Contacts of the helix formed by residues 559 - 580 (chain D) in PDB entry 4YFI
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 ASP 559 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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557D ILE 4.1 1.6 + - - -
558D LEU* 1.3 77.5 - - - +
560D LEU* 1.3 64.8 + - - +
561D GLN* 3.3 14.0 + - - +
562D SER* 2.4 39.2 + - - -
563D LYS* 3.4 11.5 + - - +
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Residues in contact with LEU 560 (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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559D ASP* 1.3 74.9 - - - +
561D GLN* 1.3 62.4 + - - +
563D LYS* 3.4 9.4 + - + +
564D LEU* 3.2 30.0 + - + +
659D LEU* 3.9 27.1 - - + -
691D PRO* 4.8 18.6 - - + -
694D ILE* 5.1 4.0 - - + -
726D ILE* 3.2 39.5 - - + -
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Residues in contact with GLN 561 (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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559D ASP* 3.3 14.1 - - - +
560D LEU* 1.3 79.0 - - - +
562D SER* 1.3 57.0 + - - +
564D LEU* 3.3 3.4 + - - +
565D ILE* 3.0 46.7 + - + +
723D LEU* 3.8 21.3 - - + +
726D ILE* 4.4 18.1 - - + +
727D GLU* 4.0 28.9 + - + +
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Residues in contact with SER 562 (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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558D LEU* 4.1 22.9 - - - +
559D ASP* 2.4 29.5 + - - -
561D GLN* 1.3 74.4 - - - +
563D LYS* 1.3 65.1 + - - +
565D ILE* 3.5 11.3 + - - +
566D ILE* 3.2 30.8 + - - +
600D GLY* 4.7 2.9 - - - +
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Residues in contact with LYS 563 (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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551D LEU* 5.7 1.6 - - - -
558D LEU* 3.5 37.8 + - + +
559D ASP 3.4 12.3 + - - +
560D LEU* 3.4 16.1 + - + +
561D GLN 3.3 0.4 - - - -
562D SER* 1.3 78.5 - - - +
564D LEU* 1.3 57.4 + - - +
566D ILE* 3.5 8.7 + - - +
567D ALA* 3.0 26.3 + - - +
658D ILE* 3.4 37.8 - - + +
659D LEU* 2.6 45.1 + - + +
660D THR 5.0 2.4 + - - -
661D GLY* 5.6 1.3 - - - +
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Residues in contact with LEU 564 (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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560D LEU* 3.2 24.8 + - + +
561D GLN 3.9 3.8 - - - +
563D LYS* 1.3 74.8 - - + +
565D ILE* 1.3 63.1 + - - +
566D ILE 3.2 0.4 - - - -
567D ALA* 4.2 7.9 - - + -
568D VAL* 2.8 36.4 + - + +
655D LEU* 5.2 1.8 - - + -
659D LEU* 5.0 5.4 - - + -
694D ILE* 3.8 25.8 - - + -
719D LEU* 4.3 19.3 - - + +
722D CYS* 4.3 13.0 - - + -
723D LEU* 4.1 21.8 - - + +
726D ILE* 3.2 35.7 - - + -
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Residues in contact with ILE 565 (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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561D GLN* 3.0 46.2 + - + +
562D SER* 3.8 8.3 - - - +
563D LYS 3.4 0.2 - - - -
564D LEU* 1.3 77.0 - - - +
566D ILE* 1.3 61.4 + - - +
568D VAL* 4.0 3.7 - - - +
569D ASP* 3.1 26.7 + - - +
599D ASP 5.7 0.4 - - - +
600D GLY 3.6 22.2 - - - +
601D HIS* 3.8 32.3 - - + +
723D LEU* 4.3 19.7 - - + -
727D GLU* 5.4 1.6 - - - +
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Residues in contact with ILE 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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547D LEU* 4.1 31.0 - - + -
550D LEU* 5.6 2.0 - - + -
558D LEU* 4.3 21.3 - - + -
562D SER* 3.2 16.0 + - - +
563D LYS* 3.6 8.7 - - - +
564D LEU 3.2 0.6 - - - -
565D ILE* 1.3 78.2 - - - +
567D ALA* 1.3 62.0 + - - +
569D ASP* 3.3 3.5 + - - +
570D VAL* 3.0 28.0 + - + +
594D ILE* 4.8 0.4 - - + -
596D LEU* 4.0 23.8 - - + -
600D GLY* 3.6 19.3 - - - +
602D ALA* 4.2 17.2 - - + +
658D ILE* 4.1 15.0 - - + -
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Residues in contact with ALA 567 (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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563D LYS 3.0 18.1 + - - +
564D LEU* 3.9 9.4 - - + +
566D ILE* 1.3 76.7 - - - +
568D VAL* 1.3 58.3 + - - +
570D VAL* 3.5 3.2 + - - -
571D ALA* 3.0 17.3 + - - +
651D TYR* 2.7 31.0 + - - +
655D LEU* 3.6 25.1 - - + -
658D ILE* 4.2 14.1 - - + -
719D LEU* 4.1 6.5 - - + -
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Residues in contact with VAL 568 (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 LEU* 2.8 23.8 + - + +
565D ILE* 4.0 4.0 - - - +
567D ALA* 1.3 74.0 - - - +
569D ASP* 1.3 64.4 + - - +
571D ALA* 3.1 7.7 + - - +
572D LYS* 2.8 55.1 + - + +
716D VAL* 4.9 3.8 - - + +
719D LEU* 3.5 42.2 - - + +
720D GLU* 4.0 18.6 - - + +
723D LEU* 4.9 10.8 - - + -
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Residues in contact with ASP 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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520D CYS* 3.2 26.6 - - - +
565D ILE* 3.1 20.8 + - - +
566D ILE 3.3 4.0 + - - +
568D VAL* 1.3 79.6 - - - +
570D VAL* 1.3 61.7 + - - +
572D LYS* 3.3 17.9 + - - -
573D GLY 3.0 18.9 + - - -
601D HIS* 2.8 36.4 + - - +
602D ALA* 3.0 36.2 + - + +
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Residues in contact with VAL 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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520D CYS 5.4 0.4 - - - -
566D ILE* 3.0 23.5 + - + +
567D ALA* 3.9 5.2 - - - +
569D ASP* 1.3 76.3 - - - +
571D ALA* 1.3 63.4 + - - +
573D GLY* 3.4 1.6 + - - -
574D MET* 3.1 23.1 + - + +
589D LEU* 4.4 9.2 - - + -
594D ILE* 3.5 49.1 - - + -
602D ALA* 4.3 7.4 - - + -
604D VAL* 4.1 21.1 - - + +
651D TYR* 3.6 25.6 - - + -
654D CYS* 5.9 0.2 - - + -
658D ILE* 5.7 2.2 - - + -
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Residues in contact with ALA 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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567D ALA 3.0 18.3 + - - +
568D VAL* 3.1 8.5 + - - +
570D VAL* 1.3 78.1 - - - +
572D LYS* 1.3 55.9 + - - +
574D MET* 3.3 2.8 + - - +
575D GLU* 2.8 28.9 + - - +
651D TYR* 3.8 11.2 - - + +
712D PHE* 3.7 15.6 - - + -
715D VAL* 3.9 16.8 - - + -
716D VAL* 3.5 21.8 - - + +
719D LEU* 4.6 0.9 - - + -
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Residues in contact with LYS 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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518D HIS* 4.1 14.7 + - + +
520D CYS* 4.1 13.6 - - - -
568D VAL* 2.8 38.3 + - + +
569D ASP* 3.7 20.8 + - - +
571D ALA* 1.3 73.7 - - - +
573D GLY* 1.3 59.9 + - - +
575D GLU* 3.2 9.0 + - - +
576D TYR* 2.8 30.7 + - - +
601D HIS* 6.2 0.4 - - - -
716D VAL* 3.9 22.2 - - + -
720D GLU* 4.4 15.1 + - - +
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Residues in contact with GLY 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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518D HIS* 4.4 0.7 - - - -
520D CYS* 3.6 27.7 - - - +
521D VAL* 3.8 11.5 - - - +
569D ASP 3.0 10.5 + - - -
570D VAL 3.4 3.8 + - - -
572D LYS* 1.3 77.1 - - - +
574D MET* 1.3 57.4 + - - +
576D TYR* 3.3 7.0 + - - +
577D LEU* 3.0 32.9 + - - +
604D VAL* 4.8 2.5 - - - -
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Residues in contact with MET 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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570D VAL* 3.1 22.0 + - + +
571D ALA 3.7 2.5 - - - +
573D GLY* 1.3 74.0 - - - +
575D GLU* 1.3 66.1 + - - +
577D LEU* 3.3 17.9 + - + -
578D HIS* 3.0 36.4 + - - +
586D HIS* 3.9 11.0 - - + -
589D LEU* 4.1 24.2 - - + -
604D VAL* 4.2 18.2 - - + -
647D ASP* 3.2 45.5 - - + +
712D PHE* 3.5 31.4 - - + -
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Residues in contact with GLU 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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571D ALA 2.8 17.1 + - - +
572D LYS* 3.6 10.0 - - - +
574D MET* 1.3 75.0 - - - +
576D TYR* 1.3 63.7 + - - +
578D HIS* 3.3 1.2 + - - +
579D ASN* 3.0 46.3 + - + +
712D PHE* 3.8 17.4 - - + +
713D SER* 3.3 34.3 - - - +
716D VAL* 3.7 20.3 - - + +
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Residues in contact with TYR 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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515D GLN 3.3 13.7 + - - -
516D LEU* 4.1 18.6 - - + -
517D ASN* 2.8 44.2 + - - +
518D HIS* 3.5 42.0 - + + +
521D VAL* 4.1 9.2 - - + -
572D LYS 2.8 12.6 + - - +
573D GLY 3.4 10.3 - - - +
574D MET 3.2 0.2 - - - -
575D GLU* 1.3 79.1 - - - +
577D LEU* 1.3 66.7 + - + +
579D ASN* 3.3 8.9 + - - +
580D LEU* 3.4 40.3 + - + +
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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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516D LEU* 3.5 31.2 - - + -
521D VAL* 4.3 5.6 - - + -
573D GLY 3.0 18.1 + - - +
574D MET* 3.6 29.2 - - + +
576D TYR* 1.3 85.5 - - + +
578D HIS* 1.3 61.7 + - + +
579D ASN 3.4 0.9 + - - -
580D LEU* 3.6 10.8 - - + +
583D PRO* 3.6 1.7 - - - +
584D ILE* 3.0 51.0 + - + +
586D HIS* 4.6 8.5 - - + -
604D VAL* 4.8 2.0 - - + -
607D PHE* 3.6 32.3 - - + -
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Residues in contact with HIS 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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574D MET* 3.0 21.4 + - + +
575D GLU* 3.3 5.1 + - - +
577D LEU* 1.3 80.1 - - + +
579D ASN* 1.3 67.4 + - - +
580D LEU 3.6 0.4 - - - -
583D PRO* 3.7 21.3 - - - +
584D ILE 3.2 19.0 + - - -
644D ILE* 3.3 58.9 - - + +
647D ASP* 3.1 26.9 + - + +
648D VAL* 4.7 1.7 - - + +
711D GLU* 5.5 3.6 + - - +
712D PHE* 3.5 34.8 + + + +
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Residues in contact with ASN 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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575D GLU* 3.0 43.9 + - + +
576D TYR* 3.3 2.9 + - - +
577D LEU 3.2 0.2 - - - -
578D HIS* 1.3 86.7 - - - +
580D LEU* 1.3 65.0 + - - +
581D THR* 3.7 2.6 + - - +
712D PHE* 5.8 0.8 - - - +
713D SER* 5.3 7.1 + - - +
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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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515D GLN* 5.0 9.4 - - + +
516D LEU* 5.0 1.6 - - + -
576D TYR* 3.4 46.7 + - + +
577D LEU* 3.6 22.4 - - + +
578D HIS 3.6 0.6 - - - -
579D ASN* 1.3 80.8 - - - +
581D THR* 1.3 66.1 + - - +
582D GLN 3.1 14.6 + - - +
583D PRO* 3.3 15.8 - - - +
584D ILE* 3.5 34.1 - - + -
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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
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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