Contacts of the helix formed by residues 917 - 942 (chain A) in PDB entry 4FUL
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 THR 917 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A SER* 3.4 8.1 - - - -
916A PRO* 1.4 83.7 - - + +
918A GLU* 1.4 59.4 + - - +
919A GLU* 3.8 10.8 + - - +
920A LYS* 3.2 30.1 + - + +
921A PHE* 3.0 21.6 + - - -
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Residues in contact with GLU 918 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
912A LYS* 3.3 31.1 - - - +
917A THR* 1.4 69.7 - - - +
919A GLU* 1.3 55.8 + - - +
921A PHE* 3.1 16.5 + - - +
922A GLN* 2.9 64.1 + - + +
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Residues in contact with GLU 919 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917A THR* 3.8 10.5 + - - +
918A GLU* 1.3 77.2 - - - +
920A LYS* 1.4 63.8 + - + +
922A GLN* 3.4 6.9 + - - +
923A ALA* 3.2 21.5 + - - +
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Residues in contact with LYS 920 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A SER* 4.1 2.9 - - - -
916A PRO* 3.8 34.6 - - + +
917A THR* 3.2 23.9 + - + +
919A GLU* 1.4 83.1 - - + +
921A PHE* 1.4 56.0 + - - +
923A ALA* 3.3 10.5 + - + +
924A ALA* 3.0 28.2 + - - +
957A THR* 5.7 0.7 + - - -
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Residues in contact with PHE 921 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ASN* 3.5 25.4 - - - -
911A LEU* 3.7 20.0 - - + -
912A LYS* 3.3 59.5 - - + -
915A SER* 3.3 20.8 + - - +
917A THR 3.0 9.5 + - - +
918A GLU* 3.1 28.9 + - - +
920A LYS* 1.4 73.7 - - - +
922A GLN* 1.3 82.2 + - - +
924A ALA* 3.4 2.8 + - + +
925A VAL* 3.2 37.1 + - + +
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Residues in contact with GLN 922 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918A GLU* 2.9 40.4 + - + +
919A GLU* 3.8 7.0 - - - +
920A LYS 3.4 0.2 - - - -
921A PHE* 1.3 93.0 - - - +
923A ALA* 1.4 58.4 + - - +
925A VAL* 3.4 8.9 + - - +
926A GLU* 3.1 26.9 + - - +
1005A HIS* 4.7 16.1 + - - -
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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
----------------------------------------------------------
919A GLU 3.2 12.7 + - - +
920A LYS* 3.4 14.8 - - + +
922A GLN* 1.4 76.1 - - - +
924A ALA* 1.4 49.8 + - - +
926A GLU* 3.3 10.0 - - - +
927A ARG* 2.8 34.2 + - - +
957A THR* 5.0 0.9 - - - +
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Residues in contact with ALA 924 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
911A LEU* 4.9 10.0 - - + +
915A SER* 4.5 7.0 - - - +
920A LYS 3.0 13.3 + - - +
921A PHE* 3.5 16.6 - - + +
922A GLN 3.3 0.2 - - - -
923A ALA* 1.4 73.8 - - - +
925A VAL* 1.4 54.8 + - - +
927A ARG 3.3 0.3 + - - -
928A PHE* 2.8 29.6 + - - +
956A GLU 4.8 2.7 - - - +
957A THR* 3.4 32.5 + - - +
958A GLY* 3.4 14.1 - - - +
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Residues in contact with VAL 925 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A ASN* 4.8 0.7 - - - +
911A LEU* 5.2 2.2 - - + -
921A PHE* 3.2 45.5 + - + +
922A GLN* 3.4 12.1 + - - +
924A ALA* 1.4 73.4 - - - +
926A GLU* 1.4 58.8 + - - +
928A PHE* 3.3 7.2 + - - +
929A VAL* 2.9 37.0 + - + +
994A VAL* 3.5 37.2 - - + +
1005A HIS* 3.6 31.6 - - + +
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Residues in contact with GLU 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922A GLN 3.1 14.1 + - - +
923A ALA* 3.3 13.5 - - - +
925A VAL* 1.4 72.6 - - - +
927A ARG* 1.4 63.7 + - - +
929A VAL* 3.3 6.5 + - - +
930A TYR* 3.0 49.9 + - + -
1005A HIS* 5.1 11.6 + - + -
1008A LYS* 3.0 38.0 + - - +
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Residues in contact with ARG 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LYS 5.4 4.8 + - - -
299A ASN* 3.3 26.1 + - - +
861A ASP* 5.3 2.6 + - - -
863A CYS* 3.7 28.4 - - + +
865A LEU* 5.3 4.6 - - - +
923A ALA 2.8 17.0 + - - +
924A ALA 3.3 1.3 + - - +
926A GLU* 1.4 71.6 - - - +
928A PHE* 1.4 52.7 + - - +
930A TYR* 3.5 5.3 + - - +
931A SER* 2.8 37.1 + - - -
957A THR* 3.4 40.3 - - - +
958A GLY 3.6 2.5 - - - -
959A ASN* 3.2 40.4 + - + +
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Residues in contact with PHE 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
907A LEU* 3.8 15.5 - - + -
911A LEU* 4.8 2.2 - - + -
924A ALA 2.8 17.4 + - - +
925A VAL* 3.5 8.7 - - - +
926A GLU 3.3 0.2 - - - -
927A ARG* 1.4 73.2 - - - +
929A VAL* 1.3 62.0 + - - +
931A SER* 3.5 1.3 + - - -
932A CYS* 2.8 40.0 + - + +
954A ILE* 3.5 20.0 - - + -
958A GLY* 3.1 13.6 + - - +
960A LEU* 3.5 28.9 - - + -
991A PHE* 3.4 54.7 - + + -
994A VAL* 3.8 21.3 - - + -
995A MET* 3.6 22.2 - - + -
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Residues in contact with VAL 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925A VAL* 2.9 26.6 + - + +
926A GLU* 3.3 8.7 + - - +
928A PHE* 1.3 76.3 - - + +
930A TYR* 1.3 62.6 + - + +
932A CYS* 4.7 1.3 - - - -
933A ALA* 3.3 21.8 + - - +
995A MET* 3.9 28.5 - - + -
1005A HIS* 3.8 37.9 - - + +
1008A LYS* 4.4 9.2 - - + -
1009A PHE* 3.6 14.7 - - + +
1012A ILE* 3.7 22.7 - - + -
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Residues in contact with TYR 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
861A ASP 3.3 22.9 - - - +
862A LEU* 3.3 11.0 - - + +
863A CYS* 3.8 21.3 - - - -
926A GLU* 3.0 58.5 + - + +
927A ARG* 3.9 0.7 - - - +
929A VAL* 1.3 75.2 - - + +
931A SER* 1.4 59.0 + - - +
933A ALA* 3.4 6.0 + - - +
934A GLY 3.0 23.6 + - - -
1008A LYS* 3.4 20.9 + - + -
1012A ILE* 3.6 40.7 - - + +
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Residues in contact with SER 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A LEU 3.4 9.0 - - - -
863A CYS* 3.4 9.6 - - - +
927A ARG 2.8 27.1 + - - -
928A PHE 3.5 2.8 + - - -
930A TYR* 1.4 70.0 - - - +
932A CYS* 1.3 60.8 + - - +
934A GLY* 3.5 0.7 + - - -
935A TYR* 3.0 37.7 + - - -
958A GLY 3.6 2.3 + - - -
959A ASN* 3.3 26.1 + - - -
960A LEU* 2.9 29.1 + - - +
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Residues in contact with CYS 932 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
928A PHE* 2.8 26.1 + - + +
929A VAL 4.0 2.9 - - - +
931A SER* 1.3 77.0 + - - +
933A ALA* 1.3 50.6 + - - +
935A TYR* 3.2 1.9 + - - +
936A CYS* 2.8 44.6 + - - -
960A LEU* 3.6 16.7 - - + +
987A LEU* 3.9 6.5 - - - -
991A PHE* 3.8 28.3 - - - -
995A MET* 3.7 26.0 - - + -
1009A PHE* 3.7 10.8 - - + -
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Residues in contact with ALA 933 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
862A LEU* 4.1 2.7 - - + -
929A VAL 3.3 12.7 + - - +
930A TYR 3.4 9.0 - - - +
932A CYS* 1.3 76.9 - - - +
934A GLY* 1.3 61.6 + - - +
936A CYS* 3.2 2.5 + - - +
937A VAL* 3.0 29.7 + - - +
1009A PHE* 3.4 16.0 - - + -
1012A ILE* 3.7 25.4 - - + -
1013A CYS* 3.6 20.9 - - - +
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Residues in contact with GLY 934 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
855A TRP* 3.7 8.5 - - - -
862A LEU* 3.5 30.4 - - - +
864A LEU* 3.6 13.2 - - - -
930A TYR 3.0 11.8 + - - -
931A SER 3.8 3.4 - - - -
933A ALA* 1.3 75.2 - - - +
935A TYR* 1.4 55.3 + - - +
937A VAL 3.5 0.2 + - - -
938A ALA* 3.1 29.8 + - - +
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Residues in contact with TYR 935 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A LEU* 4.1 23.0 - - + +
863A CYS 4.5 0.4 - - - -
864A LEU* 3.6 27.7 - - + +
865A LEU* 2.7 38.9 + - - -
866A PRO* 3.9 1.6 - - - +
931A SER 3.0 27.6 + - - +
932A CYS 3.9 2.7 - - - +
934A GLY* 1.4 71.6 - - - +
936A CYS* 1.4 56.1 + - - +
938A ALA* 4.4 3.1 - - + -
939A THR* 2.7 49.0 + - + +
960A LEU* 3.3 31.6 - - + -
961A PHE* 3.5 11.3 - - + +
962A HIS* 3.7 49.7 + + + +
965A PHE* 5.1 0.7 - + - -
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Residues in contact with CYS 936 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
932A CYS* 2.8 40.6 + - - +
933A ALA* 3.2 7.4 + - - +
935A TYR* 1.4 71.9 - - - +
937A VAL* 1.3 59.2 + - - +
939A THR* 4.2 0.2 - - - -
940A PHE* 3.1 27.2 + - - +
960A LEU* 6.1 0.9 - - - -
962A HIS* 6.3 0.7 - - - -
985A PHE* 3.4 47.7 - - + -
986A VAL 3.5 20.6 - - - -
987A LEU* 4.5 1.3 - - - -
1009A PHE* 4.2 7.4 - - - -
1013A CYS* 4.6 7.6 - - - -
1068A PHE* 3.8 1.9 - - + -
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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
----------------------------------------------------------
855A TRP* 4.4 6.3 - - + -
933A ALA 3.0 21.3 + - - +
934A GLY 4.1 2.5 - - - +
936A CYS* 1.3 75.9 - - - +
938A ALA* 1.3 58.2 + - - +
940A PHE* 3.3 2.8 + - - +
941A VAL* 2.9 34.7 + - + +
1013A CYS* 3.5 29.8 - - - +
1016A ALA* 4.1 7.6 - - + -
1017A TYR* 3.7 37.7 - - + +
1020A LEU* 3.9 18.6 - - + -
1068A PHE* 3.6 18.2 - - + -
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Residues in contact with ALA 938 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A LEU* 3.6 28.9 - - + -
851A MET* 3.7 20.2 - - - -
855A TRP* 4.5 5.5 - - + -
864A LEU* 4.9 4.5 - - + -
934A GLY 3.1 19.6 + - - +
935A TYR* 4.0 5.4 - - + +
937A VAL* 1.3 75.0 - - - +
939A THR* 1.4 58.5 + - + +
941A VAL* 3.3 3.9 + - - +
942A LEU* 3.0 36.2 + - - +
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Residues in contact with THR 939 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
848A LEU* 5.9 2.9 - - + -
935A TYR* 2.7 37.7 + - + +
936A CYS* 4.1 2.1 + - - -
938A ALA* 1.4 70.3 - - + +
940A PHE* 1.3 65.4 + - - +
942A LEU 3.4 0.3 + - - -
943A GLY 3.0 3.5 + - - -
944A ILE* 2.9 52.5 + - + +
945A GLY* 3.2 23.3 + - - -
962A HIS* 3.7 36.1 - - + +
965A PHE* 5.1 1.3 - - + -
985A PHE* 4.2 5.4 - - - +
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Residues in contact with PHE 940 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
936A CYS 3.1 20.2 + - - +
937A VAL 3.3 2.6 + - - +
938A ALA 3.3 0.6 - - - -
939A THR* 1.3 80.4 + - - +
941A VAL* 1.3 64.5 + - - +
943A GLY 3.1 4.2 + - - -
945A GLY 4.8 0.2 - - - +
984A PRO* 3.8 37.6 + - + -
985A PHE* 3.7 13.0 - + + -
1017A TYR* 4.2 9.6 - + - -
1050A TYR* 2.8 40.2 + + - -
1054A ALA* 3.5 28.9 - - + +
1067A TYR* 3.5 35.9 - + - -
1068A PHE* 3.6 21.3 - + + -
1071A GLN* 4.2 11.7 - - + -
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Residues in contact with VAL 941 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
851A MET* 3.8 20.2 - - + -
937A VAL* 2.9 30.9 + - + +
938A ALA 3.6 4.5 - - - +
940A PHE* 1.3 73.0 - - + +
942A LEU* 1.4 57.0 + - + +
1017A TYR* 4.5 12.6 - - + -
1020A LEU* 3.8 20.0 - - + -
1027A LEU* 4.7 3.1 - - + -
1050A TYR* 3.4 15.6 - - - -
1051A ILE* 3.5 37.6 - - + +
1054A ALA* 4.0 9.3 - - - +
1055A LEU* 4.3 25.6 - - + -
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Residues in contact with LEU 942 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
844A ILE* 4.3 21.8 - - + -
847A ILE* 4.0 39.0 - - + -
848A LEU* 4.3 16.4 - - + -
851A MET* 3.9 14.6 - - + -
938A ALA 3.0 17.2 + - - +
939A THR 3.4 0.2 + - - -
940A PHE 3.2 0.2 - - - -
941A VAL* 1.4 75.2 - - - +
943A GLY* 1.3 62.1 + - - +
944A ILE* 3.2 26.2 + - + +
1027A LEU* 5.8 0.4 - - + -
1031A PHE* 3.3 45.8 - - + -
1034A MET* 4.8 1.7 - - + +
1050A TYR* 4.1 1.3 - - - -
1051A ILE* 4.2 8.7 - - + -
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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
------------------------------------------------------------
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