Contacts of the helix formed by residues 413 - 434 (chain A) in PDB entry 2BVA
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 413 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411A ARG* 4.9 11.0 - - - +
412A MET* 1.3 76.4 - - - +
414A GLU* 1.3 63.4 + - - +
415A GLU* 3.1 32.7 + - - +
416A GLN* 3.3 38.8 + - - +
417A ILE* 2.7 40.4 + - - +
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Residues in contact with GLU 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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413A ASN* 1.3 74.3 + - - +
415A GLU* 1.3 57.2 - - - +
417A ILE* 3.8 10.0 - - + +
418A ALA* 2.6 38.0 + - - +
540A LYS 4.8 3.8 - - - +
541A VAL* 4.6 3.5 - - - +
542A SER* 2.9 33.9 + - - +
544A SER* 4.7 0.3 + - - -
545A LEU* 2.8 27.0 - - - +
571A PHE* 2.8 33.0 - - + -
574A LYS* 4.4 24.0 + - + +
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ASN* 3.1 23.8 + - - +
414A GLU* 1.3 78.5 - - - +
416A GLN* 1.3 67.3 + - + +
419A ALA* 3.2 12.8 + - - +
574A LYS* 3.0 19.0 - - + +
575A ALA* 3.6 1.0 - - - -
576A GLY* 3.0 45.0 + - - -
577A PRO* 3.6 4.0 - - - +
580A SER* 3.0 27.1 - - - +
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Residues in contact with GLN 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411A ARG 5.1 0.5 - - - +
412A MET* 3.3 17.5 - - + -
413A ASN* 3.3 41.5 + - - +
415A GLU* 1.3 82.7 + - + +
417A ILE* 1.3 65.3 + - - +
419A ALA* 3.3 7.6 + - - +
420A VAL* 3.1 25.8 + - - +
580A SER 3.2 25.9 + - - +
581A ILE* 4.4 15.5 - - + +
583A PRO* 5.4 1.8 - - - +
584A LEU* 3.2 40.3 - - + +
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Residues in contact with ILE 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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412A MET* 3.3 21.9 - - + +
413A ASN* 2.7 40.0 + - - +
414A GLU* 3.8 10.1 - - + +
416A GLN* 1.3 74.0 - - - +
418A ALA* 1.3 65.0 + - - +
420A VAL* 3.0 4.3 + - - +
421A CYS* 3.0 29.0 + - - -
505A VAL* 5.6 3.8 - - + -
508A MET* 3.7 39.7 - - + +
509A VAL* 4.6 11.7 - - + -
545A LEU* 4.3 17.3 - - + -
571A PHE* 3.7 17.0 - - + -
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Residues in contact with ALA 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 GLU 2.6 23.7 + - - +
416A GLN 3.3 0.2 - - - -
417A ILE* 1.3 74.2 - - - +
419A ALA* 1.3 55.5 + - - +
421A CYS* 3.4 1.8 + - - +
422A LEU* 3.0 27.7 + - - +
571A PHE* 3.5 35.0 - - + +
572A LEU* 3.7 9.7 - - + +
574A LYS* 3.9 2.5 - - + -
575A ALA* 3.5 28.1 - - + +
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Residues in contact with ALA 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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415A GLU 3.2 17.3 + - - +
416A GLN 3.4 6.1 - - - +
418A ALA* 1.3 76.0 - - - +
420A VAL* 1.3 60.9 + - - +
422A LEU* 5.5 1.9 - - - +
423A ALA* 3.0 28.6 + - - +
454A VAL* 4.6 2.1 - - - +
575A ALA* 3.8 8.2 - - + +
576A GLY 3.7 18.6 - - - +
581A ILE* 3.5 26.5 - - + -
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Residues in contact with VAL 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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403A LEU* 3.7 35.9 - - + -
412A MET* 3.7 17.3 - - + -
416A GLN 3.1 14.9 + - - +
417A ILE 3.0 6.1 + - - +
419A ALA* 1.3 74.7 - - + +
421A CYS* 1.3 63.9 + - - +
423A ALA* 3.6 2.8 - - - +
424A VAL* 2.8 37.9 + - + +
446A ILE* 4.7 11.7 - - + -
448A LEU* 6.1 0.2 - - + -
454A VAL* 4.5 13.0 - - + -
504A MET* 3.9 17.5 - - + -
508A MET* 4.1 5.2 - - - -
581A ILE* 5.2 6.3 - - + -
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Residues in contact with CYS 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 ILE* 3.0 25.0 + - - +
418A ALA 3.6 7.0 - - - +
420A VAL* 1.3 76.6 - - - +
422A LEU* 1.3 65.6 + - - +
424A VAL* 3.0 9.8 + - - +
425A LEU* 2.9 24.5 + - - +
501A LEU* 4.4 14.2 - - + +
505A VAL* 4.2 15.3 - - - -
508A MET* 3.6 24.0 - - - -
548A PHE* 4.8 11.2 - - + -
571A PHE* 4.2 16.4 - - + -
572A LEU* 4.4 4.7 - - + -
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Residues in contact with LEU 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 ALA 3.0 8.4 + - - +
419A ALA* 5.5 1.8 - - - +
421A CYS* 1.3 78.8 - - - +
423A ALA* 1.3 53.9 + - - +
425A LEU* 3.0 10.8 + - - +
426A GLN* 2.7 74.4 + - - +
567A LEU* 3.3 27.4 - - + +
572A LEU* 3.8 32.7 - - + +
575A ALA* 5.2 11.0 - - + -
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Residues in contact with ALA 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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377A ASN* 4.1 17.8 + - - +
419A ALA 3.0 22.4 + - - +
420A VAL 3.6 1.1 - - - +
421A CYS 3.2 0.6 - - - -
422A LEU* 1.3 81.2 - - - +
424A VAL* 1.3 61.5 + - - +
426A GLN* 3.2 26.0 + - - +
427A ALA* 3.5 6.4 + - - +
454A VAL* 3.3 33.9 - - + -
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Residues in contact with VAL 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A VAL* 2.8 38.0 + - + +
421A CYS* 3.2 9.0 - - - +
423A ALA* 1.3 76.7 - - + +
425A LEU* 1.3 57.9 + - - +
427A ALA* 3.6 7.4 + - - +
428A LEU* 3.3 38.6 + - + +
441A ILE* 4.8 18.8 - - + -
446A ILE* 4.4 18.4 - - + -
454A VAL* 4.9 2.2 - - + +
456A LEU* 4.9 9.6 - - + +
501A LEU* 4.3 16.6 - - + -
504A MET* 4.2 12.8 - - + -
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Residues in contact with LEU 425 (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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421A CYS 2.9 11.4 + - - +
422A LEU* 3.0 20.8 + - - +
424A VAL* 1.3 75.5 - - - +
426A GLN* 1.3 65.7 + - - +
427A ALA 3.2 1.6 - - - -
428A LEU* 3.9 11.6 - - + +
429A SER* 3.0 28.8 + - - -
498A ILE* 5.5 1.3 - - + -
501A LEU* 4.3 20.6 - - + -
548A PHE* 4.5 11.2 - - + -
563A ALA* 3.7 34.1 - - + +
566A LEU* 3.7 26.5 - - + -
567A LEU* 4.1 15.0 - - + -
572A LEU* 4.3 13.9 - - + -
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Residues in contact with GLN 426 (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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375A HIS* 3.2 19.5 + - + +
377A ASN* 3.9 16.2 + - - +
422A LEU* 2.7 62.6 + - - +
423A ALA* 3.2 15.9 + - - +
425A LEU* 1.3 73.0 - - - +
427A ALA* 1.3 64.9 + - - +
429A SER* 3.8 11.9 - - - -
430A VAL* 3.9 4.5 + - - +
567A LEU* 4.1 8.8 - - + +
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Residues in contact with ALA 427 (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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373A TYR* 4.1 0.5 + - - -
375A HIS* 4.1 12.1 + - - -
377A ASN* 4.4 16.3 - - + +
378A VAL* 4.4 8.5 - - + -
423A ALA 3.5 5.6 + - - +
424A VAL* 3.7 9.2 - - - +
425A LEU 3.2 0.2 - - - -
426A GLN* 1.3 77.5 - - - +
428A LEU* 1.3 66.7 + - - +
430A VAL* 2.8 17.2 + - - +
431A LEU* 3.0 29.4 + - + +
456A LEU* 4.0 16.2 - - + -
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Residues in contact with LEU 428 (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 VAL* 3.3 28.0 + - + +
425A LEU* 3.4 17.7 + - + +
427A ALA* 1.3 77.4 - - - +
429A SER* 1.3 55.8 + - - +
431A LEU* 4.2 9.6 - - + -
432A HIS* 2.8 51.6 + - + +
438A HIS* 4.7 2.9 - - + +
441A ILE* 3.9 20.4 - - + -
456A LEU* 4.5 8.1 - - + -
497A ASP* 3.8 48.0 - - + +
498A ILE* 4.7 7.6 - - + -
501A LEU* 5.6 3.6 - - + -
563A ALA* 4.9 4.7 - - + -
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Residues in contact with SER 429 (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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425A LEU 3.0 19.3 + - - -
426A GLN* 3.8 8.3 - - - -
428A LEU* 1.3 76.9 - - - +
430A VAL* 1.3 63.5 + - - +
432A HIS* 4.6 2.3 - - - +
433A ALA* 4.0 17.3 + - - +
563A ALA* 3.8 23.2 - - - +
564A ALA* 4.2 3.6 + - - +
567A LEU* 4.1 20.1 - - - +
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Residues in contact with VAL 430 (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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373A TYR* 3.0 22.4 - - + +
375A HIS* 4.5 10.8 - - + +
426A GLN 3.9 5.6 + - - +
427A ALA 2.8 8.1 + - - +
429A SER* 1.3 77.2 - - - +
431A LEU* 1.3 68.7 + - - +
432A HIS 3.0 3.0 + - - -
433A ALA* 4.4 2.6 - - - +
434A GLN* 3.1 46.3 + - + +
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Residues in contact with LEU 431 (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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370A MET* 4.0 24.9 - - + -
373A TYR* 3.6 34.8 - - + +
378A VAL* 4.9 3.4 - - + -
427A ALA* 3.0 29.1 + - + +
428A LEU* 3.8 10.8 - - + +
430A VAL* 1.3 79.1 - - - +
432A HIS* 1.3 58.9 + - + +
434A GLN* 3.7 5.6 - - - +
435A GLY 3.5 3.5 + - - -
436A VAL* 2.9 39.2 + - + +
438A HIS* 5.1 2.7 - - + +
456A LEU* 3.9 28.7 - - + -
459A PHE* 4.0 19.5 - - + -
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Residues in contact with HIS 432 (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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428A LEU* 2.8 35.3 + - + +
429A SER* 4.6 3.4 - - - +
431A LEU* 1.3 76.6 - - + +
433A ALA* 1.3 58.3 + - - +
434A GLN 3.0 1.1 - - - -
435A GLY* 2.5 29.3 + - - -
436A VAL 2.8 27.6 - - - -
437A ILE* 4.1 0.4 - - - +
494A PRO* 3.3 47.6 - - + +
497A ASP* 2.5 36.4 + - + -
498A ILE* 4.7 10.1 - - + +
563A ALA* 5.4 3.8 - - - +
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Residues in contact with ALA 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A SER 4.0 14.7 + - - +
430A VAL* 3.7 3.8 + - - +
432A HIS* 1.3 77.0 - - - +
434A GLN* 1.3 57.8 + - + +
435A GLY* 3.1 5.0 + - - -
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Residues in contact with GLN 434 (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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370A MET* 6.5 0.2 - - + -
372A ASP 4.3 6.9 - - - +
373A TYR* 3.0 42.6 - - + -
430A VAL* 3.1 31.3 + - + +
431A LEU* 3.7 7.6 - - - +
432A HIS 3.0 0.6 - - - -
433A ALA* 1.3 75.7 - - + +
435A GLY* 1.3 58.8 + - - +
436A VAL* 3.5 5.1 + - + +
464A GLN* 3.5 14.6 + - - +
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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
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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