Contacts of the helix formed by residues 840 - 865 (chain P) in PDB entry 5IJO
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 LYS 840 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839P LYS* 1.3 81.1 - - + +
841P HIS* 1.3 56.0 + - - +
843P GLU* 2.9 29.7 + - + +
844P LYS* 3.3 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 841 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
839P LYS 4.1 9.4 - - - +
840P LYS* 1.3 78.5 - - - +
842P LEU* 1.3 61.3 + - - +
844P LYS* 3.1 18.6 + - - +
845P ALA* 3.4 9.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 842 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759P TRP* 5.9 9.2 - - + -
826P GLY 5.5 4.0 - - - +
827P VAL* 4.7 15.5 - - - +
839P LYS* 2.9 19.0 + - - +
841P HIS* 1.3 78.9 - - - +
843P GLU* 1.3 63.1 + - - +
845P ALA* 3.1 19.3 + - - +
846P VAL* 3.2 10.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 843 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
827P VAL* 6.1 4.9 - - - +
839P LYS 3.3 4.1 + - - +
840P LYS* 2.9 22.1 + - + +
842P LEU* 1.3 78.4 - - - +
844P LYS* 1.3 59.4 + - - +
846P VAL* 3.1 19.4 + - - +
847P GLN* 3.1 12.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 844 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
840P LYS 3.3 5.1 + - - +
841P HIS* 3.1 14.8 + - - +
843P GLU* 1.3 75.1 - - - +
845P ALA* 1.3 66.5 + - - +
847P GLN* 3.0 10.4 + - - +
848P HIS* 3.0 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 845 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
759P TRP* 6.0 4.7 - - + +
762P ALA* 5.8 5.8 - - + -
763P GLU* 5.3 18.6 - - + +
766P LEU* 5.1 3.9 - - + +
822P LEU* 4.9 5.8 - - + +
841P HIS 3.4 5.7 + - - +
842P LEU* 3.1 15.5 + - - +
844P LYS* 1.3 79.5 - - - +
846P VAL* 1.3 61.7 + - - +
848P HIS* 3.3 7.8 + - - +
849P CYS* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 846 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
822P LEU* 4.9 15.3 - - - +
823P LEU* 5.9 1.8 - - - -
826P GLY* 5.4 10.5 - - - -
842P LEU 3.2 5.6 + - - +
843P GLU* 3.1 15.9 + - - +
844P LYS 3.0 0.2 - - - -
845P ALA* 1.3 76.4 - - - +
847P GLN* 1.3 66.4 + - - +
849P CYS* 3.1 17.9 + - - +
850P LEU* 3.1 12.1 + - - +
912P LEU* 6.1 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 847 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843P GLU 3.1 6.6 + - - +
844P LYS* 3.0 13.1 + - - +
846P VAL* 1.3 77.6 - - - +
848P HIS* 1.3 63.7 + - - +
850P LEU* 3.1 7.9 + - - +
851P ALA* 2.9 23.9 + - - +
911P GLU* 4.8 19.1 - - + -
912P LEU* 5.0 16.1 - - + +
915P GLU* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 848 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766P LEU* 3.8 29.1 - - + +
767P GLU* 5.2 2.7 - - - +
770P TYR* 5.7 6.9 - - + +
844P LYS 3.0 11.6 + - - +
845P ALA* 3.6 10.3 - - - +
847P GLN* 1.3 77.5 - - - +
849P CYS* 1.3 64.5 + - - +
851P ALA* 3.8 6.0 - - - +
852P LEU* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 849 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766P LEU* 5.2 2.7 - - - +
819P ALA* 3.9 18.1 - - - +
822P LEU* 3.6 31.0 - - + -
823P LEU* 4.6 8.3 - - + +
845P ALA 3.0 10.9 + - - +
846P VAL* 3.1 9.8 + - - +
848P HIS* 1.3 79.0 - - - +
850P LEU* 1.3 62.8 + - - +
852P LEU* 3.4 5.0 + - - +
853P LEU* 3.3 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 850 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
823P LEU* 6.2 2.0 - - - +
846P VAL 3.1 7.1 + - - +
847P GLN* 3.1 10.3 + - - +
849P CYS* 1.3 76.9 - - - +
851P ALA* 1.3 67.1 + - - +
853P LEU* 3.0 9.0 + - - +
854P ASN* 2.9 21.6 + - - +
912P LEU* 5.0 8.7 - - + +
915P GLU* 4.2 20.4 - - + +
916P SER* 5.1 5.8 - - - +
919P ILE* 5.8 2.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 851 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770P TYR* 6.0 5.2 - - + -
847P GLN 2.9 16.1 + - - +
848P HIS* 3.8 7.0 - - - +
850P LEU* 1.3 76.1 - - - +
852P LEU* 1.3 63.5 + - - +
854P ASN* 3.3 7.4 + - - +
855P LEU* 2.9 23.2 + - - +
915P GLU* 4.8 8.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 852 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766P LEU* 5.9 2.0 - - + +
769P PHE* 5.5 7.2 - - + -
770P TYR* 5.2 19.7 - - + +
819P ALA* 6.2 3.8 - - + -
848P HIS 2.9 17.2 + - - +
849P CYS* 3.9 6.1 - - - +
850P LEU 3.1 0.2 - - - -
851P ALA* 1.3 77.5 - - - +
853P LEU* 1.3 61.7 + - - +
855P LEU* 3.1 7.5 + - - +
856P THR* 2.9 23.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 853 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
819P ALA* 6.6 0.2 - - + -
849P CYS 3.3 9.4 + - - +
850P LEU* 3.0 11.0 + - - +
852P LEU* 1.3 77.9 - - - +
854P ASN* 1.3 65.2 + - - +
856P THR* 3.1 8.6 + - - -
857P LEU* 3.0 21.5 + - - +
919P ILE* 5.8 6.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 854 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
850P LEU 2.9 11.4 + - - +
851P ALA* 3.6 11.0 - - - +
853P LEU* 1.3 76.9 - - - +
855P LEU* 1.3 63.7 + - - +
857P LEU* 3.0 7.9 + - - +
858P GLN* 3.0 21.7 + - - +
915P GLU* 4.9 16.8 - - + +
918P LYS* 5.1 9.4 - - + -
919P ILE* 5.1 13.0 - - + +
922P CYS* 5.4 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 855 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
773P LEU* 4.4 23.8 - - + -
851P ALA 2.9 14.2 + - - +
852P LEU* 3.1 10.1 + - - +
854P ASN* 1.3 77.2 - - - +
856P THR* 1.3 63.0 + - - +
858P GLN* 3.3 7.0 + - - +
859P LYS* 3.1 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 856 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
852P LEU 2.9 13.4 + - - -
853P LEU* 3.1 10.7 + - - -
855P LEU* 1.3 76.6 - - - +
857P LEU* 1.3 52.7 + - - +
859P LYS* 3.2 2.0 + - - -
860P GLU* 2.6 41.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 857 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
853P LEU 3.0 12.2 + - - +
854P ASN* 3.0 8.0 + - - +
856P THR* 1.3 76.8 - - - +
858P GLN* 1.3 66.4 + - - +
859P LYS 3.2 0.5 + - - -
860P GLU* 3.3 14.8 + - - +
861P ASN* 4.6 1.2 + - - +
919P ILE* 6.2 0.4 - - - -
922P CYS* 3.3 34.5 - - + +
923P ILE* 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 858 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
854P ASN 3.0 12.5 + - - +
855P LEU* 3.6 10.8 - - - +
856P THR 3.2 0.2 - - - -
857P LEU* 1.3 79.9 - - - +
859P LYS* 1.3 60.3 + - + +
860P GLU 3.8 0.2 + - - -
861P ASN* 4.7 6.2 + - - +
922P CYS* 5.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 859 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778P PRO* 5.2 11.7 - - + -
855P LEU 3.1 12.6 + - - +
856P THR* 3.4 2.2 - - - -
858P GLN* 1.3 80.0 - - + +
860P GLU* 1.3 65.6 + - - +
861P ASN 3.1 2.7 - - - +
862P LEU* 3.1 26.2 + - + +
863P PHE* 3.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 860 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
856P THR* 2.6 23.2 + - - +
857P LEU* 3.3 12.7 + - - +
859P LYS* 1.3 74.8 - - - +
861P ASN* 1.3 62.1 + - - +
863P PHE* 3.2 6.3 + - - +
864P MET* 3.2 20.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 861 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
857P LEU 4.6 1.4 + - - -
858P GLN 5.1 5.2 - - - +
859P LYS* 4.1 0.6 - - - +
860P GLU* 1.3 77.3 - - - +
862P LEU* 1.3 65.9 + - - +
864P MET* 3.2 6.6 + - - +
865P ASP* 3.0 25.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 862 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
778P PRO* 5.4 9.9 - - + +
858P GLN 5.2 0.2 + - - -
859P LYS* 3.1 23.9 + - + +
861P ASN* 1.3 77.9 - - - +
863P PHE* 1.3 63.5 + - - +
865P ASP* 5.1 0.9 - - - -
866P LEU* 3.0 29.0 + - + +
867P LEU* 3.1 7.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 863 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
806P MET* 4.5 21.5 - - + -
859P LYS 3.1 9.2 + - - +
860P GLU* 3.7 9.0 - - - +
862P LEU* 1.3 80.1 - - - +
864P MET* 1.3 57.1 + - - +
867P LEU* 3.9 13.7 - - + -
868P ARG* 2.6 35.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 864 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860P GLU 3.2 9.8 + - - +
861P ASN* 3.2 9.9 + - - +
863P PHE* 1.3 80.4 - - - +
865P ASP* 1.3 63.1 + - - +
868P ARG* 3.6 15.0 - - - +
869P GLU* 4.4 1.0 + - - +
879P LEU* 6.2 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 865 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861P ASN 3.0 15.6 + - - +
862P LEU* 4.9 1.1 - - - -
864P MET* 1.3 81.1 - - + +
866P LEU* 1.3 70.4 + - + +
869P GLU* 3.5 19.6 + - - +
----------------------------------------------------------
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