Contacts of the helix formed by residues 905 - 928 (chain A) in PDB entry 3U3F
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 GLY 905 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 4.3 9.2 - - - +
902A PRO* 2.7 20.4 + - - +
904A GLU* 1.3 70.0 - - - +
906A TYR* 1.3 61.8 + - - -
907A VAL 3.0 5.8 - - - -
908A VAL* 2.9 22.2 + - - +
909A VAL* 3.5 12.3 + - - +
897C GLU* 6.1 0.7 - - - -
901C LEU* 4.2 23.5 - - - +
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Residues in contact with TYR 906 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898A LEU* 3.7 37.4 + - + -
901A LEU* 3.6 30.3 + - + -
902A PRO 3.9 5.6 - - - -
903A PRO* 3.6 39.3 - - + +
904A GLU 3.3 1.2 - - - -
905A GLY* 1.3 76.8 - - - +
907A VAL* 1.3 60.8 + - - +
909A VAL* 3.2 22.6 - - - +
910A VAL* 3.4 13.2 + - - +
957A MET* 3.8 19.3 - - + +
960A ALA* 4.4 28.5 - - + -
961A GLN* 4.5 6.7 - - + -
973A LYS* 3.6 27.1 + - + +
976A MET* 4.1 9.9 - - + -
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Residues in contact with VAL 907 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU 3.3 12.8 - - - +
905A GLY 2.9 0.4 + - - -
906A TYR* 1.3 80.3 - - - +
908A VAL* 1.3 57.6 + - - +
910A VAL* 3.6 1.9 + - - +
911A LYS* 2.9 54.4 + - - +
957A MET* 4.2 7.4 - - + -
958A ARG* 4.2 11.2 - - - +
961A GLN* 3.0 30.5 - - - +
274E LEU* 4.4 21.2 - - + +
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Residues in contact with VAL 908 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904A GLU 4.8 0.2 + - - -
905A GLY* 2.9 13.1 + - - +
907A VAL* 1.3 76.2 - - - +
909A VAL* 1.3 66.3 + - - +
911A LYS* 3.0 14.2 + - + +
912A ASN* 2.9 18.4 + - - +
897C GLU* 4.4 17.7 + - - +
901C LEU* 5.8 2.0 - - + -
908C VAL* 3.6 20.0 - - + -
909C VAL* 4.9 8.5 - - + -
912C ASN* 3.5 15.0 + - - +
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Residues in contact with VAL 909 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 4.2 18.8 - - + -
897A GLU* 3.7 25.4 - - + +
898A LEU* 4.5 7.9 - - + -
901A LEU* 3.4 32.5 - - + -
905A GLY 4.0 2.7 - - - +
906A TYR* 3.2 20.2 - - + +
908A VAL* 1.3 76.3 - - - +
910A VAL* 1.3 77.3 + - + +
912A ASN* 2.9 28.0 + - - +
913A VAL* 3.0 11.6 + - - +
976A MET* 4.8 0.7 - - + -
908C VAL* 4.0 15.5 - - + -
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Residues in contact with VAL 910 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894A LEU* 4.3 2.9 - - + -
906A TYR 3.4 16.2 + - - +
907A VAL 4.1 2.0 - - - +
908A VAL 3.3 0.2 - - - -
909A VAL* 1.3 81.6 - - + +
911A LYS* 1.3 57.4 + - - +
913A VAL* 3.1 7.5 + - - +
914A GLY* 2.7 33.4 + - - -
950A LEU* 4.4 4.3 - - + -
953A LEU* 3.8 29.2 - - + -
954A ILE* 3.9 28.3 - - + -
957A MET* 4.1 15.5 - - + -
976A MET* 3.7 24.7 - - + -
271E MET* 4.5 0.2 - - - +
274E LEU* 4.4 6.1 - - + -
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Residues in contact with LYS 911 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A VAL* 2.9 31.6 + - + +
908A VAL* 3.1 18.6 - - + +
910A VAL* 1.3 77.2 - - - +
912A ASN* 1.3 54.2 + - - +
914A GLY 3.4 0.5 + - - -
915A LEU* 3.0 36.2 + - + +
893C GLU* 3.0 37.9 + - - +
912C ASN* 3.6 15.5 - - - +
271E MET* 3.5 13.3 - - + +
274E LEU* 3.4 45.8 + - + +
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Residues in contact with ASN 912 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ALA* 5.0 6.1 - - + -
897A GLU* 5.7 0.5 - - - +
908A VAL 2.9 6.8 + - - +
909A VAL* 2.9 11.7 + - - +
911A LYS* 1.3 71.0 - - - +
913A VAL* 1.3 63.2 + - + +
914A GLY 3.1 1.3 - - - -
915A LEU* 2.9 17.9 + - - +
916A THR* 2.9 20.6 + - + +
908C VAL* 3.3 34.0 - - - +
911C LYS* 4.0 13.6 - - - +
912C ASN* 3.2 30.9 + - - +
915C LEU* 3.2 26.0 - - + +
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Residues in contact with VAL 913 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 4.3 4.4 - - + +
890A ALA* 3.7 31.2 - - + +
891A VAL* 4.5 13.0 - - + +
894A LEU* 3.9 20.2 - - + -
909A VAL 3.0 12.7 + - - +
910A VAL* 3.1 8.0 + - - +
912A ASN* 1.3 79.5 - - + +
914A GLY* 1.3 62.9 + - - +
916A THR* 3.3 9.0 + - - +
917A LEU* 3.1 23.7 + - - +
950A LEU* 4.8 1.1 - - + -
953A LEU* 4.3 11.0 - - + -
980A SER* 5.8 0.7 - - - -
983A LEU* 3.7 30.1 - - + -
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Residues in contact with GLY 914 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910A VAL 2.7 12.7 + - - -
913A VAL* 1.3 79.3 - - - +
915A LEU* 1.3 55.3 + - - +
917A LEU* 3.2 6.6 + - - +
918A ARG* 3.0 25.8 + - - +
950A LEU* 4.1 19.7 - - - +
267E LEU* 4.5 1.7 - - - +
271E MET* 3.3 29.3 - - - +
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Residues in contact with LEU 915 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A LYS* 3.0 23.1 + - + +
912A ASN 2.9 5.6 + - - +
914A GLY* 1.3 72.8 - - - +
916A THR* 1.3 64.9 + - - +
917A LEU 3.1 1.1 - - - -
918A ARG* 3.1 20.1 + - + +
919A LYS* 3.2 12.0 + - - +
912C ASN* 3.9 15.9 - - + +
915C LEU* 4.2 26.2 - - + +
916C THR* 3.6 30.1 - - + -
919C LYS* 4.0 31.2 - - - +
271E MET* 4.5 13.9 - - + -
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Residues in contact with THR 916 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ASN* 4.7 5.0 - - - +
886A GLU* 4.4 18.4 - - + +
887A LEU* 4.0 21.2 - - - +
890A ALA* 3.8 18.4 - - + +
912A ASN* 2.9 18.2 + - + +
913A VAL* 3.3 10.7 + - - -
915A LEU* 1.3 74.9 - - - +
917A LEU* 1.3 62.9 + - - +
919A LYS* 3.3 11.3 + - - +
920A LEU* 3.1 21.0 + - - +
911C LYS* 5.9 4.7 - - - +
915C LEU* 3.6 29.4 - - + -
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Residues in contact with LEU 917 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887A LEU* 3.4 23.1 - - + -
913A VAL 3.1 19.4 + - - +
914A GLY 3.2 5.4 - - - +
915A LEU 3.1 0.8 - - - -
916A THR* 1.3 76.5 + - - +
918A ARG* 1.3 59.5 + - - +
920A LEU* 3.2 4.9 + - + -
921A ILE* 2.9 52.4 + - + +
946A LEU* 4.0 29.2 - - + +
950A LEU* 4.2 22.9 - - + -
983A LEU* 4.6 12.3 - - + -
267E LEU* 4.1 21.1 - - + -
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Residues in contact with ARG 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
914A GLY 3.0 10.5 + - - +
915A LEU* 3.1 15.2 + - + +
917A LEU* 1.3 76.2 - - - +
919A LYS* 1.3 58.3 + - - +
921A ILE* 3.6 2.2 + - - +
922A GLY* 2.9 26.7 + - - -
879C LEU* 5.6 11.7 - - - +
882C LEU* 6.2 1.8 - - - +
883C ASN* 5.3 1.8 - - - +
886C GLU* 5.5 0.6 + - - -
919C LYS* 3.7 47.7 - - - +
264E THR* 4.5 20.1 - - + +
267E LEU* 3.5 27.8 - - + -
268E ASP* 2.7 42.3 + - - +
271E MET* 5.7 4.0 - - - -
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Residues in contact with LYS 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
883A ASN* 2.9 30.7 - - - +
886A GLU* 2.8 43.9 + - - +
915A LEU 3.2 7.6 + - - +
916A THR* 3.4 11.8 + - - +
918A ARG* 1.3 78.4 - - - +
920A LEU* 1.3 64.5 + - - +
922A GLY* 3.3 1.5 + - - -
923A SER* 3.0 26.0 + - - -
915C LEU* 4.4 15.3 - - + -
918C ARG* 3.1 45.3 - - - +
268G ASP* 6.0 0.2 - - - -
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Residues in contact with LEU 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A VAL* 4.0 11.2 - - + +
883A ASN* 3.6 19.2 - - + +
884A VAL* 3.6 40.4 - - + -
887A LEU* 4.2 18.6 - - + -
916A THR 3.1 12.2 + - - +
917A LEU* 3.2 10.1 + - + +
919A LYS* 1.3 71.3 - - - +
921A ILE* 1.3 65.2 + - + +
922A GLY 2.9 5.2 + - - -
923A SER* 3.0 16.5 + - - +
924A VAL* 3.0 16.7 + - + +
946A LEU* 4.4 7.6 - - + -
987A ALA* 4.4 11.4 - - + -
990A LEU* 3.7 26.2 - - + -
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Residues in contact with ILE 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917A LEU* 2.9 41.1 + - + +
918A ARG* 4.0 4.5 - - - +
920A LEU* 1.3 76.6 - - + +
922A GLY* 1.3 57.0 + - - +
924A VAL* 4.0 1.6 - - - -
925A ASP* 3.1 23.4 + - - +
943A GLN* 3.3 35.1 + - + +
946A LEU* 4.5 8.1 - - + -
947A ASN* 3.2 31.4 - - - +
990A LEU* 5.8 0.4 - - + -
263E ALA* 3.5 27.4 - - + -
264E THR* 4.0 15.5 - - + +
267E LEU* 4.5 4.5 - - + -
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Residues in contact with GLY 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A ARG 2.9 18.1 + - - -
919A LYS 3.3 1.5 + - - -
920A LEU 2.9 0.2 - - - -
921A ILE* 1.3 76.3 - - - +
923A SER* 1.3 62.2 + - - +
924A VAL 3.2 0.2 - - - -
925A ASP* 3.3 6.2 + - - +
926A ASP* 3.1 31.1 + - - +
264E THR* 4.2 13.7 - - - -
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Residues in contact with SER 923 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LEU* 4.5 19.5 - - - -
880A VAL* 3.9 18.0 - - - +
883A ASN* 2.7 28.8 + - - -
919A LYS* 3.0 6.3 + - - -
920A LEU* 3.0 11.4 + - - -
922A GLY* 1.3 73.2 - - - +
924A VAL* 1.3 64.5 + - - +
926A ASP* 3.5 23.0 + - - +
927A LEU* 3.8 6.6 + - - +
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Residues in contact with VAL 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A VAL* 3.7 32.1 - - + -
920A LEU* 3.0 17.9 + - + +
921A ILE* 4.6 0.2 - - - -
923A SER* 1.3 74.4 - - - +
925A ASP* 1.3 51.7 + - - +
926A ASP 2.6 15.8 + - - -
927A LEU* 2.7 20.9 + - + +
928A LEU* 2.9 23.0 + - + +
939A ILE* 4.3 12.6 - - + -
943A GLN* 3.2 29.4 - - + +
990A LEU* 3.8 23.3 - - + -
994A VAL* 4.6 9.6 - - + -
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Residues in contact with ASP 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921A ILE 3.1 17.6 + - - +
922A GLY* 3.3 9.2 + - - +
924A VAL* 1.3 77.8 - - - +
926A ASP* 1.3 62.4 + - - +
927A LEU 3.4 0.2 - - - -
928A LEU* 3.5 15.4 + - - +
929A PRO* 3.9 10.7 - - - +
940A GLU* 5.9 1.4 - - - +
943A GLN* 3.7 17.0 + - - +
262E SER* 4.0 10.8 + - - -
263E ALA* 3.6 29.6 + - - +
264E THR* 3.9 11.6 + - + +
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Residues in contact with ASP 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A GLY 3.1 17.8 - - - +
923A SER* 3.5 17.6 - - - +
924A VAL 2.6 6.3 + - - -
925A ASP* 1.3 76.4 - - - +
927A LEU* 1.3 60.1 + - + +
929A PRO* 3.1 20.3 - - - +
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Residues in contact with LEU 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880A VAL* 4.1 14.6 - - + -
923A SER 4.2 9.6 - - - +
924A VAL* 2.7 16.0 + - + +
926A ASP* 1.3 71.8 - - + +
928A LEU* 1.3 67.1 + - + +
929A PRO* 2.8 7.8 - - - +
930A SER* 2.9 32.3 + - - +
931A LEU* 4.4 11.4 - - + +
994A VAL* 3.9 20.2 - - + -
998A LYS* 3.6 34.5 - - + +
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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
----------------------------------------------------------
924A VAL* 2.9 50.0 - - + +
925A ASP* 3.5 19.7 - - - +
926A ASP 3.5 0.2 - - - -
927A LEU* 1.3 79.0 - - + +
929A PRO* 1.4 71.0 - - + +
930A SER 3.1 0.9 + - - -
931A LEU* 3.4 15.2 + - + +
936A ARG* 3.3 55.2 + - + +
939A ILE* 3.8 28.5 - - + -
940A GLU* 4.7 13.0 - - + +
943A GLN* 4.6 1.8 - - - +
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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