Contacts of the helix formed by residues 483 - 491 (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 ASN 483 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 3.6 35.2 - - - +
351B LYS* 5.1 6.9 + - - +
479B GLU* 5.9 2.2 - - - +
480B SER* 2.8 30.2 + - - +
482B VAL* 1.3 75.9 - - - +
484B ARG* 1.3 58.3 + - - +
486B PRO* 2.6 36.9 - - + +
487B CYS* 3.0 11.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 484 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 5.0 0.2 - - - +
201B ALA* 5.8 2.0 - - - +
205B LYS* 5.8 2.0 - - - +
206B PHE* 3.3 20.6 - - - -
454B SER* 5.1 3.0 + - - -
457B LEU* 4.5 15.0 - - + -
458B ASN* 3.3 40.0 + - - +
461B CYS* 3.9 24.3 - - - +
476B CYS 3.4 16.4 - - - +
477B CYS* 2.9 32.5 + - - +
480B SER 3.3 16.4 + - - +
481B LEU* 3.5 29.7 - - - +
482B VAL 3.5 1.8 - - - -
483B ASN* 1.3 73.0 - - - +
485B ARG* 1.3 66.4 + - - +
487B CYS* 2.8 14.6 + - - +
488B PHE* 3.0 21.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 485 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 3.9 1.3 - - - +
383B GLU* 2.8 42.6 + - - -
384B PRO* 3.8 7.5 - - - +
387B LEU* 3.4 35.6 - - - +
450B GLU* 3.4 35.8 + - + +
453B LEU* 4.1 28.0 - - + -
454B SER* 6.0 2.2 - - - +
457B LEU* 3.5 26.1 - - + +
482B VAL 5.1 0.2 + - - -
483B ASN 3.4 0.2 - - - -
484B ARG* 1.3 76.0 - - - +
486B PRO* 1.3 86.1 - - + +
488B PHE* 3.5 1.4 + - - +
489B SER* 2.9 40.0 + - - -
2001B 1FL 4.7 9.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 486 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348B ARG* 4.0 25.6 - - - +
383B GLU* 4.4 7.2 - - - +
482B VAL 4.4 0.2 - - - +
483B ASN* 2.6 33.0 - - + +
485B ARG* 1.3 117.1 - - + +
487B CYS* 1.3 59.6 + - - +
489B SER* 3.5 5.6 + - - -
490B ALA* 3.1 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 487 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B LYS* 3.9 21.9 + - - -
476B CYS* 2.0 55.6 - - + +
479B GLU* 4.7 7.6 - - - +
483B ASN* 3.0 11.6 + - + +
484B ARG* 2.8 18.2 + - - +
486B PRO* 1.3 68.4 - - - +
488B PHE* 1.3 60.2 + - - +
490B ALA* 2.8 29.5 + - - +
491B LEU* 3.4 8.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 488 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B TYR* 3.7 30.7 - + + +
414B LYS* 2.9 26.0 - - + -
415B VAL* 5.0 6.1 - - + -
457B LEU* 3.9 26.7 - - + -
460B LEU* 4.0 24.7 - - + -
461B CYS* 4.4 13.9 - - - -
473B VAL* 4.4 20.0 - - + -
476B CYS* 3.6 26.9 - - + -
477B CYS* 4.2 14.1 - - - -
484B ARG* 3.0 23.5 + - + +
485B ARG* 4.0 3.8 - - - +
487B CYS* 1.3 78.7 - - - +
489B SER* 1.3 60.9 + - - +
490B ALA 3.2 0.7 + - - -
491B LEU* 3.2 26.4 + - + +
2001B 1FL 4.6 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 489 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B GLU* 5.6 0.7 - - - -
387B LEU* 3.8 11.5 - - - +
414B LYS* 4.0 3.4 + - - +
485B ARG* 2.9 38.3 + - - -
486B PRO* 3.5 7.2 - - - -
488B PHE* 1.3 77.3 - - - +
490B ALA* 1.3 61.8 + - - +
491B LEU 3.5 6.1 - - - +
2001B 1FL 3.4 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 490 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B PRO 3.1 11.9 + - - +
487B CYS* 2.8 17.0 + - - +
489B SER* 1.3 77.8 - - - +
491B LEU* 1.3 66.7 + - + +
492B GLU* 3.5 8.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 491 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LYS* 2.8 34.1 + - + -
415B VAL* 4.7 9.0 - - + -
472B ARG* 3.5 53.4 - - + +
475B LYS* 5.0 13.0 - - - +
476B CYS* 4.0 20.2 - - - -
487B CYS 3.7 9.6 - - - +
488B PHE* 3.4 24.2 - - + +
489B SER 3.5 2.6 - - - +
490B ALA* 1.3 80.1 - - + +
492B GLU* 1.3 61.8 + - - +
----------------------------------------------------------
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