Contacts of the helix formed by residues 830 - 842 (chain A) in PDB entry 1KO6
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 ASN 830 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A LEU 2.6 13.4 + - - -
827A ALA* 3.1 11.6 + - - +
828A ASP 3.1 6.3 - - - +
829A ILE* 1.3 78.5 - - - +
831A TYR* 1.3 63.7 + - - +
832A GLU* 3.3 12.2 - - - +
833A GLY* 3.2 31.2 + - - -
834A ARG* 3.3 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 831 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780A LYS* 4.5 1.6 + - - +
809A VAL* 3.3 18.2 - - + +
810A TRP* 3.0 24.1 + - - -
811A PRO* 3.3 34.0 - - + +
826A LEU* 3.2 36.4 + - + +
829A ILE* 3.4 6.9 - - + -
830A ASN* 1.3 72.0 - - - +
832A GLU* 1.3 69.1 + - - +
834A ARG* 2.8 20.2 + - + +
835A LEU* 2.8 36.2 + - + +
849A TYR* 3.4 39.0 - + + -
868B LEU* 3.9 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 832 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A LEU* 6.4 1.6 - - + -
827A ALA* 5.7 8.0 - - - +
830A ASN* 4.6 8.9 - - - +
831A TYR* 1.3 78.1 - - + +
833A GLY* 1.3 59.0 + - - +
835A LEU* 2.8 10.1 + - - -
836A GLU* 2.6 38.1 + - - +
846A PHE* 4.6 13.6 - - + -
848A GLU* 5.9 0.2 - - - -
849A TYR* 4.2 39.7 + - + +
851A PRO* 6.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 833 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ASN* 3.2 30.5 + - - -
831A TYR 3.0 1.0 - - - -
832A GLU* 1.3 80.4 - - - +
834A ARG* 1.3 51.8 + - - +
836A GLU* 3.4 8.2 + - - +
837A ALA* 2.7 35.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 834 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
830A ASN* 3.3 9.0 + - - +
831A TYR* 2.8 26.1 + - + +
833A GLY* 1.3 67.2 - - - +
835A LEU* 1.3 75.0 + - + +
837A ALA* 2.8 10.7 + - + +
838A VAL* 2.8 34.2 + - + +
868B LEU* 5.1 12.2 - - + +
870B ASP* 5.2 15.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 835 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
809A VAL* 4.3 1.8 - - + -
831A TYR* 2.8 33.2 + - + +
832A GLU* 2.8 13.3 + - - +
834A ARG* 1.3 75.9 - - + +
836A GLU* 1.3 64.4 + - - +
838A VAL* 2.9 12.8 + - - +
839A SER* 3.0 17.6 + - - -
846A PHE* 4.5 2.2 - - + -
849A TYR* 3.2 44.2 - - + -
856A TRP* 3.5 42.6 - - + +
868B LEU* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 836 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
832A GLU* 2.6 20.3 + - - +
833A GLY* 3.8 8.0 - - - +
835A LEU* 1.3 72.7 - - - +
837A ALA* 1.3 61.5 + - - +
839A SER* 3.6 1.9 - - - -
840A ARG* 2.9 26.0 + - + +
846A PHE* 3.2 56.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 837 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A GLY 2.7 18.6 + - - +
834A ARG* 2.8 20.8 + - + +
836A GLU* 1.3 73.2 - - - +
838A VAL* 1.3 64.8 + - + +
840A ARG* 2.9 17.2 + - - +
841A LYS* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 838 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
834A ARG* 2.8 31.8 + - + +
835A LEU* 3.4 6.3 - - - +
837A ALA* 1.3 71.7 - - + +
839A SER* 1.3 55.8 + - - +
841A LYS* 2.5 40.3 + - + +
842A GLN* 2.9 42.1 + - + +
856A TRP* 4.1 9.4 - - + -
867B GLY 4.1 5.4 - - - +
868B LEU* 4.2 25.6 - - + -
869B GLN 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 839 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
835A LEU 3.0 5.0 + - - -
836A GLU* 3.6 8.8 - - - -
838A VAL* 1.3 78.3 - - - +
840A ARG* 1.3 57.1 + - - +
842A GLN* 3.5 6.7 + - - -
843A GLY 3.3 2.6 + - - -
844A ALA* 2.6 47.0 + - - +
846A PHE* 4.1 23.2 - - - -
856A TRP* 2.8 38.7 + - - -
858A PHE* 4.0 4.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 840 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A GLU* 2.9 16.2 + - + +
837A ALA* 2.9 16.4 + - - +
838A VAL 2.8 3.8 + - - -
839A SER* 1.3 73.7 - - - +
841A LYS* 1.3 56.4 + - + +
843A GLY* 2.9 21.8 + - - -
844A ALA 3.8 8.3 - - - -
846A PHE 5.3 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 841 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
837A ALA* 3.0 23.5 + - - +
838A VAL* 2.5 22.6 + - + +
840A ARG* 1.3 74.0 - - + +
842A GLN* 1.3 57.6 + - + +
843A GLY* 3.0 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 842 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
838A VAL* 2.9 33.2 + - + +
839A SER* 3.8 12.1 - - - +
841A LYS* 1.3 74.6 - - + +
843A GLY* 1.3 59.6 + - - +
844A ALA* 4.5 1.8 - - + +
856A TRP* 4.0 5.8 - - - -
858A PHE* 4.5 3.1 - - - -
865B LYS 4.0 3.6 - - - +
866B TYR* 3.0 51.2 + - + +
867B GLY* 2.5 36.7 + - - +
----------------------------------------------------------
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