Contacts of the helix formed by residues 872 - 895 (chain A) in PDB entry 6CIM
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 872 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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870A ILE* 3.1 7.6 - - - +
871A PRO* 1.3 86.3 - - - +
873A GLU* 1.3 61.9 + - - +
874A GLU* 3.4 19.4 + - - +
875A ARG* 3.6 21.8 + - - +
876A HIS* 2.8 23.7 + - - -
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Residues in contact with GLU 873 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871A PRO 3.7 2.6 + - - +
872A SER* 1.3 73.3 + - - +
874A GLU* 1.3 67.2 + - - +
875A ARG 3.1 0.9 - - - -
876A HIS* 3.1 24.7 + - + +
877A GLU* 2.9 21.0 + - - +
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Residues in contact with GLU 874 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872A SER* 3.4 10.6 + - - +
873A GLU* 1.3 76.8 - - - +
875A ARG* 1.3 59.4 + - + +
877A GLU* 3.3 17.3 + - - +
878A ALA* 3.0 25.5 + - - +
923A LYS* 5.8 1.6 + - - +
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Residues in contact with ARG 875 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811A GLU* 2.4 45.7 + - - +
814A GLU* 6.3 2.2 - - - +
816A TYR* 3.8 25.6 - - - +
870A ILE* 4.1 13.0 - - + -
871A PRO* 6.3 1.8 - - - -
872A SER* 3.6 26.8 + - - +
873A GLU 3.1 0.4 - - - -
874A GLU* 1.3 77.4 - - + +
876A HIS* 1.3 64.8 + - - +
878A ALA* 3.7 10.8 - - - +
879A LEU* 2.9 28.3 + - - +
923A LYS* 2.9 35.2 + - - +
924A PHE* 3.9 9.5 - - - -
926A TYR* 4.0 8.3 - - - -
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Residues in contact with HIS 876 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867A CYS* 3.1 50.5 + - + +
870A ILE* 2.9 38.4 + - + +
871A PRO 4.7 2.2 - - - -
872A SER 2.8 23.5 + - - -
873A GLU* 3.1 25.0 + - + +
875A ARG* 1.3 75.5 - - - +
877A GLU* 1.3 56.2 + - - +
879A LEU* 3.3 2.4 + - - +
880A ARG* 2.9 49.1 + - - +
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Residues in contact with GLU 877 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873A GLU 2.9 11.8 + - - +
874A GLU* 3.3 18.1 + - - +
876A HIS* 1.3 76.1 - - - +
878A ALA* 1.3 62.8 + - - +
880A ARG* 3.3 7.6 + - - +
881A GLU* 2.9 26.2 + - + +
923A LYS* 4.6 13.9 + - - +
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Residues in contact with ALA 878 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874A GLU 3.0 14.4 + - - +
875A ARG* 3.7 15.3 - - - +
876A HIS 3.3 0.2 - - - -
877A GLU* 1.3 77.0 + - - +
879A LEU* 1.3 56.7 + - - +
881A GLU* 3.3 5.3 + - - -
882A LEU* 2.9 29.6 + - - +
919A LEU* 3.8 8.7 - - + +
923A LYS* 4.3 27.3 - - + +
924A PHE* 3.9 24.0 - - + -
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Residues in contact with LEU 879 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A PHE* 4.8 3.6 - - + -
807A ILE* 3.7 27.4 - - + -
808A PHE* 3.8 31.4 - - + -
811A GLU* 4.5 9.9 - - + +
863A VAL* 4.0 15.7 - - + +
866A VAL* 4.7 2.0 - - + -
867A CYS* 4.8 1.3 - - - -
870A ILE* 3.4 31.9 - - + -
875A ARG 2.9 17.4 + - - +
876A HIS* 3.8 4.3 - - - +
878A ALA* 1.3 76.3 - - - +
880A ARG* 1.3 64.7 + - - +
882A LEU* 3.3 10.3 + - + +
883A MET* 3.0 26.2 + - - +
924A PHE* 3.7 14.4 - - + -
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Residues in contact with ARG 880 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A GLN* 3.4 27.9 - - - +
863A VAL* 4.1 10.5 - - + +
864A ASP* 2.7 46.7 + - - +
867A CYS* 3.6 18.5 - - - +
876A HIS* 2.9 41.1 + - - +
877A GLU* 3.8 7.1 - - - +
879A LEU* 1.3 76.0 - - - +
881A GLU* 1.3 57.4 + - - +
884A ASP* 2.9 27.9 + - - +
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Residues in contact with GLU 881 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877A GLU* 2.9 18.8 + - + +
878A ALA* 3.8 3.5 - - - +
880A ARG* 1.3 75.0 - - - +
882A LEU* 1.3 65.5 + - - +
884A ASP* 3.2 9.3 + - + +
885A LEU* 2.9 37.5 + - + +
915A ARG* 3.3 40.0 + - - +
919A LEU* 3.5 19.2 - - + +
923A LYS* 5.0 4.7 + - - -
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Residues in contact with LEU 882 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A PHE* 3.6 28.8 - - + -
807A ILE* 3.7 29.4 - - + -
878A ALA 2.9 17.7 + - - +
879A LEU* 3.8 8.1 - - + +
881A GLU* 1.3 76.3 - - - +
883A MET* 1.3 56.0 + - - +
885A LEU* 3.3 6.4 + - - +
886A TYR 3.0 21.7 + - - -
916A PHE* 3.6 31.1 - - + +
919A LEU* 3.6 22.1 - - + +
920A LEU* 3.8 25.6 - - + -
924A PHE* 4.2 11.9 - - + -
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Residues in contact with MET 883 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804A PHE* 3.5 33.5 - - + -
808A PHE* 4.4 2.7 - - + -
857A LEU 4.1 4.5 - - - +
858A MET* 4.0 32.5 - - + +
859A THR 4.0 9.9 - - - +
860A GLN* 3.5 22.7 - - - +
862A THR* 4.4 0.7 - - - +
863A VAL* 3.5 28.0 - - + -
879A LEU 3.0 17.2 + - - +
882A LEU* 1.3 73.0 - - - +
884A ASP* 1.3 60.7 + - - +
886A TYR* 3.3 23.1 + - - +
887A LEU* 2.9 31.0 + - + +
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Residues in contact with ASP 884 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860A GLN* 4.0 13.5 + - - +
880A ARG 2.9 18.6 + - - +
881A GLU* 3.2 12.5 + - + +
883A MET* 1.3 77.2 - - - +
885A LEU* 1.3 59.7 + - + +
887A LEU* 3.2 6.6 + - - +
888A LYS* 2.9 58.5 + - - +
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Residues in contact with LEU 885 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881A GLU* 2.9 27.0 + - + +
882A LEU 3.3 5.8 + - - +
884A ASP* 1.3 73.9 - - - +
886A TYR* 1.3 67.6 + - - +
888A LYS* 3.2 14.3 + - + +
889A MET* 3.0 29.7 + - + +
911A PHE* 6.4 0.2 - - + -
912A ASN* 4.2 25.4 - - + +
915A ARG* 3.6 26.0 - - + +
916A PHE* 3.6 43.1 - - + +
919A LEU* 4.3 14.6 - - + -
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Residues in contact with TYR 886 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A ASP* 3.1 27.3 + - - -
800A ASN* 3.3 48.7 - - + -
804A PHE* 4.2 11.4 - + + -
854A ALA 5.7 0.3 - - - -
855A ARG* 5.8 0.2 - - - -
858A MET* 3.5 37.7 - - + +
882A LEU 3.0 13.7 + - - +
883A MET* 3.5 21.5 - - - +
884A ASP 3.3 0.2 - - - -
885A LEU* 1.3 77.0 - - - +
887A LEU* 1.3 81.9 + - + +
889A MET* 3.1 12.8 + - - +
890A LYS* 2.9 47.3 + - + +
893A TRP* 3.9 7.6 - + - -
916A PHE* 4.3 2.4 - - + -
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Residues in contact with LEU 887 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858A MET 3.9 12.8 - - - +
859A THR* 5.1 1.8 - - + -
860A GLN* 3.7 37.5 - - + +
883A MET* 2.9 22.0 + - + +
884A ASP* 3.2 6.3 + - - +
886A TYR* 1.3 101.9 - - + +
888A LYS* 1.3 57.9 + - + +
890A LYS* 4.2 9.8 - - + +
891A PRO* 3.2 25.1 - - - +
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Residues in contact with LYS 888 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884A ASP* 2.9 43.2 + - - +
885A LEU* 3.2 14.8 + - + +
887A LEU* 1.3 79.8 - - + +
889A MET* 1.3 59.9 + - - +
891A PRO* 3.8 6.4 - - - +
905A SER* 4.0 20.2 + - - +
909A TYR* 5.8 0.2 - - - -
912A ASN* 4.1 33.6 + - - +
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Residues in contact with MET 889 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800A ASN* 4.7 4.3 - - - +
885A LEU 3.0 20.5 + - - +
886A TYR* 3.1 9.2 + - - +
888A LYS* 1.3 79.5 - - - +
890A LYS* 1.3 66.0 + - - +
891A PRO 3.4 0.4 - - - -
892A VAL* 3.1 22.7 + - - +
893A TRP* 3.6 24.7 - - + -
909A TYR* 3.6 27.3 - - + -
912A ASN* 4.0 19.1 - - + +
913A SER* 3.8 34.1 - - - -
916A PHE* 3.9 35.0 - - + -
940A LEU* 4.6 7.9 - - + -
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Residues in contact with LYS 890 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797A ASP* 3.5 22.2 + - - +
855A ARG* 4.7 20.0 + - - +
858A MET* 4.9 5.5 + - - +
886A TYR* 2.9 43.2 + - + +
887A LEU* 4.2 10.7 - - + +
889A MET* 1.3 74.6 - - - +
891A PRO* 1.3 70.0 - - + +
892A VAL 3.1 0.5 + - - -
893A TRP* 3.1 31.5 + - + +
894A ARG* 3.0 48.1 + - + +
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Residues in contact with PRO 891 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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887A LEU 3.2 20.2 - - - +
888A LYS* 3.8 5.2 - - - +
889A MET 3.4 4.5 - - - -
890A LYS* 1.3 91.4 - - + +
892A VAL* 1.3 61.5 + - - +
894A ARG* 4.5 4.9 - - + +
895A SER* 2.9 30.6 + - - -
902A CYS* 3.9 20.6 - - + -
905A SER* 4.0 13.7 - - - +
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Residues in contact with VAL 892 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888A LYS 5.0 0.4 - - - +
889A MET 3.1 12.7 + - - +
890A LYS 3.1 0.2 + - - -
891A PRO* 1.3 76.8 - - - +
893A TRP* 1.3 63.1 + - - +
895A SER 4.0 5.0 + - - +
898A PRO* 3.9 11.2 - - + +
902A CYS* 4.3 6.1 - - - -
905A SER* 3.4 43.3 - - - +
906A LEU* 3.5 31.2 - - + +
909A TYR* 3.8 13.5 - - + -
943A VAL* 4.0 12.8 - - + -
947A ILE* 3.9 27.1 - - + +
953A ILE* 4.6 1.0 + - - +
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Residues in contact with TRP 893 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A ALA* 3.1 28.9 - - + +
796A CYS* 3.4 30.5 - - + +
797A ASP* 2.7 28.4 + - - -
800A ASN* 3.1 31.6 - - - -
886A TYR* 3.9 13.2 - + - -
889A MET* 3.6 27.4 - - + -
890A LYS* 3.1 27.3 + - - +
892A VAL* 1.3 79.6 - - - +
894A ARG* 1.3 67.7 + - + +
895A SER 4.8 0.2 - - - -
909A TYR* 3.4 36.1 - + - -
939A THR* 3.6 12.1 - - + -
943A VAL* 4.6 6.3 - - + -
953A ILE* 3.5 28.8 - - + +
954A GLY 3.8 0.9 + - - -
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Residues in contact with ARG 894 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793A ALA* 4.1 11.7 - - + +
797A ASP* 5.3 2.9 - - - +
855A ARG* 2.8 50.4 - - - +
890A LYS* 3.0 43.7 + - + +
891A PRO* 4.3 3.1 - - + +
893A TRP* 1.3 84.8 - - + +
895A SER* 1.3 69.0 + - - +
896A SER* 5.0 0.9 + - - -
954A GLY* 4.5 8.1 - - - -
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Residues in contact with SER 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891A PRO* 2.9 19.1 + - - -
892A VAL 4.0 3.3 + - - +
893A TRP 3.7 0.4 - - - -
894A ARG* 1.3 82.1 - - - +
896A SER* 1.3 61.3 + - - +
898A PRO* 2.9 40.7 - - - +
901A GLU* 3.1 21.4 + - - -
902A CYS* 4.5 3.6 - - - -
952A SER* 4.6 1.9 - - - -
953A ILE 4.7 0.5 + - - -
954A GLY* 4.2 12.5 + - - -
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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