Contacts of the helix formed by residues 894 - 912 (chain A) in PDB entry 6DBV
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 894 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
836A GLU* 4.7 1.7 + - - -
838A TYR* 4.2 10.5 + - - -
839A GLN* 5.8 2.7 - - - -
892A VAL* 3.1 10.6 - - - +
893A PRO* 1.3 78.7 - - - +
895A GLU* 1.3 57.1 + - - +
896A GLU* 2.4 30.4 + - - +
897A ARG* 3.1 31.4 + - - +
898A ARG 2.8 23.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 895 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
892A VAL 3.9 3.1 - - - +
893A PRO* 2.7 23.4 - - - +
894A SER* 1.3 68.7 - - - +
896A GLU* 1.3 65.4 + - - +
898A ARG* 2.7 44.9 + - + +
899A GLU* 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 896 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A SER* 2.4 30.6 + - - +
895A GLU* 1.3 79.9 + - - +
897A ARG* 1.3 59.1 + - + +
899A GLU* 3.4 6.5 + - - +
900A ALA* 2.9 28.2 + - - +
945A MET* 4.9 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 897 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
833A GLU* 4.2 9.6 + - - +
838A TYR* 3.1 63.2 - - + +
892A VAL* 4.3 7.4 - - + -
894A SER* 3.1 22.8 + - - +
896A GLU* 1.3 73.5 - - - +
898A ARG* 1.3 66.5 + - - +
900A ALA* 3.4 6.9 - - - +
901A LEU* 2.9 29.9 + - + +
945A MET* 2.8 60.8 + - - +
946A PHE* 3.9 21.1 - - + -
948A TYR* 4.4 7.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 898 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
889A CYS* 2.5 40.6 + - + -
890A GLU* 2.6 32.2 + - - +
892A VAL* 2.4 37.1 + - + +
894A SER 2.8 13.1 + - - +
895A GLU* 2.7 39.2 + - - +
896A GLU 3.2 0.2 - - - -
897A ARG* 1.3 78.3 - - - +
899A GLU* 1.3 63.8 + - + +
901A LEU* 3.3 8.6 - - - +
902A LEU* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 899 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
895A GLU 2.9 18.6 + - - +
896A GLU* 4.0 4.8 - - - +
898A ARG* 1.3 74.5 - - - +
900A ALA* 1.3 62.3 + - - +
902A LEU* 3.5 14.1 - - + +
903A LYS* 2.9 42.4 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
896A GLU 2.9 18.8 + - - +
897A ARG* 3.4 9.9 - - - +
898A ARG 3.1 0.4 - - - -
899A GLU* 1.3 84.5 + - - +
901A LEU* 1.3 57.8 + - - +
903A LYS* 3.3 2.7 + - - +
904A LEU* 2.9 26.4 + - - +
941A LEU* 3.7 13.3 - - + +
945A MET* 3.5 31.2 - - + -
946A PHE* 4.7 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 901 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829A ILE* 6.4 1.1 - - + -
830A PHE* 5.2 17.3 - - + -
833A GLU* 4.6 19.3 - - + -
885A VAL* 3.6 26.5 - - + +
888A VAL* 5.9 2.5 - - + -
889A CYS* 3.8 17.5 - - + +
892A VAL* 4.0 24.9 - - + -
897A ARG* 2.9 19.2 + - + +
898A ARG 3.3 13.0 - - - +
900A ALA* 1.3 72.2 - - - +
902A LEU* 1.3 64.0 + - + +
904A LEU* 3.4 19.5 - - + +
905A MET* 2.9 30.0 + - - +
946A PHE* 4.8 10.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 902 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ARG* 4.5 22.5 + - + +
885A VAL* 3.8 29.6 - - + +
886A GLU* 4.5 21.1 - - - +
889A CYS* 3.8 23.6 - - - -
898A ARG* 3.0 27.5 + - + +
899A GLU* 3.5 19.3 - - + +
900A ALA 3.2 0.2 - - - -
901A LEU* 1.3 82.8 - - + +
903A LYS* 1.3 56.9 + - - +
905A MET* 3.3 5.8 + - + +
906A ASP* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 903 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ARG* 6.0 0.2 - - - +
899A GLU* 2.9 31.0 + - - +
900A ALA* 3.8 4.9 - - - +
902A LEU* 1.3 72.8 - - - +
904A LEU* 1.3 60.2 + - - +
906A ASP* 3.3 15.6 + - + +
907A LEU* 3.0 44.8 + - - +
937A GLN* 2.0 34.5 + - - +
941A LEU* 4.3 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 904 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A PHE* 4.6 22.9 - - + -
829A ILE* 5.3 15.5 - - + -
830A PHE* 6.0 3.4 - - + -
900A ALA 2.9 15.1 + - - +
901A LEU* 3.4 21.8 - - + +
902A LEU 3.2 0.2 - - - -
903A LYS* 1.3 76.0 - - - +
905A MET* 1.3 65.6 + - + +
907A LEU* 3.2 7.1 + - - +
908A TYR* 2.9 19.6 + - - +
938A PHE* 3.4 42.4 - - + +
941A LEU* 3.7 20.1 - - + +
942A LEU* 5.6 9.9 - - + -
946A PHE* 5.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 905 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
826A PHE* 4.0 17.5 - - + -
830A PHE* 4.5 11.0 - - + -
879A LEU 4.9 2.2 - - - +
880A MET* 3.7 45.8 - - - +
882A ARG* 4.4 9.2 - - + -
885A VAL* 3.5 38.1 - - + -
901A LEU 2.9 20.6 + - - +
902A LEU* 3.6 6.1 - - + +
904A LEU* 1.3 76.5 - - + +
906A ASP* 1.3 57.1 + - - +
908A TYR* 3.2 5.6 + - - +
909A LEU* 2.8 43.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 906 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
882A ARG* 2.8 28.9 + - - +
902A LEU 2.9 13.8 + - - +
903A LYS* 3.4 22.2 - - + +
904A LEU 3.2 0.2 - - - -
905A MET* 1.3 74.9 - - - +
907A LEU* 1.3 67.9 + - - +
909A LEU* 3.2 9.7 + - - +
910A GLN* 2.9 32.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 907 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
903A LYS* 3.0 28.3 + - - +
904A LEU* 3.2 7.8 + - - +
906A ASP* 1.3 77.1 + - - +
908A TYR* 1.3 62.5 + - - +
910A GLN* 3.1 6.7 + - + +
911A MET* 3.0 27.5 + - - +
934A ASN* 3.6 27.4 - - - +
937A GLN* 3.2 50.0 - - + +
938A PHE* 3.8 30.5 - - + +
941A LEU* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 908 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A ASP* 4.5 5.4 + - - -
822A ASN* 2.8 45.7 + - + +
826A PHE* 3.5 31.6 - + + -
880A MET* 3.5 40.2 - - + +
904A LEU 2.9 13.1 + - - +
905A MET* 3.4 12.3 - - - +
906A ASP 3.2 0.2 - - - -
907A LEU* 1.3 76.6 - - - +
909A LEU* 1.3 60.3 + - + +
911A MET* 3.3 14.3 - - + +
912A LYS* 2.9 50.4 + - + +
915A TRP* 4.0 12.7 - + - -
938A PHE* 4.6 12.1 - + + -
958A LEU* 6.3 1.8 - - + -
961A THR* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 909 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A MET* 3.2 40.2 - - + +
881A THR* 5.2 0.2 - - - -
882A ARG* 3.8 34.5 - - + +
905A MET* 2.8 27.6 + - + +
906A ASP* 3.7 6.7 - - - +
908A TYR* 1.3 77.8 - - + +
910A GLN* 1.3 61.5 + - - +
912A LYS* 4.9 12.1 + - - +
913A PRO* 3.2 20.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 910 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
906A ASP* 2.9 27.3 + - - +
907A LEU* 3.1 6.9 + - + +
909A LEU* 1.3 79.1 - - - +
911A MET* 1.3 58.2 + - - +
913A PRO* 4.0 4.9 - - - +
927A GLN* 3.3 41.7 + - - +
934A ASN* 3.8 19.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 911 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A LEU 3.0 19.1 + - - +
908A TYR* 3.3 16.2 - - + +
910A GLN* 1.3 77.0 - - - +
912A LYS* 1.3 69.9 + - + +
913A PRO* 3.5 2.0 - - - -
914A VAL* 3.1 25.3 - - - +
915A TRP* 4.3 3.5 + - + +
927A GLN* 5.4 0.4 - - - -
931A TYR* 3.6 31.5 - - + +
934A ASN* 3.8 20.4 - - - +
935A SER* 3.9 25.8 - - - +
938A PHE* 3.7 28.3 - - + -
961A THR* 5.6 2.2 - - - +
962A LEU* 4.3 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 912 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819A ASP* 4.2 17.9 - - - +
877A ARG* 5.5 14.9 - - - +
880A MET* 4.4 13.9 - - + +
908A TYR* 2.9 42.7 + - + +
909A LEU* 4.7 12.9 + - + +
911A MET* 1.3 74.6 - - + +
913A PRO* 1.3 67.2 - - + +
914A VAL 2.6 17.4 + - - -
915A TRP* 3.2 59.2 + - + +
916A ARG* 5.0 9.9 - - + +
----------------------------------------------------------
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