Contacts of the helix formed by residues 468 - 490 (chain A) in PDB entry 4N78
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 MET 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A LEU* 4.5 17.5 - - + -
366A TYR* 3.2 29.2 - - - +
367A SER* 3.5 20.2 - - - +
390A LEU* 5.6 1.1 - - - -
464A LEU 3.2 13.7 + - - +
465A MET 2.9 10.8 + - - +
467A ARG* 1.3 86.4 - - + +
469A GLU* 1.3 56.9 + - - +
470A SER 3.4 2.2 - - - -
471A VAL* 3.2 36.6 + - + +
472A PHE* 2.8 52.4 + - + +
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Residues in contact with GLU 469 (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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465A MET 3.2 5.1 + - - +
466A GLY* 3.1 21.8 + - - +
467A ARG 3.3 0.8 - - - -
468A MET* 1.3 77.2 - - - +
470A SER* 1.3 56.7 + - - +
472A PHE* 2.9 6.9 + - - +
473A ASN* 2.6 59.9 + - - +
608A PHE* 4.2 13.8 - - + -
609A SER* 3.3 36.7 + - - -
612A LEU* 5.9 1.2 - - - +
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Residues in contact with SER 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ARG 4.9 3.2 + - - -
468A MET 3.4 0.6 - - - -
469A GLU* 1.3 81.7 - - - +
471A VAL* 1.3 64.3 + - - +
473A ASN* 3.6 7.8 + - - +
474A HIS* 3.3 19.9 + - - +
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366A TYR 5.7 0.9 - - - +
390A LEU* 3.7 34.3 - - + -
468A MET* 3.2 34.1 + - + +
470A SER* 1.3 76.1 - - - +
472A PHE* 1.3 66.6 + - + +
474A HIS* 3.3 6.7 + - - +
475A ALA* 3.0 21.1 + - - +
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Residues in contact with PHE 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LEU* 3.9 20.4 - - + -
390A LEU* 3.6 44.9 - - + -
393A LEU* 4.5 3.4 - - + -
394A ALA* 3.8 17.0 - - + -
465A MET* 3.9 19.5 - - + -
468A MET* 2.8 42.5 + - + +
469A GLU* 3.4 8.3 - - - +
471A VAL* 1.3 78.1 - - + +
473A ASN* 1.3 54.6 + - - +
475A ALA* 3.1 2.8 + - - -
476A ILE* 2.8 49.1 + - + +
608A PHE* 3.4 35.0 - + + -
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Residues in contact with ASN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLU* 2.6 47.4 + - - +
470A SER* 3.8 7.6 - - - +
472A PHE* 1.3 72.5 - - - +
474A HIS* 1.3 61.3 + - - +
476A ILE* 3.7 2.6 + - - +
477A ARG* 3.0 59.1 + - - +
605A LEU 4.9 0.2 - - - +
606A ILE 4.9 0.4 - - - +
608A PHE* 3.7 26.7 + - - +
609A SER 5.2 0.2 + - - -
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Residues in contact with HIS 474 (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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387A TYR* 3.1 45.8 + + - -
470A SER 3.3 11.1 + - - +
471A VAL* 3.7 8.3 - - - +
472A PHE 3.2 0.8 - - - -
473A ASN* 1.3 77.7 - - - +
475A ALA* 1.3 64.4 + - - +
477A ARG* 3.5 5.2 + - - +
478A HIS* 3.0 26.3 + - + +
551A ALA* 3.6 30.3 - - + +
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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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387A TYR* 3.6 41.5 - - + +
390A LEU* 3.6 24.0 - - + -
391A PHE* 4.6 1.8 - - - +
471A VAL 3.0 17.6 + - - +
472A PHE* 3.8 2.9 - - - +
474A HIS* 1.3 78.3 - - - +
476A ILE* 1.3 57.9 + - - +
478A HIS* 3.6 1.4 + - - +
479A THR* 2.8 32.9 + - - -
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Residues in contact with ILE 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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390A LEU 5.3 0.2 - - - +
391A PHE* 3.9 27.4 - - + -
394A ALA* 4.0 22.9 - - + -
472A PHE* 2.8 29.8 + - - +
473A ASN* 4.0 4.5 - - - +
475A ALA* 1.3 72.1 - - + +
477A ARG* 1.3 60.4 + - - +
479A THR* 3.2 1.6 + - - -
480A VAL* 2.8 36.2 + - + +
605A LEU* 3.5 53.2 - - + +
606A ILE* 4.0 14.6 - - + -
608A PHE* 4.3 9.4 - - + -
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Residues in contact with ARG 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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473A ASN* 3.0 56.3 + - - +
474A HIS* 4.0 3.4 - - - +
476A ILE* 1.3 79.9 - - - +
478A HIS* 1.3 61.5 + - - +
480A VAL* 4.1 1.2 - - - +
481A TYR* 3.1 26.3 + - - +
551A ALA 3.7 24.9 - - - +
552A VAL* 3.9 12.3 + - - +
553A GLY 3.8 13.8 - - - +
605A LEU 4.9 1.6 + - - -
606A ILE* 3.0 54.1 + - + +
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Residues in contact with HIS 478 (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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382A LYS 5.3 2.2 - - - -
384A ASP* 2.8 31.2 + - - -
387A TYR* 3.3 49.4 - + + -
474A HIS* 3.0 21.4 + - - +
475A ALA 3.8 4.3 - - - +
476A ILE 3.2 0.2 - - - -
477A ARG* 1.3 78.8 - - - +
479A THR* 1.3 60.4 + - - +
481A TYR* 3.9 1.4 - - - +
482A ALA* 3.0 26.6 + - + +
549A ARG* 3.7 28.0 + - + +
550A ARG 3.6 19.8 + - - +
551A ALA* 4.2 7.3 - - + +
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Residues in contact with THR 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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384A ASP 4.9 0.5 + - - -
387A TYR* 3.3 24.8 + - - +
388A ARG* 3.6 29.9 + - + +
391A PHE* 3.7 28.8 - - + +
475A ALA 2.8 23.3 + - - -
476A ILE 3.2 3.1 + - - -
478A HIS* 1.3 77.4 - - - +
480A VAL* 1.3 61.1 + - - +
482A ALA* 3.4 4.1 + - - +
483A ALA* 2.9 31.2 + - + +
602A TYR* 5.8 1.3 - - - +
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Residues in contact with VAL 480 (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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391A PHE* 4.0 12.8 - - + -
476A ILE* 2.8 29.3 + - + +
477A ARG 4.2 2.2 - - - +
479A THR* 1.3 73.0 - - - +
481A TYR* 1.3 60.0 + - - +
483A ALA* 3.5 4.8 + - - +
484A LEU* 2.9 29.5 + - + +
553A GLY* 4.7 1.1 - - - -
554A PRO* 3.6 28.7 - - + -
602A TYR* 3.7 50.0 - - + -
606A ILE* 4.3 13.5 - - + -
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Residues in contact with TYR 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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477A ARG 3.1 20.4 + - - +
478A HIS 4.8 0.2 - - - -
480A VAL* 1.3 75.5 - - - +
482A ALA* 1.3 63.5 + - - +
484A LEU* 3.2 5.9 + - + +
485A GLN* 2.9 63.2 + - + +
520A ASP* 2.7 27.4 + - + +
548A PRO* 3.3 37.0 - - - +
549A ARG* 4.2 1.6 - - - -
550A ARG* 3.1 58.9 - - + +
552A VAL* 3.4 23.3 + - + +
553A GLY 5.8 0.9 - - - -
554A PRO* 5.3 4.0 - - + -
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Residues in contact with ALA 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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384A ASP* 4.9 4.0 - - + +
478A HIS* 3.0 22.4 + - + +
479A THR* 3.8 5.8 - - - +
481A TYR* 1.3 78.3 - - - +
483A ALA* 1.3 56.6 + - - +
485A GLN* 4.9 0.4 - - - -
486A ASP* 2.9 39.8 + - - +
549A ARG* 3.5 40.6 - - - +
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Residues in contact with ALA 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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388A ARG* 5.7 3.8 - - - +
479A THR* 2.9 21.7 + - + +
480A VAL 3.8 2.7 - - - +
482A ALA* 1.3 76.2 - - - +
484A LEU* 1.3 62.4 + - - +
486A ASP* 4.1 4.2 - - - +
487A PHE* 3.1 26.0 + - - +
595A PHE* 3.7 9.2 - - + -
598A GLU* 6.0 0.9 - - - +
602A TYR* 3.4 25.1 - - + +
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Residues in contact with LEU 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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480A VAL* 2.9 19.5 + - + +
481A TYR* 3.7 5.4 - - + +
483A ALA* 1.3 76.6 - - - +
485A GLN* 1.3 66.5 + - + +
487A PHE* 3.5 2.8 + - + +
488A SER* 2.9 32.9 + - - -
514A ILE* 6.3 0.2 - - + -
518A VAL* 4.2 32.1 - - + -
554A PRO* 3.6 39.7 - - + -
558A GLN 6.1 0.2 - - - +
559A LEU* 5.4 6.5 - - + -
562A VAL* 4.4 15.5 - - + -
595A PHE* 3.6 27.5 - - + -
602A TYR* 5.7 1.1 - - + -
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Residues in contact with GLN 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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481A TYR* 2.9 51.9 + - + +
482A ALA* 4.3 1.1 - - - +
484A LEU* 1.3 84.9 - - - +
486A ASP* 1.3 61.2 + - - +
488A SER* 3.5 3.1 + - - -
489A GLN* 2.7 63.7 + - - +
518A VAL 3.0 25.6 + - - -
519A CYS* 3.5 5.4 - - - -
520A ASP* 2.9 21.7 + - - +
547A VAL* 3.7 20.9 - - + -
548A PRO* 5.3 0.2 - - + -
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Residues in contact with ASP 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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482A ALA* 2.9 26.3 + - - +
483A ALA* 4.1 4.4 - - - +
485A GLN* 1.3 75.7 - - - +
487A PHE* 1.3 58.1 + - - +
490A VAL* 3.2 12.9 + - + +
491A THR* 3.1 26.5 + - - +
547A VAL* 3.3 19.6 - - - +
549A ARG* 2.6 36.2 + - - -
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Residues in contact with PHE 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 ALA 3.1 19.6 + - - +
484A LEU* 3.8 4.9 - - + +
486A ASP* 1.3 78.5 - - - +
488A SER* 1.3 61.8 + - - +
491A THR* 3.3 30.2 + - + -
492A LEU* 2.9 66.7 + - + +
514A ILE* 5.4 2.0 - - + -
562A VAL* 5.5 1.6 - - + -
566A LEU* 3.7 37.7 - - + -
591A ASP 3.8 14.4 - - - -
592A ILE* 4.2 10.8 - - + -
595A PHE* 3.7 42.0 - + + -
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Residues in contact with SER 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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484A LEU* 2.9 22.8 + - - -
485A GLN* 3.4 12.6 + - - -
487A PHE* 1.3 81.5 - - - +
489A GLN* 1.3 61.0 + - - +
492A LEU* 3.9 17.8 - - - +
514A ILE* 4.9 2.7 - - - -
515A ARG* 2.9 33.7 + - - +
518A VAL* 3.9 18.8 - - - +
519A CYS* 3.5 22.4 - - - -
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Residues in contact with GLN 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A GLN* 2.7 48.9 + - - +
488A SER* 1.3 79.6 - - - +
490A VAL* 1.3 64.4 + - + +
493A ARG* 3.2 14.3 - - - +
515A ARG* 3.1 21.2 + - - +
519A CYS* 3.8 13.2 - - - -
520A ASP 3.4 25.6 + - - +
521A TRP* 3.6 32.4 - - + -
522A GLU 5.1 0.2 + - - -
545A ILE* 3.9 13.0 - - + +
546A LYS 4.5 0.9 - - - +
547A VAL* 3.8 22.3 - - + +
548A PRO* 4.1 5.8 - - - +
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Residues in contact with VAL 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A ASP* 3.2 13.8 + - + +
489A GLN* 1.3 83.5 - - + +
491A THR* 1.3 71.4 + - - +
492A LEU 3.2 1.3 - - - -
493A ARG* 3.1 27.9 + - - +
494A GLU 4.5 0.9 + - - -
545A ILE* 4.5 17.0 - - + +
547A VAL* 4.0 25.8 - - + -
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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
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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