Contacts of the helix formed by residues 456 - 479 (chain F) in PDB entry 5I4V
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 ASN 456 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363F LEU* 5.9 0.2 - - - +
367F ASP* 3.7 5.2 + - - +
454F LEU* 3.3 3.3 - - - -
455F SER* 1.3 87.6 + - - +
457F PRO* 1.3 66.1 - - - +
458F SER* 3.2 21.1 + - - -
459F GLU* 3.3 49.5 + - - +
460F VAL* 3.6 10.7 + - - +
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Residues in contact with PRO 457 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449F PRO* 3.6 26.3 - - + +
454F LEU* 4.0 28.7 - - + +
455F SER 3.9 5.4 - - - +
456F ASN* 1.3 86.7 - - - +
458F SER* 1.3 60.5 + - - +
460F VAL* 3.2 1.6 + - + +
461F GLU* 2.8 30.4 + - - +
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Residues in contact with SER 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456F ASN* 3.2 15.4 + - - -
457F PRO* 1.3 77.9 - - - +
459F GLU* 1.3 64.3 + - - +
461F GLU* 3.0 13.6 + - - +
462F VAL* 2.9 32.3 + - - +
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Residues in contact with GLU 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362F SER* 5.1 3.6 + - - +
363F LEU* 3.9 27.8 - - + +
364F PRO* 4.4 13.0 - - - +
367F ASP* 5.6 0.9 - - - +
456F ASN* 3.3 36.1 + - - +
457F PRO 3.3 0.6 - - - -
458F SER* 1.3 80.1 - - - +
460F VAL* 1.3 62.0 + - - +
462F VAL* 3.3 8.6 + - - +
463F LEU* 3.3 29.2 + - + +
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Residues in contact with VAL 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363F LEU* 4.4 18.4 - - + -
367F ASP* 5.3 2.9 - - + +
371F LEU* 4.2 14.1 - - + -
447F PHE* 3.6 33.5 - - + +
448F ASN 3.8 4.7 - - - +
449F PRO* 3.7 16.6 - - + -
454F LEU* 4.2 21.3 - - + -
456F ASN 3.8 12.1 - - - +
457F PRO 3.2 7.5 + - - +
458F SER 3.1 0.2 - - - -
459F GLU* 1.3 75.1 - - - +
461F GLU* 1.3 64.4 + - - +
463F LEU* 3.2 10.1 + - - +
464F ARG* 3.1 21.0 + - - +
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Residues in contact with GLU 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362E ARG* 4.8 15.3 + - - -
420E ARG* 5.5 4.9 - - - +
424E LYS* 6.0 0.2 + - - -
449F PRO* 3.8 23.9 - - + +
457F PRO 2.8 14.6 + - - +
458F SER* 3.4 15.1 + - - +
460F VAL* 1.3 75.1 - - - +
462F VAL* 1.3 64.6 + - + +
464F ARG* 3.3 8.2 + - + +
465F GLU* 3.0 44.0 + - + +
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Residues in contact with VAL 462 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458F SER* 2.9 21.3 + - - +
459F GLU* 3.5 10.1 - - - +
460F VAL 3.2 0.2 - - - -
461F GLU* 1.3 77.3 - - + +
463F LEU* 1.3 63.6 + - + +
465F GLU* 3.3 17.3 + - + +
466F LYS* 3.1 45.3 + - + +
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Residues in contact with LEU 463 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F MET* 3.7 10.7 - - + +
359F HIS* 3.8 37.7 - - + +
363F LEU* 4.2 24.5 - - + -
447F PHE* 3.8 37.7 - - + -
459F GLU* 3.3 16.6 + - + +
460F VAL* 3.2 8.6 + - - +
462F VAL* 1.3 75.8 - - + +
464F ARG* 1.3 66.7 + - - +
466F LYS* 3.3 21.1 + - + +
467F VAL* 3.2 23.4 + - - +
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Residues in contact with ARG 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423E MET* 4.5 15.9 - - - +
426E VAL* 6.3 0.6 - - - +
444F ILE* 2.7 38.4 + - + +
445F ILE* 4.0 5.5 + - - +
447F PHE* 2.8 31.5 + - + +
448F ASN* 3.7 23.4 + - - +
449F PRO* 4.0 20.7 - - - +
450F ASP* 5.4 3.2 + - - -
460F VAL 3.1 7.4 + - - +
461F GLU* 3.5 10.5 - - - +
463F LEU* 1.3 75.7 - - - +
465F GLU* 1.3 60.0 + - - +
467F VAL* 2.8 25.8 + - - +
468F TYR* 3.0 45.9 + - + +
497F ARG* 5.3 6.3 - - - +
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Residues in contact with GLU 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416E LEU* 3.6 26.3 - - + +
420E ARG* 3.2 37.5 + - - +
461F GLU* 3.0 37.4 + - + +
462F VAL* 3.6 18.5 - - - +
463F LEU 3.2 0.2 - - - -
464F ARG* 1.3 76.7 - - + +
466F LYS* 1.3 61.0 + - - +
468F TYR* 3.2 29.8 + - + +
469F ALA* 3.2 18.7 + - - +
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Residues in contact with LYS 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297F GLU* 5.1 9.8 - - - +
298F GLU* 3.5 46.3 + - + +
299F MET* 3.7 20.6 - - + +
359F HIS* 4.6 11.3 + - - +
462F VAL* 3.1 37.8 + - + +
463F LEU* 3.5 22.7 - - + +
464F ARG 3.2 0.2 - - - -
465F GLU* 1.3 72.9 - - + +
467F VAL* 1.3 60.3 + - - +
469F ALA* 3.3 7.2 + - - +
470F SER* 2.9 33.1 + - - -
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Residues in contact with VAL 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299F MET* 3.8 23.1 - - + -
304F ILE* 4.9 2.9 - - + -
440F CYS* 3.4 43.1 - - + +
443F ALA* 4.0 19.3 - - + -
444F ILE* 3.5 14.4 - - + -
447F PHE* 4.2 10.1 - - + -
463F LEU 3.2 15.3 + - - +
464F ARG* 2.8 9.4 + - - +
466F LYS* 1.3 74.1 - - - +
468F TYR* 1.3 66.4 + - - +
470F SER* 4.5 1.1 - - - -
471F LEU* 2.8 28.1 + - - +
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Residues in contact with TYR 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E LEU* 4.0 13.5 - - + -
419E PRO* 3.8 34.3 - - + -
420E ARG* 4.4 15.1 - - + +
423E MET* 2.9 37.2 - - + +
444F ILE* 3.9 24.2 - - + -
464F ARG* 3.0 43.0 + - + -
465F GLU* 3.2 36.1 - - + +
467F VAL* 1.3 76.5 - - - +
469F ALA* 1.3 57.7 + - - +
471F LEU* 4.7 0.7 - - - -
472F GLU* 2.9 31.4 + - - +
486F PHE* 3.6 11.1 - + + -
490F LEU* 4.8 5.4 - - + -
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Residues in contact with ALA 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416E LEU* 4.4 12.1 - - + +
297F GLU* 5.0 12.3 - - + +
465F GLU 3.2 8.5 + - - +
466F LYS* 3.7 10.1 - - - +
468F TYR* 1.3 79.7 - - - +
470F SER* 1.3 63.2 + - - +
472F GLU* 3.9 4.3 - - - +
473F THR* 2.9 31.4 + - - +
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Residues in contact with SER 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297F GLU* 3.6 15.7 - - - +
299F MET* 2.6 36.2 + - - +
301F VAL* 3.6 16.9 - - - +
304F ILE* 5.7 0.4 - - - -
440F CYS* 5.6 2.0 - - - -
466F LYS 2.9 16.7 + - - -
467F VAL* 3.9 3.8 - - - -
469F ALA* 1.3 76.7 - - - +
471F LEU* 1.3 58.8 + - - +
473F THR* 3.4 6.3 + - - -
474F TYR* 2.9 29.3 + - - +
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Residues in contact with LEU 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F VAL* 4.5 0.4 - - - +
437F GLU* 4.4 12.8 - - + -
440F CYS* 3.8 36.3 - - + -
441F LEU* 4.2 16.2 - - + -
444F ILE* 4.1 19.3 - - + -
467F VAL 2.8 17.9 + - - +
468F TYR 3.7 3.1 - - - +
470F SER* 1.3 77.5 - - - +
472F GLU* 1.3 57.8 + - - +
474F TYR* 3.1 11.3 + - + +
475F CYS* 2.9 45.3 + - - -
486F PHE* 3.8 22.2 - - + -
489F LEU* 4.0 13.9 - - + -
490F LEU* 4.5 2.5 - - + -
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Residues in contact with GLU 472 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404E LEU* 5.1 1.9 - - - +
408E ARG* 3.1 42.3 + - - -
415E GLN* 4.5 8.1 + - - +
419E PRO* 5.4 0.5 - - - +
468F TYR 2.9 17.2 + - - +
469F ALA* 3.9 5.0 - - - +
471F LEU* 1.3 76.1 - - - +
473F THR* 1.3 65.8 + - - +
475F CYS* 3.1 4.5 + - - +
476F LYS* 2.9 48.7 + - + +
486F PHE* 3.3 45.4 - - + +
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Residues in contact with THR 473 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F ALA* 2.9 22.2 + - - +
470F SER* 3.5 7.5 - - - -
472F GLU* 1.3 79.5 - - - +
474F TYR* 1.3 62.9 + - - +
476F LYS* 3.2 7.1 + - - +
477F GLN* 3.0 49.3 + - + +
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Residues in contact with TYR 474 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301F VAL* 4.1 23.3 - - + -
434F ASP* 2.8 31.6 + - - -
436F THR* 3.8 35.6 + - + -
437F GLU* 3.9 18.6 - - + -
470F SER 2.9 14.2 + - - +
471F LEU* 3.3 14.1 - - + +
473F THR* 1.3 77.4 - - - +
475F CYS* 1.3 63.1 + - - +
477F GLN* 3.2 10.7 + - + +
478F LYS* 2.8 60.4 + - + +
479F TYR* 4.1 9.2 - + - -
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Residues in contact with CYS 475 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437F GLU* 4.2 9.4 - - - -
471F LEU* 2.9 24.9 + - - -
472F GLU 3.1 9.1 + - - +
474F TYR* 1.3 82.1 - - - +
476F LYS* 1.3 58.3 + - + +
479F TYR* 3.0 38.9 + - - +
482F GLN 5.0 2.9 - - - +
485F ARG* 4.2 9.0 - - + -
486F PHE* 4.1 25.1 - - + +
489F LEU* 3.6 30.7 - - - -
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Residues in contact with LYS 476 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408E ARG* 4.2 10.0 - - - +
415E GLN* 4.4 11.1 - - - +
472F GLU* 2.9 47.3 + - + +
473F THR* 3.8 6.5 - - - +
475F CYS* 1.3 76.0 - - + +
477F GLN* 1.3 63.6 + - + +
479F TYR 4.8 0.4 - - - -
480F PRO* 3.2 28.4 - - - +
482F GLN 6.1 0.2 - - - -
483F GLN 6.0 1.8 - - - -
486F PHE* 6.5 0.7 - - + -
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Residues in contact with GLN 477 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473F THR* 3.0 40.5 + - + +
474F TYR* 3.7 8.4 - - + +
476F LYS* 1.3 79.0 - - + +
478F LYS* 1.3 62.8 + - + +
480F PRO* 3.4 13.0 - - - +
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Residues in contact with LYS 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434F ASP* 5.1 1.8 + - - +
474F TYR* 2.8 52.3 + - + +
477F GLN* 1.3 74.7 - - + +
479F TYR* 1.3 92.7 + - + +
480F PRO* 3.4 5.8 - - - +
481F GLU* 4.5 1.6 - - - +
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Residues in contact with TYR 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432F ARG 4.5 3.4 + - - -
434F ASP* 2.7 32.6 + - - +
437F GLU* 3.4 17.5 - - - -
474F TYR* 4.1 3.4 - + - -
475F CYS* 3.0 27.5 + - - +
476F LYS* 4.8 0.5 - - - -
478F LYS* 1.3 111.5 - - + +
480F PRO* 1.3 59.9 - - - +
481F GLU* 3.1 16.6 - - - -
482F GLN* 2.8 43.4 + - + +
485F ARG* 3.8 38.2 + - + -
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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