Contacts of the helix formed by residues 852 - 858 (chain A) 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 A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A SER* 3.5 21.1 + - - -
832A LEU* 3.2 34.7 - - + +
848A GLU 5.1 0.7 - - - -
849A ILE 2.8 12.0 + - - +
850A ALA 3.5 15.7 - - - -
851A GLY* 1.3 84.6 + - - +
853A ILE* 1.3 63.1 + - - +
854A MET 3.4 2.0 - - - -
855A GLU* 3.4 24.9 + - - +
856A PHE* 3.0 41.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 853 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
846A LEU 5.0 0.9 - - - +
849A ILE* 3.7 36.6 - - + +
852A HIS* 1.3 77.8 - - - +
854A MET* 1.3 53.0 + - - +
856A PHE* 3.7 3.3 - - - +
857A SER* 2.7 43.9 + - - +
866A ILE* 4.1 4.9 - - + -
880A LEU* 4.5 7.2 - - + +
881A VAL* 3.8 40.2 - - + -
884A GLU* 3.0 36.6 + - + +
885A ILE* 3.4 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 854 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852A HIS 3.4 0.4 - - - -
853A ILE* 1.3 78.6 - - - +
855A GLU* 1.3 63.2 + - - +
857A SER* 3.3 3.1 + - - -
858A GLN* 3.1 49.1 + - - +
884A GLU* 3.2 29.3 + - + +
885A ILE* 3.9 5.8 - - - -
888A ALA* 3.4 33.2 - - + +
891A GLN* 3.8 8.7 - - - +
892A LEU* 3.3 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 855 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
828A GLY 3.8 5.7 - - - +
829A ARG* 3.5 9.1 - - - -
830A SER* 2.7 51.1 + - - -
833A LEU* 3.4 23.5 - - + +
852A HIS* 3.4 23.8 + - - +
853A ILE 3.2 0.4 - - - -
854A MET* 1.3 78.6 - - - +
856A PHE* 1.3 61.6 + - + +
858A GLN* 3.4 14.6 + - - +
859A ASP* 3.5 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 856 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A LEU* 4.2 7.0 - - + -
833A LEU* 3.8 39.5 - - + -
836A PHE* 3.9 22.7 - + + -
844A LEU* 3.9 14.1 - - + -
849A ILE* 3.5 37.9 - - + -
852A HIS* 3.0 43.3 + + + +
853A ILE 3.7 2.9 - - - +
855A GLU* 1.3 76.6 - - + +
857A SER* 1.3 61.4 + - - +
859A ASP* 3.1 8.4 + - - -
862A GLY* 2.9 23.8 - - - -
863A SER 2.7 27.8 + - - -
865A PHE* 4.3 7.6 - + - -
866A ILE* 3.8 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 857 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853A ILE* 2.7 29.0 + - - +
854A MET* 3.6 6.3 - - - -
856A PHE* 1.3 74.4 - - - +
858A GLN* 1.3 56.5 + - - +
859A ASP 3.2 2.8 + - - -
863A SER* 3.5 15.4 - - - +
866A ILE* 3.3 17.8 - - - +
892A LEU* 3.9 28.0 - - - +
897A PHE 3.6 0.2 - - - -
898A GLY* 3.4 21.9 + - - -
901A VAL* 3.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 858 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854A MET* 3.1 30.6 + - - +
855A GLU* 3.4 7.0 + - - +
856A PHE 3.2 0.8 - - - -
857A SER* 1.3 74.9 - - - +
859A ASP* 1.3 57.7 + - - +
860A GLN 4.3 0.2 - - - -
891A GLN* 2.8 35.9 + - - +
892A LEU* 3.5 19.7 - - + -
895A ASP* 3.1 37.0 - - - +
896A VAL* 6.0 0.2 - - - +
897A PHE* 4.5 7.6 - - - -
----------------------------------------------------------
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