Contacts of the helix formed by residues 519 - 544 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 2.9 11.3 - - - +
518A LYS* 1.3 78.3 - - - +
520A ARG* 1.3 56.3 + - - +
522A THR* 4.5 6.5 - - - -
523A LEU* 3.0 45.6 + - + +
589A CYS 5.3 2.2 + - - -
590A ILE* 3.9 42.0 - - + +
591A ARG 5.2 1.4 - - - +
630A ASP* 5.8 1.2 + - - -
766B VAL 4.1 18.1 + - - -
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Residues in contact with ARG 520 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517A ASP* 2.9 30.5 + - - +
518A LYS 2.8 0.6 - - - -
519A ARG* 1.3 80.7 - - - +
521A LYS* 1.3 61.8 + - - +
523A LEU* 3.3 24.9 - - + +
524A VAL* 3.5 13.6 + - + +
766B VAL* 5.5 9.5 - - - +
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Residues in contact with LYS 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LYS* 2.9 28.0 + - + +
520A ARG* 1.3 77.2 - - - +
522A THR* 1.3 69.4 + - - +
524A VAL* 3.0 28.4 + - - +
525A ILE* 3.4 13.6 + - + +
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Residues in contact with THR 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518A LYS* 2.9 15.3 + - - -
519A ARG* 4.1 5.4 - - - -
521A LYS* 1.3 78.5 - - - +
523A LEU* 1.3 63.4 + - - +
525A ILE* 2.9 22.0 + - + +
526A ILE* 3.0 12.0 + - + +
586A GLN* 2.7 34.0 + - - +
587A ILE* 3.9 37.7 - - + +
590A ILE* 3.8 18.4 - - + -
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Residues in contact with LEU 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519A ARG* 3.0 50.1 + - + +
520A ARG* 3.3 12.1 - - - +
521A LYS 3.2 0.4 - - - -
522A THR* 1.3 76.8 - - - +
524A VAL* 1.3 57.1 + - + +
526A ILE* 3.4 11.8 + - + +
527A GLU* 3.1 39.7 + - + +
590A ILE* 3.8 30.7 - - + -
592A LYS* 5.8 4.5 - - + -
766B VAL 6.0 0.9 - - - +
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Residues in contact with VAL 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520A ARG* 3.6 17.0 - - + +
521A LYS* 3.0 16.9 + - + +
523A LEU* 1.3 76.4 - - + +
525A ILE* 1.3 67.9 + - + +
527A GLU* 3.3 5.0 + - + +
528A LYS* 2.9 52.1 + - - +
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Residues in contact with ILE 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521A LYS* 4.0 17.3 - - + +
522A THR* 2.9 14.9 + - + +
524A VAL* 1.3 79.7 - - + +
526A ILE* 1.3 55.6 + - - +
528A LYS* 3.5 10.0 - - + +
529A THR* 2.8 41.3 + - - +
568A ASN* 3.5 34.5 + - + +
583A HIS* 3.9 21.1 - - + +
587A ILE* 3.9 16.8 - - + -
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Residues in contact with ILE 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A THR* 3.0 16.1 + - + +
523A LEU* 3.5 12.1 - - + +
525A ILE* 1.3 74.6 - - - +
527A GLU* 1.3 56.2 + - - +
529A THR* 3.0 3.1 + - - -
530A TYR* 2.5 37.2 + - + +
587A ILE* 4.0 23.6 - - + +
590A ILE* 3.7 37.9 - - + -
592A LYS* 3.6 33.0 - - + -
593A GLY* 3.8 20.9 - - - +
596A MET* 3.5 22.3 - - + +
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Residues in contact with GLU 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523A LEU* 3.1 24.0 + - + +
524A VAL* 3.9 5.4 - - - +
526A ILE* 1.3 78.0 - - - +
528A LYS* 1.3 63.1 + - - +
530A TYR* 3.5 10.7 - - - +
531A SER* 2.9 26.3 + - - -
592A LYS* 3.2 37.3 + - - +
535C ASP* 5.7 1.7 - - - +
1765C SO4 4.5 2.4 + - - -
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Residues in contact with LYS 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524A VAL* 2.9 42.1 + - - +
525A ILE* 3.5 12.8 - - + +
527A GLU* 1.3 75.6 - - - +
529A THR* 1.3 61.8 + - - +
531A SER* 3.7 6.6 + - - -
532A LEU* 3.6 21.6 + - + +
568A ASN* 4.3 13.0 - - - +
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Residues in contact with THR 529 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A ILE* 2.8 23.9 + - - +
526A ILE 3.5 3.1 - - - -
528A LYS* 1.3 74.6 - - - +
530A TYR* 1.3 65.4 + - - +
532A LEU* 3.1 8.8 + - - +
533A LEU 3.0 16.6 + - - -
565A MET* 3.8 38.8 - - + +
568A ASN* 3.0 27.9 + - + +
569A LEU* 4.6 3.2 - - + +
596A MET* 4.0 10.5 - - + -
600A ILE* 3.9 20.4 - - + -
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Residues in contact with TYR 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526A ILE* 2.5 21.7 + - + +
527A GLU* 3.1 17.2 + - - +
529A THR* 1.3 73.7 - - - +
531A SER* 1.3 62.4 + - - +
533A LEU* 3.0 19.7 + - + +
534A LEU* 3.1 32.7 + - + +
592A LYS* 4.0 33.0 - - + -
595A ARG* 6.4 0.7 - - + -
596A MET* 3.8 30.0 - - + -
599A ARG* 2.8 33.7 + - - -
535C ASP* 5.5 4.5 - - - -
538C ASP* 2.7 29.9 + - - -
542C ARG* 3.2 14.7 + - - -
1767C SO4 5.7 1.3 - - - -
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Residues in contact with SER 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A GLU 2.9 15.4 + - - -
528A LYS* 3.8 7.2 - - - -
530A TYR* 1.3 79.7 - - - +
532A LEU* 1.3 61.4 + - - +
533A LEU 3.4 0.2 + - - -
534A LEU* 3.4 10.2 + - - +
535A ASP* 3.3 21.1 + - - +
531C SER* 4.1 22.9 + - - -
534C LEU* 5.7 0.3 - - - +
535C ASP* 5.6 2.2 + - - -
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Residues in contact with LEU 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
528A LYS* 3.6 15.4 + - + +
529A THR* 3.1 13.6 + - - +
531A SER* 1.3 78.4 - - - +
533A LEU* 1.3 62.8 + - - +
535A ASP* 3.4 6.4 + - + +
536A VAL* 3.1 29.1 + - - +
561A LYS* 4.0 34.0 - - + +
564A SER* 3.8 29.2 - - - -
565A MET* 3.9 21.3 - - + +
568A ASN* 4.5 7.6 - - - +
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Residues in contact with LEU 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529A THR 3.0 8.7 + - - +
530A TYR* 3.2 16.6 - - + +
532A LEU* 1.3 76.9 - - - +
534A LEU* 1.3 59.0 + - + +
536A VAL* 3.1 3.8 + - + -
537A GLU* 2.8 64.2 + - + +
565A MET* 3.4 26.6 - - + +
596A MET* 4.0 24.5 - - + +
599A ARG* 3.6 37.9 - - + +
600A ILE* 4.2 0.7 - - + -
603A PHE* 3.8 17.9 - - + -
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Residues in contact with LEU 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
530A TYR* 3.1 38.3 + - + +
531A SER* 3.9 9.6 - - - +
533A LEU* 1.3 76.7 - - + +
535A ASP* 1.3 57.3 + - - +
537A GLU* 3.3 8.3 + - - +
538A ASP* 2.8 31.4 + - - +
541A ARG* 4.9 3.6 + - - +
599A ARG* 3.5 19.3 - - - +
531C SER 5.5 0.4 - - - +
534C LEU* 3.9 24.5 - - + +
535C ASP* 4.2 15.3 - - + +
538C ASP* 3.4 40.4 - - + +
541C ARG* 6.0 1.3 - - - +
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Residues in contact with ASP 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531A SER 3.3 11.0 + - - +
532A LEU* 3.6 11.0 - - + +
533A LEU 3.2 0.6 - - - -
534A LEU* 1.3 78.1 - - - +
536A VAL* 1.3 61.3 + - - +
538A ASP* 3.2 3.8 + - - +
539A TYR* 3.2 22.0 + - - +
558A ARG* 3.2 23.4 + - - -
561A LYS* 3.0 34.6 - - + +
527C GLU* 4.8 8.3 - - - +
530C TYR* 4.7 9.0 - - - -
531C SER* 6.0 1.6 - - - +
534C LEU* 3.8 19.5 - - + +
592C LYS* 4.8 2.1 + - - -
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Residues in contact with VAL 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532A LEU 3.1 16.4 + - - +
533A LEU* 3.1 8.0 + - - +
535A ASP* 1.3 76.2 - - - +
537A GLU* 1.3 61.2 + - - +
539A TYR* 3.6 5.2 + - - +
540A GLU* 3.3 22.0 + - - +
555A MET* 6.2 4.5 - - + -
558A ARG* 5.3 10.5 - - + +
561A LYS* 4.2 26.9 - - + -
562A ILE* 3.9 18.2 - - + -
565A MET* 4.5 7.0 - - - -
603A PHE* 3.3 37.9 - - + -
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Residues in contact with GLU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
533A LEU* 2.8 36.9 + - - +
534A LEU* 3.5 15.3 - - - +
536A VAL* 1.3 75.0 - - - +
538A ASP* 1.3 60.2 + - - +
540A GLU* 3.7 8.9 - - - +
541A ARG* 3.0 49.4 + - - +
599A ARG* 2.9 49.4 + - - +
603A PHE* 3.7 20.1 - - + -
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Residues in contact with ASP 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU 2.8 17.3 + - - +
535A ASP* 3.4 7.3 - - - +
537A GLU* 1.3 76.2 - - - +
539A TYR* 1.3 66.7 + - - +
541A ARG* 3.3 13.3 + - - +
542A ARG* 3.0 47.7 + - - +
558A ARG* 5.9 0.3 + - - -
530C TYR* 2.6 37.1 + - + -
534C LEU* 3.8 15.1 - - + +
592C LYS* 5.1 2.3 + - - -
599C ARG* 3.4 21.8 + - - -
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Residues in contact with TYR 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A ASP 3.2 10.8 + - - +
536A VAL* 3.6 5.4 + - - +
538A ASP* 1.3 81.4 + - - +
540A GLU* 1.3 59.1 + - - +
542A ARG* 3.9 18.5 - - - +
543A TYR* 3.0 55.4 + + + +
551A ARG* 4.2 12.8 + - - -
553A ALA* 3.8 4.5 - - + -
554A LEU* 2.9 41.4 + - + +
555A MET* 3.6 31.0 - - + -
558A ARG* 3.6 44.6 - - + +
1766C SO4 5.7 2.7 - - - -
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Residues in contact with GLU 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A VAL 3.3 10.7 + - - +
537A GLU* 3.7 7.0 - - - +
539A TYR* 1.3 82.2 - - - +
541A ARG* 1.3 57.9 + - - +
543A TYR* 4.5 4.0 - - - -
544A LEU* 3.0 58.3 + - + +
602A PRO* 6.2 0.2 - - - +
603A PHE* 2.5 41.6 - - + -
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Residues in contact with ARG 541 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A LEU* 4.9 3.2 + - - +
537A GLU* 3.0 45.3 + - - +
538A ASP* 3.7 12.8 + - - +
539A TYR 3.3 0.2 - - - -
540A GLU* 1.3 80.7 - - - +
542A ARG* 1.3 68.9 + - + +
544A LEU* 3.1 16.3 + - - +
545A LEU* 3.2 27.8 + - + +
534C LEU* 6.4 0.2 - - - +
541C ARG* 3.9 45.5 - - - +
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Residues in contact with ARG 542 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538A ASP* 3.0 43.9 + - - +
539A TYR* 4.3 21.7 - - - +
541A ARG* 1.3 81.8 - - + +
543A TYR* 1.3 61.1 + - - +
544A LEU 3.4 0.2 - - - -
545A LEU* 3.9 7.5 + - - +
546A SER* 3.5 18.7 + - - -
558A ARG* 5.4 1.0 - - - +
530C TYR* 3.7 1.6 + - - -
591C ARG* 4.8 5.5 - - - +
592C LYS* 5.1 4.6 - - - +
595C ARG* 3.3 41.6 - - - +
599C ARG* 3.8 17.9 - - - +
1766C SO4 4.0 12.9 + - - -
----------------------------------------------------------
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Residues in contact with TYR 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A TYR* 3.0 44.2 + + + +
540A GLU* 3.9 3.4 - - - +
542A ARG* 1.3 77.2 - - - +
544A LEU* 1.3 77.9 + - + +
545A LEU 3.3 0.2 - - - -
546A SER* 3.2 19.7 + - - -
547A LEU* 3.8 26.5 - - + +
551A ARG* 3.2 36.8 + - - +
552A PRO* 4.2 1.8 - - - +
553A ALA* 3.3 39.9 + - + +
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Residues in contact with LEU 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A GLU* 3.0 48.7 + - + +
541A ARG* 3.1 6.9 + - - +
543A TYR* 1.3 96.0 - - + +
545A LEU* 1.3 61.6 + - + +
546A SER 3.3 3.6 + - - -
547A LEU* 3.6 24.3 + - + +
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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