Contacts of the helix formed by residues 518 - 540 (chain B) in PDB entry 5ZR1
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 518 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B LEU* 1.3 78.9 - - - +
519B VAL* 1.3 68.7 + - + +
520B ASN* 3.2 17.7 - - + +
521B SER* 3.2 20.2 + - - +
522B LYS* 3.0 31.0 + - - +
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Residues in contact with VAL 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B LEU 4.1 1.5 + - - +
518B THR* 1.3 79.4 - - + +
520B ASN* 1.3 61.8 + - + +
522B LYS* 3.9 18.6 - - - +
523B LYS* 3.0 39.4 + - + +
620B LEU 6.5 1.3 - - - -
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Residues in contact with ASN 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B THR* 3.2 12.0 - - + +
519B VAL* 1.3 83.7 - - + +
521B SER* 1.3 59.5 + - - +
523B LYS* 4.0 10.0 + - - +
524B MET* 3.6 7.3 + - - +
567B PHE 4.4 4.0 + - - +
568B ILE* 3.3 61.7 + - - +
578B MET* 4.2 13.2 - - + +
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Residues in contact with SER 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B LEU* 4.6 7.6 - - - -
518B THR* 3.2 29.1 + - - +
520B ASN* 1.3 79.6 - - - +
522B LYS* 1.3 61.3 + - - +
523B LYS 3.5 0.2 - - - -
524B MET* 4.0 4.8 - - - +
525B TYR 3.5 10.2 + - - -
578B MET* 4.5 12.2 - - - +
581B GLU* 3.1 25.2 + - - -
582B PHE* 3.4 27.8 - - - -
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Residues in contact with LYS 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B LEU* 3.2 44.7 + - + +
515B GLN* 4.8 6.9 + - - +
517B LEU* 4.0 12.8 - - + +
518B THR 3.0 22.4 + - - +
519B VAL* 3.4 19.4 + - - +
520B ASN 3.4 0.2 - - - -
521B SER* 1.3 77.5 - - - +
523B LYS* 1.3 59.8 + - + +
524B MET 3.2 0.4 - - - -
525B TYR* 4.6 2.2 - - - -
526B LYS* 2.9 31.8 + - - +
616B VAL* 4.8 16.2 + - + +
617B LEU* 3.7 16.8 - - + +
619B THR* 5.9 2.2 - - - +
620B LEU* 6.0 0.4 + - - -
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Residues in contact with LYS 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B VAL* 3.0 28.5 + - + +
520B ASN* 4.3 9.2 + - - +
522B LYS* 1.3 77.1 - - + +
524B MET* 1.3 61.1 + - - +
526B LYS* 3.9 9.4 - - + +
527B LEU* 3.1 22.5 + - - +
566B ASP* 4.2 12.8 + - - -
567B PHE* 5.3 4.6 + - - +
568B ILE* 3.9 29.9 - - + +
620B LEU* 4.8 21.1 - - + -
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Residues in contact with MET 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ASN 3.6 9.8 + - - +
521B SER* 4.1 2.7 - - - +
522B LYS 3.2 0.4 - - - -
523B LYS* 1.3 78.1 - - - +
525B TYR* 1.3 64.5 + - + +
527B LEU* 3.1 7.3 + - - +
528B LEU* 2.9 28.1 + - + +
559B PHE* 3.6 18.4 - - + -
563B CYS* 5.1 1.8 - - + -
568B ILE* 3.7 23.3 - - + +
575B LEU* 3.7 22.4 - - + -
578B MET* 3.3 50.3 - - + +
579B LEU* 3.7 19.5 - - + -
582B PHE* 3.6 21.3 - - + -
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Residues in contact with TYR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B ALA* 5.0 0.2 - - - +
514B LEU* 3.9 34.8 - - + -
521B SER 3.5 15.0 + - - +
522B LYS 3.5 4.1 + - - +
524B MET* 1.3 81.7 - - + +
526B LYS* 1.3 57.2 + - - +
528B LEU* 3.3 16.7 + - + +
529B ILE* 2.9 54.8 + - + +
582B PHE* 3.6 35.4 - + + -
587B MET* 3.2 36.7 + - + +
588B ALA* 4.7 0.4 - - + -
602B VAL* 3.5 22.3 - - + +
604B TYR* 3.7 14.4 - - - -
612B LEU* 3.9 9.8 - - + +
617B LEU* 4.1 5.6 - - + -
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Residues in contact with LYS 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B LYS 2.9 19.2 + - - +
523B LYS* 3.9 8.7 - - + +
525B TYR* 1.3 77.2 - - - +
527B LEU* 1.3 57.4 + - - +
529B ILE* 3.4 1.6 + - - +
530B GLU* 3.0 54.5 + - - +
613B LEU* 3.7 20.5 - - + +
617B LEU* 3.6 34.9 - - + +
618B ASN* 3.3 43.3 - - - +
620B LEU* 4.5 11.9 - - + -
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Residues in contact with LEU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LYS* 4.8 15.3 - - + +
523B LYS 3.1 14.6 + - - +
524B MET* 3.1 8.6 + - - +
526B LYS* 1.3 75.8 - - - +
528B LEU* 1.3 59.0 + - - +
530B GLU* 4.1 12.0 - - + +
531B THR* 2.7 42.3 + - - +
559B PHE* 4.2 10.5 - - + -
562B LEU* 3.5 43.7 - - + +
563B CYS* 3.7 17.7 - - + +
566B ASP* 4.0 17.5 - - - +
568B ILE* 4.6 7.2 - - + -
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Residues in contact with LEU 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B MET* 2.9 15.9 + - + +
525B TYR* 3.6 17.3 - - + +
527B LEU* 1.3 77.2 - - - +
529B ILE* 1.3 64.2 + - - +
531B THR* 4.2 1.8 - - - -
532B GLN* 3.2 23.7 + - - +
554B VAL* 4.1 12.8 - - + -
559B PHE* 3.7 16.5 - - + -
579B LEU* 5.0 9.0 - - + -
588B ALA* 4.1 19.3 - - + -
600B ILE* 3.7 43.7 - - + +
601B TRP 5.4 0.9 - - - -
602B VAL* 3.8 26.9 - - + -
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Residues in contact with ILE 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B TYR* 2.9 42.8 + - + +
526B LYS 3.8 3.8 - - - +
528B LEU* 1.3 77.1 - - - +
530B GLU* 1.3 56.9 + - - +
531B THR 3.3 0.3 + - - -
532B GLN* 3.3 4.8 + - - +
533B MET* 2.8 39.6 + - + +
602B VAL* 3.7 27.4 - - + -
609B LEU* 3.7 54.9 - - + +
612B LEU* 4.8 4.3 - - + -
613B LEU* 3.9 15.7 - - + -
617B LEU* 4.4 6.1 - - + -
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Residues in contact with GLU 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A LYS* 5.3 8.1 - - - +
526B LYS* 3.0 54.7 + - - +
527B LEU* 4.2 12.8 - - + +
529B ILE* 1.3 76.1 - - - +
531B THR* 1.3 58.8 + - - +
533B MET* 3.6 9.0 + - - +
534B GLN* 3.2 22.5 + - - +
613B LEU* 3.8 24.0 - - + +
618B ASN* 5.4 0.5 + - - -
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Residues in contact with THR 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576A GLN* 5.7 3.4 - - - +
609A LEU 5.9 2.0 - - - +
613A ILE* 5.7 6.5 - - + -
527B LEU* 2.7 30.3 + - - +
528B LEU* 4.9 0.2 - - - -
529B ILE 3.2 0.2 - - - -
530B GLU* 1.3 76.2 - - - +
532B GLN* 1.3 64.3 + - - +
534B GLN* 3.3 10.6 + - + +
535B ASN* 3.3 29.3 + - - +
554B VAL* 3.7 26.0 - - + -
558B LEU* 5.4 2.9 - - + -
559B PHE* 5.6 0.4 - - - -
562B LEU* 3.9 28.4 - - + +
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Residues in contact with GLN 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528B LEU* 3.2 16.2 + - - +
529B ILE* 3.9 2.7 - - - +
531B THR* 1.3 75.9 - - - +
533B MET* 1.3 59.9 + - - +
535B ASN* 3.0 3.5 + - - +
536B MET* 2.8 36.2 + - + +
548B GLY* 4.1 8.9 - - - -
549B THR 4.1 5.7 + - - -
552B THR* 3.2 42.8 + - - +
553B GLY* 4.4 0.6 - - - -
554B VAL* 4.2 6.6 - - + +
600B ILE 4.9 0.2 - - - +
601B TRP* 3.8 7.3 - - - +
602B VAL* 2.9 58.9 + - - +
609B LEU* 4.5 7.3 - - + +
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Residues in contact with MET 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B ILE* 2.8 28.5 + - + +
530B GLU* 3.7 8.3 - - - +
532B GLN* 1.3 72.9 - - - +
534B GLN* 1.3 64.1 + - - +
536B MET* 4.5 0.9 - - - +
537B GLY* 3.4 17.3 + - - -
606B TYR* 3.6 33.5 + - + +
609B LEU* 3.4 44.1 - - + +
610B GLU* 3.7 17.3 - - + +
613B LEU* 3.8 20.6 - - + -
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Residues in contact with GLN 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A GLU 3.9 7.9 + - - -
607A ARG* 2.9 27.8 + - - +
608A GLN 4.1 11.0 - - - +
609A LEU 4.1 15.0 - - - +
610A GLY* 3.7 16.8 - - - -
611A ASN* 4.8 4.9 + - - +
530B GLU 3.2 13.6 + - - +
531B THR* 3.3 14.1 - - + +
532B GLN 3.2 0.2 - - - -
533B MET* 1.3 78.6 - - - +
535B ASN* 1.3 62.7 + - - +
537B GLY* 3.7 1.0 + - - -
538B ASN* 3.3 24.0 + - - +
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Residues in contact with ASN 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A GLN* 3.2 39.2 + - - +
608A GLN 4.4 5.7 - - - +
531B THR* 3.3 20.6 + - - +
532B GLN* 3.0 3.3 + - - +
534B GLN* 1.3 77.7 - - - +
536B MET* 1.3 60.4 + - - +
538B ASN* 3.9 8.6 + - - +
539B LEU* 3.2 32.8 + - + +
551B ARG 5.1 2.2 - - - +
552B THR* 3.3 38.1 + - - +
553B GLY 4.3 9.5 + - - -
554B VAL* 4.5 5.7 - - - +
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Residues in contact with MET 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLN* 2.8 22.6 + - + +
535B ASN* 1.3 75.5 - - - +
537B GLY* 1.3 63.8 + - - +
538B ASN 3.2 0.4 - - - -
540B SER* 3.2 32.8 + - - +
542B ASN 5.4 1.0 - - - +
546B LYS* 3.3 27.1 - - + +
547B ARG 4.7 0.2 - - - -
548B GLY* 4.0 20.9 - - - +
552B THR* 3.7 24.7 - - + -
604B TYR 4.6 1.1 - - - +
605B THR 4.3 0.2 - - - -
606B TYR* 3.7 40.2 - - + +
609B LEU* 3.9 28.3 - - - -
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Residues in contact with GLY 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B MET 3.4 12.9 + - - -
534B GLN 4.1 2.7 - - - -
536B MET* 1.3 78.1 - - - +
538B ASN* 1.3 59.5 + - - +
540B SER 4.7 0.7 - - - -
541B ALA* 4.3 11.7 + - - -
542B ASN 6.1 1.1 - - - -
606B TYR* 4.3 12.4 - - - -
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Residues in contact with ASN 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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576A GLN* 5.5 0.6 - - - +
607A ARG* 3.4 31.2 + - - +
608A GLN* 3.1 45.3 + - - +
534B GLN* 3.3 18.8 + - - +
535B ASN* 4.1 8.6 + - - +
536B MET 3.2 0.8 - - - -
537B GLY* 1.3 79.4 - - - +
539B LEU* 1.3 65.7 + - + +
541B ALA* 4.2 8.1 + - - +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573A THR 5.7 3.6 - - - +
574A LYS 4.5 13.9 - - - +
535B ASN* 3.2 17.0 + - + +
538B ASN* 1.3 81.6 - - + +
540B SER* 1.3 66.7 + - - +
541B ALA* 3.6 1.3 - - - +
551B ARG* 3.5 71.8 - - + +
552B THR* 4.8 8.7 - - + -
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Residues in contact with SER 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B MET* 3.2 19.8 + - - -
539B LEU* 1.3 84.3 - - - +
541B ALA* 1.3 69.5 + - - +
542B ASN* 3.3 30.0 + - - +
544B GLY 5.5 1.0 + - - -
546B LYS* 5.0 17.8 - - - +
552B THR* 6.3 1.1 - - - -
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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) + - + + + + + -
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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