Contacts of the helix formed by residues 890 - 907 (chain A) in PDB entry 2WAC
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 LEU 890 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A LEU* 4.5 5.8 - - + -
849A GLU* 3.7 43.7 - - + +
850A LEU* 4.1 20.4 - - + -
858A LEU* 4.3 8.7 - - + -
885A ARG* 4.3 13.7 - - + +
887A GLU* 2.9 40.8 + - + +
889A LYS* 1.3 85.7 - - + +
891A LYS* 1.3 57.8 + - - +
892A GLU 3.4 2.2 - - - -
893A LEU* 3.3 16.7 + - + +
894A VAL* 2.8 40.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 891 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
885A ARG 5.8 1.1 - - - -
887A GLU 3.4 3.6 + - - +
888A ARG* 3.0 62.1 + - - +
889A LYS 3.5 0.6 - - - -
890A LEU* 1.3 77.8 - - - +
892A GLU* 1.3 56.9 + - - +
894A VAL* 3.3 6.2 + - - +
895A ASP* 2.9 64.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 892 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A ARG 4.8 0.4 + - - -
889A LYS 5.1 2.4 + - - +
890A LEU 3.4 0.6 - - - -
891A LYS* 1.3 79.9 - - - +
893A LEU* 1.3 57.8 + - - +
895A ASP* 3.4 6.6 + - - +
896A GLN* 3.0 59.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 893 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ALA* 4.7 2.0 - - + -
818A LEU* 3.7 21.5 - - + -
849A GLU* 3.9 35.4 - - + +
860A THR* 4.0 13.7 - - + -
869A ASP* 4.5 7.4 - - - +
872A LYS* 6.2 0.2 - - + -
889A LYS 5.7 0.8 + - - +
890A LEU* 3.3 15.8 + - + +
892A GLU* 1.3 76.1 - - - +
894A VAL* 1.3 60.3 + - - +
896A GLN* 3.4 15.3 + - - +
897A TYR* 3.0 57.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 894 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
818A LEU* 3.8 29.8 - - + -
883A GLU 4.1 13.0 - - - +
884A GLN* 3.5 37.9 - - - +
885A ARG* 3.9 20.6 - - + +
890A LEU* 2.8 28.4 + - + +
891A LYS* 3.6 6.7 - - - +
893A LEU* 1.3 73.7 - - - +
895A ASP* 1.3 64.1 + - - +
897A TYR* 3.5 2.8 + - - +
898A LYS* 3.0 34.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A GLN* 5.4 1.0 - - - +
891A LYS* 2.9 52.8 + - - +
892A GLU* 3.7 6.8 - - - +
894A VAL* 1.3 82.8 - - - +
896A GLN* 1.3 58.4 + - + +
898A LYS* 3.3 8.2 + - - +
899A ALA* 3.0 28.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LYS* 3.8 27.5 + - + +
892A GLU* 3.0 47.6 + - + +
893A LEU* 3.8 21.3 - - - +
894A VAL 3.3 0.2 - - - -
895A ASP* 1.3 78.3 - - + +
897A TYR* 1.3 59.3 + - + +
899A ALA* 3.3 8.0 + - - +
900A ALA* 3.1 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
817A ALA 3.4 20.9 + - - -
818A LEU* 3.8 25.1 - - + -
819A VAL* 4.3 3.4 - - + -
860A THR* 3.8 11.6 - - - +
869A ASP* 2.6 37.2 + - - -
871A GLY* 4.1 6.6 - - - -
872A LYS* 3.6 34.6 + - + -
875A VAL* 3.4 23.5 - - + +
882A ALA* 3.5 14.0 - - + +
883A GLU 5.5 1.1 - - - +
893A LEU* 3.0 48.0 + - + +
894A VAL* 3.9 4.3 - - - +
896A GLN* 1.3 73.9 - - + +
898A LYS* 1.3 59.8 - - - +
900A ALA* 3.4 5.7 + - - -
901A GLN 3.0 23.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ALA* 3.4 36.3 + - - -
883A GLU 4.4 1.3 - - - -
884A GLN* 3.9 37.4 - - - +
894A VAL* 3.0 23.0 + - + +
895A ASP* 3.4 12.3 - - - +
897A TYR* 1.3 76.6 - - - +
899A ALA* 1.3 57.1 + - - +
901A GLN* 3.3 29.2 + - - +
902A GLU* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A ASP 3.0 12.8 + - - +
896A GLN* 3.3 10.7 + - - +
898A LYS* 1.3 72.3 - - - +
900A ALA* 1.3 61.6 + - - +
902A GLU* 3.3 9.1 + - - +
903A ALA* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 900 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A LYS* 4.2 22.2 - - + -
875A VAL* 3.9 13.5 - - + -
876A ALA* 3.9 22.3 - - + +
896A GLN 3.1 14.0 + - - +
897A TYR 3.6 9.0 - - - +
899A ALA* 1.3 74.1 - - - +
901A GLN* 1.3 63.3 + - - +
903A ALA* 3.3 8.5 + - - +
904A ALA* 3.1 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL* 3.4 18.5 - - + +
880A VAL 5.4 0.9 - - - +
881A LEU* 3.7 14.5 - - - +
882A ALA* 3.0 29.8 + - + +
897A TYR 3.0 14.0 + - - +
898A LYS* 3.5 31.6 + - - +
900A ALA* 1.3 74.6 - - - +
902A GLU* 1.3 60.1 + - - +
904A ALA* 3.3 4.3 + - - +
905A ARG* 2.9 27.2 + - + +
912A TRP* 3.6 33.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LYS 3.0 15.5 + - - +
899A ALA* 3.4 12.6 - - - +
900A ALA 3.3 0.2 - - - -
901A GLN* 1.3 78.6 + - + +
903A ALA* 1.3 59.5 + - - +
905A ARG* 3.0 45.8 + - - +
906A VAL* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
876A ALA* 5.8 3.4 - - + +
899A ALA 2.9 13.6 + - - +
900A ALA* 3.3 11.6 + - - +
902A GLU* 1.3 75.0 - - - +
904A ALA* 1.3 58.6 + - - +
906A VAL* 3.4 7.7 + - - +
907A ALA* 3.0 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
875A VAL 3.6 17.0 - - - +
876A ALA 3.4 24.5 + - - +
878A GLY* 3.8 10.1 - - - +
900A ALA 3.1 6.7 + - - +
901A GLN 3.3 8.3 + - - +
903A ALA* 1.3 74.7 - - - +
905A ARG* 1.3 57.3 - - - +
907A ALA* 3.5 3.2 + - - -
908A HIS 3.1 6.8 + - - -
909A LEU* 3.0 33.8 + - + -
912A TRP* 3.8 13.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A GLN* 2.9 14.9 + - + +
902A GLU* 3.0 43.6 + - - +
904A ALA* 1.3 73.4 - - - +
906A VAL* 1.3 83.9 + - - +
908A HIS* 3.1 25.5 + - - -
912A TRP* 3.8 41.0 - - + +
915A GLY* 6.1 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
902A GLU* 2.9 26.9 + - - +
903A ALA* 3.4 6.7 + - - +
905A ARG* 1.3 98.8 - - - +
907A ALA* 1.3 61.3 + - - +
908A HIS* 3.2 14.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A ALA 3.0 18.2 + - - +
904A ALA 4.0 0.4 - - - +
905A ARG 3.2 0.2 - - - -
906A VAL* 1.3 74.9 - - - +
908A HIS* 1.3 70.3 + - - +
909A LEU* 3.4 29.3 + - + +
888B ARG* 6.5 1.3 - - - +
----------------------------------------------------------
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