Contacts of the helix formed by residues 872 - 895 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
814C GLU* 4.7 3.3 + - - -
816C TYR* 5.2 4.7 - - - -
870C ILE* 3.4 8.2 - - - +
871C PRO* 1.3 79.4 - - - +
873C GLU* 1.3 60.4 + - - +
874C GLU* 3.5 25.1 + - - +
875C ARG* 3.5 22.9 + - - +
876C HIS* 3.1 19.9 - - - -
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Residues in contact with GLU 873 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
871C PRO 4.0 9.2 - - - +
872C SER* 1.3 69.6 + - - +
874C GLU* 1.3 63.1 + - - +
875C ARG 3.1 2.2 - - - -
876C HIS* 2.9 40.8 + - + +
877C GLU* 3.0 15.6 + - - +
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Residues in contact with GLU 874 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
872C SER* 3.5 11.6 + - - +
873C GLU* 1.3 77.2 - - - +
875C ARG* 1.3 62.1 + - + +
877C GLU* 3.4 32.3 - - - +
878C ALA* 3.5 6.8 + - - +
923C LYS* 5.6 6.9 + - - +
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Residues in contact with ARG 875 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
811C GLU* 2.9 45.3 + - - +
816C TYR* 3.3 34.4 - - - -
870C ILE* 4.3 9.0 - - + -
872C SER* 3.5 25.9 + - - +
873C GLU 3.1 0.6 - - - -
874C GLU* 1.3 75.6 - - + +
876C HIS* 1.3 62.5 + - - +
877C GLU 3.3 0.2 - - - -
878C ALA* 3.3 8.6 + - - +
879C LEU* 2.9 32.3 + - - +
923C LYS* 2.7 52.1 + - - +
924C PHE* 3.8 11.2 - - - -
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Residues in contact with HIS 876 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
867C CYS* 3.1 48.3 + - + +
870C ILE* 2.8 40.1 + - + +
871C PRO 4.5 0.7 - - - -
872C SER 3.1 15.5 + - - -
873C GLU* 2.9 38.6 + - + +
875C ARG* 1.3 74.5 - - - +
877C GLU* 1.3 63.8 + - - +
879C LEU* 3.9 0.3 - - - +
880C ARG* 2.9 39.9 + - - +
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Residues in contact with GLU 877 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
873C GLU 3.0 15.7 + - - +
874C GLU* 3.4 23.0 - - - +
875C ARG 3.3 0.2 - - - -
876C HIS* 1.3 75.6 - - - +
878C ALA* 1.3 56.6 + - - +
880C ARG* 3.8 4.7 - - - +
881C GLU* 3.0 30.5 + - - +
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Residues in contact with ALA 878 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
874C GLU 3.5 7.7 + - - +
875C ARG* 3.3 12.9 + - - +
876C HIS 3.2 0.6 - - - -
877C GLU* 1.3 76.3 - - - +
879C LEU* 1.3 67.1 + - - +
881C GLU* 3.3 3.2 + - - -
882C LEU* 2.9 24.3 + - - +
919C LEU* 3.6 13.7 - - + +
923C LYS* 4.2 24.7 - - + -
924C PHE* 3.9 22.7 - - + -
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Residues in contact with LEU 879 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C PHE* 4.9 4.9 - - + -
807C ILE* 3.8 19.7 - - + -
808C PHE* 3.4 39.7 - - + -
811C GLU* 4.3 9.2 - - + -
863C VAL* 4.1 10.0 - - + +
866C VAL* 4.9 1.8 - - + -
867C CYS* 4.8 5.4 - - - -
870C ILE* 3.6 31.6 - - + -
875C ARG 2.9 16.2 + - - +
876C HIS* 4.0 4.5 - - - +
878C ALA* 1.3 77.7 - - - +
880C ARG* 1.3 58.4 + - - +
882C LEU* 3.3 12.0 + - + +
883C MET* 3.0 28.6 + - - +
924C PHE* 4.2 15.3 - - + -
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Residues in contact with ARG 880 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLN* 3.6 20.7 + - - +
863C VAL* 3.6 15.5 - - + -
864C ASP* 3.2 43.0 + - - +
867C CYS* 4.1 18.5 - - - +
876C HIS* 2.9 27.6 + - - +
877C GLU* 3.8 4.9 - - - +
879C LEU* 1.3 75.3 - - - +
881C GLU* 1.3 59.0 + - - +
883C MET 3.4 0.9 + - - -
884C ASP* 2.9 28.6 + - - +
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Residues in contact with GLU 881 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
877C GLU 3.0 17.1 + - - +
878C ALA* 3.9 4.4 - - - +
880C ARG* 1.3 76.3 - - - +
882C LEU* 1.3 64.3 + - - +
884C ASP* 3.1 9.2 + - + +
885C LEU* 2.9 33.6 + - + +
915C ARG* 3.0 41.1 + - - +
919C LEU* 3.6 16.5 - - + +
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Residues in contact with LEU 882 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C PHE* 3.6 28.5 - - + -
807C ILE* 3.7 29.6 - - + -
878C ALA 2.9 17.8 + - - +
879C LEU* 3.5 9.4 - - + +
881C GLU* 1.3 77.8 - - - +
883C MET* 1.3 63.2 + - - +
885C LEU* 3.3 5.8 + - - +
886C TYR 3.0 17.7 + - - -
916C PHE* 3.6 41.0 - - + +
919C LEU* 4.0 18.1 - - + +
920C LEU* 4.4 9.0 - - + -
924C PHE* 3.9 18.8 - - + -
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Residues in contact with MET 883 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
804C PHE* 3.5 33.6 - - + -
808C PHE* 4.3 2.7 - - + -
857C LEU 4.0 4.9 - - - +
858C MET* 3.8 37.2 - - + +
859C THR 3.6 13.9 - - - +
860C GLN* 3.5 28.9 - - - +
863C VAL* 3.4 29.4 - - + -
879C LEU 3.0 10.7 + - - +
880C ARG 3.8 0.2 - - - +
882C LEU* 1.3 76.0 - - - +
884C ASP* 1.3 57.0 + - - +
886C TYR* 3.2 14.4 + - - +
887C LEU* 2.9 31.9 + - + +
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Residues in contact with ASP 884 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
860C GLN* 3.7 14.2 + - - +
880C ARG 2.9 17.8 + - - +
881C GLU* 3.1 10.0 + - - +
883C MET* 1.3 77.2 - - - +
885C LEU* 1.3 62.7 + - - +
887C LEU* 3.1 8.2 + - - +
888C LYS* 2.9 55.9 + - - +
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Residues in contact with LEU 885 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
881C GLU* 2.9 31.2 + - + +
882C LEU* 3.3 7.2 + - - +
884C ASP* 1.3 76.3 - - + +
886C TYR* 1.3 63.7 + - - +
888C LYS* 3.1 17.9 + - - +
889C MET* 2.9 29.5 + - - +
912C ASN* 3.8 36.1 - - + +
915C ARG* 3.8 21.8 - - + +
916C PHE* 3.6 44.0 - - + +
919C LEU* 5.0 4.0 - - + -
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Residues in contact with TYR 886 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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797C ASP* 2.7 30.8 + - - -
800C ASN* 3.2 48.2 - - + -
804C PHE* 4.0 18.2 - + + -
854C ALA 5.1 0.3 + - - -
858C MET* 3.4 39.3 - - + +
882C LEU 3.0 13.2 + - - +
883C MET* 3.2 11.2 + - - +
885C LEU* 1.3 75.8 - - - +
887C LEU* 1.3 80.6 + - + +
889C MET* 3.2 9.5 + - + +
890C LYS* 2.9 44.8 + - + +
893C TRP* 3.5 10.1 - + - -
916C PHE* 4.5 5.3 - + + -
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Residues in contact with LEU 887 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
858C MET 3.4 17.9 - - - +
859C THR* 4.7 2.2 - - + -
860C GLN* 4.2 26.9 - - + +
883C MET* 2.9 34.7 + - + +
884C ASP* 3.1 8.0 + - - +
886C TYR* 1.3 101.0 - - + +
888C LYS* 1.3 58.1 + - - +
890C LYS* 4.0 14.6 - - - +
891C PRO* 3.2 22.5 - - - +
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Residues in contact with LYS 888 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
884C ASP* 2.9 47.9 + - - +
885C LEU* 3.5 20.6 - - - +
887C LEU* 1.3 78.6 - - - +
889C MET* 1.3 62.7 + - - +
891C PRO* 3.2 10.0 - - - +
892C VAL* 4.2 0.5 - - - +
905C SER* 3.7 23.9 + - - +
912C ASN* 3.7 33.8 + - - +
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Residues in contact with MET 889 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
800C ASN* 6.1 0.9 - - - +
885C LEU 2.9 22.8 + - - +
886C TYR* 3.8 4.9 - - - +
888C LYS* 1.3 77.5 - - - +
890C LYS* 1.3 65.2 + - - +
892C VAL* 3.2 19.1 + - - +
893C TRP* 3.4 21.0 - - + -
909C TYR* 3.3 43.2 - - + +
912C ASN* 4.0 22.2 - - + +
913C SER* 3.6 35.0 - - - +
916C PHE* 4.4 17.0 - - - -
939C THR 4.5 0.2 - - - +
940C LEU* 4.1 17.9 - - + -
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Residues in contact with LYS 890 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
797C ASP* 3.2 21.3 - - - +
858C MET* 5.2 3.1 - - - -
886C TYR* 2.9 51.8 + - - +
887C LEU* 4.0 16.2 - - - +
889C MET* 1.3 76.3 - - - +
891C PRO* 1.3 70.1 - - + +
892C VAL 3.1 0.5 + - - -
893C TRP* 3.3 21.2 + - + +
894C ARG* 3.0 34.2 + - + +
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Residues in contact with PRO 891 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887C LEU 3.2 20.6 - - - +
888C LYS* 3.2 13.7 - - - +
889C MET 3.4 0.7 - - - -
890C LYS* 1.3 92.7 - - + +
892C VAL* 1.3 60.8 + - - +
894C ARG* 4.4 4.9 - - + +
895C SER* 2.9 30.1 + - - +
902C CYS* 3.8 23.1 - - + -
905C SER* 4.5 7.2 - - - +
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Residues in contact with VAL 892 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
888C LYS 4.2 2.0 - - - +
889C MET 3.4 9.6 - - - +
890C LYS 3.1 0.6 + - - -
891C PRO* 1.3 76.6 - - - +
893C TRP* 1.3 59.8 + - - +
895C SER* 3.9 4.0 + - - +
898C PRO* 3.7 12.3 - - + +
902C CYS* 4.0 8.1 - - - -
905C SER* 3.6 35.7 - - - +
906C LEU* 3.5 20.4 - - + +
909C TYR* 3.5 33.2 - - + -
943C VAL* 4.3 3.4 - - + -
947C ILE* 3.3 36.5 - - + +
953C ILE* 4.4 2.4 - - - +
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Residues in contact with TRP 893 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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793C ALA* 3.3 25.9 + - + +
796C CYS* 3.4 33.8 - - + +
797C ASP* 3.2 29.3 + - - -
800C ASN* 3.2 24.0 - - - -
886C TYR* 3.5 20.9 - + - -
889C MET* 3.4 35.7 - - + -
890C LYS* 3.3 24.3 + - - +
892C VAL* 1.3 77.9 - - - +
894C ARG* 1.3 68.0 + - + +
895C SER 3.6 1.3 - - - +
909C TYR* 3.6 15.7 - + - -
939C THR* 3.7 18.2 - - + -
943C VAL* 4.3 11.0 - - + -
953C ILE* 3.3 35.5 - - + +
954C GLY 4.3 0.5 + - - -
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Residues in contact with ARG 894 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
793C ALA* 4.1 19.3 - - + +
794C LEU* 5.4 11.3 - - - +
797C ASP* 2.4 38.7 + - - -
851C GLY 5.7 1.2 + - - -
855C ARG* 5.0 19.6 - - - +
890C LYS* 3.0 34.6 + - + +
891C PRO* 4.2 3.6 - - + +
893C TRP* 1.3 79.8 - - + +
895C SER* 1.3 67.2 + - - +
896C SER* 4.9 1.6 + - - -
954C GLY* 5.4 2.4 - - - -
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Residues in contact with SER 895 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
891C PRO* 2.9 15.4 + - - +
892C VAL 3.9 1.6 + - - +
893C TRP 3.6 3.6 - - - +
894C ARG* 1.3 83.2 - - - +
896C SER* 1.3 60.2 + - - +
898C PRO* 2.9 41.2 - - - +
901C GLU* 3.2 22.2 - - - -
902C CYS* 4.3 3.4 - - - -
952C SER* 4.2 1.0 + - - -
953C ILE 4.5 3.3 + - - -
954C GLY* 3.9 16.5 + - - -
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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