Contacts of the helix formed by residues 469 - 490 (chain A) in PDB entry 5UFL
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 SER 469 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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465A LYS* 4.0 0.2 + - - -
468A ASP* 1.3 85.6 + - - +
470A GLU* 1.3 63.5 + - - +
471A LEU* 4.2 7.3 - - - +
472A CYS* 2.9 36.7 + - - +
473A LYS* 3.3 25.0 + - - +
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Residues in contact with GLU 470 (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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410A ARG* 3.9 26.5 - - - +
468A ASP 4.1 1.1 + - - +
469A SER* 1.3 70.6 - - - +
471A LEU* 1.3 60.5 + - - +
473A LYS* 2.9 35.0 + - - +
474A LEU* 2.9 47.7 + - + +
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Residues in contact with LEU 471 (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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406A GLU* 3.7 32.8 - - - +
409A THR* 3.9 29.8 - - + -
410A ARG* 3.9 25.8 - - + +
413A CYS* 4.2 16.8 - - + -
455A TYR 4.5 8.7 - - - +
456A GLY* 3.9 25.1 - - - +
457A LYS* 5.5 6.1 - - + -
469A SER* 3.3 7.3 - - - +
470A GLU* 1.3 79.0 - - - +
472A CYS* 1.3 57.9 + - - +
474A LEU* 3.9 1.3 - - - -
475A ALA* 3.0 32.9 + - - +
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Residues in contact with CYS 472 (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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456A GLY 4.5 5.2 - - - -
457A LYS 4.0 17.0 - - - -
458A ILE* 3.4 13.8 - - + +
465A LYS* 2.9 35.9 - - - +
468A ASP 5.5 0.7 - - - +
469A SER* 2.9 29.0 + - - +
470A GLU 3.3 0.6 - - - -
471A LEU* 1.3 80.0 - - - +
473A LYS* 1.3 58.3 + - - +
476A ALA* 3.1 31.7 + - - +
515A PHE* 3.7 15.2 - - + -
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Residues in contact with LYS 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ALA* 3.8 38.9 + - + +
468A ASP 5.0 3.0 + - - -
469A SER 3.3 16.6 + - - +
470A GLU* 2.9 41.1 + - - +
472A CYS* 1.3 78.2 - - - +
474A LEU* 1.3 57.7 + - + +
476A ALA* 3.8 1.7 - - - +
477A ASP* 3.0 28.6 + - - +
515A PHE* 4.0 10.2 - - + +
524A GLN* 5.4 1.7 + - - -
557A ARG* 4.3 17.4 - - - +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ARG* 3.8 43.3 - - + +
413A CYS* 4.0 13.7 - - + +
414A GLU* 4.5 25.6 - - + -
417A ALA* 5.5 3.8 - - + +
470A GLU* 2.9 34.7 + - + +
471A LEU* 3.9 2.9 - - - +
473A LYS* 1.3 75.5 - - + +
475A ALA* 1.3 59.3 + - - +
477A ASP* 3.2 10.0 + - + +
478A VAL* 3.0 33.6 + - - +
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Residues in contact with ALA 475 (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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413A CYS* 4.5 5.5 - - - +
452A GLN* 3.4 28.9 - - - +
456A GLY* 3.8 25.8 - - - -
458A ILE* 4.0 9.2 - - + -
471A LEU* 3.0 18.2 + - + +
474A LEU* 1.3 76.0 - - - +
476A ALA* 1.3 61.5 + - - +
478A VAL* 3.5 3.6 + - - +
479A ILE* 3.3 27.3 + - - +
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Residues in contact with ALA 476 (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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458A ILE* 3.6 9.1 - - + +
472A CYS 3.1 20.2 + - - +
473A LYS 3.8 2.0 - - - +
475A ALA* 1.3 76.6 - - - +
477A ASP* 1.3 62.1 + - - +
479A ILE* 3.2 6.1 + - - +
480A LEU* 3.1 20.7 + - - +
512A PRO* 3.7 35.5 - - + +
515A PHE* 3.7 24.2 - - + -
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Residues in contact with ASP 477 (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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417A ALA* 4.6 7.5 - - + +
473A LYS 3.0 19.7 + - - +
474A LEU* 3.2 11.5 + - + +
476A ALA* 1.3 74.1 - - - +
478A VAL* 1.3 60.3 + - - +
480A LEU* 3.4 6.5 + - - +
481A LYS* 2.7 67.2 + - - +
524A GLN* 3.1 32.3 + - - +
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Residues in contact with VAL 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A CYS* 3.4 27.4 - - + +
416A ILE* 3.6 22.7 - - + -
417A ALA* 4.0 13.7 - - + +
420A ILE* 5.1 2.5 - - + -
448A LEU* 4.5 3.4 - - + -
452A GLN* 3.5 31.2 - - + +
474A LEU 3.0 19.7 + - - +
475A ALA 3.7 7.9 - - - +
476A ALA 3.3 0.2 - - - -
477A ASP* 1.3 74.9 - - - +
479A ILE* 1.3 54.7 + - - +
481A LYS* 3.8 6.4 - - - +
482A THR* 2.7 46.6 + - - +
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Residues in contact with ILE 479 (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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449A ILE* 3.6 27.0 - - + +
452A GLN* 3.5 25.6 - - + +
453A PHE* 3.5 46.7 - - + +
458A ILE* 4.7 2.5 - - + -
475A ALA 3.3 18.3 + - - +
476A ALA* 3.2 12.0 + - - +
478A VAL* 1.3 78.3 - - - +
480A LEU* 1.3 59.0 + - + +
483A LEU* 3.0 31.5 + - + +
503A ILE* 5.8 0.2 - - + -
509A LEU* 4.1 24.7 - - + -
512A PRO* 4.7 5.2 - - + -
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Residues in contact with LEU 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476A ALA 3.1 11.7 + - - +
477A ASP* 4.0 7.4 - - - +
479A ILE* 1.3 74.3 - - - +
481A LYS* 1.3 60.3 - - + +
483A LEU* 3.4 4.7 + - - +
484A ASP* 2.9 28.2 + - - +
509A LEU* 3.7 22.2 - - + -
512A PRO* 3.3 40.2 - - + +
513A LEU* 4.2 9.9 - - + +
516A ALA* 3.4 33.2 - - + -
524A GLN* 5.3 0.7 - - - +
527A SER* 4.0 10.8 + - - +
528A GLY* 3.8 19.1 - - - +
531A ILE* 4.5 10.2 - - + +
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Residues in contact with LYS 481 (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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417A ALA* 4.1 22.2 - - + +
420A ILE* 3.6 22.9 - - + +
421A GLU* 3.4 36.6 + - + -
424A LEU* 4.1 10.5 - - + +
477A ASP* 2.7 52.3 + - - +
478A VAL* 3.8 4.0 - - - +
480A LEU* 1.3 74.6 - - + +
482A THR* 1.3 59.7 + - - +
484A ASP* 3.2 9.1 + - - +
485A LEU 2.9 23.4 + - - -
524A GLN* 5.2 5.9 - - - +
527A SER* 5.0 5.4 - - - +
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Residues in contact with THR 482 (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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420A ILE* 3.8 16.7 - - + +
445A CYS* 4.0 24.9 - - + +
448A LEU* 3.5 28.1 - - + +
449A ILE* 3.6 25.1 - - + -
478A VAL* 2.7 27.7 + - - +
481A LYS* 1.3 75.9 - - - +
483A LEU* 1.3 57.3 + - - +
485A LEU* 3.3 5.4 + - + +
486A ILE* 2.9 34.3 + - + +
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Residues in contact with LEU 483 (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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449A ILE* 4.4 6.5 - - + -
479A ILE* 3.0 25.7 + - + +
480A LEU* 3.6 7.0 - - - +
481A LYS 3.3 0.2 - - - -
482A THR* 1.3 73.1 - - - +
484A ASP* 1.3 60.4 + - - +
486A ILE* 3.3 11.5 + - + +
487A ASN* 2.8 30.1 + - - +
500A PHE* 3.5 20.1 - - + -
503A ILE* 3.8 20.9 - - + -
504A LEU* 3.6 23.6 - - + -
509A LEU* 3.4 41.3 - - + -
531A ILE* 3.8 19.7 - - + -
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Residues in contact with ASP 484 (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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424A LEU* 3.8 18.2 - - + +
480A LEU 2.9 15.4 + - - +
481A LYS* 3.2 12.0 + - - +
483A LEU* 1.3 76.6 - - - +
485A LEU* 1.3 61.3 + - - +
487A ASN* 3.5 11.0 + - - +
488A LYS* 3.2 35.1 + - - +
527A SER* 4.1 16.5 + - - +
530A ARG* 2.6 35.1 + - - +
531A ILE* 4.0 7.4 - - + +
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Residues in contact with LEU 485 (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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397A LEU* 5.2 0.7 - - + -
420A ILE* 4.1 21.5 - - + -
423A LEU* 3.9 38.1 - - + +
424A LEU* 3.6 13.6 - - + +
427A CYS* 3.8 22.4 - - - -
436A ILE* 5.0 1.3 - - + -
440A LEU* 3.7 23.3 - - + -
445A CYS* 5.1 5.2 - - - -
481A LYS 2.9 12.7 + - - +
482A THR* 3.5 9.9 - - + +
484A ASP* 1.3 73.3 - - - +
486A ILE* 1.3 63.2 + - - +
488A LYS* 3.3 3.9 + - - +
489A LEU* 3.1 42.2 + - + +
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Residues in contact with ILE 486 (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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445A CYS* 3.8 35.9 - - + -
446A THR* 5.2 1.1 - - + +
449A ILE* 4.8 2.9 - - + -
482A THR* 2.9 28.6 + - + +
483A LEU* 3.3 14.1 + - + +
485A LEU* 1.3 75.4 - - - +
487A ASN* 1.3 56.7 + - - +
489A LEU* 3.2 2.1 + - - -
490A LYS* 2.9 29.7 + - + +
496A MET* 3.6 31.3 - - + +
499A SER* 6.3 0.2 - - - -
500A PHE* 3.5 30.1 - - + +
503A ILE* 4.4 22.2 - - + -
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Residues in contact with ASN 487 (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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483A LEU 2.8 17.4 + - - +
484A ASP* 3.5 14.1 + - - +
485A LEU 3.3 0.2 - - - -
486A ILE* 1.3 77.7 - - - +
488A LYS* 1.3 60.3 + - - +
490A LYS* 3.3 42.0 + - - +
491A PRO* 4.7 1.6 - - - +
500A PHE* 3.7 20.7 - - + -
530A ARG* 4.1 25.1 + - - +
531A ILE* 4.7 4.9 - - + +
534A GLU* 3.8 14.2 + - - +
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Residues in contact with LYS 488 (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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424A LEU* 3.9 32.5 - - + +
427A CYS* 3.8 33.2 - - + -
433A LYS* 3.6 26.2 + - + +
484A ASP* 3.2 29.9 + - - +
485A LEU 3.7 6.3 - - - +
486A ILE 3.2 0.4 - - - -
487A ASN* 1.3 80.1 - - + +
489A LEU* 1.3 61.4 + - - +
490A LYS 3.6 0.2 + - - -
491A PRO* 3.9 9.9 - - - +
492A LEU* 5.3 0.3 - - - +
530A ARG* 3.9 11.5 - - - +
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Residues in contact with LEU 489 (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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427A CYS* 4.2 5.4 - - - -
433A LYS* 3.8 39.0 - - + +
436A ILE* 3.9 9.2 - - + -
437A ALA* 4.0 17.0 - - + +
440A LEU* 3.7 27.4 - - + -
445A CYS* 5.6 0.4 - - - -
485A LEU* 3.1 39.6 + - + +
486A ILE* 3.6 0.9 - - - -
488A LYS* 1.3 76.3 - - - +
490A LYS* 1.3 65.9 - - - +
491A PRO* 3.5 2.0 - - - -
492A LEU* 3.3 13.6 + - - +
493A VAL* 3.3 16.7 + - + +
496A MET* 3.7 19.7 - - + -
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Residues in contact with LYS 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ILE* 2.9 21.9 + - + +
487A ASN* 3.3 31.1 + - - +
489A LEU* 1.3 75.1 - - - +
491A PRO* 1.4 71.7 - - + +
493A VAL 3.0 22.0 - - - +
496A MET* 4.4 9.0 - - - +
497A GLU* 3.6 39.7 + - - +
500A PHE* 3.6 27.7 - - + -
501A TYR* 3.2 22.6 + - + +
534A GLU* 3.6 12.5 + - - -
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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