Contacts of the helix formed by residues 483 - 492 (chain A) in PDB entry 5E92
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 CYS 483 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA* 4.1 2.2 - - - -
479A ARG* 3.8 23.7 - - - +
481A HIS 3.7 2.0 + - - -
482A PRO* 1.3 77.1 - - - +
484A VAL* 1.3 66.3 + - - +
485A ALA* 4.0 11.0 - - + +
486A SER* 3.2 30.6 + - - -
487A MET* 3.2 21.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 484 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLN* 3.5 39.9 - - + +
422A ALA* 4.1 15.7 - - + -
425A MET* 4.2 17.0 - - + -
430A LEU* 3.8 23.0 - - + +
483A CYS* 1.3 71.3 - - - +
485A ALA* 1.3 59.1 + - - +
487A MET* 3.2 2.8 + - - +
488A ALA* 2.8 28.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 485 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A CYS* 3.3 10.6 - - - +
484A VAL* 1.3 77.1 - - - +
486A SER* 1.4 57.3 + - - +
488A ALA* 3.3 7.1 + - - +
489A ASP* 3.0 37.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 486 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478A VAL* 3.9 12.5 - - - +
479A ARG* 5.5 3.5 + - - +
482A PRO* 3.7 12.3 - - - +
483A CYS* 3.2 32.0 + - - -
484A VAL 3.4 0.4 - - - -
485A ALA* 1.4 76.7 - - - +
487A MET* 1.3 61.8 + - - +
489A ASP* 3.5 11.1 + - - +
490A ASN* 3.0 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
422A ALA* 3.4 23.3 - - + +
423A ARG* 3.5 32.3 - - - +
425A MET 5.8 0.2 - - - +
430A LEU* 3.7 19.3 - - + -
474A PHE* 3.6 23.8 - - + -
478A VAL* 3.9 27.1 - - - -
482A PRO* 3.9 11.9 - - + -
483A CYS 3.2 13.6 + - - +
484A VAL* 3.2 7.4 + - - +
486A SER* 1.3 78.7 + - - +
488A ALA* 1.4 59.2 + - - +
490A ASN* 3.1 3.8 + - + -
491A VAL* 3.0 49.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 4.0 30.2 - - + +
484A VAL* 2.8 17.7 + - + +
485A ALA* 3.3 8.7 + - - +
487A MET* 1.4 73.9 - - - +
489A ASP* 1.4 60.8 + - - +
492A LEU* 3.0 37.8 + - + +
493A ALA* 3.1 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 489 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485A ALA* 3.0 19.2 + - - +
486A SER* 3.6 14.6 - - - +
488A ALA* 1.4 77.5 - - - +
490A ASN* 1.4 61.1 + - - +
493A ALA* 3.4 12.7 - - + +
494A ASP* 3.0 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 490 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A PHE* 4.6 16.4 - - + -
477A LYS* 3.3 36.3 + - - +
478A VAL* 3.6 16.7 - - + +
486A SER* 3.0 21.8 + - - +
487A MET* 3.1 8.7 + - + +
489A ASP* 1.4 78.9 - - - +
491A VAL* 1.3 57.9 + - + +
494A ASP* 3.4 14.1 + - - +
495A ALA 3.3 7.6 + - - -
496A GLY* 2.7 32.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425A MET 5.0 0.7 - - - +
427A PRO* 3.9 30.2 - - + +
430A LEU* 3.8 12.3 - - + -
448A TYR* 3.4 20.6 - - + +
474A PHE* 3.6 30.3 - - + -
487A MET* 3.0 33.1 + - + +
490A ASN* 1.3 70.5 - - - +
492A LEU* 1.3 58.4 + - - +
495A ALA* 3.5 8.8 - - - -
496A GLY 3.6 7.4 - - - -
497A ARG* 3.0 31.2 + - - +
523A HIS* 5.3 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 492 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A PRO* 3.9 25.1 - - + +
430A LEU* 5.0 1.1 - - + -
431A ALA* 3.7 31.4 - - + +
488A ALA* 3.0 27.0 + - + +
491A VAL* 1.3 76.7 - - + +
493A ALA* 1.3 66.5 + - - +
495A ALA* 3.0 16.1 + - - +
523A HIS* 3.6 32.4 + - + -
----------------------------------------------------------
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