Contacts of the helix formed by residues 470 - 479 (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 SER 470 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B VAL* 3.8 8.8 - - - +
417B GLN* 3.8 25.1 + - - -
418B VAL* 4.7 2.9 - - - -
464B HIS* 3.2 16.0 + - - -
468B PRO* 6.2 0.4 - - - -
469B VAL* 1.3 82.0 - - - +
471B ASP* 1.3 63.9 + - - +
472B ARG* 3.4 19.6 + - - +
473B VAL* 3.0 26.2 + - - +
474B THR* 3.1 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 471 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B VAL 4.3 0.6 - - - +
470B SER* 1.3 72.0 + - - +
472B ARG* 1.3 64.3 + - + +
474B THR* 3.0 11.3 + - - -
475B LYS* 2.9 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 472 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LYS 2.9 28.4 + - - -
415B VAL* 4.1 8.1 - - + -
470B SER* 3.1 10.5 - - - +
471B ASP* 1.3 81.4 - - + +
473B VAL* 1.3 61.1 + - - +
475B LYS* 4.0 7.1 + - - +
476B CYS* 3.4 26.3 + - - +
491B LEU* 3.5 45.6 - - + +
492B GLU 4.0 5.3 - - - +
493B VAL 3.9 7.5 + - - -
494B ASP* 3.2 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 473 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B VAL* 3.6 26.0 - - + -
418B VAL* 4.0 15.7 - - + -
460B LEU* 4.8 9.0 - - + -
464B HIS* 3.5 32.8 - - + +
470B SER* 3.0 18.5 + - - +
472B ARG* 1.3 72.8 - - - +
474B THR* 1.3 70.2 + - - +
475B LYS 3.1 0.7 + - - -
476B CYS* 3.1 3.3 + - - +
477B CYS* 2.9 40.3 + - - -
488B PHE* 4.4 17.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 474 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B HIS* 3.5 20.0 + - - -
468B PRO* 4.6 9.0 - - - +
470B SER 3.1 5.5 + - - -
471B ASP* 3.0 13.7 + - - -
473B VAL* 1.3 80.6 - - - +
475B LYS* 1.3 56.5 + - - +
477B CYS* 4.0 4.0 - - - -
478B THR* 2.7 50.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 475 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471B ASP 2.9 15.8 + - - +
472B ARG* 4.0 7.3 + - - +
473B VAL 3.2 0.2 - - - -
474B THR* 1.3 76.8 - - - +
476B CYS* 1.3 60.0 + - - +
477B CYS 3.2 0.3 + - - -
478B THR* 4.2 3.1 - - - -
479B GLU* 2.9 65.1 + - + +
487B CYS* 3.9 23.4 - - - -
491B LEU* 5.0 11.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 476 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B ARG 3.4 16.8 + - - +
473B VAL 3.1 4.4 + - - +
475B LYS* 1.3 83.1 - - - +
477B CYS* 1.3 59.5 + - - +
479B GLU* 4.5 1.9 + - - +
480B SER 4.0 5.9 + - - +
484B ARG* 3.4 23.9 - - - +
487B CYS* 2.0 61.9 - - + +
488B PHE* 3.6 22.2 - - + -
491B LEU* 4.0 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 477 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.4 8.5 - - - -
461B CYS* 2.0 56.5 - - + +
464B HIS* 5.7 0.7 - - - -
473B VAL* 2.9 34.6 + - - +
474B THR* 4.0 4.7 - - - +
476B CYS* 1.3 78.2 - - - +
478B THR* 1.3 63.6 + - + +
480B SER 4.5 1.5 - - - +
484B ARG* 2.9 33.7 + - - +
488B PHE* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 478 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 3.9 15.3 - - - -
465B GLU* 6.5 1.1 - - + -
474B THR* 2.7 35.3 + - + +
475B LYS* 3.8 2.8 + - - -
477B CYS* 1.3 80.9 - - + +
479B GLU* 1.3 70.7 + - - +
480B SER 3.4 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 479 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206B PHE* 4.9 1.2 - - - -
475B LYS* 2.9 45.6 + - + +
476B CYS* 4.9 2.0 - - - +
478B THR* 1.3 82.0 + - - +
480B SER* 1.3 67.2 + - - +
483B ASN* 5.9 2.6 - - - +
487B CYS* 4.7 7.4 - - - +
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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