Contacts of the helix formed by residues 851 - 855 (chain B) in PDB entry 4XUF
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 PRO 851 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B ARG 4.9 7.4 - - - +
811B ASP* 3.3 26.0 - - + +
815B ARG* 3.2 23.6 - - - +
841B ASN 3.6 12.3 - - - +
842B TYR* 3.5 18.3 - - + -
850B LEU* 1.3 85.8 - - + +
852B VAL* 1.3 64.3 + - - +
853B LYS 3.4 2.6 + - - -
854B TRP* 3.6 15.9 + - + +
855B MET* 3.1 24.1 - - + +
865B TYR* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 852 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B ASN 4.1 6.1 + - - +
843B VAL* 3.6 32.8 - - + -
845B ARG* 4.4 6.1 - - - -
850B LEU* 3.2 20.7 + - + -
851B PRO* 1.3 72.1 - - - +
853B LYS* 1.3 74.0 + - + +
854B TRP 3.2 5.1 + - - -
855B MET* 3.3 21.7 + - - +
860B LEU* 4.1 16.9 - - + +
894B VAL* 4.1 17.7 - - + -
898B PHE* 4.7 9.9 - - + -
899B TYR* 3.9 22.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
841B ASN 6.0 0.2 - - - +
851B PRO 3.4 0.8 - - - -
852B VAL* 1.3 82.6 - - + +
854B TRP* 1.3 76.5 + - + +
855B MET 3.6 1.3 - - - -
872B TRP* 5.1 0.6 + - - -
876B ILE* 3.4 20.3 - - - +
887B ASN* 3.7 18.1 + - - +
888B PRO* 3.2 30.2 + - + +
889B TYR* 3.7 24.1 + - + -
890B PRO* 5.9 0.2 - - - +
892B ILE 3.2 26.3 + - - -
893B PRO* 4.3 5.2 - - - +
894B VAL* 4.4 19.9 - - - +
898B PHE* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811B ASP* 5.2 1.1 - - - +
812B LEU 3.6 14.6 - - - +
813B ALA* 3.4 20.6 - - + +
815B ARG* 3.2 24.9 - - - +
841B ASN* 3.4 47.3 - - + -
851B PRO* 3.6 20.3 + - + +
852B VAL 3.2 0.8 - - - -
853B LYS* 1.3 99.7 - - + +
855B MET* 1.3 59.1 + - + +
872B TRP* 3.6 4.0 - - - -
873B SER* 2.7 39.0 + - - +
876B ILE* 3.5 24.5 - - + +
877B LEU 4.7 1.3 - - - -
880B GLU* 3.0 41.1 + - - -
887B ASN* 4.6 0.9 - - - -
888B PRO* 3.5 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
810B ARG 5.4 3.1 - - - +
850B LEU* 3.6 32.3 - - + -
851B PRO* 3.1 30.7 - - + +
852B VAL* 3.3 8.1 + - - +
853B LYS 3.6 0.7 - - - -
854B TRP* 1.3 78.8 - - + +
856B ALA* 1.3 59.2 + - - +
857B PRO 4.0 0.2 - - - -
859B SER* 3.3 35.4 - - - +
860B LEU* 3.5 24.7 - - + +
865B TYR* 3.2 31.2 - - + +
869B SER* 5.6 0.4 - - - -
872B TRP* 2.7 28.3 + - - -
873B SER* 4.5 2.9 - - - +
902B ILE* 5.7 0.9 - - - +
----------------------------------------------------------
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