Contacts of the helix formed by residues 841 - 848 (chain A) in PDB entry 1CEZ
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 VAL 841 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549A MET* 3.6 47.6 - - + -
728A VAL 6.1 0.4 - - - +
730A PRO* 3.9 15.0 - - + -
782A PHE* 4.1 14.2 - - + -
786A GLN* 3.4 26.5 - - - +
836A TYR* 4.1 10.3 - - + -
839A CYS* 3.5 11.8 + - + +
840A ASP* 1.3 71.9 - - - +
842A LEU* 1.3 58.0 + - + +
844A ASP* 3.6 9.9 - - - +
845A PHE* 2.7 34.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A PHE* 5.5 0.4 - - + -
549A MET* 3.6 30.5 - - + +
550A LEU* 3.5 33.2 - - + -
695A ALA* 4.6 8.5 - - + -
698A TRP* 4.3 16.5 - - + +
699A LEU* 4.6 14.6 - - + -
782A PHE* 3.6 20.4 - - + -
840A ASP* 3.1 7.3 + - - +
841A VAL* 1.3 77.7 - - - +
843A ALA* 1.3 61.7 + - - +
845A PHE* 3.0 7.3 + - + +
846A TYR* 2.8 27.9 + - - +
864A LEU* 4.1 13.3 - - + +
865A PRO* 4.0 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840A ASP* 3.0 32.3 + - + +
842A LEU* 1.3 77.2 - - - +
844A ASP* 1.3 58.4 + - - +
846A TYR* 3.1 10.1 + - - +
847A ASP* 2.9 38.0 + - - +
864A LEU* 4.3 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728A VAL 5.7 4.7 - - - +
839A CYS* 4.2 10.0 - - - +
840A ASP* 2.7 37.4 + - - +
841A VAL* 3.5 9.8 + - - +
843A ALA* 1.3 76.8 - - - +
845A PHE* 1.3 61.8 + - - +
847A ASP* 3.5 15.3 + - - +
848A GLN* 3.1 21.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A TRP* 4.5 9.6 - - - -
699A LEU* 3.5 28.3 - - + -
702A ALA* 4.3 14.8 - - + -
725A VAL* 3.5 32.1 - - + -
726A HIS 3.8 4.3 - - - -
727A TRP* 3.3 39.0 - + + -
778A ILE* 4.2 11.0 - - + -
782A PHE* 4.4 12.1 - + + -
841A VAL 2.7 17.4 + - - +
842A LEU* 3.2 7.4 - - - +
844A ASP* 1.3 75.8 - - - +
846A TYR* 1.3 65.5 + - - +
848A GLN* 2.8 20.9 + - - +
849A PHE* 3.0 42.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
698A TRP* 3.3 35.9 - + + -
842A LEU 2.8 13.1 + - - +
843A ALA* 3.3 13.5 - - - +
845A PHE* 1.3 76.9 - - - +
847A ASP* 1.3 61.8 + - - +
848A GLN 2.8 10.6 + - - -
849A PHE* 3.1 29.8 + + + -
850A ALA* 3.4 25.0 + - + +
861A MET* 5.2 4.0 - - + -
862A PRO* 4.6 16.8 - - + +
863A ALA 5.3 0.9 - - - -
864A LEU* 4.1 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A ALA* 2.9 27.4 + - - +
844A ASP* 3.9 11.1 - - - +
845A PHE 3.2 0.8 - - - -
846A TYR* 1.3 81.0 - - - +
848A GLN* 1.3 64.1 + - - +
850A ALA* 4.6 8.8 - - - +
851A ASP* 5.7 1.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A HIS* 4.0 35.6 + - - +
727A TRP* 4.7 4.5 - - - -
728A VAL* 3.2 37.7 - - - +
844A ASP 3.1 24.3 + - - +
845A PHE* 2.8 12.5 + - - +
846A TYR 2.8 0.2 + - - -
847A ASP* 1.3 82.0 - - - +
849A PHE* 1.3 58.1 + - - +
850A ALA 3.4 4.6 + - - -
851A ASP* 5.1 1.5 - - - +
852A GLN* 4.2 16.6 + - - +
----------------------------------------------------------
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