Contacts of the helix formed by residues 491 - 515 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D LEU* 4.0 31.9 - - + +
165D ARG* 5.3 3.1 - - - +
489D ALA 3.3 3.0 + - - -
490D GLN* 1.3 81.0 - - + +
492D LEU* 1.3 61.2 + - - +
493D SER* 3.5 2.2 - - - +
494D ALA* 4.3 4.9 - - - +
495D ILE* 3.5 24.4 + - + +
542D CYS 4.0 9.0 + - - -
543D TYR* 4.3 7.9 - - + -
546D CYS* 3.2 46.9 - - - +
547D ASN* 4.8 11.7 - - - +
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Residues in contact with LEU 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 5.2 5.2 - - + +
161D ILE* 3.7 28.9 - - + -
162D SER* 3.6 32.5 - - - +
165D ARG* 4.3 12.8 - - + +
250D TYR* 3.4 43.3 - - + -
253D ILE* 5.6 3.6 - - + -
489D ALA* 3.5 19.2 + - - +
490D GLN 2.9 4.4 - - - +
491D THR* 1.3 78.9 - - - +
493D SER* 1.3 66.4 + - - +
494D ALA 3.4 0.2 - - - -
495D ILE* 4.9 1.8 - - - -
496D LEU* 2.9 40.9 + - + +
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Residues in contact with SER 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D TYR* 2.8 41.1 + - - -
254D TYR* 5.0 3.6 - - - -
489D ALA* 4.0 10.5 + - - +
491D THR 5.8 0.4 - - - -
492D LEU* 1.3 78.1 - - - +
494D ALA* 1.3 68.2 + - - +
496D LEU* 4.5 2.3 - - - +
497D LEU* 2.9 32.8 + - - +
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Residues in contact with ALA 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491D THR* 4.3 4.8 - - - +
492D LEU 3.4 0.4 - - - -
493D SER* 1.3 82.0 - - - +
495D ILE* 1.3 65.1 + - - +
497D LEU* 3.4 5.0 - - - +
498D ALA* 2.9 19.8 + - - +
542D CYS* 4.2 24.5 - - + +
545D LEU* 5.9 4.7 - - + -
546D CYS* 4.1 25.3 - - - -
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Residues in contact with ILE 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D LEU* 5.1 2.7 - - + -
109D LEU* 4.2 10.3 - - + -
158D LEU* 3.4 28.7 - - + -
161D ILE* 6.0 0.7 - - + -
491D THR* 3.5 21.0 + - - +
492D LEU* 3.6 2.6 + - - +
493D SER 3.5 0.2 - - - -
494D ALA* 1.3 78.6 - - - +
496D LEU* 1.3 64.7 + - - +
498D ALA* 3.0 8.1 + - - +
499D PHE* 2.9 20.4 + - - +
539D ASN* 3.2 38.1 - - - +
542D CYS* 3.2 29.8 - - + -
543D TYR* 3.5 22.4 - - + -
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Residues in contact with LEU 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 4.4 10.3 - - + -
162D SER* 4.7 2.5 - - - +
243D VAL 5.5 0.4 - - - +
246D MET* 3.5 54.3 - - + +
247D THR* 4.6 6.7 - - + +
250D TYR* 4.5 16.6 - - + -
492D LEU* 2.9 35.8 + - + +
493D SER* 4.5 4.0 - - - +
495D ILE* 1.3 76.5 - - - +
497D LEU* 1.3 72.9 + - + +
499D PHE* 3.1 10.8 + - + +
500D ILE* 3.0 32.1 + - + +
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Residues in contact with LEU 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493D SER* 2.9 25.7 + - - +
494D ALA* 3.4 4.7 - - - +
496D LEU* 1.3 84.5 - - + +
498D ALA* 1.3 62.4 + - - +
500D ILE* 2.9 26.0 - - + +
501D ILE* 3.0 51.7 + - + +
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Residues in contact with ALA 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494D ALA 2.9 11.9 + - - +
495D ILE* 3.2 12.8 - - - +
497D LEU* 1.3 76.3 - - - +
499D PHE* 1.3 64.7 + - - +
501D ILE* 2.9 9.3 + - - +
502D THR* 2.9 30.9 + - + +
535D ASN* 3.8 12.1 - - - +
538D VAL* 4.7 11.9 - - + -
539D ASN* 5.1 2.5 - - - +
542D CYS* 4.4 14.8 - - - -
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Residues in contact with PHE 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D SER* 5.2 3.6 - - - -
155D VAL* 3.5 41.1 - - + -
158D LEU* 3.6 29.6 - - + -
239D PHE* 3.6 22.4 - + - -
242D PRO* 6.3 0.4 - - + -
243D VAL* 3.8 15.0 - - + -
246D MET* 4.0 18.8 - - + -
495D ILE* 2.9 9.6 + - + +
496D LEU* 3.3 10.1 - - + +
498D ALA* 1.3 75.5 - - - +
500D ILE* 1.3 68.6 + - + +
503D TRP* 2.9 65.8 + + - +
535D ASN* 3.1 21.3 - - - +
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Residues in contact with ILE 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D PHE* 4.8 0.2 - - - -
243D VAL* 4.5 21.3 - - + -
247D THR* 5.9 1.6 - - - +
496D LEU* 3.0 21.4 + - + +
497D LEU* 2.9 34.1 - - + +
499D PHE* 1.3 82.0 - - + +
501D ILE* 1.3 56.1 + - + +
503D TRP* 4.7 0.4 - - - -
504D THR* 2.7 62.4 + - + +
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Residues in contact with ILE 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497D LEU* 3.0 48.9 + - + +
498D ALA* 2.9 8.9 + - - +
500D ILE* 1.3 79.4 - - + +
502D THR* 1.3 66.9 + - + +
503D TRP 3.3 0.2 - - - -
504D THR* 4.4 2.0 - - - -
505D PRO* 2.9 26.2 - - - +
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Residues in contact with THR 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498D ALA* 2.9 24.5 + - + +
501D ILE* 1.3 82.7 - - + +
503D TRP* 1.3 61.5 + - - +
505D PRO* 4.0 3.9 - - - +
506D TYR 5.5 0.2 + - - -
531D LEU* 3.3 27.8 - - + +
532D CYS* 3.3 23.2 + - - -
534D ILE* 4.1 21.5 - - + +
535D ASN* 2.8 33.1 - - - +
538D VAL* 5.8 4.0 - - + -
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Residues in contact with TRP 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116D ILE* 5.7 0.7 - - + -
151D SER* 3.6 38.4 - - - -
154D SER* 5.5 3.1 - - - -
155D VAL* 3.8 17.3 - - + -
239D PHE* 3.4 26.2 - + + -
499D PHE* 2.9 39.7 + + - +
502D THR* 1.3 93.7 - - - +
504D THR* 1.3 68.0 + - - +
505D PRO* 3.2 2.2 - - - -
506D TYR* 2.8 24.3 + - - +
507D ASN* 3.4 7.1 + - - -
532D CYS* 3.2 28.0 + - - -
535D ASN* 3.6 16.6 + - + +
536D SER* 5.7 2.5 - - - -
2000D 0HK 3.4 55.9 - + + -
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Residues in contact with THR 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D PHE* 3.3 30.9 - - + -
240D TYR* 6.2 2.5 - - + -
243D VAL* 5.1 2.2 - - + -
500D ILE* 2.7 48.5 + - + +
501D ILE* 4.0 2.1 + - - -
503D TRP* 1.3 72.0 - - - +
505D PRO* 1.3 74.9 - - - +
506D TYR 2.9 0.5 + - - -
507D ASN* 3.0 4.6 + - - +
508D ILE* 2.8 40.2 + - - +
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Residues in contact with PRO 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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501D ILE 2.9 25.1 - - - +
502D THR 4.0 0.7 - - - -
503D TRP 3.2 6.1 - - - +
504D THR* 1.3 95.5 - - - +
506D TYR* 1.3 56.2 + - - +
508D ILE* 3.4 14.2 + - + +
509D MET* 2.9 28.3 + - - +
528D GLY* 5.8 0.4 - - - -
531D LEU* 3.9 28.0 - - + -
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Residues in contact with TYR 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D TYR* 4.6 4.9 + - - -
502D THR 5.5 0.2 + - - -
503D TRP 2.8 11.6 + - - +
505D PRO* 1.3 78.6 - - - +
507D ASN* 1.3 56.6 + - - +
509D MET* 2.7 43.8 + - + +
510D VAL* 2.9 28.7 + - + +
525D TRP* 4.0 28.1 - + + -
528D GLY* 3.6 25.4 - - - +
529D TYR* 3.6 33.5 - + - -
531D LEU* 5.5 0.6 - - + +
532D CYS* 3.7 17.7 - - - -
2000D 0HK 3.6 47.1 - - + +
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Residues in contact with ASN 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ALA* 3.4 14.4 - - - +
239D PHE* 3.4 40.6 - - + +
240D TYR* 2.6 35.0 + - + +
503D TRP* 3.4 16.0 + - - +
504D THR* 3.0 5.7 + - - +
506D TYR* 1.3 78.5 - - - +
508D ILE* 1.3 55.1 + - - +
510D VAL* 3.3 11.4 + - - +
511D LEU 2.9 20.3 + - - -
2000D 0HK 3.1 39.4 + - - +
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Residues in contact with ILE 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240D TYR* 3.9 9.6 - - + +
504D THR* 2.8 42.3 + - - +
505D PRO* 3.4 11.2 - - + +
507D ASN* 1.3 74.7 - - + +
509D MET* 1.3 62.3 + - - +
511D LEU* 3.2 14.4 + - + +
512D VAL* 2.9 35.9 + - + +
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Residues in contact with MET 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505D PRO 2.9 11.5 + - - +
506D TYR* 2.7 44.3 + - + +
508D ILE* 1.3 78.6 - - - +
510D VAL* 1.3 54.4 + - - +
512D VAL* 3.5 8.1 + - - +
513D ASN* 2.9 26.7 + - - +
520D ILE* 3.8 30.4 - - + +
524D TYR* 3.6 24.0 - - - +
525D TRP* 3.5 43.3 - - + +
528D GLY* 4.2 4.7 - - - -
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Residues in contact with VAL 510 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D PRO* 4.8 1.3 - - + +
231D THR* 3.6 28.0 - - + +
232D PHE* 4.1 19.7 - - + -
235D ALA* 4.8 6.3 - - + -
506D TYR* 2.9 41.9 + - + +
507D ASN* 3.4 10.8 - - - +
508D ILE 3.2 0.2 - - - -
509D MET* 1.3 72.5 - - - +
511D LEU* 1.3 66.8 + - - +
512D VAL 3.1 1.6 - - - -
513D ASN* 2.9 18.0 + - + +
514D THR* 2.9 13.6 + - - +
525D TRP* 4.1 14.8 - - + -
2000D 0HK 4.6 9.4 - - + -
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Residues in contact with LEU 511 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D PHE* 3.1 40.1 - - + -
240D TYR* 3.8 13.7 - - + +
507D ASN 2.9 14.7 + - - +
508D ILE* 3.3 19.1 - - + +
510D VAL* 1.3 75.7 - - - +
512D VAL* 1.3 66.4 + - + +
514D THR* 3.4 3.8 + - - -
515D PHE* 3.2 38.4 - - + -
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Residues in contact with VAL 512 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508D ILE* 2.9 25.0 + - + +
509D MET* 3.7 5.6 - - - +
511D LEU* 1.3 77.8 - - + +
513D ASN* 1.3 61.9 + - - +
514D THR 3.0 6.1 + - - -
515D PHE* 3.1 17.5 + - - +
516D CYS* 3.4 16.5 + - - -
519D CYS* 5.2 1.1 - - + -
520D ILE* 3.8 26.2 - - + -
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Residues in contact with ASN 513 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228D PRO* 3.8 17.5 - - - +
509D MET 2.9 16.9 + - - +
510D VAL* 2.9 7.9 + - + +
512D VAL* 1.3 73.5 - - - +
514D THR* 1.3 62.3 - - - +
515D PHE 3.2 0.2 - - - -
516D CYS* 3.5 21.2 - - - +
517D ASP* 3.6 22.8 + - - +
519D CYS* 4.4 0.8 - - - -
520D ILE* 4.3 10.6 + - + +
525D TRP* 3.3 37.1 - - + +
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Residues in contact with THR 514 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 5.2 6.3 - - + -
252C ARG* 3.2 21.9 + - - +
228D PRO* 3.6 18.8 + - - +
229D THR* 4.5 18.6 - - + -
232D PHE* 3.3 34.5 - - + +
510D VAL 2.9 12.2 + - - -
511D LEU 3.4 11.7 - - - -
512D VAL 3.0 0.8 - - - -
513D ASN* 1.3 81.1 - - - +
515D PHE* 1.3 81.5 + - + +
516D CYS 3.7 3.8 + - - +
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Residues in contact with PHE 515 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248C ILE* 4.2 36.6 - - + -
252C ARG* 3.9 17.8 + - - +
232D PHE* 5.4 2.9 - + - -
511D LEU* 3.2 38.6 - - + -
512D VAL* 3.1 9.5 + - - +
514D THR* 1.3 89.7 - - + +
516D CYS* 1.3 60.1 + - - +
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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