Contacts of the helix formed by residues 491 - 516 (chain A) in PDB entry 4DAJ
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 THR 491 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A LEU* 4.5 14.5 - - + +
165A ARG* 5.7 0.2 - - - -
489A ALA 3.6 1.4 + - - -
490A GLN* 1.3 89.3 + - - +
492A LEU* 1.3 62.3 + - - +
493A SER* 3.2 4.8 + - - +
494A ALA* 3.3 3.3 + - - +
495A ILE* 3.0 40.6 + - + +
542A CYS 4.4 2.5 - - - +
543A TYR* 4.3 15.9 - - + -
546A CYS* 3.1 42.0 - - + +
547A ASN* 3.2 5.2 + - - -
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Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.3 6.3 - - + +
161A ILE* 3.4 33.2 - - + -
162A SER* 3.8 28.3 - - - +
165A ARG* 4.2 14.8 - - - +
250A TYR* 4.0 26.9 - - + -
253A ILE* 4.9 14.4 - - + -
489A ALA* 3.9 15.9 - - - +
490A GLN 2.9 7.0 + - - +
491A THR* 1.3 74.7 - - - +
493A SER* 1.3 68.2 + - - +
495A ILE* 4.7 7.6 - - + -
496A LEU* 2.9 32.2 + - + +
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Residues in contact with SER 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A TYR* 2.8 32.3 + - - -
254A TYR* 4.9 4.7 - - - -
489A ALA 3.9 9.2 + - - -
491A THR 5.0 2.2 + - - -
492A LEU* 1.3 80.1 - - - +
494A ALA* 1.3 65.1 + - - +
496A LEU* 3.5 3.1 - - - +
497A LEU* 2.9 34.2 + - - +
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Residues in contact with ALA 494 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491A THR* 3.3 8.7 + - - +
492A LEU 3.3 0.4 - - - -
493A SER* 1.3 81.2 - - - +
495A ILE* 1.3 65.3 + - - +
497A LEU* 3.1 6.2 + - - +
498A ALA* 2.9 24.3 + - - +
542A CYS* 3.7 28.0 - - + -
546A CYS* 3.7 20.4 - - - -
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Residues in contact with ILE 495 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A LEU* 5.1 4.7 - - + -
109A LEU* 4.2 7.0 - - + -
158A LEU* 3.4 36.3 - - + -
161A ILE* 6.5 0.2 - - + -
491A THR* 3.0 25.2 + - + +
492A LEU* 4.2 7.4 - - + +
494A ALA* 1.3 75.0 - - - +
496A LEU* 1.3 64.0 + - - +
498A ALA* 3.4 3.6 + - - +
499A PHE* 2.9 22.0 + - - +
539A ASN* 3.7 25.5 - - + +
542A CYS* 3.6 22.9 - - + -
543A TYR* 3.6 29.4 - - + -
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Residues in contact with LEU 496 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.2 2.9 - - + -
243A VAL* 5.7 2.0 - - + +
246A MET* 4.2 42.0 - - + +
247A THR* 5.1 12.1 - - + +
250A TYR* 4.5 31.2 - - + -
492A LEU* 2.9 25.1 + - + +
493A SER* 3.5 3.4 - - - +
495A ILE* 1.3 77.8 - - - +
497A LEU* 1.3 66.8 + - + +
499A PHE* 3.0 12.2 + - + +
500A ILE* 2.9 36.7 + - + +
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Residues in contact with LEU 497 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493A SER* 2.9 24.8 + - - +
494A ALA* 3.5 5.8 - - - +
496A LEU* 1.3 79.0 - - + +
498A ALA* 1.3 64.9 + - - +
500A ILE* 3.2 15.6 - - + +
501A ILE* 2.9 33.3 + - + +
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Residues in contact with ALA 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A ALA 2.9 16.3 + - - +
495A ILE 3.6 3.8 - - - +
497A LEU* 1.3 75.0 - - - +
499A PHE* 1.3 65.6 + - - +
501A ILE* 3.1 10.1 - - - +
502A THR* 3.0 29.6 + - + +
535A ASN* 3.9 10.3 - - - +
538A VAL* 4.2 27.4 - - + -
539A ASN* 4.5 4.7 - - - +
542A CYS* 4.3 7.6 - - - -
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Residues in contact with PHE 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154A SER* 5.5 2.9 - - - -
155A VAL* 3.8 22.4 - - + -
158A LEU* 3.8 26.2 - - + -
239A PHE* 3.9 12.1 - + - -
243A VAL* 3.4 27.1 - - + -
246A MET* 3.8 14.8 - - + -
495A ILE* 2.9 14.0 + - + +
496A LEU* 3.3 11.7 - - + +
498A ALA* 1.3 77.6 - - - +
500A ILE* 1.3 76.9 + - + +
502A THR* 3.1 2.4 + - - -
503A TRP* 2.9 78.8 + + - +
535A ASN* 3.3 19.0 - - - +
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Residues in contact with ILE 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 5.0 1.3 - - + -
243A VAL* 3.7 28.5 - - + -
247A THR* 5.1 6.3 - - - +
496A LEU* 2.9 27.6 + - + +
497A LEU* 3.2 28.9 - - + +
499A PHE* 1.3 82.2 - - + +
501A ILE* 1.3 71.9 + - + +
503A TRP* 4.9 0.7 - - - -
504A THR* 2.6 58.5 + - + +
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Residues in contact with ILE 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A LEU* 2.9 28.3 + - + +
498A ALA* 3.1 16.4 - - - +
500A ILE* 1.3 85.3 - - + +
502A THR* 1.3 64.0 + - + +
504A THR* 4.0 4.9 - - - -
505A PRO* 3.3 21.3 - - + +
531A LEU* 4.7 2.8 - - - +
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Residues in contact with THR 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A ALA* 3.0 24.3 + - + +
499A PHE 3.2 0.2 + - - -
501A ILE* 1.3 83.8 - - + +
503A TRP* 1.3 66.9 + - - +
505A PRO* 4.0 3.9 - - - +
506A TYR* 5.2 0.2 - - - +
528A GLY 4.2 0.2 - - - +
531A LEU* 3.2 38.8 - - + +
532A CYS* 3.4 12.0 + - - -
534A ILE* 3.6 30.3 - - + +
535A ASN* 3.0 29.3 - - - +
538A VAL* 5.6 2.2 - - + -
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Residues in contact with TRP 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ILE* 6.4 0.4 - - + -
151A SER* 3.7 31.2 - - - -
154A SER* 5.0 4.9 - - - -
155A VAL* 3.5 29.4 - - + -
239A PHE* 3.3 25.4 - + + -
499A PHE* 2.9 43.2 + + + +
502A THR* 1.3 94.9 - - - +
504A THR* 1.3 55.5 + - - +
505A PRO* 3.2 3.1 - - - -
506A TYR* 2.7 31.7 + - - +
507A ASN* 3.0 12.3 + - - +
532A CYS* 3.6 28.3 + - - -
535A ASN* 3.7 14.9 - - - +
2000A 0HK 3.1 53.6 - - + +
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Residues in contact with THR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A PHE* 3.3 31.2 - - + -
240A TYR* 5.6 2.7 - - + -
243A VAL* 5.7 0.7 - - + -
500A ILE* 2.6 44.7 + - + +
501A ILE* 4.0 3.5 - - - -
503A TRP* 1.3 68.5 - - - +
505A PRO* 1.3 74.7 - - - +
507A ASN* 4.2 2.5 - - - +
508A ILE* 2.8 42.1 + - + +
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Residues in contact with PRO 505 (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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501A ILE* 3.3 23.6 - - + +
502A THR 4.6 0.7 - - - +
503A TRP 3.3 5.6 - - - +
504A THR* 1.3 98.8 - - - +
506A TYR* 1.3 57.3 + - + +
508A ILE* 3.7 6.9 - - + +
509A MET* 2.9 30.9 + - + +
528A GLY* 5.3 4.0 - - - -
531A LEU* 3.8 26.0 - - + -
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Residues in contact with TYR 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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148A TYR* 4.3 3.3 + - - -
502A THR 5.2 0.2 - - - +
503A TRP 2.7 15.2 + - - +
505A PRO* 1.3 73.6 - - - +
507A ASN* 1.3 64.7 + - - +
509A MET* 3.1 19.2 + - + +
510A VAL* 2.9 46.4 + - + +
525A TRP* 4.1 22.0 - + + -
528A GLY* 3.9 6.5 - - - +
529A TYR* 3.5 49.9 - + - -
532A CYS* 3.9 18.6 - - - -
2000A 0HK 3.6 46.3 - - + +
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Residues in contact with ASN 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A ALA* 3.6 13.9 - - - +
239A PHE* 3.1 56.5 - - + +
240A TYR* 2.6 32.5 + - + +
503A TRP* 3.0 15.0 + - - +
504A THR 3.4 3.8 + - - +
506A TYR* 1.3 80.7 - - - +
508A ILE* 1.3 55.1 + - - +
510A VAL* 3.3 6.9 + - - +
511A LEU* 2.9 22.7 + - - +
2000A 0HK 3.3 29.8 + - - +
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Residues in contact with ILE 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A TYR* 3.6 12.1 - - + +
504A THR* 2.8 36.0 + - + +
505A PRO* 3.7 6.3 - - + +
507A ASN* 1.3 73.9 - - - +
509A MET* 1.3 61.3 + - - +
511A LEU* 3.7 13.6 - - + +
512A VAL* 2.8 45.1 + - + +
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Residues in contact with MET 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A PRO 2.9 15.0 + - - +
506A TYR* 3.3 26.9 - - + +
508A ILE* 1.3 78.4 - - - +
510A VAL* 1.3 55.3 + - - +
512A VAL* 3.5 8.5 - - - +
513A ASN* 2.9 27.2 + - - +
520A ILE* 3.8 26.9 - - + +
524A TYR* 3.3 50.0 - - - +
525A TRP* 3.7 25.5 - - + -
528A GLY* 4.2 6.1 - - - -
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Residues in contact with VAL 510 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 4.9 1.8 - - - +
231A THR* 3.6 33.4 - - + +
232A PHE* 4.2 17.0 - - + +
235A ALA* 4.4 9.4 - - + -
506A TYR* 2.9 46.2 + - + +
507A ASN* 3.4 9.4 - - - +
508A ILE 3.2 0.2 - - - -
509A MET* 1.3 72.2 - - - +
511A LEU* 1.3 67.6 + - - +
512A VAL 3.0 1.3 - - - -
513A ASN* 3.0 3.9 + - - +
514A THR* 2.9 24.2 + - - +
525A TRP* 3.8 17.7 - - + -
2000A 0HK 5.0 2.0 - - + -
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Residues in contact with LEU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 3.6 42.3 - - + -
240A TYR* 4.0 14.8 - - + +
507A ASN 2.9 16.7 + - - +
508A ILE* 3.7 16.4 - - + +
510A VAL* 1.3 74.8 - - - +
512A VAL* 1.3 66.7 + - + +
514A THR* 3.1 17.8 - - - -
515A PHE* 3.8 17.5 - - + -
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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
----------------------------------------------------------
508A ILE* 2.8 39.2 + - + +
509A MET* 3.5 7.9 - - - +
511A LEU* 1.3 76.3 - - + +
513A ASN* 1.3 58.1 + - - +
514A THR 2.9 4.5 - - - -
515A PHE* 2.8 25.5 + - - +
516A CYS* 3.4 25.8 + - - -
519A CYS* 5.3 0.7 - - + -
520A ILE* 4.2 18.6 - - + -
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Residues in contact with ASN 513 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 3.3 24.6 - - - +
509A MET 2.9 18.8 + - - +
510A VAL* 3.0 5.6 + - + +
512A VAL* 1.3 76.7 - - - +
514A THR* 1.3 63.5 + - - +
515A PHE 3.2 0.6 + - - -
516A CYS 3.5 19.0 + - - +
517A ASP* 3.7 23.0 + - - +
520A ILE* 4.5 11.8 + - + +
525A TRP* 3.7 31.4 - - + +
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Residues in contact with THR 514 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A PRO* 3.5 20.7 + - - +
229A THR* 4.6 19.1 - - + +
232A PHE* 3.2 40.7 - - + +
510A VAL 2.9 15.8 + - - -
511A LEU 3.1 13.7 + - - -
513A ASN* 1.3 80.0 + - - +
515A PHE* 1.3 80.3 + - + +
516A CYS 5.4 0.2 - - - -
517A ASP* 5.6 0.7 - - - +
248B ILE* 4.9 8.7 - - + -
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Residues in contact with PHE 515 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A PHE* 5.5 1.6 - + - -
511A LEU* 3.8 23.6 - - + -
512A VAL* 2.8 14.4 + - - +
514A THR* 1.3 93.7 - - + +
516A CYS* 1.3 59.1 + - - +
517A ASP* 4.4 4.1 - - - +
248B ILE* 4.0 37.7 - - + -
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Residues in contact with CYS 516 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
512A VAL* 3.4 18.9 + - - -
513A ASN* 3.5 15.6 + - - +
515A PHE* 1.3 80.6 - - - +
517A ASP* 1.3 64.6 + - - +
518A SER 3.5 0.4 - - - +
519A CYS* 2.0 68.7 - - + +
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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