Contacts of the helix formed by residues 924 - 952 (chain A) in PDB entry 1OY6
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 ASP 924 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A TYR* 4.9 2.2 - - - -
562A SER 3.2 11.2 - - - +
563A PHE 3.6 13.9 - - - +
564A LEU* 4.2 0.4 - - - -
565A PRO* 3.7 17.0 - - + +
869A SER 6.0 1.1 - - - -
921A LEU* 5.4 1.2 - - - +
922A THR* 3.0 37.6 + - + +
923A ASN* 1.3 76.2 - - - +
925A VAL* 1.3 58.9 + - - +
926A TYR* 3.1 43.5 + - - +
927A PHE* 3.5 6.9 + - - +
928A GLN* 3.1 28.9 + - - +
1002A ALA* 4.0 11.5 - - - +
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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
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393A LEU* 5.0 4.3 - - + -
463A THR* 4.7 0.2 - - + -
466A ILE* 3.4 41.3 - - + +
467A TYR* 3.7 28.5 - - + +
470A PHE* 4.5 11.9 - - + -
563A PHE* 3.1 28.5 + - + +
564A LEU* 3.7 17.9 - - + +
869A SER* 6.2 1.3 - - - +
924A ASP* 1.3 75.3 + - - +
926A TYR* 1.3 68.3 + - + +
928A GLN* 3.2 3.1 + - - +
929A VAL* 3.2 22.9 + - - +
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Residues in contact with TYR 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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35A TYR* 4.7 2.6 - - - -
392A THR* 3.9 16.1 - - + +
393A LEU* 5.0 10.1 - - + -
396A PHE* 3.4 34.6 - + - -
470A PHE* 3.9 19.4 - + - -
564A LEU* 3.6 33.3 - - + +
565A PRO* 3.6 11.2 - - + -
567A GLU* 4.9 2.8 + - - -
924A ASP* 3.1 17.0 + - - +
925A VAL* 1.3 78.9 - - + +
927A PHE* 1.3 56.9 + - - +
929A VAL* 3.5 1.6 + - - +
930A GLY* 2.8 26.2 + - - -
999A ALA* 3.4 24.9 - - + +
1002A ALA* 3.6 24.2 - - + +
1003A VAL* 3.5 25.3 - - + +
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Residues in contact with PHE 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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556A PHE* 6.1 0.4 - + - -
559A LEU* 4.2 18.2 - - + -
912A ALA* 3.3 44.0 - - + -
913A LEU* 3.6 13.2 - - + -
916A ALA* 4.1 9.6 - - + -
921A LEU* 6.5 0.2 - - + -
922A THR 3.7 18.4 - - - +
923A ASN* 3.4 31.4 - - - -
924A ASP* 3.5 11.3 + - - +
925A VAL 3.3 0.4 - - - -
926A TYR* 1.3 78.0 - - - +
928A GLN* 1.3 58.0 + - - +
929A VAL 3.3 0.2 - - - -
930A GLY* 4.3 1.3 - - - +
931A LEU* 2.9 47.5 + - + +
1002A ALA 3.9 8.4 + - - +
1003A VAL 5.4 0.4 - - - -
1006A GLY* 3.5 25.8 - - - -
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Residues in contact with GLN 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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456A MET* 4.9 4.0 - - - -
467A TYR* 2.7 39.0 + - + +
556A PHE* 6.1 4.2 - - - -
869A SER* 3.6 20.8 - - - -
873A ALA* 4.2 10.9 - - - +
877A TYR* 3.3 44.9 + - + +
923A ASN* 3.8 15.7 + - - +
924A ASP 3.1 16.1 + - - +
925A VAL 3.2 6.9 + - - +
927A PHE* 1.3 78.1 - - - +
929A VAL* 1.3 57.2 + - - +
931A LEU* 3.5 12.6 - - - +
932A LEU* 3.4 15.8 + - - +
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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
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400A LEU* 3.7 15.0 - - + -
453A PHE* 4.8 2.2 - - + -
456A MET* 4.5 2.9 - - + -
467A TYR* 4.0 19.3 - - + -
470A PHE* 3.4 54.5 - - + -
474A ILE* 4.2 7.0 - - + -
925A VAL 3.2 9.4 + - - +
928A GLN* 1.3 76.4 - - - +
930A GLY* 1.3 58.0 + - - +
931A LEU 3.0 4.9 - - - -
932A LEU* 3.1 24.4 + - + +
933A THR* 3.0 29.1 + - - +
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Residues in contact with GLY 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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400A LEU* 4.5 4.2 - - - +
926A TYR 2.8 19.6 + - - -
927A PHE* 3.6 5.6 - - - -
929A VAL* 1.3 75.6 - - - +
931A LEU* 1.3 56.7 + - - +
933A THR* 4.6 3.1 - - - -
934A THR* 3.1 27.6 + - - -
1003A VAL* 4.9 1.3 - - - -
1006A GLY 4.4 4.0 - - - +
1007A VAL* 3.7 32.8 - - - +
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Residues in contact with LEU 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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556A PHE* 5.1 14.6 - - + -
877A TYR* 4.8 8.5 - - + +
909A VAL* 3.7 36.8 - - + +
912A ALA* 3.8 21.3 - - + -
913A LEU* 5.2 0.9 - - + -
923A ASN* 4.4 6.1 - - - +
927A PHE* 2.9 48.8 + - + +
928A GLN* 3.5 17.5 - - + +
929A VAL 3.0 0.4 - - - -
930A GLY* 1.3 76.7 - - - +
932A LEU* 1.3 64.8 + - - +
933A THR 3.3 0.2 - - - -
934A THR* 3.1 4.8 + - + -
935A ILE* 3.0 33.3 + - + +
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Residues in contact with LEU 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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452A VAL* 3.6 27.8 - - + +
453A PHE* 3.5 33.5 - - + -
456A MET* 3.3 41.5 - - + -
471A SER* 5.0 1.1 - - - -
877A TYR* 3.7 30.3 - - + -
928A GLN 3.4 10.3 + - - +
929A VAL* 3.1 24.1 + - + +
931A LEU* 1.3 78.2 - - - +
933A THR* 1.3 56.7 + - - +
935A ILE* 3.2 11.8 + - + +
936A GLY 2.9 22.5 + - - -
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Residues in contact with THR 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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400A LEU* 3.2 49.0 - - + +
404A LEU* 4.1 16.8 - - + -
453A PHE* 3.5 16.5 - - + -
474A ILE* 4.5 2.2 - - + +
929A VAL 3.0 15.6 + - - -
930A GLY 4.3 2.9 - - - -
932A LEU* 1.3 73.0 - - - +
934A THR* 1.3 65.6 + - - +
936A GLY* 4.2 1.1 - - - +
937A LEU* 3.0 43.0 + - + +
982A PHE* 4.4 4.0 - - + -
1007A VAL* 4.9 1.6 - - + -
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Residues in contact with THR 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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905A VAL 5.3 0.2 - - - +
908A GLY* 3.5 37.2 - - - +
909A VAL* 3.7 12.3 - - + +
912A ALA* 4.4 2.7 - - + -
930A GLY 3.1 17.0 + - - -
931A LEU* 3.1 12.7 + - - +
933A THR* 1.3 77.7 - - - +
935A ILE* 1.3 57.8 + - - +
937A LEU* 4.1 7.7 + - - +
938A SER* 3.2 25.3 + - - -
1006A GLY 4.1 2.4 + - - -
1007A VAL* 3.9 14.4 + - - +
1010A GLY* 3.9 18.6 - - - -
1011A MET* 4.5 2.7 + - - +
1014A ALA* 4.9 3.2 - - + +
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Residues in contact with ILE 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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452A VAL* 3.9 30.5 - - + -
877A TYR* 5.2 13.2 - - + -
905A VAL* 3.8 33.2 - - + +
909A VAL* 3.7 28.7 - - + -
931A LEU* 3.0 29.0 + - + +
932A LEU* 3.2 9.6 + - + +
934A THR* 1.3 74.8 - - - +
936A GLY* 1.3 60.8 - - - +
938A SER* 3.3 6.8 - - - -
939A ALA* 3.0 27.7 + - + +
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Residues in contact with GLY 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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404A LEU* 4.6 7.0 - - - -
448A VAL 5.9 0.4 - - - -
449A LEU* 3.5 26.7 - - - +
452A VAL* 4.8 9.2 - - - +
453A PHE* 5.1 2.2 - - - -
932A LEU 2.9 14.1 + - - -
933A THR* 3.2 4.4 + - - -
935A ILE* 1.3 73.7 - - - +
937A LEU* 1.3 64.7 + - - +
939A ALA* 3.1 9.5 + - - +
940A LYS* 3.1 16.8 + - - +
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Residues in contact with LEU 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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404A LEU* 4.3 15.2 - - + +
407A ASP* 3.6 27.4 - - + +
933A THR* 3.0 27.6 + - + +
934A THR* 4.2 3.6 - - - +
936A GLY* 1.3 72.3 - - - +
938A SER* 1.3 63.3 + - - +
940A LYS* 3.1 16.9 + - - +
941A ASN* 3.1 23.4 + - - +
978A THR* 4.5 7.2 - - + -
982A PHE* 3.2 50.3 - - + -
1007A VAL* 4.9 0.7 - - + -
1011A MET* 3.6 30.7 - - + -
1014A ALA* 6.0 0.2 - - + -
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Residues in contact with SER 938 (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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904A VAL* 2.9 53.0 + - - +
905A VAL* 4.7 1.1 - - - -
908A GLY* 4.0 3.3 + - - -
934A THR 3.2 19.6 + - - -
935A ILE* 3.3 11.9 - - - -
936A GLY 3.2 0.4 - - - -
937A LEU* 1.3 78.1 - - - +
939A ALA* 1.3 62.6 + - - +
941A ASN* 3.8 7.4 + - - +
942A ALA 3.3 16.3 + - - -
1014A ALA* 3.9 17.9 - - - +
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Residues in contact with ALA 939 (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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448A VAL* 5.0 14.6 - - + +
449A LEU* 5.1 4.0 - - + -
901A VAL* 3.7 20.5 - - + +
904A VAL* 4.4 1.3 - - - -
935A ILE* 3.0 14.0 + - + +
936A GLY* 3.1 10.3 + - - +
938A SER* 1.3 73.9 - - - +
940A LYS* 1.3 56.5 + - - +
942A ALA 3.2 0.9 + - - -
943A ILE* 2.8 54.7 + - + +
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Residues in contact with LYS 940 (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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404A LEU* 4.3 9.4 + - + +
407A ASP* 3.1 42.8 + - - +
408A ASP* 3.2 28.2 + - - +
411A VAL* 3.5 26.5 - - - -
445A ILE* 3.4 43.8 - - + +
449A LEU* 5.2 6.4 - - + +
936A GLY 3.1 11.2 + - - +
937A LEU* 3.1 11.5 + - - +
939A ALA* 1.3 77.5 - - - +
941A ASN* 1.3 66.9 + - - +
943A ILE* 3.7 1.7 - - - +
944A LEU* 3.0 37.1 + - + +
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Residues in contact with ASN 941 (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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407A ASP* 5.4 2.8 - - - +
937A LEU* 3.1 25.3 + - - +
938A SER* 4.0 7.4 - - - +
940A LYS* 1.3 81.9 - - - +
942A ALA* 1.3 61.2 + - - +
944A LEU* 3.4 5.2 + - - +
945A ILE* 3.2 27.0 + - + +
975A ILE* 3.6 40.1 - - + +
978A THR* 5.6 5.0 - - - +
979A SER* 5.8 0.3 - - - -
1011A MET* 5.1 3.2 - - - +
1014A ALA* 5.0 4.2 - - - +
1015A THR* 3.4 33.6 - - + +
1018A ALA* 5.2 12.3 - - + +
1019A ILE 6.1 0.4 - - - +
1024A VAL* 4.6 0.9 - - + -
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Residues in contact with ALA 942 (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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900A SER* 5.3 3.6 - - - +
901A VAL* 3.4 15.0 - - + +
904A VAL* 3.4 33.9 - - + -
938A SER 3.3 2.3 + - - +
939A ALA 3.2 0.4 + - - -
940A LYS 3.2 1.0 - - - -
941A ASN* 1.3 74.1 - - - +
943A ILE* 1.3 62.2 + - - +
944A LEU 3.1 1.8 - - - -
945A ILE* 2.8 29.6 + - - +
946A VAL* 3.3 8.4 - - - +
1024A VAL* 3.5 24.4 - - + +
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Residues in contact with ILE 943 (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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441A ALA* 4.9 6.5 - - + -
445A ILE* 3.5 26.2 - - + -
448A VAL* 3.8 25.4 - - + -
888A LEU* 4.1 8.3 - - + -
892A TYR* 3.1 37.5 - - + +
897A ILE* 5.7 2.5 - - + -
901A VAL* 3.7 13.9 - - + -
939A ALA* 2.8 36.8 + - + +
940A LYS 3.8 2.7 - - - +
942A ALA* 1.3 72.5 - - - +
944A LEU* 1.3 55.7 + - + +
946A VAL* 4.1 8.1 - - + -
947A GLU* 2.7 37.1 + - + +
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Residues in contact with LEU 944 (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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407A ASP* 5.7 1.1 - - - +
411A VAL* 4.3 31.4 - - + -
441A ALA* 4.5 19.5 - - + -
445A ILE* 5.5 2.2 - - + -
940A LYS* 3.0 41.0 + - + +
941A ASN* 3.5 6.7 - - - +
943A ILE* 1.3 74.8 - - + +
945A ILE* 1.3 53.1 + - - +
946A VAL 3.0 9.3 + - - -
947A GLU* 5.0 1.1 - - + -
948A PHE* 3.2 29.0 + - + +
971A ARG* 2.7 31.3 + - + -
974A PRO* 5.6 7.9 - - + -
975A ILE* 3.7 26.7 - - + -
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Residues in contact with ILE 945 (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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941A ASN* 3.2 16.2 - - + +
942A ALA 2.8 12.4 + - - +
944A LEU* 1.3 73.3 - - - +
946A VAL* 1.3 61.2 + - - +
949A ALA* 4.4 7.6 - - + +
950A LYS* 4.3 1.2 + - - -
967A ALA* 5.5 0.2 - - + -
971A ARG* 3.3 42.4 - - - +
975A ILE* 5.1 1.1 - - + -
1019A ILE* 3.7 29.2 - - + -
1024A VAL* 3.1 39.5 - - + +
1025A PHE* 3.3 26.5 - - + -
1028A VAL* 4.0 10.9 - - - +
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Residues in contact with VAL 946 (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 TYR* 4.6 3.4 - - + -
897A ILE* 3.4 46.0 - - + -
900A SER* 3.2 28.9 - - - +
901A VAL* 5.6 1.1 - - + +
942A ALA 3.3 11.9 - - - +
943A ILE* 3.5 9.4 - - - +
944A LEU 3.0 1.8 + - - -
945A ILE* 1.3 89.3 - - - +
947A GLU* 1.3 69.4 + - - +
948A PHE 3.1 0.9 - - - +
949A ALA 2.9 2.7 + - - +
950A LYS* 2.8 38.5 + - + +
1027A VAL* 5.4 0.9 - - + -
1028A VAL* 4.3 7.9 - - + -
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Residues in contact with GLU 947 (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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437A GLN 3.8 11.2 - - - +
440A GLY* 3.1 30.8 - - - +
441A ALA* 3.6 28.9 - - + +
891A LEU* 4.4 6.8 - - - +
892A TYR* 3.2 27.7 - - + -
943A ILE* 2.7 20.5 + - + +
944A LEU* 5.0 1.3 - - - -
946A VAL* 1.3 76.1 - - - +
948A PHE* 1.3 60.7 + - + +
950A LYS* 4.2 5.7 - - - +
951A ASP* 2.9 40.9 + - - +
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Residues in contact with PHE 948 (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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411A VAL* 5.7 7.2 - - + -
415A ASN* 3.1 31.0 - - - -
418A ARG* 4.9 6.7 - - - -
437A GLN* 3.5 39.6 - - + +
438A ILE* 4.8 2.9 - - + -
944A LEU* 3.2 24.6 + - + +
946A VAL 3.1 0.6 - - - -
947A GLU* 1.3 79.7 - - + +
949A ALA* 1.3 58.3 + - - +
950A LYS 3.1 2.0 + - - -
951A ASP* 3.1 6.6 + - - +
952A LEU* 3.0 34.6 + - + +
967A ALA* 4.4 6.7 - - + -
970A MET* 4.4 16.4 - - + -
971A ARG* 3.5 45.3 - - + +
974A PRO* 5.7 2.5 - - + -
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Residues in contact with ALA 949 (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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945A ILE* 4.4 10.5 - - + +
946A VAL* 2.9 3.7 + - - +
948A PHE* 1.3 77.4 - - - +
950A LYS* 1.3 78.1 + - - +
952A LEU* 3.6 14.9 - - - +
953A MET* 2.9 25.5 + - - +
963A ALA* 3.9 12.2 - - - +
964A THR* 4.4 12.1 - - + -
967A ALA* 3.9 17.5 - - + -
971A ARG* 5.6 0.2 - - - +
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Residues in contact with LYS 950 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A ILE* 4.2 23.6 - - + -
946A VAL* 2.8 45.0 + - - +
947A GLU* 4.3 6.5 - - - +
949A ALA* 1.3 93.7 + - - +
951A ASP* 1.3 62.7 + - - +
952A LEU 3.1 0.9 - - - -
953A MET* 3.5 11.2 - - - +
954A ASP* 3.1 38.8 + - - +
964A THR* 5.0 0.4 - - - +
1028A VAL* 2.9 42.7 - - + +
1032A ARG* 3.4 31.4 - - + +
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Residues in contact with ASP 951 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436A GLY 4.6 2.0 - - - +
437A GLN* 3.5 41.9 + - - +
947A GLU* 2.9 28.7 + - - +
948A PHE 3.1 8.5 + - - +
950A LYS* 1.3 78.0 - - - +
952A LEU* 1.3 58.7 + - - +
955A LYS* 3.1 57.9 + - - +
956A GLU* 3.5 8.7 + - - +
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Residues in contact with LEU 952 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A GLN* 4.8 11.9 - - - +
948A PHE* 3.0 22.4 + - + +
949A ALA* 3.6 8.3 - - - +
950A LYS 3.1 0.4 - - - -
951A ASP* 1.3 79.2 - - - +
953A MET* 1.3 51.2 + - - +
954A ASP 3.5 0.7 - - - -
956A GLU* 3.2 37.0 - - + +
957A GLY 2.8 26.2 - - - +
963A ALA* 3.8 16.7 - - + +
966A ASP* 4.0 17.7 - - - +
967A ALA* 3.6 38.1 - - + +
970A MET* 5.1 16.6 - - + -
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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