Contacts of the helix formed by residues 836 - 849 (chain A) in PDB entry 1OY6
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 SER 836 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
561A SER 5.7 0.7 + - - -
678A THR* 3.7 19.7 + - - +
831A ALA* 3.9 6.7 - - - -
835A LYS* 1.3 79.2 - - - +
837A THR* 1.3 75.1 + - - +
838A GLY 2.8 1.8 + - - -
839A GLU* 2.7 31.1 + - - +
840A ALA 4.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
677A ALA* 4.1 2.6 - - - -
678A THR* 3.0 26.4 + - - +
679A GLY 3.3 18.4 + - - +
680A PHE* 6.1 0.7 - - - -
831A ALA* 3.4 15.8 - - - +
836A SER* 1.3 72.7 + - - +
838A GLY* 1.3 60.4 + - - +
840A ALA* 2.9 6.8 + - - +
841A MET* 2.8 54.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A SER* 2.8 4.9 + - - -
837A THR* 1.3 80.8 - - - +
839A GLU* 1.3 56.8 + - - -
841A MET* 4.3 9.5 - - - +
842A GLU* 3.2 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LYS* 3.5 33.8 + - + +
836A SER* 2.7 36.4 + - - +
838A GLY* 1.3 72.8 - - - +
840A ALA* 1.3 58.3 + - - +
842A GLU* 3.4 6.8 + - - +
843A LEU* 3.0 38.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A PHE* 4.5 12.3 - - + -
714A THR* 4.8 9.3 - - + +
831A ALA* 3.6 34.3 - - + -
832A ALA* 4.2 5.8 - - + +
835A LYS* 4.9 5.3 - - + +
836A SER 3.5 1.9 + - - +
837A THR 2.9 8.3 + - - +
839A GLU* 1.3 79.8 - - - +
841A MET* 1.3 57.3 + - - +
843A LEU* 3.1 32.4 - - - +
844A MET* 3.2 9.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679A GLY 5.5 0.2 - - - +
680A PHE* 3.9 18.2 - - + -
837A THR* 2.8 45.0 + - - +
838A GLY* 4.3 7.4 - - - +
840A ALA* 1.3 69.8 - - - +
842A GLU* 1.3 64.5 + - - +
844A MET* 3.4 3.6 - - - +
845A GLU* 3.2 34.4 + - - +
859A TRP* 3.6 54.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A GLY 3.2 18.5 + - - +
839A GLU* 3.7 5.3 - - - +
840A ALA 3.4 0.2 - - - -
841A MET* 1.3 77.6 - - - +
843A LEU* 1.3 75.9 + - - +
844A MET 3.2 1.5 + - - -
845A GLU* 4.1 11.9 + - - +
846A GLN* 3.3 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 843 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
714A THR* 5.4 4.5 - - - +
835A LYS* 3.7 36.1 - - + +
839A GLU* 3.0 26.1 + - + +
840A ALA* 3.1 13.0 - - - +
842A GLU* 1.3 92.8 - - - +
844A MET* 1.3 62.6 + - - +
846A GLN* 3.1 26.8 - - + +
847A LEU* 4.5 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 844 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A PHE* 4.3 31.2 - - + -
682A PHE* 4.6 15.5 - - + -
702A LEU* 4.3 26.5 - - + -
706A ALA* 4.4 11.0 - - + -
714A THR* 5.4 6.1 - - + -
716A VAL* 5.0 6.5 - - - -
827A ILE* 5.9 1.1 - - - -
840A ALA 3.2 15.0 - - - +
841A MET* 3.4 9.4 - - - +
842A GLU 3.2 0.8 - - - -
843A LEU* 1.3 80.9 - - - +
845A GLU* 1.3 62.6 + - - +
846A GLN* 3.0 6.3 + - - -
847A LEU* 3.3 38.4 + - + +
848A ALA* 3.1 25.8 + - - +
859A TRP* 4.2 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 845 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PHE* 5.3 1.1 - - - -
841A MET* 3.2 22.6 + - - +
842A GLU* 4.1 9.4 + - - +
844A MET* 1.3 76.6 - - - +
846A GLN* 1.3 58.2 + - - +
847A LEU 3.2 0.4 - - - -
848A ALA* 4.0 2.8 - - - +
849A SER* 3.2 27.4 + - - -
857A TYR* 3.1 40.7 + - + +
859A TRP* 3.4 31.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 846 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
709A HIS* 5.2 6.1 + - - -
842A GLU* 3.3 25.1 + - - +
843A LEU* 3.1 25.1 - - + +
844A MET 3.0 13.9 + - - -
845A GLU* 1.3 79.4 - - - +
847A LEU* 1.3 90.7 + - - +
849A SER* 3.0 19.4 + - - +
850A LYS* 3.5 27.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 847 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
702A LEU* 5.1 8.1 - - + +
705A GLU* 3.5 32.5 - - + +
706A ALA* 4.0 23.3 - - + +
709A HIS* 3.9 20.9 - - + +
843A LEU 4.5 5.2 - - - +
844A MET* 3.3 33.0 + - + -
845A GLU 3.2 0.6 - - - -
846A GLN* 1.3 100.5 + - - +
848A ALA* 1.3 60.7 + - - +
849A SER 3.2 2.0 - - - -
850A LYS* 3.4 29.3 + - + +
851A LEU* 3.9 11.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 848 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682A PHE* 3.6 30.5 - - + -
684A LEU* 5.6 1.1 - - + -
702A LEU* 4.0 10.9 - - + +
844A MET 3.1 10.6 + - - +
845A GLU 3.6 2.0 + - - +
847A LEU* 1.3 72.3 - - - +
849A SER* 1.3 58.7 + - - +
850A LYS 3.2 5.9 + - - -
851A LEU* 3.5 29.5 + - + +
855A VAL 4.2 9.9 - - - +
856A GLY 5.7 0.7 - - - +
857A TYR* 3.9 20.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 849 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
845A GLU 3.2 16.0 + - - -
846A GLN* 3.0 22.0 + - - -
848A ALA* 1.3 76.7 - - - +
850A LYS* 1.3 57.2 + - - +
851A LEU 3.4 6.0 - - - +
857A TYR* 5.4 5.8 - - - -
----------------------------------------------------------
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