Contacts of the helix formed by residues 902 - 928 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B GLN 4.2 10.1 - - - +
901B LEU* 4.3 4.5 - - + -
902B PRO* 3.9 22.9 - - + -
901D LEU* 1.3 100.5 - - + +
903D PRO* 1.3 79.9 - - + +
904D GLU* 3.4 17.7 - - - +
905D GLY* 2.8 17.8 + - - +
906D TYR* 3.4 12.4 + - - -
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Residues in contact with PRO 903 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901D LEU 4.7 0.2 - - - +
902D PRO* 1.3 87.2 - - + -
904D GLU* 1.3 77.3 + - - +
906D TYR* 2.9 45.2 + - + +
961D GLN* 3.3 23.4 + - + +
964D ALA* 3.6 30.7 - - + -
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Residues in contact with GLU 904 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
900B GLN* 3.4 53.8 + - + +
901B LEU* 5.2 1.1 - - + -
902D PRO* 3.4 25.8 - - + +
903D PRO* 1.3 85.2 - - - +
905D GLY* 1.3 60.4 + - - +
907D VAL* 3.4 21.5 - - - +
908D VAL* 4.5 0.9 + - - +
961D GLN* 4.5 4.5 - - - +
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Residues in contact with GLY 905 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901B LEU* 3.9 24.3 - - - +
901D LEU* 4.0 9.7 - - - +
902D PRO 2.8 10.5 + - - -
904D GLU* 1.3 76.3 - - - +
906D TYR* 1.3 64.4 + - - +
907D VAL 3.0 3.6 + - - -
908D VAL* 3.2 18.9 + - - +
909D VAL* 3.3 18.4 + - - +
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Residues in contact with TYR 906 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
898D LEU* 3.3 40.9 + - + +
901D LEU* 3.9 19.8 + - + -
902D PRO 3.4 7.7 + - - -
903D PRO* 2.9 48.6 + - + +
905D GLY* 1.3 75.5 - - - +
907D VAL* 1.3 61.8 + - - +
909D VAL* 3.7 6.3 + - - +
910D VAL* 3.2 28.4 + - - +
957D MET* 4.0 17.9 - - + -
960D ALA* 4.2 21.5 - - + -
961D GLN* 4.3 14.1 - - + -
964D ALA* 5.3 1.9 - - + +
969D SER* 6.1 0.3 - - - -
973D LYS* 3.6 28.3 + - + +
976D MET* 4.9 4.4 - - - +
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Residues in contact with VAL 907 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
904D GLU 3.4 16.6 - - - +
905D GLY 3.0 0.6 - - - -
906D TYR* 1.3 75.1 - - - +
908D VAL* 1.3 56.1 - - - +
910D VAL* 3.0 4.2 + - - +
911D LYS* 2.6 42.7 + - + +
957D MET* 4.2 17.7 - - + -
958D ARG* 5.1 4.5 - - - +
961D GLN* 3.5 29.6 - - - +
274H LEU* 4.0 29.6 - - + +
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Residues in contact with VAL 908 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
897B GLU* 5.1 9.0 - - - +
901B LEU* 5.6 3.1 - - + -
908B VAL* 3.7 17.0 - - + -
909B VAL* 4.7 15.3 - - + -
912B ASN* 4.2 10.5 - - - +
904D GLU 4.5 0.6 + - - -
905D GLY* 3.2 13.6 + - - +
907D VAL* 1.3 76.9 - - - +
909D VAL* 1.3 57.5 + - - +
911D LYS* 3.1 12.2 - - - +
912D ASN* 2.4 34.1 + - - -
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Residues in contact with VAL 909 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B VAL* 4.1 6.3 - - + -
890D ALA 5.2 1.3 - - - +
893D GLU* 5.8 0.2 - - + -
894D LEU* 3.5 37.7 - - + +
897D GLU* 3.0 26.0 - - + +
898D LEU* 5.1 3.8 - - + -
901D LEU* 3.3 26.7 - - + -
905D GLY 3.3 16.6 - - - +
906D TYR* 3.8 7.9 - - - +
907D VAL 3.1 0.6 - - - -
908D VAL* 1.3 75.5 - - - +
910D VAL* 1.3 56.8 + - - +
912D ASN* 2.7 37.2 + - + +
913D VAL* 3.1 7.6 + - + +
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Residues in contact with VAL 910 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
894D LEU* 4.1 8.7 - - + -
906D TYR 3.2 15.5 - - - +
907D VAL 3.0 6.5 + - - +
909D VAL* 1.3 74.7 - - - +
911D LYS* 1.3 64.0 + - - +
913D VAL* 3.1 10.8 + - - +
914D GLY* 2.9 20.3 + - - -
950D LEU* 4.6 4.3 - - + +
953D LEU* 4.1 22.7 - - + -
954D ILE* 4.3 14.8 - - + -
957D MET* 3.9 26.7 - - + -
976D MET* 3.6 29.2 - - + -
274H LEU* 4.6 5.4 - - + +
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Residues in contact with LYS 911 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
890B ALA* 5.0 5.9 - - - +
893B GLU* 2.5 43.5 + - - +
912B ASN* 4.0 19.1 - - - +
916B THR* 5.9 3.2 - - - +
907D VAL* 2.6 22.7 + - + +
908D VAL* 3.1 17.9 - - - +
910D VAL* 1.3 72.9 - - - +
912D ASN* 1.3 48.2 + - - +
914D GLY 3.1 0.3 + - - -
915D LEU* 2.8 44.6 + - + +
271H MET* 3.1 15.6 - - + +
274H LEU* 4.1 32.6 - - + +
275H SER* 6.3 2.1 - - - +
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Residues in contact with ASN 912 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
908B VAL* 3.2 24.0 - - - +
911B LYS* 3.3 33.0 - - - +
912B ASN* 2.5 27.9 + - - +
915B LEU* 4.4 6.6 - - + +
890D ALA* 5.2 5.4 - - + +
897D GLU* 6.0 0.2 - - - -
908D VAL 2.4 32.3 + - - -
909D VAL* 2.7 17.2 + - + +
911D LYS* 1.3 68.9 - - - +
913D VAL* 1.3 59.3 + - + +
915D LEU* 3.3 5.9 + - - +
916D THR* 3.0 34.9 + - + +
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Residues in contact with VAL 913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D LEU* 4.3 15.3 - - + +
890D ALA* 3.9 24.5 - - + +
891D VAL* 4.3 9.2 - - + +
894D LEU* 4.2 16.4 - - + -
909D VAL* 3.1 13.1 + - + +
910D VAL* 3.5 12.3 - - - +
912D ASN* 1.3 73.8 - - + +
914D GLY* 1.3 66.1 + - - +
916D THR* 3.2 7.0 + - - -
917D LEU* 3.0 23.2 + - - +
950D LEU* 5.0 0.9 - - + -
953D LEU* 4.1 12.1 - - + -
980D SER* 6.2 0.4 - - - -
983D LEU* 3.9 28.5 - - + -
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Residues in contact with GLY 914 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
910D VAL 2.9 11.9 + - - -
911D LYS 3.5 4.0 - - - -
913D VAL* 1.3 77.3 - - - +
915D LEU* 1.3 63.1 + - - +
917D LEU* 2.9 4.6 + - - +
918D ARG* 2.9 23.4 + - - +
950D LEU* 4.2 19.2 - - - +
267H LEU* 4.8 1.9 - - - +
271H MET* 3.5 23.7 - - - +
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Residues in contact with LEU 915 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
886B GLU* 4.9 3.4 - - - +
912B ASN* 3.5 30.3 - - - +
915B LEU* 4.1 25.0 - - + +
916B THR* 3.7 38.1 - - + +
919B LYS* 4.6 17.4 - - + +
911D LYS* 2.8 29.9 + - + +
912D ASN 3.7 4.0 - - - +
914D GLY* 1.3 71.6 - - - +
916D THR* 1.3 61.2 + - - +
918D ARG* 3.4 12.2 + - - +
919D LYS* 3.2 19.6 + - - +
271H MET* 3.3 13.8 - - + +
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Residues in contact with THR 916 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B LEU* 3.7 26.5 - - + -
883D ASN* 4.7 3.3 - - - +
886D GLU* 4.5 17.4 - - + +
887D LEU* 4.0 17.2 - - - +
890D ALA* 3.8 23.4 - - + +
912D ASN* 3.0 17.4 + - + +
913D VAL* 3.2 9.2 + - - -
915D LEU* 1.3 73.0 - - - +
917D LEU* 1.3 66.8 + - - +
919D LYS* 3.5 10.6 + - - +
920D LEU* 3.2 20.6 + - - +
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Residues in contact with LEU 917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
887D LEU* 3.5 26.9 - - + -
913D VAL* 3.0 16.1 + - + +
914D GLY* 2.9 10.6 + - - +
916D THR* 1.3 73.5 + - - +
918D ARG* 1.3 68.9 + - - +
920D LEU* 2.9 7.6 + - + +
921D ILE* 2.8 35.3 + - + +
946D LEU* 4.0 38.6 - - + +
947D ASN* 3.9 10.5 - - - +
950D LEU* 4.0 14.4 - - + -
983D LEU* 4.7 8.1 - - + -
267H LEU* 3.8 21.5 - - + -
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Residues in contact with ARG 918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879B LEU* 6.1 3.0 - - - +
883B ASN* 5.7 0.2 - - - +
919B LYS* 3.3 49.0 - - - +
914D GLY 2.9 9.4 + - - +
915D LEU* 3.4 17.0 - - + +
917D LEU* 1.3 76.3 - - - +
919D LYS* 1.3 54.8 + - - +
921D ILE* 3.1 5.4 + - + +
922D GLY* 2.8 34.0 + - - -
264H THR* 5.5 10.3 - - + +
267H LEU* 3.4 25.1 - - + +
268H ASP* 3.1 35.8 + - - -
271H MET* 5.8 4.5 - - + -
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Residues in contact with LYS 919 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
915B LEU* 3.2 33.0 + - - +
918B ARG* 3.4 43.9 - - - +
883D ASN* 3.3 28.8 - - + +
886D GLU* 2.7 28.3 - - - +
915D LEU 3.2 9.0 + - - +
916D THR* 3.7 11.9 - - - +
917D LEU 3.2 0.2 - - - -
918D ARG* 1.3 81.5 - - - +
920D LEU* 1.3 62.2 + - - +
922D GLY* 3.5 1.3 + - - -
923D SER* 3.2 21.1 + - - -
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Residues in contact with LEU 920 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D VAL* 3.7 11.4 - - + +
883D ASN* 3.5 32.5 - - + +
884D VAL* 3.6 35.7 - - + +
887D LEU* 3.7 24.2 - - + -
916D THR 3.2 9.6 + - - +
917D LEU* 2.9 15.1 + - + +
919D LYS* 1.3 77.2 - - - +
921D ILE* 1.3 67.2 + - - +
923D SER* 2.7 20.0 + - - +
924D VAL* 3.3 5.9 + - - +
946D LEU* 4.4 6.5 - - + -
987D ALA* 4.8 3.6 - - + -
990D LEU* 4.2 23.3 - - + -
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Residues in contact with ILE 921 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
917D LEU* 2.8 35.1 + - + +
918D ARG* 3.5 8.7 - - + +
920D LEU* 1.3 73.4 - - + +
922D GLY* 1.3 66.4 + - - +
924D VAL* 3.0 17.8 + - - +
925D ASP* 3.1 16.2 + - - +
943D GLN* 4.0 29.3 + - + +
946D LEU* 5.3 4.7 - - + -
947D ASN* 3.4 32.5 - - - +
263H ALA* 4.6 9.2 - - + -
264H THR* 4.1 25.1 - - + +
267H LEU* 4.2 15.0 - - + -
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Residues in contact with GLY 922 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
918D ARG* 2.8 21.1 + - - -
919D LYS* 3.8 1.8 - - - -
920D LEU 3.2 0.2 - - - -
921D ILE* 1.3 74.3 - - - +
923D SER* 1.3 65.0 + - - +
924D VAL 3.0 1.4 + - - -
925D ASP* 3.1 17.5 + - - +
926D ASP* 3.4 15.1 + - - +
264H THR* 5.6 4.3 - - - -
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Residues in contact with SER 923 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
879D LEU* 4.3 22.7 - - - -
880D VAL* 4.0 12.1 - - - +
883D ASN* 2.8 29.2 + - - +
919D LYS 3.2 7.1 + - - -
920D LEU* 2.7 19.6 + - - -
922D GLY* 1.3 74.8 - - - +
924D VAL* 1.3 61.5 + - - +
926D ASP* 3.2 22.6 - - - +
927D LEU* 3.3 14.6 - - - +
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Residues in contact with VAL 924 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
880D VAL* 4.0 26.0 - - + -
920D LEU 3.8 9.6 - - - +
921D ILE* 3.0 9.5 + - - +
922D GLY 3.0 0.4 - - - -
923D SER* 1.3 77.6 + - - +
925D ASP* 1.3 56.8 + - - +
926D ASP 2.7 15.6 + - - -
927D LEU* 2.8 16.5 + - - +
928D LEU* 3.0 23.8 + - + -
939D ILE* 4.4 11.4 - - + -
943D GLN* 3.4 25.8 - - + +
990D LEU* 4.0 25.4 - - + -
994D VAL* 4.7 10.1 - - + -
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Residues in contact with ASP 925 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921D ILE* 3.1 10.1 + - - +
922D GLY* 3.1 10.3 + - - +
924D VAL* 1.3 74.7 - - - +
926D ASP* 1.3 62.2 + - - +
928D LEU* 3.9 17.4 - - - +
929D PRO* 3.6 14.6 - - - +
943D GLN* 2.7 30.2 + - - -
262H SER 5.3 4.0 + - - -
263H ALA* 4.6 8.5 + - - +
264H THR* 4.0 21.8 + - + +
----------------------------------------------------------
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Residues in contact with ASP 926 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
922D GLY 3.7 11.8 - - - +
923D SER* 3.2 15.4 + - - +
924D VAL 2.7 2.4 + - - -
925D ASP* 1.3 80.9 - - - +
927D LEU* 1.3 65.9 + - + +
929D PRO* 3.3 15.1 - - - +
930D SER* 5.2 0.3 + - - -
----------------------------------------------------------
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Residues in contact with LEU 927 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
878D ASP* 5.9 0.9 - - - +
879D LEU* 5.8 6.7 - - + -
880D VAL* 4.0 23.1 - - + -
923D SER* 3.3 19.5 - - - +
924D VAL* 2.8 10.8 + - - +
926D ASP* 1.3 76.3 - - + +
928D LEU* 1.3 68.5 + - - +
929D PRO 3.2 1.3 - - - -
930D SER* 2.8 34.4 + - - +
931D LEU* 4.3 7.7 - - + +
994D VAL* 4.9 12.1 - - + -
998D LYS* 6.0 4.3 - - + -
----------------------------------------------------------
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Residues in contact with LEU 928 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924D VAL* 3.0 23.4 + - + +
925D ASP* 3.9 27.6 - - - +
927D LEU* 1.3 75.9 - - - +
929D PRO* 1.3 72.0 - - + +
931D LEU* 2.9 49.5 - - + +
936D ARG* 4.5 12.1 - - + +
939D ILE* 4.0 22.0 - - + -
940D GLU* 4.4 17.7 - - + +
943D GLN* 4.1 10.5 - - - +
----------------------------------------------------------
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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