Contacts of the helix formed by residues 520 - 541 (chain A) in PDB entry 1UZF
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 TYR 520 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLN* 3.5 0.5 + - - -
457A PHE* 3.3 26.3 - + - -
460A PHE* 3.4 27.4 - + - -
461A SER* 3.7 24.4 - - - +
464A VAL* 3.6 29.2 - - + -
465A ASP* 2.9 9.5 + - - +
468A ARG* 3.1 12.8 - - - +
511A LYS* 3.8 5.6 - - + -
513A HIS* 3.3 42.6 - + + -
519A PRO* 1.3 72.3 - - - +
521A ILE* 1.3 65.9 + - - +
522A ARG 2.9 7.6 + - - -
523A TYR* 2.9 38.2 + + - +
524A PHE 3.9 1.6 + - - -
702A MCO 2.7 19.0 + - - -
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Residues in contact with ILE 521 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TRP 6.5 0.2 - - - -
221A ARG* 6.3 0.9 - - - -
224A TYR* 3.5 28.7 - - + +
229A LEU* 5.4 2.0 - - + -
233A LEU* 3.5 33.2 - - + -
461A SER 4.2 10.8 - - - +
462A TYR* 4.5 16.4 - - + +
465A ASP* 2.8 24.6 + - + +
466A GLN* 5.0 0.9 - - - +
469A TRP* 4.3 21.3 - - + +
519A PRO* 5.6 0.2 - - + -
520A TYR* 1.3 71.3 - - - +
522A ARG* 1.3 66.0 + - - +
523A TYR 3.1 0.4 - - - -
524A PHE* 3.0 32.1 + - + -
525A VAL* 3.1 16.1 + - + +
704A CL 3.8 6.5 - - + -
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Residues in contact with ARG 522 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A MET* 3.8 18.4 - - - +
224A TYR* 3.1 20.0 - - - +
407A PRO* 3.7 27.7 - - + +
408A GLY* 3.5 7.0 - - - -
411A GLU* 3.9 18.2 + - + +
518A VAL* 3.8 16.8 - - - +
519A PRO* 3.4 35.7 + - - +
520A TYR 2.9 0.6 + - - -
521A ILE* 1.3 81.9 - - - +
523A TYR* 1.3 84.0 + - + +
525A VAL* 3.5 1.0 + - - -
526A SER* 2.8 29.7 + - - -
704A CL 3.1 19.3 - - + +
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Residues in contact with TYR 523 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 5.3 0.2 - + - -
411A GLU* 3.2 37.5 + - + -
457A PHE* 3.6 23.7 - - + -
513A HIS* 3.0 37.4 + + - -
518A VAL* 4.1 6.2 - - - +
519A PRO 3.8 9.2 - - - -
520A TYR* 2.9 46.5 + + + +
522A ARG* 1.3 87.1 + - + +
524A PHE* 1.3 58.6 + - - +
526A SER* 4.0 4.3 - - - -
527A PHE* 3.0 37.3 + + + +
702A MCO 3.3 40.4 + - + +
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Residues in contact with PHE 524 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A LEU* 3.7 51.8 - - + -
236A LEU* 4.1 12.6 - - + -
237A PHE* 3.9 14.6 - - + -
458A ILE* 3.6 37.2 - - + +
461A SER* 3.3 37.4 - - - +
462A TYR* 3.8 19.5 - + + -
520A TYR 3.9 0.2 + - - -
521A ILE* 3.0 22.0 + - + +
523A TYR* 1.3 74.1 - - - +
525A VAL* 1.3 71.6 + - - +
527A PHE* 3.3 5.5 + - - +
528A ILE* 3.2 29.7 + - + +
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Residues in contact with VAL 525 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A TYR* 4.0 21.3 - - + +
229A LEU* 5.4 1.1 - - + -
233A LEU* 4.0 26.0 - - + -
236A LEU* 6.3 0.2 - - - -
406A ASN* 4.3 9.4 - - - +
408A GLY* 3.9 17.9 - - - -
409A PHE* 5.7 0.2 - - + -
521A ILE* 3.1 13.9 + - + +
522A ARG 3.7 7.0 - - - +
524A PHE* 1.3 78.9 - - + +
526A SER* 1.3 63.8 + - - +
528A ILE* 3.1 6.5 + - - +
529A ILE* 2.9 37.1 + - + +
587A MET* 4.0 23.6 - - + -
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Residues in contact with SER 526 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A HIS* 5.4 0.3 - - - -
408A GLY 3.7 6.3 - - - -
411A GLU* 3.3 22.2 + - - +
412A ALA* 3.3 21.0 + - - -
415A ASP* 4.3 0.9 + - - -
522A ARG 2.8 17.9 + - - -
523A TYR* 3.5 8.1 - - - -
524A PHE 3.2 0.2 - - - -
525A VAL* 1.3 77.2 - - - +
527A PHE* 1.3 62.1 + - - +
529A ILE* 3.6 8.7 - - - +
530A GLN* 2.9 43.7 + - - +
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Residues in contact with PHE 527 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A THR* 5.7 0.9 - - + -
383A HIS* 6.3 0.7 - + - -
415A ASP* 3.6 16.4 - - - -
453A ASP* 4.2 9.2 - - - -
454A LYS* 3.4 54.1 - - + -
457A PHE* 3.3 46.7 - + + -
458A ILE* 4.1 14.6 - - + -
523A TYR* 3.0 23.2 + + + +
524A PHE* 3.3 4.5 + - - +
526A SER* 1.3 79.8 - - - +
528A ILE* 1.3 59.2 + - - +
530A GLN* 3.4 12.6 - - - +
531A PHE* 3.1 30.1 - - - -
592A MET* 3.7 5.3 - - + +
702A MCO 4.6 15.3 - - + -
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Residues in contact with ILE 528 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 4.3 26.2 - - + -
240A LEU* 3.1 35.7 - - + -
458A ILE* 4.1 10.8 - - + -
524A PHE* 3.2 28.6 + - + +
525A VAL* 3.1 9.3 + - - +
527A PHE* 1.3 78.9 - - - +
529A ILE* 1.3 67.4 + - + +
531A PHE* 3.4 14.9 + - - +
532A GLN* 3.6 15.3 + - - +
587A MET* 4.9 0.7 - - + -
588A SER 3.4 27.7 - - - +
589A ALA* 4.5 5.6 - - + -
592A MET* 4.3 7.4 + - - +
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Residues in contact with ILE 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A GLY 3.8 21.3 - - - +
409A PHE* 3.7 31.9 - - + +
412A ALA* 3.9 5.4 - - + -
525A VAL* 2.9 26.4 + - + +
526A SER* 3.6 6.1 - - - +
528A ILE* 1.3 75.9 - - + +
530A GLN* 1.3 63.3 + - - +
531A PHE 3.1 0.2 - - - -
532A GLN* 2.9 24.6 + - - +
533A PHE* 2.8 46.9 + - + -
578A MET* 3.8 15.7 - - + -
587A MET* 4.0 17.0 - - + -
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Residues in contact with GLN 530 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A ALA* 4.1 7.9 - - + +
415A ASP* 2.9 34.5 + - + +
416A VAL* 3.8 24.6 - - + +
419A LEU* 4.0 10.8 - - + +
454A LYS* 2.9 31.4 + - - +
526A SER* 2.9 31.3 + - - +
527A PHE* 3.4 24.2 - - - +
529A ILE* 1.3 77.5 - - - +
531A PHE* 1.3 67.8 + - + +
533A PHE* 3.6 5.1 - - - +
534A HIS* 2.9 28.1 + - - +
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Residues in contact with PHE 531 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A LEU* 3.9 18.2 - - + -
450A MET* 5.5 0.2 - - + -
454A LYS* 3.8 24.5 - - + -
527A PHE 3.1 21.8 - - - -
528A ILE 3.4 4.7 + - - +
529A ILE 3.1 0.8 - - - -
530A GLN* 1.3 89.7 - - + +
532A GLN* 1.3 62.8 + - - +
534A HIS* 3.7 5.2 - + - +
535A GLU* 2.9 24.6 + - - +
547A LEU* 4.7 2.0 - - + +
591A ALA* 3.2 11.6 - - - +
592A MET* 3.4 49.8 - - + +
595A TYR* 3.5 54.1 - + + -
596A PHE* 3.8 11.9 - + - -
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Residues in contact with GLN 532 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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528A ILE* 3.6 4.3 + - - +
529A ILE* 2.9 28.1 + - - +
531A PHE* 1.3 80.4 - - - +
533A PHE* 1.3 58.6 + - + +
535A GLU* 3.6 5.3 - - - +
536A ALA* 3.0 29.1 + - - +
578A MET* 3.9 6.1 - - - -
582A THR* 3.8 12.6 - - + +
584A GLN* 3.3 14.3 - - - +
586A ASN 3.0 24.5 + - - -
587A MET* 3.5 7.3 - - - -
588A SER* 2.9 48.0 + - - +
591A ALA* 3.5 14.8 - - + +
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Residues in contact with PHE 533 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 3.7 29.8 - + - -
412A ALA* 4.0 22.2 - - + -
413A ILE* 4.6 12.8 - - + -
416A VAL* 3.7 24.9 - - + -
529A ILE* 2.8 32.0 + - + -
530A GLN 3.6 6.1 - - - +
532A GLN* 1.3 76.9 - - + +
534A HIS* 1.3 55.4 + - - +
536A ALA* 3.2 1.4 + - - +
537A LEU* 2.7 43.6 + - + +
562A LEU* 4.9 3.4 - - + -
578A MET* 3.9 26.2 - - + -
581A ILE* 3.7 41.7 - - + -
582A THR* 4.0 2.5 - - + -
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Residues in contact with HIS 534 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL* 4.3 13.6 + - + +
419A LEU* 3.8 31.0 - - + +
420A SER* 3.9 15.6 + - - -
423A THR* 6.0 0.2 - - + -
530A GLN 2.9 18.1 + - - +
531A PHE* 3.7 6.1 - + - +
532A GLN 3.4 0.2 - - - -
533A PHE* 1.3 73.8 - - - +
535A GLU* 1.3 58.4 + - - +
537A LEU* 3.3 2.9 + - - +
538A CYS* 2.8 55.1 + - - -
547A LEU* 3.5 39.7 + - + -
548A HIS* 5.0 0.6 - - - -
550A CYS* 3.8 16.4 + - - +
552A ILE* 4.8 2.8 - - - +
595A TYR* 4.1 20.8 - + - -
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Residues in contact with GLU 535 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531A PHE 2.9 18.1 + - - +
532A GLN* 3.6 5.6 - - - +
534A HIS* 1.3 77.3 - - - +
536A ALA* 1.3 64.1 + - - +
538A CYS* 3.7 1.7 - - - +
539A GLN* 3.0 24.8 + - + +
547A LEU* 3.7 26.4 - - + +
590A SER* 5.0 2.3 - - - -
591A ALA* 3.7 26.1 + - + +
594A SER* 4.4 12.8 + - - -
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Residues in contact with ALA 536 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532A GLN 3.0 17.6 + - - +
533A PHE 3.2 3.6 + - - +
535A GLU* 1.3 77.0 + - - +
537A LEU* 1.3 59.2 + - - +
539A GLN* 3.3 10.5 + - - +
540A ALA* 2.9 27.3 + - - +
561A ARG* 4.0 6.9 + - - +
581A ILE* 3.4 27.4 - - + +
582A THR* 3.8 19.1 - - + +
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Residues in contact with LEU 537 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A VAL* 3.7 28.7 - - + -
533A PHE* 2.7 23.1 + - + +
534A HIS* 3.9 3.6 - - - +
536A ALA* 1.3 73.4 - - - +
538A CYS* 1.3 58.0 + - - +
540A ALA* 3.1 6.5 + - - +
541A ALA* 2.9 28.1 + - - +
552A ILE* 4.1 19.7 - - + -
558A ALA* 3.4 39.8 - - + +
561A ARG* 4.0 19.5 - - + -
562A LEU* 3.8 30.7 - - + -
581A ILE* 4.7 7.9 - - + -
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Residues in contact with CYS 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534A HIS* 2.8 50.0 + - - +
535A GLU 3.7 3.8 - - - +
537A LEU* 1.3 69.0 - - - +
539A GLN* 1.3 66.3 + - - +
541A ALA* 3.0 9.1 + - - +
542A GLY 3.1 0.2 + - - -
543A HIS* 3.0 30.7 + - + +
547A LEU* 4.1 9.4 - - + -
550A CYS* 2.0 53.8 - - + -
552A ILE* 3.7 6.5 - - - -
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Residues in contact with GLN 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A GLU* 3.0 18.2 + - + +
536A ALA* 3.6 8.4 + - - +
538A CYS* 1.3 76.5 - - - +
540A ALA* 1.3 68.7 + - - +
542A GLY* 3.1 13.9 + - - +
543A HIS 4.7 8.1 - - - +
561A ARG* 4.0 17.0 - - - +
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Residues in contact with ALA 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA 2.9 14.3 + - - +
537A LEU* 3.1 14.1 + - - +
539A GLN* 1.3 85.3 - - - +
541A ALA* 1.3 56.8 + - - +
542A GLY 3.2 1.0 + - - -
557A GLU* 3.5 39.1 - - + +
558A ALA* 4.8 0.2 - - - -
561A ARG* 4.0 28.3 - - - +
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Residues in contact with ALA 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A LEU 2.9 14.7 + - - +
538A CYS* 3.0 9.6 + - - +
540A ALA* 1.3 76.5 - - - +
542A GLY* 1.3 60.4 + - - +
543A HIS* 3.4 3.5 + - + +
550A CYS* 5.7 0.9 - - - -
551A ASP 5.6 1.3 - - - +
552A ILE* 4.8 10.5 - - + -
555A SER* 3.6 30.0 + - - +
557A GLU* 4.9 3.8 - - - +
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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