Contacts of the helix formed by residues 902 - 926 (chain C) 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 PRO 902 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900A GLN 4.0 15.3 - - - +
901A LEU* 4.3 1.6 - - + -
902A PRO* 3.8 17.9 - - + -
900C GLN 4.4 0.2 - - - +
901C LEU* 1.3 101.7 - - + +
903C PRO* 1.3 67.9 - - + +
904C GLU* 3.6 16.6 - - - +
905C GLY* 2.8 28.2 + - - +
906C TYR* 3.3 12.3 + - - -
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Residues in contact with PRO 903 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901C LEU 4.7 0.2 - - - +
902C PRO* 1.3 83.6 - - + +
904C GLU* 1.3 74.1 + - - +
906C TYR* 3.1 35.4 + - + +
961C GLN* 2.9 31.0 + - + +
964C ALA* 3.5 32.1 - - + -
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Residues in contact with GLU 904 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897A GLU* 6.5 0.4 - - + -
900A GLN* 4.1 44.5 - - + +
901A LEU* 5.0 2.2 - - + -
902C PRO* 3.6 21.7 - - - +
903C PRO* 1.3 80.2 - - - +
905C GLY* 1.3 62.0 + - - +
906C TYR 3.1 1.4 + - - -
907C VAL* 3.3 21.2 + - - +
908C VAL* 4.2 4.3 + - - +
961C GLN* 4.5 3.8 - - - +
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Residues in contact with GLY 905 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901A LEU* 3.8 24.3 - - - +
901C LEU* 3.7 13.8 - - - +
902C PRO 2.8 11.6 + - - -
904C GLU* 1.3 78.1 - - - +
906C TYR* 1.3 63.5 + - - +
907C VAL 3.0 1.0 + - - -
908C VAL* 3.2 18.8 + - - +
909C VAL* 3.3 15.6 + - - +
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Residues in contact with TYR 906 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898C LEU* 3.6 36.6 + - + +
901C LEU* 3.8 26.7 + - + -
902C PRO 3.3 4.4 + - - -
903C PRO* 3.1 44.6 + - + +
905C GLY* 1.3 77.7 - - - +
907C VAL* 1.3 62.4 + - - +
909C VAL* 3.6 7.3 + - - +
910C VAL* 3.2 28.4 + - - +
957C MET* 3.9 18.6 - - + -
960C ALA* 4.1 25.1 - - + -
961C GLN* 4.2 15.0 - - + +
964C ALA* 5.2 2.1 - - + +
969C SER* 5.0 3.6 + - - -
973C LYS* 3.7 22.4 - - + +
976C MET* 4.8 5.1 - - - +
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Residues in contact with VAL 907 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904C GLU* 3.4 11.9 - - - +
905C GLY 3.0 0.2 - - - -
906C TYR* 1.3 74.7 - - - +
908C VAL* 1.3 58.4 + - + +
910C VAL* 3.1 3.6 + - - +
911C LYS* 2.6 42.9 + - + +
957C MET* 4.0 22.2 - - + +
958C ARG* 4.5 8.7 - - - +
961C GLN* 3.4 29.2 - - - +
273G SER 6.0 2.2 - - - +
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Residues in contact with VAL 908 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
893A GLU* 5.8 2.5 - - - +
897A GLU* 3.6 32.1 - - - +
901A LEU* 4.9 4.7 - - + -
908A VAL* 3.6 27.4 - - + -
909A VAL* 3.9 16.4 - - + +
912A ASN* 3.3 18.1 - - - +
901C LEU* 6.3 0.2 - - + -
904C GLU 4.9 6.3 - - - +
905C GLY* 3.2 13.4 + - - +
907C VAL* 1.3 81.6 - - + +
909C VAL* 1.3 63.3 + - - +
911C LYS* 3.0 12.4 + - + +
912C ASN* 2.9 25.6 + - - -
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Residues in contact with VAL 909 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 4.9 6.1 - - + -
890C ALA 5.3 0.4 - - - +
894C LEU* 3.4 46.4 - - + -
897C GLU* 3.8 18.8 - - + +
898C LEU* 5.5 3.8 - - + -
901C LEU* 3.2 35.4 - - + -
905C GLY 3.4 5.2 - - - +
906C TYR* 3.7 8.1 - - - +
907C VAL 3.2 0.2 - - - -
908C VAL* 1.3 76.3 - - - +
910C VAL* 1.3 63.0 + - - +
912C ASN* 2.9 25.4 + - + +
913C VAL* 3.0 12.6 + - + +
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Residues in contact with VAL 910 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894C LEU* 4.2 8.5 - - + -
906C TYR 3.2 14.8 + - - +
907C VAL 3.1 7.4 + - - +
909C VAL* 1.3 79.0 - - - +
911C LYS* 1.3 65.6 + - - +
913C VAL* 3.1 9.7 + - - +
914C GLY* 2.9 19.2 + - - -
950C LEU* 4.6 3.8 - - + +
953C LEU* 4.0 22.9 - - + -
954C ILE* 4.3 17.3 - - + -
957C MET* 3.6 24.7 - - + -
976C MET* 3.6 29.4 - - + -
271G MET* 4.7 0.7 - - - +
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Residues in contact with LYS 911 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890A ALA* 5.1 5.7 - - - +
893A GLU* 2.6 42.7 + - - +
912A ASN* 4.0 18.6 + - - +
916A THR* 5.9 3.9 - - - +
907C VAL* 2.6 21.2 + - + +
908C VAL* 3.0 18.2 - - + +
910C VAL* 1.3 77.9 - - - +
912C ASN* 1.3 54.6 + - - +
914C GLY 3.1 1.7 + - - -
915C LEU* 2.9 37.2 + - + +
271G MET* 3.2 29.4 - - + +
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Residues in contact with ASN 912 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908A VAL* 3.5 23.7 + - - +
911A LYS* 3.6 27.6 - - - +
912A ASN* 3.2 24.2 + - - +
915A LEU* 3.9 8.9 - - + +
890C ALA* 5.1 4.3 - - + -
908C VAL* 2.9 31.9 + - - +
909C VAL* 2.9 10.9 + - + +
911C LYS* 1.3 73.6 - - - +
913C VAL* 1.3 64.6 + - + +
915C LEU* 3.3 3.6 + - - +
916C THR* 2.9 34.4 + - + +
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Residues in contact with VAL 913 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887C LEU* 4.6 5.4 - - + +
890C ALA* 3.8 28.9 - - + +
891C VAL* 4.4 13.0 - - + +
894C LEU* 3.9 21.8 - - + -
909C VAL* 3.0 13.4 + - + +
910C VAL* 3.1 8.9 + - - +
912C ASN* 1.3 76.7 - - + +
914C GLY* 1.3 62.3 + - - +
916C THR* 3.4 7.6 + - - -
917C LEU* 3.1 22.0 + - - +
950C LEU* 5.0 1.8 - - + -
953C LEU* 4.0 10.5 - - + -
980C SER* 6.2 0.2 - - - -
983C LEU* 3.6 31.2 - - + -
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Residues in contact with GLY 914 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910C VAL 2.9 12.5 + - - -
911C LYS 3.4 4.0 - - - -
913C VAL* 1.3 75.5 - - - +
915C LEU* 1.3 65.9 + - - +
917C LEU* 2.9 5.2 + - - +
918C ARG* 2.9 22.7 + - - +
950C LEU* 4.2 18.6 - - - +
267G LEU* 4.7 1.9 - - - +
271G MET* 3.6 24.2 - - - +
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Residues in contact with LEU 915 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886A GLU* 4.8 3.1 - - - +
912A ASN* 3.2 37.2 - - + +
915A LEU* 4.2 19.6 - - + +
916A THR* 3.6 38.1 - - + +
919A LYS* 4.4 18.2 - - + -
911C LYS* 2.9 25.2 + - + +
912C ASN* 3.3 4.2 + - - +
914C GLY* 1.3 72.8 - - - +
916C THR* 1.3 58.1 + - - +
918C ARG* 3.2 13.6 + - - +
919C LYS* 3.0 24.1 + - - +
271G MET* 3.7 12.7 - - + +
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Residues in contact with THR 916 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A LEU* 3.6 25.1 - - + -
883C ASN* 4.6 4.5 - - - +
886C GLU* 5.1 13.1 - - + +
887C LEU* 3.8 28.0 - - - +
890C ALA* 3.9 15.0 - - + +
912C ASN* 2.9 18.6 + - + +
913C VAL 3.4 8.1 + - - -
915C LEU* 1.3 72.8 - - - +
917C LEU* 1.3 66.6 + - - +
919C LYS* 3.5 12.3 + - - +
920C LEU* 3.2 20.4 + - - +
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Residues in contact with LEU 917 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887C LEU* 3.4 24.9 - - + -
913C VAL* 3.1 15.3 + - + +
914C GLY 2.9 9.5 + - - +
916C THR* 1.3 74.4 + - - +
918C ARG* 1.3 62.2 + - - +
920C LEU* 3.0 7.7 + - + +
921C ILE* 2.8 40.2 + - + +
946C LEU* 3.9 48.2 - - + +
947C ASN* 4.1 10.3 - - - +
950C LEU* 3.8 30.1 - - + -
983C LEU* 4.5 6.5 - - + -
267G LEU* 4.1 3.1 - - + -
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Residues in contact with ARG 918 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879A LEU* 6.0 4.9 - - - +
883A ASN* 5.6 2.2 - - - +
886A GLU* 5.7 0.9 - - - -
919A LYS* 3.1 43.8 - - - +
914C GLY 2.9 10.7 + - - +
915C LEU* 3.4 15.3 - - - +
917C LEU* 1.3 77.3 - - - +
919C LYS* 1.3 63.6 + - - +
921C ILE* 3.2 1.3 + - - +
922C GLY* 2.8 24.5 + - - +
264G THR* 4.7 17.6 - - + +
267G LEU* 3.4 25.6 - - + -
268G ASP* 2.7 47.3 + - - +
271G MET* 6.2 1.6 - - + -
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Residues in contact with LYS 919 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915A LEU* 4.0 22.8 - - - +
918A ARG* 3.7 50.7 - - - +
883C ASN* 3.0 29.4 - - + +
886C GLU* 2.8 31.4 + - - +
915C LEU 3.0 12.6 + - - +
916C THR* 3.6 12.1 - - - +
917C LEU 3.3 0.2 - - - -
918C ARG* 1.3 76.1 - - - +
920C LEU* 1.3 61.6 + - - +
922C GLY* 3.6 1.1 + - - -
923C SER* 3.2 22.2 + - - -
268E ASP* 4.4 3.0 + - - -
271E MET* 6.2 1.6 - - - +
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Residues in contact with LEU 920 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C VAL* 3.8 11.2 - - + +
883C ASN* 3.6 26.9 - - + +
884C VAL* 3.6 37.7 - - + -
887C LEU* 3.9 23.3 - - + -
916C THR 3.2 10.3 + - - +
917C LEU* 3.0 15.8 + - + +
919C LYS* 1.3 76.4 - - - +
921C ILE* 1.3 68.8 + - - +
922C GLY 3.1 0.2 + - - -
923C SER* 3.0 19.8 + - - +
924C VAL* 3.2 6.6 + - + +
946C LEU* 4.5 6.5 - - + -
987C ALA* 4.7 5.4 - - + -
990C LEU* 4.1 23.1 - - + -
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Residues in contact with ILE 921 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917C LEU* 2.8 32.0 + - + +
918C ARG* 3.7 4.7 - - + +
920C LEU* 1.3 72.5 - - + +
922C GLY* 1.3 68.6 + - - +
924C VAL* 3.1 6.6 + - - +
925C ASP* 3.0 21.4 + - - +
943C GLN* 3.7 33.6 + - + +
946C LEU* 5.1 3.8 - - + -
947C ASN* 3.4 30.7 - - - +
990C LEU* 6.1 2.2 - - + -
263G ALA* 4.3 8.1 - - + -
264G THR* 3.9 31.6 - - + +
267G LEU* 3.7 19.3 - - + -
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Residues in contact with GLY 922 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918C ARG* 2.8 20.2 + - - -
919C LYS* 3.9 1.6 - - - -
921C ILE* 1.3 78.3 - - - +
923C SER* 1.3 63.4 + - - +
924C VAL 2.9 1.9 + - - -
925C ASP* 3.0 14.3 + - - +
926C ASP* 3.3 16.9 + - - +
264G THR* 5.2 6.5 - - - -
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Residues in contact with SER 923 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879C LEU* 4.7 17.3 - - - -
880C VAL* 3.9 15.7 - - - +
883C ASN* 2.9 27.9 + - - -
919C LYS 3.2 6.2 + - - -
920C LEU* 3.0 16.9 + - - -
922C GLY* 1.3 73.9 - - - +
924C VAL* 1.3 56.9 + - - +
926C ASP* 3.1 27.0 - - - +
927C LEU* 3.3 16.2 - - - +
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Residues in contact with VAL 924 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880C VAL* 3.5 33.7 - - + -
920C LEU* 3.2 8.7 + - + +
921C ILE* 3.1 8.5 + - - +
922C GLY 2.9 1.0 + - - -
923C SER* 1.3 74.5 + - - +
925C ASP* 1.3 59.3 + - - +
926C ASP 2.8 10.8 + - - -
927C LEU* 2.8 15.1 + - - +
928C LEU* 3.2 17.1 + - + +
939C ILE* 4.2 18.2 - - + -
943C GLN* 3.1 28.5 - - + +
990C LEU* 4.1 18.4 - - + -
994C VAL* 4.7 8.3 - - + -
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Residues in contact with ASP 925 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921C ILE* 3.0 12.7 + - - +
922C GLY* 3.5 9.9 - - - +
924C VAL* 1.3 73.0 - - - +
926C ASP* 1.3 62.8 + - - +
927C LEU 3.4 0.6 + - - -
928C LEU* 4.0 16.5 - - - +
929C PRO* 3.8 14.4 - - - +
943C GLN* 2.7 35.5 + - - +
262G SER 3.9 17.2 + - - -
263G ALA* 4.4 4.4 + - - +
264G THR* 3.9 21.2 - - + +
----------------------------------------------------------
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Residues in contact with ASP 926 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922C GLY* 3.4 12.8 - - - +
923C SER* 3.1 19.2 + - - +
924C VAL 2.8 2.0 + - - -
925C ASP* 1.3 82.6 - - - +
927C LEU* 1.3 64.8 + - + +
929C PRO* 3.9 12.2 - - - +
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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