Contacts of the helix formed by residues 861 - 877 (chain A) in PDB entry 3LXK
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 GLY 861 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 4.5 2.7 - - - +
859A HIS* 3.6 3.7 + - - -
860A SER* 1.3 75.4 - - - +
862A PRO* 1.4 72.5 - - - +
863A ASP 3.6 1.1 - - - -
864A GLN* 3.8 23.1 - - - -
865A GLN* 3.2 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 862 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A GLY* 1.4 84.9 - - - +
863A ASP* 1.3 71.3 + - - +
864A GLN* 4.7 0.6 - - - +
865A GLN* 3.5 5.5 + - + +
866A ARG* 3.2 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 863 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A PRO* 1.3 84.4 - - - +
864A GLN* 1.3 75.2 + - - +
866A ARG* 3.4 34.8 + - - +
867A ASP* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 864 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A PHE* 3.6 58.8 - - + -
857A LEU* 3.6 24.3 - - + +
859A HIS* 5.4 4.4 + - - +
861A GLY* 3.8 19.4 - - - +
862A PRO* 3.3 1.3 - - - +
863A ASP* 1.3 91.0 - - - +
865A GLN* 1.3 51.1 + - - +
867A ASP* 3.3 10.2 + - - +
868A PHE* 2.8 35.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 865 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857A LEU* 3.6 20.0 - - - +
860A SER* 5.9 2.6 - - - +
861A GLY 3.2 19.7 + - - +
862A PRO* 3.6 7.4 - - + +
863A ASP 3.3 0.2 - - - -
864A GLN* 1.3 76.0 - - - +
866A ARG* 1.3 64.9 + - - +
868A PHE* 3.3 9.2 + - - +
869A GLN* 3.0 26.9 + - - +
896A GLN* 3.7 32.4 - - + +
897A SER* 3.0 29.7 + - - +
898A LEU* 6.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 866 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A PRO 3.2 10.1 + - - +
863A ASP* 3.4 43.9 + - - +
865A GLN* 1.3 79.4 - - - +
867A ASP* 1.3 89.2 + - - +
869A GLN* 3.5 6.3 + - - +
870A ARG* 3.2 55.4 + - - +
972A LYS* 4.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 867 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
863A ASP* 3.1 15.2 + - - +
864A GLN* 3.6 12.8 + - - +
866A ARG* 1.3 110.1 + - - +
868A PHE* 1.3 57.1 + - - +
870A ARG* 3.2 11.7 + - - +
871A GLU* 2.9 29.5 + - - +
969A GLY 5.4 7.5 - - - +
972A LYS* 3.7 19.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 868 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A LYS* 3.5 44.4 - - + -
856A GLN* 3.9 8.5 - - - -
857A LEU* 4.1 24.2 - - + -
864A GLN 2.8 20.6 + - - +
865A GLN* 3.7 13.9 - - - +
866A ARG 3.3 0.2 - - - -
867A ASP* 1.3 71.3 - - - +
869A GLN* 1.3 65.0 + - - +
871A GLU* 3.2 23.9 + - - +
872A ILE* 3.0 44.6 + - + +
897A SER* 4.2 11.4 - - - -
898A LEU 3.5 25.6 - - - -
900A LEU* 3.8 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 869 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
865A GLN* 3.0 18.4 + - + +
866A ARG* 3.8 5.8 - - - +
868A PHE* 1.3 76.5 - - - +
870A ARG* 1.3 63.2 + - + +
872A ILE* 3.5 11.7 + - - +
873A GLN* 3.2 29.3 + - + +
897A SER* 5.2 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 870 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
866A ARG* 3.2 57.4 + - - +
867A ASP* 3.2 12.5 + - - +
868A PHE 3.2 0.6 - - - -
869A GLN* 1.3 76.0 - - + +
871A GLU* 1.3 57.9 + - - +
873A GLN* 3.1 8.3 + - - +
874A ILE* 2.9 39.2 + - + +
971A ALA 6.1 0.7 - - - +
972A LYS* 4.3 16.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A LYS* 2.8 38.8 + - - +
867A ASP 2.9 13.1 + - - +
868A PHE* 3.4 29.5 - - - +
870A ARG* 1.3 76.6 - - - +
872A ILE* 1.3 57.3 + - - +
874A ILE* 3.3 10.3 + - - +
875A LEU* 3.0 29.4 + - + +
900A LEU* 4.4 10.6 - - + +
967A ASP* 4.3 0.3 - - - +
968A PHE* 3.5 27.7 + - + +
969A GLY* 3.6 25.5 + - - +
971A ALA 5.9 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 872 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
868A PHE* 3.0 41.2 + - + +
869A GLN* 3.6 9.0 - - - +
870A ARG 3.3 0.2 - - - -
871A GLU* 1.3 75.2 - - - +
873A GLN* 1.3 69.0 + - - +
875A LEU* 3.4 1.1 + - - +
876A LYS* 2.9 34.3 + - + +
886A TYR* 4.2 12.7 - - + +
889A VAL* 3.7 28.9 - - + -
897A SER* 3.7 32.5 - - - +
899A ARG 4.8 1.1 - - - +
900A LEU* 4.1 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 873 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
869A GLN* 3.2 14.9 + - + +
870A ARG* 3.1 11.4 + - - +
872A ILE* 1.3 81.0 - - - +
874A ILE* 1.3 67.9 + - + +
876A LYS* 3.6 24.5 + - - +
877A ALA* 3.3 22.2 + - - +
973A LEU* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 874 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
870A ARG* 2.9 25.5 + - + +
871A GLU* 3.5 10.3 - - - +
873A GLN* 1.3 76.3 - - + +
875A LEU* 1.3 64.6 + - - +
877A ALA* 3.1 15.1 + - - +
878A LEU* 3.3 32.4 + - + +
945A CYS* 4.1 18.8 - - + -
968A PHE* 4.8 9.4 - - + -
971A ALA* 3.7 35.0 - - + +
972A LYS* 4.4 2.7 - - - +
973A LEU* 3.7 39.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 875 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A GLU* 3.0 17.0 + - + +
872A ILE* 4.1 3.8 - - - +
874A ILE* 1.3 75.7 - - - +
876A LYS* 1.3 64.5 + - - +
878A LEU* 3.0 23.8 + - + +
883A ILE* 3.6 10.8 - - + -
884A VAL* 3.5 24.7 - - + +
886A TYR* 4.0 18.4 - - + +
900A LEU* 4.0 18.4 - - + -
902A MET* 3.8 37.0 - - + -
968A PHE* 3.6 35.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 876 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
815A THR* 5.8 6.1 + - - +
872A ILE* 2.9 23.3 + - + +
873A GLN* 3.9 27.1 - - - +
874A ILE 3.3 0.2 - - - -
875A LEU* 1.3 73.9 - - - +
877A ALA* 1.3 59.3 + - - +
878A LEU 3.5 1.2 + - - +
879A HIS* 3.6 19.4 + - - -
886A TYR* 3.8 49.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 877 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A GLN 3.3 14.3 + - - +
874A ILE* 3.1 7.3 + - - +
875A LEU 3.1 0.8 - - - -
876A LYS* 1.3 77.5 - - + +
878A LEU* 1.3 63.8 + - + +
879A HIS* 3.6 16.2 - - - -
939A TYR* 3.7 6.1 + - - -
943A ARG* 4.9 9.2 + - - +
----------------------------------------------------------
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