Contacts of the helix formed by residues 486 - 513 (chain B) in PDB entry 1IW1
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 486 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU* 1.3 77.1 - - - +
487B ASP* 1.3 66.1 + - - +
488B GLU* 3.6 13.6 + - - +
489B GLN* 2.9 38.9 + - - +
490B ARG* 2.9 22.1 + - - +
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Residues in contact with ASP 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B LEU 5.4 0.2 - - - +
486B SER* 1.3 73.3 - - - +
488B GLU* 1.3 72.5 + - - +
490B ARG* 3.3 5.7 + - - +
491B GLU* 3.0 24.8 + - - +
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Residues in contact with GLU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B SER* 3.2 12.7 + - - +
487B ASP* 1.3 86.6 + - - +
489B GLN* 1.3 63.8 + - + +
491B GLU* 3.4 7.7 + - - +
492B HIS* 3.0 25.1 + - - +
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Residues in contact with GLN 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B PHE* 4.3 12.5 - - - -
423B PRO* 3.8 34.5 - - + +
484B GLU 4.1 3.1 + - - +
485B LEU* 3.4 17.1 - - + +
486B SER* 2.9 44.8 + - - +
488B GLU* 1.3 79.1 - - + +
490B ARG* 1.3 57.5 + - - +
492B HIS* 3.3 6.2 + - - +
493B LEU* 2.9 29.5 + - - +
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Residues in contact with ARG 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLY* 3.7 17.0 + - - +
308B LEU* 3.8 35.4 - - + +
311B GLU* 3.6 29.5 + - - +
485B LEU* 4.3 17.6 - - + +
486B SER 2.9 16.2 + - - +
487B ASP* 3.8 6.3 - - - +
489B GLN* 1.3 75.7 - - - +
491B GLU* 1.3 58.9 + - - +
493B LEU* 3.2 7.0 + - - +
494B LEU* 2.9 47.9 + - + +
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Residues in contact with GLU 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B ASP 3.0 17.4 + - - +
488B GLU* 3.8 7.4 - - - +
490B ARG* 1.3 76.6 - - - +
492B HIS* 1.3 62.7 + - - +
494B LEU* 3.4 8.3 + - - +
495B LYS* 2.9 60.1 + - + +
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Residues in contact with HIS 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 4.1 15.7 - - - -
421B ASP* 2.7 39.7 + - - -
423B PRO* 4.4 6.3 - - + -
424B ALA* 3.9 12.3 - - + +
488B GLU 3.0 17.9 + - - +
489B GLN* 3.6 5.4 - - - +
491B GLU* 1.3 78.1 - - - +
493B LEU* 1.3 61.4 + - - +
495B LYS* 3.4 9.2 + - - +
496B GLU* 2.9 30.5 + - - +
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Residues in contact with LEU 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 4.0 14.8 - - + -
312B LEU* 3.9 32.5 - - + -
423B PRO* 3.3 35.9 - - + +
426B VAL* 3.9 22.0 - - + -
427B ALA* 3.4 13.5 - - + +
483B LEU* 5.2 0.9 - - + -
485B LEU* 3.9 25.8 - - + -
489B GLN 2.9 16.6 + - - +
490B ARG* 3.5 6.3 - - - +
492B HIS* 1.3 76.4 - - - +
494B LEU* 1.3 63.3 + - - +
496B GLU* 3.2 3.0 + - - -
497B ALA* 3.0 18.9 + - - +
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Residues in contact with LEU 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 4.2 7.6 - - + -
311B GLU* 3.6 38.1 - - + +
312B LEU* 3.8 29.2 - - + +
315B SER* 3.9 18.0 + - - +
490B ARG* 2.9 39.2 + - + +
491B GLU* 3.9 7.0 - - - +
493B LEU* 1.3 75.5 - - - +
495B LYS* 1.3 62.8 + - + +
497B ALA* 3.3 12.6 + - - +
498B THR* 3.3 14.6 + - - -
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Residues in contact with LYS 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491B GLU* 2.9 57.3 + - + +
492B HIS* 3.8 8.7 - - - +
494B LEU* 1.3 75.0 - - + +
496B GLU* 1.3 63.5 + - - +
498B THR* 3.1 9.7 + - - -
499B ASP* 3.0 27.9 + - - +
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Residues in contact with GLU 496 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B ARG* 2.8 47.3 + - - +
424B ALA* 3.7 20.6 - - + +
427B ALA* 3.7 5.6 - - + -
428B HIS* 2.8 38.4 + - + +
492B HIS* 2.9 23.0 + - - +
493B LEU 3.2 4.5 + - - +
495B LYS* 1.3 78.0 - - - +
497B ALA* 1.3 57.7 + - - +
499B ASP* 3.1 19.2 + - - +
500B ALA* 2.8 28.1 + - - +
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Residues in contact with ALA 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B LEU* 3.6 31.6 - - + -
316B THR* 3.9 13.7 - - + -
427B ALA* 3.6 12.1 - - + +
431B VAL* 3.8 14.0 - - + +
493B LEU 3.0 10.6 + - - +
494B LEU* 3.7 7.6 - - + +
495B LYS 3.2 0.2 - - - -
496B GLU* 1.3 74.9 - - - +
498B THR* 1.3 62.4 + - - +
500B ALA* 3.2 4.0 + - - +
501B PHE* 3.1 27.5 + - - -
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Residues in contact with THR 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315B SER* 3.9 19.6 + - - -
316B THR* 4.2 9.2 - - - +
319B ALA* 5.3 8.0 - - + +
494B LEU 3.3 8.1 + - - -
495B LYS* 3.1 10.8 + - - -
497B ALA* 1.3 79.0 - - - +
499B ASP* 1.3 65.8 + - - +
501B PHE* 3.2 7.8 + - - +
502B VAL* 3.1 30.6 + - + +
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Residues in contact with ASP 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B LYS* 3.0 22.3 + - - +
496B GLU* 3.1 24.2 + - - +
498B THR* 1.3 80.2 - - - +
500B ALA* 1.3 61.8 + - - +
502B VAL* 3.2 9.8 + - - +
503B PHE* 3.0 41.1 + - + -
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Residues in contact with ALA 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B TYR* 5.2 0.7 - - - +
428B HIS* 3.5 35.6 - - + +
431B VAL* 3.9 22.7 - - + -
496B GLU 2.8 19.4 + - - +
497B ALA* 3.5 7.0 - - - +
498B THR 3.2 0.2 - - - -
499B ASP* 1.3 74.0 - - - +
501B PHE* 1.3 61.0 + - - +
503B PHE* 3.3 5.1 + - - +
504B ASN* 2.9 32.5 + - - +
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Residues in contact with PHE 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316B THR* 3.5 32.5 - - + -
319B ALA* 3.6 25.3 - - + +
320B HIS* 3.6 43.5 - + + -
323B ALA* 4.7 5.8 - - + +
430B TYR* 4.6 3.6 - + - -
431B VAL* 3.8 20.0 - - + -
497B ALA 3.1 20.7 + - - -
498B THR 3.2 4.9 + - - +
500B ALA* 1.3 76.7 - - - +
502B VAL* 1.3 56.2 + - - +
504B ASN* 3.2 4.6 + - - +
505B HIS* 2.9 30.0 + - - +
902B HEM 3.5 49.4 - + + -
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Residues in contact with VAL 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA* 5.6 4.7 - - + -
498B THR* 3.1 25.8 + - + +
499B ASP* 3.5 11.9 - - - +
501B PHE* 1.3 74.1 - - + +
503B PHE* 1.3 67.7 + - + +
505B HIS* 3.2 7.2 + - - +
506B GLN* 2.9 48.7 + - + +
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Residues in contact with PHE 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ALA* 4.3 2.6 - - - +
408B ASP* 3.8 25.1 - - + -
409B TYR* 3.7 42.0 - + + -
412B ARG* 3.8 39.0 - - + -
428B HIS* 4.2 5.8 - + - -
499B ASP* 3.0 37.0 + - + -
500B ALA* 3.6 10.1 - - - +
502B VAL* 1.3 77.6 - - + +
504B ASN* 1.3 57.6 + - - +
506B GLN* 3.2 22.1 + - - +
507B VAL* 3.0 31.3 + - - +
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Residues in contact with ASN 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B PHE* 3.9 5.7 - - - -
409B TYR* 3.0 33.6 + - - -
431B VAL* 4.0 8.7 - - - +
432B ARG* 2.9 35.9 + - - +
500B ALA 2.9 24.0 + - - +
501B PHE 3.6 6.7 - - - +
502B VAL 3.2 0.2 - - - -
503B PHE* 1.3 77.7 - - - +
505B HIS* 1.3 64.6 + - - +
507B VAL* 3.2 17.3 + - - +
508B PHE* 3.3 19.3 + - + -
902B HEM 3.6 24.7 - - + -
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Residues in contact with HIS 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B ALA 5.2 1.4 + - - +
322B LYS* 3.5 37.9 + - + +
323B ALA* 4.0 14.2 + - + +
326B SER* 3.8 12.7 - - - -
501B PHE 2.9 16.4 + - - +
502B VAL* 3.7 7.6 - - - +
504B ASN* 1.3 76.1 - - - +
506B GLN* 1.3 59.1 + - + +
508B PHE* 3.1 10.4 + - - +
509B ALA* 2.9 25.2 + - + +
910B SO4 2.7 39.6 + - - -
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Residues in contact with GLN 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405B ALA* 3.5 18.6 - - + +
408B ASP* 5.0 6.7 + - - -
502B VAL* 2.9 36.6 + - + +
503B PHE* 3.5 30.9 - - - +
505B HIS* 1.3 75.5 - - + +
507B VAL* 1.3 65.3 + - - +
509B ALA* 3.2 8.5 + - + +
510B ASP* 2.9 29.0 + - - +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B LEU* 4.4 13.0 - - + -
348B GLN* 4.5 6.5 - - + -
352B PHE* 4.2 20.4 - - + -
403B SER* 5.0 1.7 + - - +
405B ALA* 3.8 9.0 - - + -
406B VAL* 3.8 30.5 - - + +
409B TYR* 4.3 7.4 - - + -
503B PHE 3.0 21.1 + - - +
504B ASN* 3.4 13.9 - - - +
505B HIS 3.2 0.2 - - - -
506B GLN* 1.3 78.4 - - - +
508B PHE* 1.3 64.7 + - + +
510B ASP* 3.3 3.9 + - - +
511B LEU* 3.1 38.1 + - + +
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Residues in contact with PHE 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323B ALA 3.5 15.7 - - - -
326B SER* 3.4 28.7 - - - +
328B PHE* 3.3 32.5 - + + +
329B MET* 3.6 35.4 - - + -
345B LEU* 3.9 23.3 - - + -
432B ARG* 5.8 2.5 - - - -
504B ASN* 3.3 11.2 + - + -
505B HIS* 3.1 10.9 + - - +
507B VAL* 1.3 78.9 - - + +
509B ALA* 1.3 64.9 + - - +
511B LEU* 3.2 2.3 + - + +
512B GLY 2.9 18.7 + - - -
902B HEM 3.4 41.3 - - + -
910B SO4 5.0 0.4 - - - -
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Residues in contact with ALA 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 5.4 0.4 - - - -
505B HIS* 2.9 14.5 + - + +
506B GLN* 3.2 12.5 + - + +
508B PHE* 1.3 76.5 - - - +
510B ASP* 1.3 62.7 + - - +
512B GLY* 3.2 3.6 + - - +
513B LYS* 3.2 38.5 + - + +
910B SO4 3.9 22.2 + - - +
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Residues in contact with ASP 510 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B SER* 3.0 18.2 + - - +
404B PRO* 3.3 16.0 - - - +
405B ALA* 2.7 33.2 + - - +
506B GLN* 2.9 16.1 + - - +
507B VAL 3.6 7.9 - - - +
509B ALA* 1.3 77.6 - - - +
511B LEU* 1.3 62.8 + - + +
513B LYS* 3.0 28.4 + - - +
515B LEU* 2.9 39.0 + - + +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B PHE* 3.6 34.5 - - + -
341B GLU* 6.0 0.7 - - - +
344B ARG* 3.9 36.1 - - + +
345B LEU* 3.6 36.1 - - + -
348B GLN* 4.5 9.6 - - + -
507B VAL* 3.1 28.8 + - + +
508B PHE* 3.6 6.1 - - - +
510B ASP* 1.3 76.0 - - + +
512B GLY* 1.3 62.9 + - - +
514B GLY* 3.1 14.2 + - - -
515B LEU* 3.6 16.2 - - - +
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Residues in contact with GLY 512 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B THR* 6.5 0.7 - - - -
328B PHE* 3.7 19.6 - - - -
508B PHE 2.9 14.5 + - - -
509B ALA* 3.2 4.9 + - - -
510B ASP 3.2 0.4 - - - -
511B LEU* 1.3 76.4 - - - +
513B LYS* 1.3 58.3 + - - +
514B GLY 3.3 2.8 + - - -
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Residues in contact with LYS 513 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
509B ALA* 3.2 25.8 + - + +
510B ASP* 3.0 31.9 + - - +
512B GLY* 1.3 77.7 - - - +
514B GLY* 1.3 61.5 + - - +
515B LEU* 3.2 27.9 + - + +
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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