Contacts of the helix formed by residues 893 - 912 (chain A) in PDB entry 3BA6
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 ALA 893 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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855A TRP* 4.7 5.6 - - + +
889A GLU 4.4 1.2 + - - -
890A ILE* 3.2 28.8 + - + +
892A GLU* 1.3 76.6 - - - +
894A PRO* 1.3 65.7 - - - +
895A GLU* 3.0 15.9 - - - +
896A PRO* 3.0 34.8 - - + +
897A MET* 3.2 8.5 - - - +
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Residues in contact with PRO 894 (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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892A GLU 3.1 8.5 - - - +
893A ALA* 1.3 84.2 - - + +
895A GLU* 1.3 56.8 + - - +
896A PRO 3.7 0.2 - - - -
897A MET* 3.5 14.7 + - + +
898A THR* 2.9 35.7 + - - +
958A LYS* 3.5 21.5 - - + -
959A LEU* 3.2 57.0 - - + +
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Residues in contact with GLU 895 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TRP* 3.5 38.7 - - + -
861A ASP* 4.8 2.6 - - - +
893A ALA* 3.0 18.9 - - - +
894A PRO* 1.3 78.9 - - - +
896A PRO* 1.3 67.8 - - + +
897A MET 2.9 4.3 - - - -
898A THR* 3.5 6.6 + - - -
899A MET* 2.8 27.7 + - - +
959A LEU* 4.4 14.8 - - + +
960A LYS 4.6 13.9 - - - +
961A ALA* 4.9 8.3 - - + -
962A LEU* 6.1 0.2 - - - +
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Residues in contact with PRO 896 (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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785A GLU 5.9 1.1 - - - +
852A ALA* 3.3 27.1 - - + +
855A TRP* 3.2 41.3 - - + +
856A PHE* 3.6 35.4 - - + -
890A ILE 4.7 0.7 - - - +
892A GLU 5.7 0.7 - - - +
893A ALA* 3.0 32.8 - - + +
895A GLU* 1.3 84.6 - - + +
897A MET* 1.3 63.2 + - + +
899A MET* 3.4 11.3 - - + +
900A ALA* 3.5 3.5 + - - +
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Residues in contact with MET 897 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
785A GLU* 4.0 17.9 - - - +
786A ALA* 3.6 28.2 - - - +
787A LEU* 4.3 3.8 - - - +
788A ILE* 5.3 7.2 - - + -
791A GLN* 3.8 26.2 - - - +
892A GLU* 3.8 24.5 - - - +
893A ALA 3.2 24.0 - - - +
894A PRO* 3.5 14.6 + - + +
895A GLU 2.9 1.8 - - - -
896A PRO* 1.3 80.8 - - + +
898A THR* 1.3 65.3 + - - +
899A MET 3.0 1.1 - - - -
900A ALA* 3.0 13.3 + - - +
901A LEU* 3.0 14.0 + - - +
958A LYS* 3.9 12.6 - - + -
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Residues in contact with THR 898 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791A GLN* 4.7 1.3 - - - +
894A PRO 2.9 18.1 + - - +
895A GLU* 3.5 8.0 + - - -
897A MET* 1.3 75.1 - - - +
899A MET* 1.3 65.2 + - - +
901A LEU* 3.9 12.2 - - + +
902A SER* 2.8 27.9 + - - -
944A HIS* 5.2 0.3 + - - -
948A LEU* 5.2 13.9 - - + -
958A LYS* 3.2 28.5 - - + +
959A LEU 3.0 26.3 + - - +
960A LYS 4.0 5.8 + - - -
961A ALA* 4.2 8.3 - - - +
962A LEU* 5.0 2.4 - - - +
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Residues in contact with MET 899 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A ALA* 3.6 25.1 - - + +
852A ALA* 4.7 0.2 - - - -
854A TRP* 3.7 25.1 - - + -
855A TRP* 4.3 12.6 - - + -
895A GLU 2.8 19.6 + - - +
896A PRO* 3.4 12.1 - - + +
898A THR* 1.3 80.7 + - - +
900A ALA* 1.3 58.7 + - - +
902A SER* 3.5 3.9 - - - -
903A VAL* 3.1 31.7 + - + +
962A LEU* 3.8 24.5 - - + -
966A GLN* 3.2 22.7 - - - +
969A MET* 3.8 14.6 - - + -
970A VAL* 3.7 15.7 - - + +
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Residues in contact with ALA 900 (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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774A CYS* 5.6 0.4 - - - -
786A ALA* 4.3 17.0 - - + +
787A LEU* 5.1 2.7 - - + -
848A THR* 3.4 34.7 + - - +
851A ALA* 4.8 1.5 - - - +
852A ALA* 4.4 6.5 - - + -
896A PRO 3.5 8.0 + - - +
897A MET 3.0 8.5 + - - +
899A MET* 1.3 73.6 - - - +
901A LEU* 1.3 59.4 + - - +
902A SER 2.9 1.8 - - - -
903A VAL* 2.9 8.4 + - - +
904A LEU* 2.8 35.5 + - - +
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Residues in contact with LEU 901 (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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787A LEU* 3.5 21.2 - - + +
791A GLN* 3.3 42.4 - - + +
794A TRP* 3.9 20.4 - - + -
795A VAL* 3.5 26.2 - - + +
897A MET 3.0 12.6 + - - +
898A THR* 3.9 11.4 - - + +
900A ALA* 1.3 75.9 - - - +
902A SER* 1.3 60.4 + - - +
904A LEU* 3.6 4.9 + - - +
905A VAL* 3.2 30.8 + - - +
944A HIS* 4.1 13.5 - - + -
947A ILE* 5.4 4.9 - - + -
948A LEU* 6.0 2.5 - - + -
957A PHE* 5.8 5.6 - - + -
958A LYS 6.3 0.2 - - - +
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Residues in contact with SER 902 (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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898A THR 2.8 20.1 + - - -
899A MET 3.5 5.8 - - - -
900A ALA 2.9 0.2 - - - -
901A LEU* 1.3 78.6 - - - +
903A VAL* 1.3 60.6 + - - +
905A VAL* 3.8 2.6 + - - +
906A THR* 3.2 24.8 + - - -
944A HIS* 3.5 17.5 + - - -
948A LEU* 4.8 1.7 - - - +
962A LEU* 3.6 12.4 - - - +
967A TRP* 3.1 34.3 - - - -
970A VAL* 3.5 9.1 - - - +
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Residues in contact with VAL 903 (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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847A ALA* 3.9 22.4 - - + +
848A THR* 4.6 2.7 - - - -
851A ALA* 3.9 17.9 - - + -
899A MET* 3.1 17.0 - - + +
900A ALA* 2.9 8.4 + - - +
902A SER* 1.3 76.3 - - - +
904A LEU* 1.3 54.9 + - - +
906A THR 3.0 1.0 + - - -
907A ILE* 2.6 43.9 + - + +
970A VAL* 3.5 31.6 - - + -
973A ILE* 4.0 14.4 - - + -
974A SER* 3.1 16.2 + - - +
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Residues in contact with LEU 904 (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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771A GLU* 4.7 26.7 - - + +
774A CYS* 5.1 2.0 - - + -
787A LEU* 3.7 28.9 - - + -
792A LEU* 5.8 0.4 - - + -
795A VAL* 3.4 30.7 - - + -
844A VAL* 4.3 17.3 - - + -
848A THR* 3.1 36.3 - - + +
900A ALA 2.8 16.9 + - - +
901A LEU* 3.6 4.0 - - - +
903A VAL* 1.3 69.6 - - - +
905A VAL* 1.3 67.5 + - - +
907A ILE* 3.2 4.3 - - + +
908A GLU* 2.9 33.8 + - - +
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Residues in contact with VAL 905 (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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794A TRP* 4.6 2.2 - - + -
795A VAL* 3.9 11.9 - - + +
798A VAL* 3.7 34.1 - - + -
799A THR* 4.0 13.3 - - + +
901A LEU 3.2 18.1 + - - +
902A SER 3.9 4.3 - - - +
904A LEU* 1.3 78.1 - - - +
906A THR* 1.3 59.3 + - - +
908A GLU* 3.5 2.3 - - - +
909A MET* 2.8 33.1 + - - +
941A MET* 3.9 28.3 - - + +
944A HIS* 4.0 26.0 - - + +
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Residues in contact with THR 906 (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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902A SER 3.2 15.6 + - - -
903A VAL 3.0 2.0 + - - -
905A VAL* 1.3 79.3 - - - +
907A ILE* 1.3 61.6 + - - +
909A MET* 3.3 7.9 + - - +
910A CYS* 3.1 29.4 + - - -
941A MET* 4.0 15.6 - - - +
967A TRP* 3.6 17.3 - - - -
970A VAL* 3.8 9.4 - - + -
971A LEU* 4.3 19.0 - - + +
974A SER* 3.2 26.2 - - - +
975A LEU* 6.1 0.2 - - + -
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Residues in contact with ILE 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
843A TYR* 3.5 33.7 - - + +
844A VAL* 3.6 42.7 - - + +
847A ALA* 4.2 9.2 - - + -
848A THR* 5.9 0.7 - - - -
903A VAL* 2.6 28.4 + - + +
904A LEU* 3.2 17.0 - - + +
906A THR* 1.3 72.9 - - - +
908A GLU* 1.3 59.4 + - - +
910A CYS* 3.2 4.7 + - - +
911A ASN* 3.2 20.6 + - - +
974A SER* 3.2 32.3 + - - +
977A VAL* 3.7 10.2 - - + +
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Residues in contact with GLU 908 (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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763A TYR* 3.1 20.7 + - - +
767A SER* 3.5 23.6 - - - +
771A GLU* 2.6 39.8 - - - +
795A VAL* 5.3 0.2 - - - -
799A THR* 2.4 35.5 + - + +
844A VAL* 5.0 6.3 - - + +
904A LEU* 2.9 30.8 + - - +
905A VAL 3.5 2.9 - - - +
907A ILE* 1.3 80.0 - - + +
909A MET* 1.3 61.3 + - - +
910A CYS 2.7 10.2 + - - -
911A ASN* 3.1 20.5 - - - +
912A ALA 3.2 2.3 + - - -
1004A CA 2.9 6.9 - - - -
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Residues in contact with MET 909 (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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763A TYR* 2.9 29.6 - - + +
798A VAL 3.8 14.6 - - - +
799A THR* 3.7 20.4 - - + -
803A PRO* 3.9 19.5 - - + -
905A VAL* 2.8 20.1 + - - +
906A THR* 3.3 8.5 + - - +
908A GLU* 1.3 75.0 - - - +
910A CYS* 1.3 59.7 + - - +
912A ALA* 4.3 5.4 - - + -
913A LEU* 3.8 18.2 + - - +
937A ILE* 3.1 47.5 - - + +
940A SER* 3.8 17.0 - - - -
941A MET* 4.5 8.7 - - - +
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Residues in contact with CYS 910 (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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906A THR* 3.1 26.1 + - - +
907A ILE* 3.3 11.7 - - - +
908A GLU 2.7 3.2 - - - -
909A MET* 1.3 81.0 - - - +
911A ASN* 1.3 57.0 + - - +
912A ALA 3.1 4.3 - - - -
913A LEU* 2.9 32.2 + - - +
914A ASN 3.5 1.7 + - - -
974A SER 4.4 8.5 - - - -
975A LEU* 4.4 17.9 - - - -
977A VAL* 3.3 18.4 - - + -
978A ILE* 3.8 23.6 - - + +
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Residues in contact with ASN 911 (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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762A ARG* 4.9 1.1 + - - +
763A TYR* 3.5 5.2 - - - +
766A SER* 2.9 28.3 + - - -
767A SER* 3.1 22.7 + - - +
840A ILE* 3.4 18.2 - - + +
844A VAL* 5.3 2.2 - - - +
907A ILE 3.2 5.1 + - - -
908A GLU* 3.1 19.1 - - - +
910A CYS* 1.3 74.8 - - - +
912A ALA* 1.3 60.8 + - - +
913A LEU 3.2 0.4 - - - -
914A ASN* 3.2 38.1 + - + +
915A SER* 3.3 13.3 + - - -
977A VAL* 3.7 17.0 - - + +
981A ASP* 5.9 0.2 - - - -
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Residues in contact with ALA 912 (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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763A TYR* 3.1 36.8 - - + +
803A PRO* 5.2 2.5 - - + -
807A LEU* 4.2 4.8 - - + +
908A GLU 3.2 8.0 + - - +
909A MET* 4.5 10.3 - - + +
910A CYS 3.1 0.6 - - - -
911A ASN* 1.3 75.4 + - - +
913A LEU* 1.3 58.8 - - - +
914A ASN 3.0 4.9 - - - -
915A SER* 3.2 19.0 + - - +
933A LEU* 3.4 32.1 - - + +
937A ILE* 5.4 2.7 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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