Contacts of the helix formed by residues 565 - 582 (chain B) in PDB entry 2BXE
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 GLU 565 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ASP* 3.0 11.0 + - - -
564B LYS* 1.3 82.1 - - + +
566B THR* 1.3 69.4 + - - +
568B PHE* 2.8 38.6 + - + +
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Residues in contact with THR 566 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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563B ASP* 3.1 11.4 + - - +
564B LYS* 4.7 7.5 + - - +
565B GLU* 1.3 77.8 + - - +
567B CYS* 1.3 67.9 + - - +
568B PHE 2.9 1.2 + - - -
569B ALA* 3.0 7.9 + - - +
570B GLU* 2.9 29.6 + - + -
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Residues in contact with CYS 567 (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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558B CYS* 2.0 53.8 - - + -
561B ALA* 3.8 9.6 - - + -
563B ASP* 2.5 35.1 + - - +
566B THR* 1.3 72.7 - - - +
568B PHE* 1.3 61.6 + - - +
570B GLU* 2.8 4.2 + - - -
571B GLU* 2.5 60.6 + - - +
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Residues in contact with PHE 568 (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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508B THR* 3.4 33.9 - - + +
509B PHE 3.0 31.5 - - - +
510B HIS* 3.2 26.5 - - + +
511B ALA* 4.5 14.4 - - + +
558B CYS* 3.5 10.0 - - - +
563B ASP* 3.9 0.4 + - - -
565B GLU* 2.8 31.0 + - + +
567B CYS* 1.3 75.2 - - - +
569B ALA* 1.3 76.0 + - + -
572B GLY* 3.8 11.8 + - - -
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Residues in contact with ALA 569 (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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508B THR* 6.2 1.3 - - - -
566B THR* 3.0 8.7 + - - +
568B PHE* 1.3 93.6 - - + +
570B GLU* 1.3 64.3 + - - +
572B GLY* 3.8 3.0 + - - -
573B LYS* 3.6 13.9 + - - +
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Residues in contact with GLU 570 (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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566B THR* 2.9 28.1 + - + +
567B CYS* 2.8 7.4 + - - +
569B ALA* 1.3 74.4 - - - +
571B GLU* 1.3 57.6 + - - +
572B GLY 2.9 1.3 - - - -
573B LYS* 2.7 35.0 + - - +
574B LYS* 3.7 2.4 + - - +
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Residues in contact with GLU 571 (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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554B PHE* 4.9 7.0 - - - +
557B LYS* 2.9 48.6 - - + +
558B CYS* 3.0 10.8 - - - +
561B ALA* 5.4 1.7 - - - +
567B CYS* 2.5 38.7 + - - +
570B GLU* 1.3 75.2 - - - +
572B GLY* 1.3 57.9 + - - -
574B LYS* 3.1 23.2 + - + +
575B LEU* 3.3 10.7 + - - +
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Residues in contact with GLY 572 (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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509B PHE* 5.9 1.6 - - - -
558B CYS* 5.0 0.4 - - - -
567B CYS 3.6 4.2 + - - -
568B PHE 3.8 13.8 + - - -
569B ALA* 4.1 4.5 - - - -
570B GLU 2.9 1.4 - - - -
571B GLU* 1.3 80.6 - - - +
573B LYS* 1.3 56.1 + - - +
574B LYS 3.3 0.2 - - - -
575B LEU* 3.6 9.5 - - - +
576B VAL* 3.1 37.1 + - - +
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Residues in contact with LYS 573 (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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569B ALA 3.6 7.2 + - - +
570B GLU* 2.7 19.8 + - - +
572B GLY* 1.3 76.9 - - - +
574B LYS* 1.3 61.8 + - - +
575B LEU 3.2 0.2 - - - -
576B VAL* 4.5 3.4 - - - +
577B ALA* 3.2 24.9 + - - +
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Residues in contact with LYS 574 (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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570B GLU 3.7 1.4 + - - +
571B GLU* 3.1 19.6 + - - +
573B LYS* 1.3 78.9 - - - +
575B LEU* 1.3 60.5 - - - +
577B ALA* 3.8 4.4 - - - +
578B ALA* 3.3 21.7 + - - +
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Residues in contact with LEU 575 (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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551B PHE* 6.4 0.9 - - + -
554B PHE* 4.2 25.4 - - + +
571B GLU 3.3 9.6 + - - +
572B GLY* 3.6 12.8 - - - +
573B LYS 3.2 0.6 - - - -
574B LYS* 1.3 75.7 - - - +
576B VAL* 1.3 54.6 + - + +
577B ALA 3.1 1.3 - - - -
578B ALA* 3.1 6.4 + - - +
579B SER* 2.6 41.8 + - - +
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Residues in contact with VAL 576 (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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502B PHE* 5.6 12.8 - - + -
507B PHE* 5.0 20.6 - - + +
572B GLY* 3.1 17.5 + - - +
573B LYS* 4.5 3.1 - - - +
575B LEU* 1.3 76.7 - - + +
577B ALA* 1.3 52.9 + - - +
579B SER* 3.1 11.3 - - - -
580B GLN* 2.6 39.4 + - + +
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Residues in contact with ALA 577 (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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573B LYS 3.2 19.2 + - - +
574B LYS* 3.8 7.0 - - - +
575B LEU 3.1 0.6 - - - -
576B VAL* 1.3 81.9 - - - +
578B ALA* 1.3 62.7 + - - +
580B GLN* 3.3 5.9 + - - +
581B ALA* 3.3 17.5 + - - +
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Residues in contact with ALA 578 (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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547B VAL* 4.9 2.5 - - - +
550B ASP* 4.9 18.1 - - + +
574B LYS 3.3 14.2 + - - +
575B LEU* 3.1 5.6 + - - +
577B ALA* 1.3 79.9 - - - +
579B SER* 1.3 61.8 + - - +
581B ALA* 3.5 8.9 - - - +
582B ALA* 3.4 22.2 + - - +
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Residues in contact with SER 579 (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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507B PHE* 4.9 20.8 - - - -
532B LEU* 6.0 2.6 - - - +
547B VAL* 4.4 19.4 - - - +
551B PHE* 6.0 2.4 - - - -
575B LEU* 2.6 24.0 + - - +
576B VAL* 3.0 20.7 + - - -
578B ALA* 1.3 76.2 - - - +
580B GLN* 1.3 58.7 + - - +
581B ALA 3.1 5.2 + - - -
582B ALA* 3.8 13.3 + - - +
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Residues in contact with GLN 580 (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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576B VAL* 2.6 23.1 + - + +
577B ALA* 3.9 6.5 - - - +
579B SER* 1.3 74.4 - - - +
581B ALA* 1.3 61.8 + - - +
582B ALA 4.8 1.1 - - - -
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Residues in contact with ALA 581 (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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577B ALA 3.3 11.7 + - - +
578B ALA* 3.5 14.6 - - - +
579B SER 3.1 0.6 - - - -
580B GLN* 1.3 79.8 - - - +
582B ALA* 1.3 68.5 + - - +
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Residues in contact with ALA 582 (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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543B GLN* 4.5 23.7 - - + +
546B ALA* 5.3 6.1 - - + -
547B VAL* 4.0 30.7 - - + +
578B ALA 3.4 10.7 + - - +
579B SER 3.8 10.0 + - - +
580B GLN 3.8 1.5 - - - -
581B ALA* 1.3 85.4 - - - +
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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
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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