Contacts of the helix formed by residues 413 - 434 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG* 3.5 14.8 - - - +
412B MET* 1.3 73.5 - - - +
414B GLU* 1.3 54.2 + - + +
415B GLU* 3.2 17.4 + - - +
416B GLN* 2.7 62.7 + - - +
417B ILE* 2.5 39.9 + - - +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG* 6.3 0.9 - - - +
413B ASN* 1.3 72.5 - - + +
415B GLU* 1.3 58.5 + - - +
417B ILE* 3.9 11.8 - - + +
418B ALA* 2.6 36.4 + - - +
540B LYS 3.3 22.5 - - - +
541B VAL* 3.9 2.8 - - - +
542B SER* 2.9 39.0 + - - -
545B LEU* 3.7 17.9 - - + +
571B PHE* 3.9 7.0 - - + -
574B LYS* 3.7 18.1 + - + +
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASN* 3.2 16.3 + - - +
414B GLU* 1.3 78.2 - - - +
416B GLN* 1.3 61.6 + - - +
418B ALA* 3.5 1.4 - - - +
419B ALA* 3.0 17.5 + - - +
574B LYS* 3.8 17.8 - - + +
576B GLY* 3.4 39.3 + - - +
577B PRO* 4.3 5.9 - - - +
580B SER* 3.7 18.7 - - - +
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Residues in contact with GLN 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B ARG 4.7 0.7 - - - +
412B MET* 3.5 19.2 - - + -
413B ASN* 2.7 62.0 + - - +
415B GLU* 1.3 71.7 - - - +
417B ILE* 1.3 55.3 + - - +
419B ALA* 2.7 31.6 + - - +
420B VAL* 3.3 8.1 + - - +
580B SER* 3.0 40.6 + - - +
581B ILE* 5.4 3.8 - - + +
583B PRO* 5.1 3.6 - - - +
584B LEU* 3.0 37.9 - - + +
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Residues in contact with ILE 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B MET* 3.8 30.7 - - + +
413B ASN 2.5 29.9 + - - +
414B GLU* 3.9 8.7 - - + +
416B GLN* 1.3 72.6 - - - +
418B ALA* 1.3 63.7 + - - +
419B ALA 3.3 0.5 + - - -
420B VAL 3.6 1.2 + - - -
421B CYS* 3.6 18.7 + - - +
505B VAL* 4.7 8.7 - - + -
508B MET* 3.6 46.9 - - + +
509B VAL* 4.4 14.1 - - + -
545B LEU* 4.0 26.5 - - + -
571B PHE* 4.2 7.0 - - + -
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Residues in contact with ALA 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B GLU 2.6 25.0 + - - +
415B GLU 3.5 4.5 - - - +
417B ILE* 1.3 73.7 - - - +
419B ALA* 1.3 62.7 + - - +
421B CYS* 3.4 4.6 + - - +
422B LEU* 3.2 18.2 + - - +
571B PHE* 4.0 31.6 - - + +
572B LEU* 4.1 4.5 - - - +
574B LYS* 4.1 4.7 - - + -
575B ALA* 3.5 28.8 - - + +
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Residues in contact with ALA 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLU 3.0 9.9 + - - +
416B GLN* 2.7 24.2 + - - +
418B ALA* 1.3 70.2 - - - +
420B VAL* 1.3 63.8 + - - +
421B CYS 3.4 0.2 + - - -
422B LEU* 3.6 3.3 + - - +
423B ALA* 3.5 18.2 + - - +
454B VAL* 5.7 1.2 - - - +
575B ALA* 3.7 8.5 - - - -
576B GLY 3.6 24.5 - - - +
577B PRO 5.1 0.9 - - - +
580B SER* 4.6 4.3 - - - +
581B ILE* 4.7 14.1 - - + -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403B LEU* 4.3 12.6 - - + -
412B MET* 3.8 28.7 - - + -
416B GLN 3.3 3.3 + - - +
418B ALA 3.4 0.2 - - - -
419B ALA* 1.3 76.0 - - - +
421B CYS* 1.3 63.4 + - - +
423B ALA* 3.3 8.7 + - - +
424B VAL* 3.3 23.8 + - + +
446B ILE* 4.5 2.0 - - + -
448B LEU* 5.0 0.7 - - + -
454B VAL* 4.4 32.3 - - + +
504B MET* 4.3 20.2 - - + -
508B MET* 4.0 24.2 - - + -
581B ILE* 4.7 7.0 - - + -
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Residues in contact with CYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417B ILE* 3.6 13.8 + - - +
418B ALA* 3.5 11.7 - - - +
420B VAL* 1.3 77.6 - - - +
422B LEU* 1.3 67.6 + - - +
423B ALA 3.2 0.2 + - - -
424B VAL* 3.3 3.3 + - - +
425B LEU* 2.9 30.8 + - + +
501B LEU* 4.9 12.3 - - - -
505B VAL* 4.4 17.5 - - - -
508B MET* 4.9 5.4 - - - -
548B PHE* 3.2 40.2 - - + -
571B PHE* 5.1 1.8 - - + -
572B LEU* 3.9 9.4 - - + -
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418B ALA 3.2 7.7 + - - +
419B ALA* 3.8 9.4 - - - +
421B CYS* 1.3 77.0 - - - +
423B ALA* 1.3 56.7 + - - +
425B LEU* 3.4 2.7 + - - +
426B GLN* 2.8 68.9 + - + +
567B LEU* 4.1 10.0 - - + +
572B LEU* 3.3 27.6 - - + +
575B ALA* 3.7 23.1 - - + -
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B ASN* 3.5 33.3 - - + +
419B ALA 3.5 8.6 + - - +
420B VAL 3.3 10.9 + - - +
421B CYS 3.2 0.6 - - - -
422B LEU* 1.3 79.1 - - - +
424B VAL* 1.3 62.9 + - + +
426B GLN* 3.2 13.4 + - - -
427B ALA 3.2 15.9 + - - -
454B VAL* 4.0 22.7 - - + +
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Residues in contact with VAL 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377B ASN* 5.5 0.7 - - - -
420B VAL* 3.3 15.6 + - + +
421B CYS 4.1 1.8 - - - +
423B ALA* 1.3 80.3 - - + +
425B LEU* 1.3 60.1 + - - +
427B ALA* 3.1 6.8 + - - +
428B LEU* 2.8 57.7 + - + +
441B ILE* 5.0 9.9 - - + -
446B ILE* 3.8 33.7 - - + -
454B VAL* 6.0 1.6 - - + -
456B LEU* 4.9 8.5 - - + -
501B LEU* 3.7 28.0 - - + -
504B MET* 5.3 5.2 - - + -
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421B CYS* 2.9 23.0 + - + +
422B LEU* 3.9 3.1 - - - +
424B VAL* 1.3 78.3 - - + +
426B GLN* 1.3 57.7 + - - +
428B LEU* 4.4 2.7 - - + -
429B SER* 3.0 28.3 + - - -
498B ILE* 4.2 2.0 - - + -
501B LEU* 4.0 24.2 - - + -
548B PHE* 4.4 13.7 - - + -
552B LEU* 6.0 1.3 - - + -
563B ALA* 3.8 27.4 - - + +
566B LEU* 3.7 35.4 - - + -
567B LEU* 3.5 15.3 - - + +
572B LEU* 3.7 28.5 - - + -
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Residues in contact with GLN 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375B HIS* 3.9 13.7 - - + +
376B GLU* 5.0 2.7 - - - +
377B ASN* 2.8 26.4 + - - +
422B LEU* 2.8 50.4 + - + +
423B ALA* 3.6 9.0 - - - +
424B VAL 3.1 0.2 - - - -
425B LEU* 1.3 75.8 - - - +
427B ALA* 1.3 61.9 + - - +
429B SER* 3.0 21.8 - - - -
430B VAL* 3.1 15.2 + - - +
567B LEU* 3.8 12.3 - - + +
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Residues in contact with ALA 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B TYR* 3.5 7.9 + - - -
375B HIS* 4.0 7.3 + - + -
377B ASN* 4.0 11.0 - - + +
378B VAL* 3.7 28.9 - - + -
423B ALA 3.2 9.3 + - - +
424B VAL* 3.1 9.5 + - - +
426B GLN* 1.3 76.0 - - - +
428B LEU* 1.3 54.5 + - - +
430B VAL* 2.6 23.7 + - - +
431B LEU* 2.7 20.9 + - + +
456B LEU* 5.0 11.4 - - + -
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Residues in contact with LEU 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B VAL* 2.8 49.8 + - + +
425B LEU* 4.2 7.0 - - + +
427B ALA* 1.3 71.4 - - - +
429B SER* 1.3 51.8 + - - +
431B LEU* 4.4 7.6 - - + +
432B HIS* 2.5 50.6 + - + +
438B HIS* 5.2 1.3 - - + -
441B ILE* 4.4 13.9 - - + -
456B LEU* 5.0 11.4 - - + -
497B ASP* 3.6 37.7 - - + +
498B ILE* 4.7 5.6 - - + -
501B LEU* 3.7 21.1 - - + -
563B ALA* 3.5 14.4 - - + -
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Residues in contact with SER 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425B LEU 3.0 10.5 + - - -
426B GLN* 3.0 16.8 - - - -
428B LEU* 1.3 77.3 - - - +
430B VAL* 1.3 59.1 + - - +
432B HIS* 4.0 1.4 - - - +
433B ALA* 3.7 21.0 + - - +
563B ALA* 3.1 10.6 - - - +
564B ALA* 3.2 25.2 + - - +
567B LEU* 2.8 29.3 - - - +
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Residues in contact with VAL 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373B TYR* 2.9 34.9 - - + +
374B GLN 5.8 1.3 - - - +
375B HIS* 3.3 35.0 - - + +
426B GLN 3.1 7.3 + - - +
427B ALA 2.6 16.0 + - - +
429B SER* 1.3 72.7 - - - +
431B LEU* 1.3 61.5 + - - +
432B HIS 3.3 0.2 - - - -
433B ALA* 4.2 1.6 + - - +
434B GLN* 4.0 24.9 + - - +
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Residues in contact with LEU 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370B MET* 4.1 13.0 - - + -
373B TYR* 3.3 39.9 - - + +
378B VAL* 5.0 1.8 - - + -
427B ALA 2.7 18.1 + - - +
428B LEU* 4.0 8.1 - - + +
430B VAL* 1.3 73.6 - - - +
432B HIS* 1.3 60.8 + - + +
434B GLN* 3.6 2.6 + - - -
435B GLY 3.1 3.8 + - - -
436B VAL* 2.5 78.2 + - + +
438B HIS* 5.3 8.1 - - + +
456B LEU* 4.9 8.1 - - + -
459B PHE* 3.7 28.0 - - + -
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Residues in contact with HIS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B LEU* 2.5 46.0 + - + +
429B SER* 4.0 6.1 - - - +
430B VAL 3.3 0.2 - - - -
431B LEU* 1.3 71.5 - - + +
433B ALA* 1.3 56.7 + - - +
435B GLY* 2.5 30.1 + - - -
436B VAL 4.0 13.2 - - - -
437B ILE* 5.6 0.4 - - - +
494B PRO* 3.3 49.1 + - + +
495B GLU* 5.2 0.4 - - - -
497B ASP* 4.0 14.7 - - - +
498B ILE* 4.0 15.3 - - + -
562B THR* 4.6 7.4 - - + +
563B ALA* 3.3 31.6 + - + +
564B ALA 5.9 0.4 - - - +
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Residues in contact with ALA 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B SER 3.7 13.6 + - - +
430B VAL* 4.8 2.2 - - - +
431B LEU 3.6 0.2 - - - -
432B HIS* 1.3 77.4 - - - +
434B GLN* 1.3 60.3 + - + +
435B GLY* 3.2 3.8 + - - -
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Residues in contact with GLN 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B ASP 5.1 6.1 - - - +
373B TYR* 6.0 5.7 - - - -
430B VAL* 4.0 20.8 + - - +
431B LEU* 3.6 3.5 + - - +
432B HIS 3.2 1.0 - - - -
433B ALA* 1.3 78.9 - - + +
435B GLY* 1.3 50.8 + - - +
436B VAL* 3.5 7.4 - - + -
464B GLN* 2.5 30.4 + - - +
465B VAL 4.1 2.4 - - - +
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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