Contacts of the helix formed by residues 403 - 424 (chain A) in PDB entry 4BSN
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 PRO 403 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383A GLU* 3.3 27.4 - - - +
384A SER* 3.6 25.1 - - - +
388A THR* 4.8 14.1 - - + +
401A ASP 3.6 7.6 - - - +
402A VAL* 1.3 92.0 - - + +
404A PRO* 1.3 67.6 - - + +
406A ARG* 3.5 19.5 - - + +
407A GLN* 2.9 27.0 + - - +
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Residues in contact with PRO 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383A GLU* 3.3 10.5 - - + +
402A VAL 3.4 6.2 - - - +
403A PRO* 1.3 84.2 - - + +
405A ARG* 1.3 62.4 + - + +
407A GLN* 3.5 18.0 + - + +
408A LEU* 3.8 7.8 + - - +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASP* 3.9 6.1 + - - -
335A GLN* 4.4 19.3 + - - +
338A GLU* 2.8 37.8 + - - -
379A GLU* 2.8 34.0 + - + +
380A LEU* 4.1 24.9 - - + +
383A GLU* 3.1 26.2 + - + +
404A PRO* 1.3 77.4 - - + +
406A ARG* 1.3 67.1 + - - +
407A GLN 3.5 0.2 + - - -
408A LEU* 3.6 9.0 + - - +
409A TYR* 3.8 18.0 - - - +
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Residues in contact with ARG 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 4.6 16.2 - - + -
383A GLU* 3.7 6.1 + - - +
384A SER* 2.5 41.9 + - - +
386A PHE 2.6 28.5 + - - -
388A THR* 3.1 27.6 + - - +
402A VAL* 4.8 3.4 - - + -
403A PRO* 3.1 22.5 + - + +
405A ARG* 1.3 75.8 - - - +
407A GLN* 1.3 60.8 + - - +
408A LEU 3.2 0.2 + - - -
409A TYR 3.3 2.1 + - - -
410A LEU* 2.8 38.1 + - + +
413A LEU* 4.7 13.4 - - + +
466A HIS 3.8 1.0 + - - -
467A LEU* 3.0 52.7 + - + +
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Residues in contact with GLN 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ARG* 6.4 0.4 - - - +
402A VAL* 3.4 28.9 + - + +
403A PRO 2.9 16.2 + - - +
404A PRO* 3.6 11.0 - - + +
405A ARG 3.3 0.4 - - - -
406A ARG* 1.3 77.2 - - - +
408A LEU* 1.3 60.4 + - - +
410A LEU* 3.5 30.5 - - - +
411A PRO* 4.3 2.9 - - - +
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Residues in contact with LEU 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLU* 3.6 40.6 - - + +
344A ARG* 3.7 51.1 - - + +
347A LEU* 4.1 19.3 - - + -
348A MET* 3.2 37.2 - - + +
404A PRO 3.8 6.8 + - - +
405A ARG* 3.6 5.8 + - - +
406A ARG 3.2 1.0 - - - -
407A GLN* 1.3 81.4 - - - +
409A TYR* 1.3 71.8 + - + +
410A LEU 3.2 1.1 + - - -
411A PRO* 3.7 3.5 - - - +
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Residues in contact with TYR 409 (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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330A LEU* 5.4 0.2 - - - +
334A ASP* 3.7 20.4 + - - +
338A GLU* 3.0 37.7 + - + -
347A LEU* 3.9 16.9 - - + +
348A MET* 5.1 1.3 - - - -
351A LEU* 3.8 20.9 - - + -
372A TYR* 4.0 9.5 + - - -
376A LEU* 3.6 36.6 - - + -
380A LEU* 4.1 22.0 - - + -
405A ARG* 3.8 15.0 + - - +
406A ARG 3.3 5.1 + - - +
408A LEU* 1.3 87.0 - - + +
410A LEU* 1.3 63.5 + - - +
411A PRO* 3.5 2.5 - - - -
412A MET* 3.1 17.9 + - + -
413A LEU* 3.2 19.7 + - + +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A THR* 6.0 2.7 - - - +
402A VAL* 5.2 7.4 - - + -
406A ARG* 2.8 22.5 + - + +
407A GLN* 3.5 29.4 - - - +
408A LEU 3.2 0.4 - - - -
409A TYR* 1.3 76.9 - - - +
411A PRO* 1.3 70.1 - - + +
412A MET 3.2 1.0 + - - -
413A LEU* 3.3 26.6 + - + +
414A PHE* 4.3 6.6 - - - -
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Residues in contact with PRO 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A MET* 4.4 19.1 - - + -
407A GLN 4.3 3.1 - - - +
408A LEU 3.7 9.4 - - - +
409A TYR 3.6 1.8 - - - -
410A LEU* 1.3 96.1 - - + +
412A MET* 1.3 65.6 + - + +
413A LEU 3.4 0.4 - - - -
414A PHE* 3.1 34.2 - - + -
415A LYS* 5.3 0.9 - - - +
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Residues in contact with MET 412 (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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348A MET* 4.1 34.5 - - + +
351A LEU* 3.7 38.1 - - + +
352A HIS* 4.9 15.5 - - + -
355A LEU* 4.8 10.8 - - + -
373A TRP* 5.6 1.8 - - + -
409A TYR* 3.1 8.7 + - + +
411A PRO* 1.3 84.5 - - + +
413A LEU* 1.3 63.4 + - - +
414A PHE 3.6 0.9 - - - -
415A LYS* 3.8 42.9 + - + +
416A VAL* 3.2 18.6 - - + +
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Residues in contact with LEU 413 (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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376A LEU* 4.4 16.4 - - + -
380A LEU* 4.4 20.0 - - + -
406A ARG* 4.7 15.3 - - + +
409A TYR* 3.2 25.1 + - + +
410A LEU* 3.3 27.0 + - + +
412A MET* 1.3 75.0 - - - +
414A PHE* 1.3 61.8 + - - +
415A LYS 3.1 2.0 - - - -
416A VAL* 3.0 28.5 + - + +
417A ARG* 3.5 27.1 + - - +
464A LEU* 4.4 4.7 - - + +
467A LEU* 4.0 31.2 - - + -
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Residues in contact with PHE 414 (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 LEU 4.3 4.5 - - - -
411A PRO* 3.1 35.2 - - + -
413A LEU* 1.3 78.0 - - - +
415A LYS* 1.3 80.9 + - + +
416A VAL 3.2 0.2 - - - -
417A ARG* 3.5 16.2 + - - +
418A LEU* 3.1 27.2 + - + +
471A ASP* 3.2 25.9 - - - +
474A ARG* 5.9 3.4 - - - +
475A ILE* 5.1 4.2 - - + +
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Residues in contact with LYS 415 (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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352A HIS* 4.6 16.8 + - - -
355A LEU* 3.8 32.2 - - + +
356A LEU* 5.9 1.2 - - - +
411A PRO 5.3 1.1 - - - +
412A MET* 3.8 34.7 + - - +
413A LEU 3.1 0.6 - - - -
414A PHE* 1.3 101.6 - - + +
416A VAL* 1.3 58.0 + - - +
418A LEU* 3.6 10.5 + - + +
419A LEU* 3.0 29.1 + - - +
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Residues in contact with VAL 416 (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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355A LEU* 5.2 2.9 - - + -
373A TRP* 3.6 50.7 - - + +
376A LEU* 5.1 2.9 - - + -
412A MET 3.2 20.4 - - - +
413A LEU* 3.0 17.4 + - + +
415A LYS* 1.3 76.0 - - + +
417A ARG* 1.3 55.2 + - - +
419A LEU* 3.2 7.2 + - + +
420A MET* 2.7 47.5 + - + +
464A LEU* 3.6 27.1 - - + -
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Residues in contact with ARG 417 (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 LEU* 3.5 26.2 + - - +
414A PHE* 3.5 22.4 - - - +
415A LYS 3.4 0.2 - - - -
416A VAL* 1.3 76.3 - - - +
418A LEU* 1.3 62.6 + - - +
420A MET* 4.0 4.7 - - - +
421A VAL* 3.2 34.1 + - + +
461A LEU* 4.6 8.7 - - + -
464A LEU* 2.9 38.3 + - + +
465A THR* 5.8 0.2 - - - -
467A LEU* 3.8 18.0 - - - +
468A ASP* 3.6 27.7 + - - +
471A ASP* 2.5 39.4 + - - +
472A THR* 3.5 26.5 - - + +
475A ILE* 5.0 7.9 - - + -
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Residues in contact with LEU 418 (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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414A PHE* 3.1 20.6 + - + +
415A LYS* 3.8 11.2 - - + +
417A ARG* 1.3 77.9 - - - +
419A LEU* 1.3 59.0 + - - +
421A VAL* 4.2 1.6 + - - +
422A SER* 3.5 21.4 + - - +
475A ILE* 3.9 39.6 - - + +
479A LYS* 4.5 13.5 - - - +
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Residues in contact with LEU 419 (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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355A LEU* 4.1 22.0 - - + +
358A SER* 4.0 29.4 - - - +
359A GLU* 3.2 38.6 - - + +
366A PHE* 5.5 7.4 - - + -
373A TRP* 4.7 10.1 - - + +
415A LYS 3.0 18.8 + - - +
416A VAL* 3.5 8.3 - - + +
418A LEU* 1.3 78.2 - - - +
420A MET* 1.3 69.0 + - + +
421A VAL 3.3 1.0 + - - -
422A SER* 3.4 10.3 + - - -
423A ARG* 3.4 21.4 + - + +
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Residues in contact with MET 420 (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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366A PHE* 5.7 2.5 - - + -
370A LEU* 4.9 6.5 - - + -
373A TRP* 4.3 15.0 - - + -
416A VAL* 2.7 36.6 + - + +
417A ARG* 3.4 0.9 + - - +
419A LEU* 1.3 78.7 - - + +
421A VAL* 1.3 63.0 + - - +
422A SER 3.4 0.3 + - - -
423A ARG* 3.6 1.5 + - - -
424A MET* 3.5 22.7 + - - +
457A MET* 3.7 42.4 - - + +
460A THR* 3.7 25.1 - - + -
461A LEU* 3.8 40.8 - - + +
464A LEU* 4.4 1.6 - - + -
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Residues in contact with VAL 421 (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 ARG* 3.2 19.8 + - + +
418A LEU 4.5 4.3 - - - +
419A LEU 3.3 0.2 - - - -
420A MET* 1.3 78.6 - - - +
422A SER* 1.3 60.1 + - - +
423A ARG 3.6 0.3 + - - -
424A MET* 4.0 3.3 + - - +
461A LEU* 4.2 13.7 - - + -
472A THR* 5.7 1.3 - - + -
475A ILE* 4.5 14.4 - - + -
476A MET* 3.8 34.3 - - + -
479A LYS* 4.4 20.2 - - - +
496A THR* 3.2 21.3 - - - +
497A LEU* 4.5 11.7 - - + -
500A ALA* 3.8 20.4 - - + +
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Residues in contact with SER 422 (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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418A LEU* 3.5 10.2 + - - +
419A LEU* 3.4 7.4 + - - -
420A MET 3.3 0.6 - - - -
421A VAL* 1.3 78.4 - - - +
423A ARG* 1.3 63.9 + - - +
424A MET 3.6 0.4 - - - -
479A LYS* 2.7 30.4 + - - +
492A LYS* 5.0 6.8 + - - -
496A THR* 3.3 31.7 + - - +
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Residues in contact with ARG 423 (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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358A SER 4.0 4.1 + - - +
359A GLU* 2.8 67.6 + - - +
360A VAL 3.5 12.3 + - - -
361A GLU* 3.5 26.5 + - - +
366A PHE* 3.6 41.6 - - + -
419A LEU* 3.4 21.5 + - + +
420A MET 3.6 0.2 + - - -
421A VAL 3.4 0.2 - - - -
422A SER* 1.3 82.2 - - - +
424A MET* 1.3 66.5 + - - +
425A ALA* 3.5 3.5 + - - +
453A LEU* 6.1 0.2 - - - +
457A MET* 3.7 12.3 - - + +
496A THR* 5.4 0.4 - - - -
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Residues in contact with MET 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A MET 3.5 13.3 + - - +
421A VAL 4.0 8.2 + - - +
422A SER 3.6 1.6 - - - -
423A ARG* 1.3 78.5 - - - +
425A ALA* 1.3 71.1 + - - +
454A TYR* 3.7 17.7 - - + +
457A MET* 3.6 24.2 - - + +
458A ARG* 3.5 31.4 - - + +
461A LEU* 4.3 10.1 - - + -
496A THR* 4.3 10.1 - - - +
499A TRP* 3.3 54.3 - - + +
500A ALA* 3.8 2.9 - - - -
503A SER* 3.5 19.5 - - - +
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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
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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