Contacts of the helix formed by residues 917 - 937 (chain A) in PDB entry 3H2V
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 ASN 917 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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912A TRP* 5.5 0.4 - - - +
913A SER 4.0 5.8 + - - +
914A SER 2.9 18.1 + - - +
916A GLY* 1.3 77.1 - - - +
918A ASP* 1.3 58.8 + - - +
919A ILE* 3.2 13.0 + - - +
920A ILE* 3.2 26.7 + - + +
921A ALA* 3.2 18.4 + - - +
1056A LEU* 3.1 26.8 - - - +
1057A ARG 2.9 28.6 + - - +
1058A TRP* 3.5 29.5 - - - -
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Residues in contact with ASP 918 (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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914A SER 5.0 1.6 - - - +
916A GLY* 4.1 2.8 + - - -
917A ASN* 1.3 72.5 + - - +
919A ILE* 1.3 65.4 + - - +
920A ILE 3.2 0.2 - - - -
921A ALA* 3.6 12.6 - - - +
922A ALA* 2.9 26.5 + - - +
925A ARG* 4.7 4.7 + - - +
963A ARG* 5.3 4.0 + - - -
964A LEU* 3.4 26.2 - - + +
1054A PHE* 6.5 0.4 - - + -
1056A LEU* 3.9 6.5 - - + +
73F GLN* 5.2 13.2 + - - +
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Residues in contact with ILE 919 (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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917A ASN* 3.2 10.9 + - - +
918A ASP* 1.3 80.5 - - - +
920A ILE* 1.3 57.6 + - - +
922A ALA* 3.4 4.3 + - - +
923A ALA* 2.9 28.4 + - - +
961A VAL* 4.0 22.3 - - + +
964A LEU* 3.8 18.4 - - + +
965A ALA* 3.9 28.7 - - + +
968A VAL* 5.0 0.9 - - + -
1037A THR* 4.4 4.3 - - + -
1038A VAL* 4.0 27.6 - - + -
1041A ALA* 4.1 15.0 - - + -
1056A LEU* 3.6 20.6 - - + +
1058A TRP* 4.6 10.3 - - + -
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Residues in contact with ILE 920 (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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909A ALA* 3.1 32.3 - - + +
912A TRP* 3.7 26.7 - - + +
913A SER 4.3 3.8 - - - +
914A SER* 4.3 2.5 - - - +
917A ASN* 3.2 32.9 + - + +
918A ASP 3.2 0.2 - - - -
919A ILE* 1.3 76.5 - - + +
921A ALA* 1.3 64.4 + - - +
923A ALA* 3.8 3.0 - - - +
924A LYS* 3.0 40.8 + - + +
1038A VAL* 4.4 13.5 - - + -
1058A TRP* 3.7 24.5 - - + -
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Residues in contact with ALA 921 (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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914A SER* 4.5 18.4 - - - +
917A ASN 3.2 12.1 + - - +
918A ASP* 3.7 16.8 - - - +
919A ILE 3.3 0.6 - - - -
920A ILE* 1.3 78.8 - - - +
922A ALA* 1.3 60.7 + - - +
924A LYS* 3.5 6.2 + - - +
925A ARG* 3.1 38.3 + - - +
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Residues in contact with ALA 922 (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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918A ASP 2.9 18.4 + - - +
919A ILE* 3.7 3.4 - - - +
921A ALA* 1.3 74.7 - - - +
923A ALA* 1.3 56.5 + - - +
925A ARG* 2.9 28.3 + - - +
926A MET* 2.8 38.6 + - - +
957A ALA* 4.0 10.7 - - + +
960A GLU* 4.9 6.3 - - + -
961A VAL* 3.8 22.7 - - + +
964A LEU* 6.1 0.2 - - + -
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Residues in contact with ALA 923 (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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905A LEU* 3.2 23.0 - - + +
909A ALA* 4.0 17.9 - - + -
919A ILE 2.9 18.1 + - - +
920A ILE* 3.8 6.1 - - - +
922A ALA* 1.3 77.6 - - - +
924A LYS* 1.3 62.2 + - - +
926A MET* 3.3 3.2 + - - +
927A ALA 3.0 19.1 + - - -
961A VAL* 4.6 0.8 - - + +
1034A VAL* 4.2 22.9 - - + -
1038A VAL* 4.9 9.6 - - + -
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Residues in contact with LYS 924 (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 HIS* 4.5 21.2 - - + +
909A ALA* 3.1 34.1 - - + -
910A ARG* 3.9 9.7 - - - +
912A TRP 2.9 23.4 + - - -
913A SER* 4.4 0.6 - - - +
914A SER* 2.8 32.2 + - - +
920A ILE* 3.0 20.2 + - - +
921A ALA* 3.7 5.8 - - - +
923A ALA* 1.3 74.4 - - - +
925A ARG* 1.3 63.1 + - + +
927A ALA* 3.4 6.8 + - - +
928A LEU* 3.1 32.6 + - + +
1061A LYS* 4.6 9.7 - - - +
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Residues in contact with ARG 925 (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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918A ASP* 4.7 5.5 + - - +
921A ALA* 3.1 21.2 + - - +
922A ALA* 2.9 44.1 + - - +
924A LYS* 1.3 72.6 - - - +
926A MET* 1.3 66.9 + - - +
928A LEU* 3.0 12.6 + - + +
929A LEU* 2.9 32.7 + - + +
957A ALA* 4.4 18.1 - - + +
960A GLU* 5.6 6.3 - - - +
69E ASP* 4.3 24.0 - - + -
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Residues in contact with MET 926 (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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905A LEU* 4.1 4.7 - - + -
922A ALA 2.8 13.3 + - - +
923A ALA 3.6 7.2 - - - +
925A ARG* 1.3 71.0 - - - +
927A ALA* 1.3 54.6 + - - +
929A LEU* 2.8 12.4 + - - +
930A MET* 2.7 37.1 + - - +
954A ILE* 4.2 10.8 - - + +
957A ALA* 3.2 24.9 - - + +
958A SER* 3.8 27.6 - - - +
961A VAL* 4.3 4.5 - - - -
1030A LEU* 3.8 16.2 - - + -
1031A MET* 3.7 22.9 - - + -
1034A VAL* 3.3 42.8 - - + -
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Residues in contact with ALA 927 (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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885A PHE* 4.2 4.3 - - + -
902A ALA* 3.4 29.2 - - - +
905A LEU* 3.6 19.0 - - + +
906A HIS* 3.8 22.4 - - + +
923A ALA 3.0 8.3 + - - +
924A LYS 3.7 8.1 - - - +
926A MET* 1.3 74.2 - - - +
928A LEU* 1.3 56.6 + - - +
930A MET* 3.2 9.0 + - - +
931A ALA* 3.0 28.2 + - - +
1031A MET* 4.9 0.2 - - - -
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Residues in contact with LEU 928 (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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885A PHE* 3.6 29.8 - - + -
906A HIS* 5.2 6.3 - - - +
924A LYS* 3.1 26.8 + - + +
925A ARG* 3.0 13.2 + - + +
927A ALA* 1.3 75.9 - - - +
929A LEU* 1.3 58.5 + - - +
930A MET 3.4 0.2 - - - -
931A ALA* 3.7 6.1 - - + +
932A GLU* 3.3 16.6 + - - +
935A ARG* 4.3 2.6 + - - -
68E GLY* 3.3 32.3 - - - +
69E ASP* 5.0 2.2 - - - -
91E LYS* 3.8 39.4 - - + +
92E TYR* 4.2 4.5 - - - +
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Residues in contact with LEU 929 (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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925A ARG* 2.9 28.2 + - + +
926A MET* 2.8 15.0 + - - +
928A LEU* 1.3 70.7 - - - +
930A MET* 1.3 60.6 + - - +
931A ALA 3.3 0.2 - - - -
932A GLU* 3.3 7.4 + - - +
933A MET* 3.0 21.1 + - - +
950A CYS* 3.5 12.4 - - - +
953A ASP* 3.6 35.2 - - + +
954A ILE* 3.8 23.7 - - + +
957A ALA* 4.9 3.6 - - + -
68E GLY* 4.1 3.6 - - - -
69E ASP* 3.5 44.0 - - + +
121E ARG* 3.8 11.0 - - - +
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Residues in contact with MET 930 (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 MET* 3.5 35.7 - - + +
902A ALA* 3.6 16.4 - - + +
926A MET 2.7 15.1 + - - +
927A ALA 3.4 8.7 - - - +
929A LEU* 1.3 69.2 - - - +
931A ALA* 1.3 67.2 + - - +
933A MET* 3.0 16.3 + - - +
934A SER* 3.1 12.8 + - - -
954A ILE* 3.2 35.4 - - + -
995A LEU* 5.0 2.2 - - + -
1027A ALA* 3.9 17.9 - - + -
1030A LEU* 4.8 2.0 - - + -
1031A MET* 3.3 43.5 - - + -
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Residues in contact with ALA 931 (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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885A PHE* 4.5 9.4 - - + -
899A MET* 3.5 38.4 - - + +
902A ALA* 3.7 5.5 - - + +
927A ALA 3.0 15.9 + - - +
928A LEU* 3.7 10.8 - - + +
930A MET* 1.3 76.2 - - - +
932A GLU* 1.3 63.4 + - - +
933A MET 3.0 0.2 + - - -
934A SER* 2.9 18.8 + - - -
935A ARG* 3.4 12.3 + - - +
92E TYR* 4.5 7.2 - - + +
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Residues in contact with GLU 932 (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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928A LEU 3.3 10.2 + - - +
929A LEU* 3.5 9.9 - - - +
930A MET 3.2 0.2 - - - -
931A ALA* 1.3 77.9 - - - +
933A MET* 1.3 56.4 + - - +
935A ARG* 3.3 33.3 - - - +
936A LEU* 2.9 51.7 + - + +
946A ALA* 4.9 0.2 - - - +
950A CYS* 4.1 7.0 - - - -
65E GLY 5.2 0.7 - - - +
66E LEU 4.1 5.6 - - - +
67E PRO* 4.1 4.5 - - - +
68E GLY* 2.5 33.7 + - - -
121E ARG* 3.0 38.1 + - - +
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Residues in contact with MET 933 (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 MET* 3.7 20.4 - - + -
929A LEU 3.0 13.0 + - - +
930A MET* 3.3 13.2 - - - +
931A ALA 3.0 0.8 - - - -
932A GLU* 1.3 77.5 - - - +
934A SER* 1.3 66.9 + - - +
936A LEU* 3.6 4.7 - - - -
937A VAL* 2.8 29.9 + - + +
947A LEU* 3.1 46.9 - - + +
950A CYS* 3.6 19.3 - - - -
951A ALA* 3.6 18.2 - - + +
954A ILE* 4.0 14.6 - - - -
995A LEU* 4.7 14.4 - - - -
999A SER* 4.6 3.1 - - - -
1023A LEU* 5.1 10.8 - - + -
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Residues in contact with SER 934 (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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894A ILE* 3.5 6.3 - - - +
895A ASN* 3.4 29.4 - - - -
898A MET* 3.3 30.4 - - - +
899A MET* 2.9 23.9 - - - +
930A MET 3.1 6.8 + - - -
931A ALA 2.9 15.6 + - - -
933A MET* 1.3 76.4 - - - +
935A ARG* 1.3 63.0 + - - +
937A VAL* 3.4 9.6 + - - +
938A ARG* 3.5 13.5 - - - +
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Residues in contact with ARG 935 (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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893A VAL 4.3 5.4 - - - +
894A ILE* 3.5 28.3 - - + +
899A MET* 4.4 3.6 - - + +
928A LEU 4.3 3.4 + - - -
931A ALA* 3.4 9.4 + - - +
932A GLU* 3.3 47.5 + - - +
933A MET 3.0 0.2 - - - -
934A SER* 1.3 77.1 + - - +
936A LEU* 1.3 65.9 + - + +
938A ARG* 3.0 19.6 + - - +
939A GLY* 3.5 5.9 + - - -
65E GLY* 5.7 4.6 - - - +
66E LEU 4.3 7.7 + - - -
68E GLY* 4.7 3.2 - - - -
91E LYS 4.1 7.7 + - - -
92E TYR 3.7 22.0 + - - -
93E LYS* 3.5 34.5 + - - +
94E GLY* 4.0 9.1 + - - +
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Residues in contact with LEU 936 (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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932A GLU* 2.9 47.3 + - + +
933A MET* 3.6 4.9 - - - +
935A ARG* 1.3 72.4 - - + +
937A VAL* 1.3 57.3 + - - +
938A ARG 3.1 5.0 + - - -
939A GLY* 3.3 8.2 + - - -
943A THR* 3.6 40.4 + - + -
946A ALA* 3.6 22.0 - - + +
947A LEU* 3.5 43.9 - - + +
950A CYS* 4.0 7.6 - - + -
1006A LEU* 4.3 6.2 - - - +
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Residues in contact with VAL 937 (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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895A ASN* 3.7 30.5 - - + +
898A MET* 4.5 11.2 - - - -
933A MET* 2.8 23.0 + - + +
934A SER* 3.5 12.6 - - - +
935A ARG 3.1 0.8 + - - -
936A LEU* 1.3 72.0 - - - +
938A ARG* 1.3 65.6 + - - +
947A LEU* 4.9 7.2 - - + -
1002A LYS* 4.7 20.1 - - + -
1006A LEU* 5.3 6.8 - - - +
1020A THR* 4.8 14.9 + - + +
1023A LEU* 4.3 25.1 - - + -
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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