15.8 + - - +
370A PHE* 4.0 35.4 - - + -
474A ILE* 3.5 21.5 - - + +
505A TRP* 2.9 41.8 + - + +
506A LEU* 3.8 24.4 - - + +
508A ALA* 1.3 74.7 - - - +
510A ALA* 1.3 61.1 + - - +
512A VAL* 3.4 4.6 - - - +
513A ILE* 3.1 29.8 + - + +
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Residues in contact with ALA 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
506A LEU 3.0 18.9 + - - +
507A LEU* 3.6 9.9 - - - +
509A LYS* 1.3 75.7 - - - +
511A HIS* 1.3 61.0 + - - +
513A ILE* 3.4 2.3 + - - -
514A VAL* 3.1 27.5 + - - +
734A PRO* 3.8 10.7 - - + +
760A TYR* 3.8 26.2 - - + +
763A THR* 5.2 5.6 - - + -
764A ILE* 4.3 14.8 - - + -
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Residues in contact with HIS 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453A LYS 3.7 9.6 - - - -
454A ALA* 4.8 0.2 - - - +
455A TYR* 3.5 36.5 + + + +
457A THR* 4.0 5.2 - - + -
476A LEU* 3.8 17.9 - - + -
507A LEU 3.2 21.6 + - - -
508A ALA 3.1 8.7 + - - +
510A ALA* 1.3 74.1 - - - +
512A VAL* 1.3 65.4 + - - +
514A VAL* 3.0 19.9 + - - +
515A ASN* 3.3 12.1 + - - -
737A ALA* 3.5 32.0 - - + +
739A ARG* 3.2 27.0 + - - -
740A PHE* 4.6 2.2 - - - -
741A ILE* 4.5 7.9 - - + -
763A THR* 3.5 13.7 - - + +
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Residues in contact with VAL 512 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 3.9 17.5 - - + -
433A LEU* 4.0 18.8 - - + +
435A TYR* 4.4 1.5 - - + -
457A THR* 3.5 22.7 + - - +
459A THR* 3.3 21.1 - - - +
474A ILE* 3.3 32.3 - - + -
508A ALA 3.0 16.4 + - - +
509A LYS* 3.4 8.7 - - - +
511A HIS* 1.3 74.4 - - - +
513A ILE* 1.3 58.2 + - + +
515A ASN* 3.5 5.9 - - - +
516A ASP* 3.1 23.2 + - - +
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Residues in contact with ILE 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370A PHE* 3.6 34.1 - - + +
374A VAL* 6.0 2.9 - - + -
433A LEU* 5.5 2.7 - - + -
509A LYS* 3.1 18.3 + - + +
510A ALA* 3.8 4.7 - - - +
512A VAL* 1.3 76.7 - - + +
514A VAL* 1.3 59.9 + - - +
516A ASP* 3.8 16.6 - - + -
517A SER* 2.8 31.4 + - - -
732A ASN 3.6 24.2 - - - +
733A ARG* 3.6 34.5 - - - +
734A PRO* 3.1 9.4 - - + +
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Residues in contact with VAL 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ALA* 5.3 0.2 - - + -
510A ALA 3.1 17.9 - - - +
511A HIS 3.0 9.5 + - - +
513A ILE* 1.3 74.2 - - - +
515A ASN* 1.4 64.8 + - - +
517A SER* 3.5 2.1 + - - -
518A GLY* 3.0 20.4 + - - -
584A LEU* 3.7 22.6 - - + +
734A PRO* 3.6 22.2 - - + +
735A THR 3.5 20.0 - - - +
736A LEU 3.8 16.4 - - - +
737A ALA* 3.6 32.1 - - + +
764A ILE* 5.4 2.5 - - + -
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Residues in contact with ASN 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A TYR* 3.6 17.7 - - + +
439A PHE* 3.5 35.3 - - + -
454A ALA* 5.2 0.4 - - - +
455A TYR 2.8 23.3 + - - +
456A ALA* 3.7 1.4 - - - -
457A THR* 2.8 38.8 + - - +
511A HIS* 3.3 9.8 + - - -
512A VAL 3.5 7.2 - - - +
514A VAL* 1.4 73.5 - - - +
516A ASP* 1.4 52.2 + - - +
518A GLY* 3.1 3.3 + - - -
519A TYR* 2.8 34.1 + - - +
584A LEU* 4.4 8.1 - - - +
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Residues in contact with ASP 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A VAL* 5.6 1.9 - - - +
379A ASN* 3.3 19.7 + - - +
433A LEU* 3.6 18.0 - - + +
435A TYR* 3.1 32.8 + - + -
512A VAL 3.1 13.6 + - - +
513A ILE* 3.8 18.3 - - + +
515A ASN* 1.4 74.9 - - - +
517A SER* 1.3 59.7 + - - +
519A TYR* 3.8 0.5 - - - +
520A HIS* 2.8 26.9 + - - +
733A ARG* 2.6 27.6 + - - +
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Residues in contact with SER 517 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
513A ILE* 2.8 24.6 + - - +
514A VAL 3.8 2.5 - - - -
516A ASP* 1.3 73.0 - - - +
518A GLY* 1.3 64.7 + - - +
520A HIS* 4.0 3.6 + - - +
521A GLN* 3.2 24.9 + - - +
583A PHE* 3.6 18.6 - - - -
733A ARG* 3.0 33.2 + - - +
734A PRO 3.1 17.1 + - - -
735A THR* 4.4 6.2 - - - +
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Residues in contact with GLY 518 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A PHE* 4.9 4.7 - - - -
514A VAL 3.0 14.4 + - - -
515A ASN 3.1 4.7 + - - -
517A SER* 1.3 75.5 - - - +
519A TYR* 1.3 62.6 + - - +
521A GLN* 3.8 0.5 - - - +
522A LEU* 3.1 41.6 + - - +
583A PHE* 4.2 15.5 - - - -
584A LEU* 5.5 1.1 - - - -
585A PRO* 4.9 7.4 - - - -
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Residues in contact with TYR 519 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A ASN* 4.1 1.3 - - - -
382A VAL* 3.6 29.0 - - + +
435A TYR* 3.6 40.6 - + + +
438A ALA* 4.4 20.0 - - + -
439A PHE* 4.6 7.6 - + + -
515A ASN 2.8 15.8 + - - +
516A ASP 3.8 0.7 - - - +
518A GLY* 1.3 73.0 - - - +
520A HIS* 1.3 58.8 + - - +
522A LEU* 5.0 0.9 - - - -
523A VAL* 2.7 70.1 + - + +
524A SER* 3.1 13.8 + - - -
592A MET* 5.9 4.5 - - - -
596A VAL* 4.4 12.7 - - + +
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Residues in contact with HIS 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A VAL* 3.2 32.6 + - + +
379A ASN* 3.6 24.9 - - + -
516A ASP 2.8 22.9 + - - +
517A SER* 4.0 6.8 + - - +
519A TYR* 1.3 72.3 - - - +
521A GLN* 1.3 63.7 + - - +
524A SER* 3.2 15.8 + - - -
525A HIS* 2.7 38.2 + - + +
719A VAL* 2.8 34.3 + - + +
723A GLN* 3.9 26.2 + - + -
733A ARG* 4.5 6.3 + - - +
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Residues in contact with GLN 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A SER 3.2 16.2 + - - +
518A GLY 3.8 2.9 - - - +
520A HIS* 1.3 82.7 + - - +
522A LEU* 1.3 55.8 + - + +
525A HIS* 3.6 21.2 + - - +
526A TRP* 2.7 39.3 + - + +
573A ILE* 6.4 0.2 - - + -
579A ILE* 3.8 34.3 - - + +
583A PHE* 3.6 34.6 - - + -
723A GLN* 2.9 28.9 + - - +
777A ILE* 4.8 4.2 - - - +
780A LEU* 4.6 6.1 - - - +
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Residues in contact with LEU 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A GLY* 3.1 24.6 + - - +
519A TYR* 5.1 0.4 - - - -
521A GLN* 1.3 75.8 - - + +
523A VAL* 1.3 64.8 + - + +
526A TRP* 3.6 8.6 - - + +
527A LEU* 3.1 25.3 + - - +
573A ILE* 5.5 1.1 - - + -
579A ILE* 3.7 21.8 - - + -
583A PHE* 5.5 2.7 - - + -
585A PRO* 4.1 25.1 - - + -
589A SER* 3.5 41.5 - - - +
590A ILE* 4.0 9.2 - - + -
592A MET* 4.5 11.9 - - + -
593A SER* 3.6 18.7 - - - +
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Residues in contact with VAL 523 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A TYR* 2.7 55.1 + - + +
521A GLN 3.5 0.2 - - - -
522A LEU* 1.3 83.3 - - + +
524A SER* 1.3 65.8 + - - +
525A HIS 3.2 1.1 - - - -
527A LEU* 4.1 5.4 - - + -
528A ASN* 3.0 48.2 + - - +
592A MET* 5.6 3.4 - - + -
593A SER* 4.8 4.7 - - - -
596A VAL* 3.5 39.3 - - + -
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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