Contacts of the helix formed by residues 564 - 585 (chain D) in PDB entry 2BKU
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 GLU 564 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C GLU* 3.4 35.3 - - - +
176C PHE* 3.8 3.1 - - - +
177C VAL* 3.1 50.4 + - + +
565D ASP* 1.3 64.0 + - - +
566D ALA* 3.3 5.7 - - - +
567D GLN* 3.5 16.8 + - - +
568D SER* 2.9 35.1 + - - -
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Residues in contact with ASP 565 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564D GLU* 1.3 80.2 - - - +
566D ALA* 1.3 53.3 + - - +
568D SER* 3.6 8.1 + - - -
569D LEU* 2.7 38.5 + - - +
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Residues in contact with ALA 566 (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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564D GLU 3.3 3.4 - - - +
565D ASP* 1.3 77.6 - - - +
567D GLN* 1.3 61.5 + - + +
569D LEU* 3.1 9.4 + - + +
570D GLN* 2.5 55.7 + - - +
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Residues in contact with GLN 567 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ARG* 3.0 52.4 + - - +
33C GLY* 3.7 14.5 - - - -
154C ASN* 2.9 23.5 + - - +
157C PHE* 3.8 26.6 - - + -
564D GLU* 3.5 17.0 + - - +
565D ASP 3.4 0.2 - - - -
566D ALA* 1.3 78.3 - - + +
568D SER* 1.3 59.0 + - - +
570D GLN* 3.1 30.8 + - - +
571D GLU* 2.9 27.0 + - - +
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Residues in contact with SER 568 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511D ASP* 5.8 1.6 - - - +
512D ASN* 5.2 5.9 + - - +
517D ARG* 3.6 24.5 + - - -
564D GLU* 2.9 22.0 + - - -
565D ASP* 3.7 11.7 + - - -
567D GLN* 1.3 76.8 - - - +
569D LEU* 1.3 61.7 + - - +
571D GLU* 3.5 13.6 - - - +
572D LEU* 3.2 15.4 + - - +
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Residues in contact with LEU 569 (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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517D ARG* 5.4 0.7 - - - +
553D THR* 4.0 45.3 - - + +
556D VAL* 4.3 13.0 - - + +
565D ASP* 2.7 27.6 + - - +
566D ALA* 3.1 10.3 + - + +
568D SER* 1.3 71.3 - - - +
570D GLN* 1.3 67.5 + - + +
572D LEU* 3.0 22.9 + - + +
573D GLN* 3.0 23.7 + - - +
608D LYS* 5.9 1.6 - - - +
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Residues in contact with GLN 570 (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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29C ARG* 3.1 27.0 + - - +
33C GLY* 4.0 10.1 + - - +
154C ASN* 5.6 0.2 - - - -
566D ALA* 2.5 32.3 + - - +
567D GLN* 3.1 23.0 + - - +
569D LEU* 1.3 73.2 - - + +
571D GLU* 1.3 64.3 + - - +
573D GLN* 3.0 9.4 + - - +
574D SER* 3.0 25.6 + - - -
610D ASP* 4.2 12.6 + - - +
613D PHE* 3.2 47.4 - - + -
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Residues in contact with GLU 571 (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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153C SER 3.4 20.6 - - - +
154C ASN* 3.4 25.7 - - + +
155C TYR* 3.7 14.9 - - - -
156C ASN 4.6 1.1 + - - -
512D ASN* 3.2 33.7 + - + +
515D ASN* 4.3 1.4 - - - +
517D ARG* 6.2 0.2 - - - +
518D ALA* 4.2 8.7 - - - +
567D GLN 2.9 18.6 + - - +
568D SER* 3.5 14.6 - - - +
569D LEU 3.2 0.2 - - - -
570D GLN* 1.3 76.6 - - - +
572D LEU* 1.3 52.8 + - - +
574D SER* 3.2 4.5 + - - -
575D ASN* 2.6 50.1 + - - +
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Residues in contact with LEU 572 (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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507D ALA 5.0 0.2 - - - +
517D ARG* 3.3 43.5 - - + +
521D PHE* 3.3 35.4 - - + -
549D LYS* 4.6 14.1 - - - -
553D THR* 3.8 22.9 - - + -
568D SER 3.2 10.1 + - - +
569D LEU* 3.0 18.2 + - + +
571D GLU* 1.3 79.9 - - - +
573D GLN* 1.3 56.6 + - - +
575D ASN* 3.2 9.6 + - - +
576D ILE* 2.9 40.0 + - + +
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Residues in contact with GLN 573 (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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550D LEU* 4.7 8.5 - - + +
553D THR* 3.3 37.0 + - - +
554D MET* 4.2 4.9 - - - +
569D LEU* 3.0 18.5 + - - +
570D GLN* 3.0 12.4 + - - +
572D LEU* 1.3 72.3 - - - +
574D SER* 1.3 60.8 + - - +
576D ILE* 3.2 10.5 + - - +
577D LEU* 2.9 34.1 + - + +
605D LEU* 4.0 12.6 - - + +
608D LYS* 3.0 30.4 + - - +
613D PHE* 3.1 29.5 - - + -
614D ILE* 4.5 6.5 - - + -
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Residues in contact with SER 574 (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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152C LYS 3.9 1.4 + - - -
153C SER* 3.9 31.8 - - - -
570D GLN 3.0 14.9 + - - -
571D GLU* 3.3 8.5 - - - -
573D GLN* 1.3 73.8 - - - +
575D ASN* 1.3 64.8 + - - +
577D LEU* 3.3 3.8 + - - +
578D THR* 3.1 26.0 + - - -
613D PHE* 3.6 18.9 + - - -
614D ILE* 4.3 10.6 - - - +
617D ASP* 4.9 11.2 + - - +
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Residues in contact with ASN 575 (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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153C SER* 5.7 3.2 - - - -
512D ASN* 5.2 1.2 - - - +
517D ARG* 5.6 1.2 - - - +
518D ALA* 3.5 34.6 - - - +
521D PHE* 3.8 25.9 - - + +
522D SER* 5.1 2.3 + - - -
571D GLU* 2.6 49.0 + - - +
572D LEU* 3.2 13.8 - - - +
574D SER* 1.3 75.7 - - - +
576D ILE* 1.3 63.7 + - - +
578D THR* 3.2 22.2 - - - -
579D VAL* 3.5 10.6 + - - +
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Residues in contact with ILE 576 (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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521D PHE* 3.7 26.7 - - + -
546D VAL* 3.6 31.6 - - + +
549D LYS* 4.1 10.3 - - + -
550D LEU* 4.0 41.5 - - + +
553D THR* 4.1 7.9 - - + -
572D LEU* 2.9 37.3 + - + +
573D GLN* 3.2 11.6 + - - +
575D ASN* 1.3 75.8 - - - +
577D LEU* 1.3 58.6 + - - +
579D VAL* 3.1 7.0 + - - +
580D LEU* 2.9 25.8 + - + +
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Residues in contact with LEU 577 (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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550D LEU* 4.9 4.3 - - + -
573D GLN 2.9 15.7 + - - +
574D SER* 3.3 5.4 + - - +
576D ILE* 1.3 73.9 - - - +
578D THR* 1.3 60.0 - - - +
580D LEU* 4.0 10.8 - - + -
581D ALA* 2.8 33.1 + - + +
602D PHE* 3.8 26.0 - - + -
605D LEU* 3.6 20.4 - - + -
614D ILE* 3.9 16.2 - - + -
617D ASP* 4.1 23.1 - - + +
618D VAL* 3.5 24.9 - - + -
621D ALA* 4.0 19.7 - - + -
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Residues in contact with THR 578 (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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521D PHE 5.3 0.7 - - - +
522D SER* 5.5 4.3 - - - +
525D THR* 3.3 28.3 - - + +
574D SER 3.1 15.8 + - - -
575D ASN* 3.2 13.4 - - - -
577D LEU* 1.3 77.0 - - - +
579D VAL* 1.3 61.3 + - - +
581D ALA* 3.8 4.7 - - - +
582D ALA* 3.2 21.3 + - - +
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Residues in contact with VAL 579 (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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521D PHE* 3.2 42.4 - - + +
524D LEU* 4.0 7.9 - - + -
525D THR* 3.4 10.3 - - - +
528D VAL* 4.6 4.7 - - + -
542D ILE* 3.4 32.8 - - + -
546D VAL* 3.6 17.7 - - + -
575D ASN 3.5 9.6 + - - +
576D ILE 3.1 7.7 + - - +
578D THR* 1.3 75.0 - - - +
580D LEU* 1.3 64.6 + - - +
582D ALA* 2.9 16.9 + - - +
583D VAL* 3.0 15.8 + - + +
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Residues in contact with LEU 580 (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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543D SER* 4.6 5.8 - - - +
546D VAL* 3.3 29.4 - - + -
547D MET* 3.9 19.7 - - + +
550D LEU* 3.5 32.3 - - + -
576D ILE* 2.9 18.8 + - + +
577D LEU* 3.4 11.4 + - + +
579D VAL* 1.3 76.3 - - - +
581D ALA* 1.3 62.7 + - - +
583D VAL* 3.5 6.8 + - + +
584D ILE* 3.2 30.6 + - + +
591D VAL* 5.3 3.1 - - + -
598D LEU* 3.7 25.1 - - + -
602D PHE* 3.7 14.1 - - + -
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Residues in contact with ALA 581 (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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577D LEU* 2.8 19.8 + - + +
578D THR* 3.8 6.1 - - - +
580D LEU* 1.3 77.2 - - - +
582D ALA* 1.3 62.2 + - - +
584D ILE* 3.3 11.2 + - - +
585D ARG* 3.0 40.8 + - - +
617D ASP 5.6 1.3 - - - +
620D TYR* 6.2 1.8 - - + -
621D ALA* 4.7 17.9 - - + +
624D ALA* 5.5 0.2 - - - +
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Residues in contact with ALA 582 (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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525D THR* 3.9 21.5 - - + +
528D VAL* 3.4 18.9 - - + +
529D GLU* 4.3 15.6 - - - +
578D THR 3.2 10.8 + - - +
579D VAL* 2.9 9.9 + - - +
581D ALA* 1.3 75.0 - - - +
583D VAL* 1.3 67.4 + - - +
585D ARG* 3.1 25.7 + - - +
586D LYS* 3.4 9.0 - - - +
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Residues in contact with VAL 583 (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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528D VAL* 3.4 26.4 - - + +
539D SER* 4.8 5.6 - - - +
542D ILE* 4.4 2.0 - - + -
543D SER* 3.8 36.1 - - - +
546D VAL* 5.2 0.4 - - + -
579D VAL* 3.0 26.3 + - + +
580D LEU* 3.6 11.4 - - + +
581D ALA 3.3 0.2 - - - -
582D ALA* 1.3 75.1 - - - +
584D ILE* 1.3 57.1 + - - +
586D LYS 3.3 0.2 + - - -
587D SER* 2.9 48.8 + - - +
590D SER* 3.9 5.8 - - - +
591D VAL* 4.2 13.5 - - + -
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Residues in contact with ILE 584 (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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580D LEU* 3.2 20.5 + - + +
581D ALA* 3.6 6.5 - - - +
582D ALA 3.3 0.4 - - - -
583D VAL* 1.3 77.1 - - + +
585D ARG* 1.3 57.3 + - - +
586D LYS 3.2 3.9 + - - -
588D PRO* 3.9 23.5 - - + +
591D VAL* 4.0 9.2 - - + -
598D LEU* 3.7 32.5 - - + -
602D PHE* 4.2 16.4 - - + -
621D ALA* 4.1 17.0 - - + +
624D ALA* 3.7 12.5 - - + +
625D LEU* 3.3 42.2 - - + +
628D SER* 4.6 4.0 + - - +
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Residues in contact with ARG 585 (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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529D GLU* 5.6 3.3 - - - +
581D ALA* 3.0 29.6 + - - +
582D ALA* 3.1 8.6 + - - +
584D ILE* 1.3 77.2 - - - +
586D LYS* 1.3 68.2 + - - +
620D TYR* 3.3 37.6 + - - +
621D ALA* 5.7 0.4 - - - +
623D SER* 5.5 1.6 - - - -
624D ALA* 3.8 22.8 - - + +
658D THR* 6.2 1.0 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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