Contacts of the helix formed by residues 852 - 858 (chain B) in PDB entry 1M8X
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 HIS 852 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830B SER* 3.5 22.5 + - - -
832B LEU* 3.5 28.8 - - + +
848B GLU 4.8 0.9 - - - -
849B ILE* 2.8 12.3 + - + +
850B ALA 3.5 15.6 + - - -
851B GLY* 1.3 84.3 + - - +
853B ILE* 1.3 64.0 + - - +
854B MET 3.3 2.9 + - - -
855B GLU* 3.1 28.1 + - - +
856B PHE* 3.0 42.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 853 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846B LEU 4.7 2.7 - - - +
849B ILE* 3.4 39.0 - - + +
850B ALA* 4.8 1.8 - - - +
852B HIS* 1.3 78.6 - - - +
854B MET* 1.3 61.1 + - - +
856B PHE* 3.5 4.0 + - - +
857B SER* 2.8 34.0 + - - +
866B ILE* 4.4 3.1 - - + -
880B LEU 4.5 1.8 - - - +
881B VAL* 3.9 41.7 - - + +
884B GLU* 2.9 38.0 + - + +
885B ILE* 3.5 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 854 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852B HIS 3.3 0.8 - - - -
853B ILE* 1.3 78.7 - - - +
855B GLU* 1.3 59.2 + - - +
857B SER* 2.9 19.8 + - - -
858B GLN* 3.1 34.0 + - - +
884B GLU* 3.4 27.8 + - + +
885B ILE* 4.0 5.4 - - - -
888B ALA* 3.9 21.1 - - + -
891B GLN* 3.8 12.3 - - - +
892B LEU* 3.5 44.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 855 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828B GLY 4.3 4.7 - - - +
829B ARG* 4.0 7.4 - - - -
830B SER* 2.5 43.6 + - - -
833B LEU* 3.8 22.0 - - + +
851B GLY 5.6 0.2 - - - +
852B HIS* 3.1 36.2 + - + +
854B MET* 1.3 79.1 - - - +
856B PHE* 1.3 61.2 + - + +
858B GLN* 3.4 10.5 + - - +
859B ASP* 3.3 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 856 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832B LEU* 4.2 10.8 - - + -
833B LEU* 3.7 39.0 - - + -
836B PHE* 3.9 31.0 - + + -
844B LEU* 4.8 2.0 - - + -
849B ILE* 3.6 35.7 - - + -
852B HIS* 3.0 40.3 + - + +
853B ILE 3.9 3.4 - - - +
855B GLU* 1.3 79.3 - - - +
857B SER* 1.3 56.0 + - - +
859B ASP* 3.4 5.1 - - - +
862B GLY* 2.8 25.5 - - - -
863B SER 2.6 32.6 + - - -
865B PHE* 4.4 8.5 - + - -
866B ILE* 3.9 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 857 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853B ILE* 2.8 27.0 + - - +
854B MET* 2.9 7.7 + - - -
856B PHE* 1.3 78.7 - - - +
858B GLN* 1.3 56.6 + - - +
859B ASP 3.3 1.5 + - - -
863B SER* 3.8 4.0 - - - +
866B ILE* 3.5 13.4 - - - +
885B ILE* 4.2 1.9 - - - +
892B LEU* 4.0 22.9 - - - -
897B PHE 3.3 6.8 - - - +
898B GLY* 3.1 24.9 + - - -
901B VAL* 3.6 25.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 858 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854B MET* 3.1 31.5 + - - +
855B GLU* 3.4 9.1 + - - +
856B PHE 3.3 0.4 - - - -
857B SER* 1.3 76.1 - - - +
859B ASP* 1.3 57.3 + - - +
860B GLN 4.4 0.3 + - - -
891B GLN* 2.8 33.6 + - - +
892B LEU* 3.5 19.1 - - + -
895B ASP* 3.5 30.6 - - - +
896B VAL* 5.4 1.0 - - - +
897B PHE* 4.1 11.9 - - - +
----------------------------------------------------------
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