Contacts of the helix formed by residues 519 - 544 (chain B) in PDB entry 2XER
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 ARG 519 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ASP* 3.2 8.4 - - + +
518B LYS* 1.3 82.4 - - + +
520B ARG* 1.3 57.6 + - + +
521B LYS 3.4 0.2 - - - -
522B THR* 3.9 7.7 - - - -
523B LEU* 3.1 49.3 + - + +
586B GLN* 5.7 0.4 - - - -
589B CYS* 4.7 10.1 + - - +
590B ILE* 4.0 38.6 - - + +
591B ARG 5.5 0.4 - - - +
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Residues in contact with ARG 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ASP* 3.2 34.9 - - - +
518B LYS 2.8 0.2 - - - -
519B ARG* 1.3 80.6 - - + +
521B LYS* 1.3 59.7 + - + +
523B LEU* 3.7 8.3 + - + +
524B VAL* 3.1 29.6 + - - +
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Residues in contact with LYS 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ASP 5.0 2.7 - - - +
518B LYS* 2.8 19.7 + - + +
520B ARG* 1.3 75.9 - - + +
522B THR* 1.3 62.3 + - - +
524B VAL* 3.5 8.6 + - - +
525B ILE* 3.2 28.1 + - - +
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Residues in contact with THR 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B LYS 3.2 8.3 + - - -
519B ARG* 4.0 9.1 - - - -
520B ARG 3.3 0.2 - - - -
521B LYS* 1.3 74.4 - - - +
523B LEU* 1.3 56.7 + - - +
524B VAL 3.0 4.7 - - - -
525B ILE* 3.0 9.0 + - + +
526B ILE* 2.9 27.5 + - + +
583B HIS* 5.1 7.2 + - + +
586B GLN* 2.8 29.6 + - + +
587B ILE* 4.0 35.2 - - + +
590B ILE* 3.7 22.4 - - + -
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B ARG* 3.1 45.7 + - + +
520B ARG* 4.1 9.2 - - + +
521B LYS 3.5 0.2 - - - -
522B THR* 1.3 76.4 - - - +
524B VAL* 1.3 58.5 + - + +
526B ILE* 4.0 10.2 - - + +
527B GLU* 3.1 32.9 + - - +
590B ILE* 3.7 35.2 - - + -
592B LYS* 6.1 2.0 - - + -
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Residues in contact with VAL 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520B ARG 3.1 17.4 + - - +
521B LYS* 3.6 11.7 - - - +
522B THR 3.0 0.2 - - - -
523B LEU* 1.3 78.7 - - + +
525B ILE* 1.3 61.4 + - + +
526B ILE 3.3 0.2 - - - -
527B GLU* 3.4 5.2 + - + +
528B LYS* 2.9 55.3 + - + +
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Residues in contact with ILE 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521B LYS 3.2 17.0 + - - +
522B THR* 3.0 10.4 + - - +
524B VAL* 1.3 75.1 - - + +
526B ILE* 1.3 63.9 + - - +
528B LYS* 3.3 12.4 + - + +
529B THR* 2.7 40.0 + - - +
568B ASN* 4.3 23.3 + - + +
569B LEU* 5.9 0.4 - - + -
583B HIS* 3.7 29.6 - - + +
587B ILE* 3.9 26.9 - - + -
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Residues in contact with ILE 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B THR* 2.9 18.8 + - + +
523B LEU* 4.0 10.5 - - + +
525B ILE* 1.3 77.6 - - - +
527B GLU* 1.3 56.2 + - - +
529B THR 3.2 1.2 + - - -
530B TYR* 2.6 35.0 + - + +
587B ILE* 4.0 22.2 - - + -
590B ILE* 3.6 37.5 - - + -
592B LYS* 4.3 27.1 - - + -
593B GLY* 3.6 24.9 - - - +
596B MET* 3.5 20.8 - - + +
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Residues in contact with GLU 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LEU* 3.1 22.0 + - - +
524B VAL* 3.4 6.8 + - - +
525B ILE 3.3 0.4 - - - -
526B ILE* 1.3 78.3 - - - +
528B LYS* 1.3 65.8 + - - +
530B TYR* 3.8 6.9 - - - +
531B SER* 3.0 25.3 + - - -
592B LYS* 2.9 40.2 + - - +
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Residues in contact with LYS 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524B VAL* 2.9 41.6 + - + +
525B ILE* 3.7 14.4 - - + +
527B GLU* 1.3 77.0 - - - +
529B THR* 1.3 61.2 - - - +
531B SER* 3.6 7.6 - - - -
532B LEU* 3.5 24.4 + - + +
568B ASN* 4.5 9.2 - - - +
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Residues in contact with THR 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B ILE* 2.7 24.8 + - - +
526B ILE 3.7 2.9 - - - -
528B LYS* 1.3 75.4 - - - +
530B TYR* 1.3 59.6 + - - +
531B SER 3.1 2.0 - - - -
532B LEU* 3.0 8.6 + - - +
533B LEU 2.9 23.6 + - - -
565B MET* 3.5 47.5 - - + +
568B ASN* 2.8 23.2 + - + +
569B LEU* 4.8 2.1 - - + +
596B MET* 4.0 20.4 - - + -
600B ILE* 4.2 3.6 - - + -
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Residues in contact with TYR 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B ILE 2.6 22.8 + - - +
527B GLU* 3.2 10.1 + - - +
529B THR* 1.3 73.5 - - - +
531B SER* 1.3 57.0 + - - +
533B LEU* 3.8 7.9 - - + +
534B LEU* 3.2 51.2 + - + +
592B LYS* 3.9 36.6 - - + -
595B ARG* 4.6 13.2 + - - -
596B MET* 3.7 31.6 - - + -
599B ARG* 3.5 37.4 + - - -
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Residues in contact with SER 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527B GLU 3.0 16.2 + - - -
528B LYS* 3.6 8.5 - - - -
530B TYR* 1.3 78.0 - - - +
532B LEU* 1.3 61.7 + - - +
534B LEU* 3.7 8.0 + - - +
535B ASP* 3.3 29.8 + - - +
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Residues in contact with LEU 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528B LYS* 3.5 15.7 + - + +
529B THR* 3.0 13.2 + - - +
531B SER* 1.3 77.0 - - - +
533B LEU* 1.3 66.4 + - - +
535B ASP* 3.0 12.6 + - - +
536B VAL* 2.9 24.8 + - - +
560B HIS* 6.4 0.9 - - + -
561B LYS* 4.0 32.8 - - + +
564B SER* 3.9 24.2 - - - +
565B MET* 3.7 25.1 - - + +
568B ASN* 4.3 10.8 - - - +
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Residues in contact with LEU 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B THR 2.9 10.2 + - - +
530B TYR* 3.8 14.1 - - + +
532B LEU* 1.3 76.3 - - - +
534B LEU* 1.3 53.3 + - + +
536B VAL* 3.0 3.1 + - + -
537B GLU* 2.8 73.9 + - + +
565B MET* 3.4 26.3 - - + +
596B MET* 4.1 21.5 - - + +
599B ARG* 3.5 51.8 - - + +
600B ILE* 4.4 0.4 - - + -
603B PHE* 3.9 9.6 - - + -
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Residues in contact with LEU 534 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530B TYR* 3.2 47.6 + - + +
531B SER* 4.0 8.5 - - - +
532B LEU 3.3 0.2 - - - -
533B LEU* 1.3 78.1 - - - +
535B ASP* 1.3 58.2 + - - +
537B GLU* 3.9 16.3 - - + +
538B ASP* 3.0 29.3 + - - +
599B ARG* 4.2 8.1 - - - +
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Residues in contact with ASP 535 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B SER* 3.3 17.7 + - - +
532B LEU* 3.0 15.8 + - - +
534B LEU* 1.3 78.3 - - - +
536B VAL* 1.3 59.0 + - - +
538B ASP* 2.9 26.3 + - - +
539B TYR* 2.9 17.2 - - + -
561B LYS* 3.3 36.9 + - + +
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Residues in contact with VAL 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU 2.9 19.4 + - - +
533B LEU* 3.6 8.3 - - - +
535B ASP* 1.3 75.5 - - - +
537B GLU* 1.3 60.4 + - - +
538B ASP 3.5 0.3 + - - -
539B TYR* 3.5 22.9 + - - +
540B GLU* 4.1 7.4 - - - +
558B ARG* 3.6 25.4 - - + -
561B LYS* 3.8 27.6 - - + -
562B ILE* 3.8 17.0 - - + -
565B MET* 4.3 7.2 - - - -
603B PHE* 3.6 34.3 - - + -
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Residues in contact with GLU 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533B LEU* 2.8 49.2 + - + +
534B LEU* 4.1 11.6 - - + +
536B VAL* 1.3 70.0 - - - +
538B ASP* 1.3 63.9 + - - +
539B TYR 3.2 0.4 + - - -
540B GLU* 3.7 18.2 + - - +
541B ARG* 4.4 2.3 + - - +
599B ARG* 3.0 48.6 + - - +
603B PHE* 3.7 18.0 - - + -
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Residues in contact with ASP 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B LEU 3.0 18.9 + - - +
535B ASP* 2.9 10.7 + - - +
537B GLU* 1.3 77.9 - - - +
539B TYR* 1.3 57.1 + - - +
540B GLU 3.1 1.1 - - - -
541B ARG* 2.9 50.4 + - - +
542B ARG* 3.0 34.6 + - - +
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Residues in contact with TYR 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ASP* 2.9 34.5 + - + -
536B VAL* 3.5 20.6 - - - +
537B GLU 3.2 0.4 - - - -
538B ASP* 1.3 77.4 - - - +
540B GLU* 1.3 52.7 + - - +
542B ARG* 3.4 19.8 + - - +
543B TYR* 2.6 66.3 + - + -
554B LEU* 3.4 33.7 - - + -
555B MET* 5.8 1.2 - - - +
556B ASP* 3.6 14.8 + - - -
557B ASP* 3.4 18.9 + - - +
558B ARG* 3.8 15.3 - - - +
561B LYS* 3.1 33.3 + - + -
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Residues in contact with GLU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL 4.1 8.0 - - - +
537B GLU* 3.7 11.1 + - - +
538B ASP 3.1 0.8 - - - -
539B TYR* 1.3 77.8 - - - +
541B ARG* 1.3 60.3 + - - +
543B TYR* 3.9 9.8 - - + +
544B LEU* 3.9 17.5 + - - +
558B ARG* 4.1 9.4 + - - +
603B PHE* 4.0 24.4 - - - -
638C SER* 3.3 30.1 + - - +
642C LEU* 6.0 2.5 - - - +
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Residues in contact with ARG 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B GLU 4.4 1.8 + - - +
538B ASP* 2.9 32.7 + - - +
540B GLU* 1.3 79.8 - - - +
542B ARG* 1.3 68.6 + - + +
543B TYR 3.2 2.0 + - - -
544B LEU* 3.6 7.3 + - - +
545B LEU* 3.5 17.5 + - + +
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Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B ASP* 3.0 40.9 + - - +
539B TYR* 3.4 20.5 + - - +
541B ARG* 1.3 84.5 - - + +
543B TYR* 1.3 60.3 + - - +
545B LEU* 3.1 32.4 - - + +
546B SER* 4.3 2.6 + - - -
554B LEU* 3.2 54.6 - - + +
555B MET* 4.9 5.5 - - - +
737C ILE* 5.4 0.2 - - - +
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Residues in contact with TYR 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B TYR* 2.6 47.3 + + + +
540B GLU* 3.9 15.3 - - + +
541B ARG 3.2 0.4 - - - -
542B ARG* 1.3 71.3 - - - +
544B LEU* 1.3 59.7 + - - +
545B LEU 2.8 9.1 + - - -
546B SER 3.3 10.2 + - - -
554B LEU* 3.8 20.0 - - + -
556B ASP* 3.1 30.6 + - - +
558B ARG* 3.1 33.3 + - - -
637C LEU* 5.8 7.4 - - + -
638C SER* 4.6 10.5 - - - -
641C SER* 5.5 2.0 - - - -
737C ILE* 3.3 27.5 - - + +
738C SER* 3.6 29.4 - - - -
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B GLU 3.9 10.4 + - - +
541B ARG* 3.6 9.8 + - - +
542B ARG 3.5 0.2 - - - -
543B TYR* 1.3 79.2 - - - +
545B LEU* 1.3 51.9 + - - +
546B SER 3.3 0.9 + - - -
547B LEU* 2.4 50.7 + - + +
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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