Contacts of the helix formed by residues 845 - 873 (chain A) in PDB entry 3U44
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 845 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A TYR* 5.3 1.5 - - + +
331A HIS* 5.3 4.5 - - - +
334A SER* 5.4 4.4 + - - -
335A LEU* 3.3 32.3 - - + +
338A MET* 5.3 2.9 - - - +
832A THR* 2.9 29.8 + - - +
833A LYS 3.6 0.7 - - - -
834A TYR* 3.2 22.9 + - - +
843A TYR* 3.4 3.0 + - - -
844A PRO* 1.3 75.2 - - - +
846A LEU* 1.3 71.1 + - + +
847A PRO* 3.2 19.5 - - + -
848A LEU* 3.0 14.7 + - - +
849A ILE* 3.0 13.8 + - - +
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Residues in contact with LEU 846 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ILE* 5.2 11.9 - - + -
218A PHE* 4.0 22.4 - - + -
219A TYR* 5.8 3.1 - - + -
222A VAL* 4.8 4.4 - - + +
274A PHE* 4.2 18.4 - - + -
323A TYR* 3.8 33.0 - - + -
328A PRO* 5.9 0.2 - - + -
331A HIS* 3.9 55.3 + - + +
332A LEU* 6.3 1.1 - - + -
335A LEU* 5.5 1.6 - - + -
844A PRO 4.1 0.4 + - - -
845A THR* 1.3 76.6 - - + +
847A PRO* 1.3 70.1 - - + +
849A ILE* 3.1 13.2 + - + +
850A ALA* 2.9 21.7 + - - +
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Residues in contact with PRO 847 (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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204A LEU* 4.1 21.3 - - + -
205A TYR* 5.3 1.3 - - - +
218A PHE* 3.4 42.1 - - + -
335A LEU* 3.6 21.5 - - + -
828A LEU* 6.5 0.2 - - + -
831A GLY* 5.1 7.2 - - - -
845A THR* 3.2 15.7 - - + -
846A LEU* 1.3 96.9 - - + +
848A LEU* 1.3 51.8 + - - +
850A ALA* 3.1 1.9 + - - +
851A MET* 2.7 43.6 + - + +
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Residues in contact with LEU 848 (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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820A LYS 4.7 2.0 - - - +
821A SER 3.8 9.0 - - - +
822A TYR* 5.2 1.1 - - - -
823A LEU* 4.3 7.9 - - + -
831A GLY* 4.6 4.5 - - - +
832A THR* 3.3 44.7 + - - +
833A LYS* 3.3 27.1 - - + +
844A PRO* 4.1 7.9 - - + -
845A THR* 3.0 16.9 + - - +
847A PRO* 1.3 78.6 - - - +
849A ILE* 1.3 65.1 + - + +
851A MET* 3.1 9.0 + - - +
852A LYS* 3.0 54.5 + - + +
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Residues in contact with ILE 849 (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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322A ASP* 3.0 44.6 - - - +
323A TYR* 3.6 20.2 - - + -
331A HIS* 5.9 0.7 - - + -
844A PRO* 4.0 30.1 - - + +
845A THR 3.0 11.9 + - - +
846A LEU* 3.5 16.8 - - + +
848A LEU* 1.3 77.6 - - + +
850A ALA* 1.3 62.3 + - - +
852A LYS* 3.2 8.7 + - + +
853A LYS* 3.1 52.8 + - - +
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Residues in contact with ALA 850 (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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218A PHE* 3.5 36.3 - - + +
221A TYR* 3.7 10.8 - - + +
222A VAL* 3.7 18.1 - - + +
323A TYR* 5.4 0.4 - - - -
828A LEU* 6.2 0.7 - - + -
846A LEU 2.9 13.0 + - - +
847A PRO* 3.1 8.5 + - + +
849A ILE* 1.3 78.4 - - - +
851A MET* 1.3 60.2 + - - +
852A LYS 3.3 0.2 + - - -
853A LYS* 3.4 6.7 + - - +
854A LYS* 3.1 23.6 + - - +
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Residues in contact with MET 851 (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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204A LEU* 5.8 0.2 - - - -
218A PHE* 5.9 0.4 - - + -
823A LEU* 3.1 44.4 - - + +
824A LEU 3.7 1.3 - - - +
825A ASP* 3.3 30.9 - - + +
828A LEU* 4.1 28.5 - - + -
829A GLY 3.7 6.5 - - - +
830A PHE 4.2 2.0 - - - +
831A GLY* 3.7 28.0 - - - -
847A PRO* 2.7 25.1 + - + +
848A LEU* 3.1 6.0 + - - +
850A ALA* 1.3 73.7 - - + +
852A LYS* 1.3 58.0 + - - +
854A LYS* 3.8 8.6 - - - +
855A MET* 2.9 33.5 + - - +
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Residues in contact with LYS 852 (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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818A LEU* 3.2 51.6 - - + +
819A ASN* 3.4 9.3 + - - +
820A LYS 3.6 19.0 + - - -
823A LEU* 3.4 18.2 - - + +
833A LYS* 6.0 1.2 - - - +
848A LEU* 3.0 40.4 + - + +
849A ILE* 3.5 10.8 - - + +
850A ALA 3.2 0.2 - - - -
851A MET* 1.3 75.8 - - - +
853A LYS* 1.3 62.2 + - + +
855A MET 3.1 0.2 + - - -
856A ARG* 2.7 38.4 + - - +
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Residues in contact with LYS 853 (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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221A TYR* 4.4 12.6 - - + +
225A ASP* 3.2 43.3 + - + +
318A LYS* 5.7 3.6 - - - +
322A ASP* 3.5 19.7 + - - -
323A TYR* 3.6 10.5 - - - +
849A ILE* 3.1 30.4 + - + +
850A ALA* 3.7 8.7 - - - +
852A LYS* 1.3 79.9 - - + +
854A LYS* 1.3 66.2 + - - +
856A ARG* 3.4 2.6 + - - +
857A ARG* 3.3 25.4 + - - +
911A TYR* 4.2 24.1 + - + +
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Residues in contact with LYS 854 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A TYR* 3.3 51.7 - - + +
825A ASP* 2.9 41.2 + - - +
826A LYS* 3.9 9.5 - - - +
827A GLU* 3.6 16.4 + - - +
828A LEU* 3.6 13.9 - - + +
850A ALA 3.1 12.2 + - - +
851A MET* 3.8 4.9 - - - +
853A LYS* 1.3 78.2 - - - +
855A MET* 1.3 65.0 + - - +
857A ARG* 3.1 14.1 + - + +
858A GLU* 3.0 53.7 + - + +
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Residues in contact with MET 855 (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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187A TYR* 5.1 9.4 - - - +
817A ASP* 2.9 37.7 - - + +
818A LEU* 3.3 29.4 - - + -
823A LEU* 4.2 13.0 - - + -
824A LEU 4.9 10.3 - - - +
825A ASP* 5.6 5.8 - - - +
851A MET* 2.9 20.8 + - - +
852A LYS 3.1 0.4 + - - +
854A LYS* 1.3 79.9 - - - +
856A ARG* 1.3 57.0 + - - +
858A GLU* 3.9 9.9 - - + +
859A LEU* 2.8 43.9 + - + +
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Residues in contact with ARG 856 (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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815A MET* 4.1 36.5 - - + +
818A LEU* 3.6 16.1 - - + +
852A LYS 2.7 20.9 + - - +
853A LYS* 3.8 5.4 - - - +
854A LYS 3.1 0.2 + - - -
855A MET* 1.3 75.4 - - - +
857A ARG* 1.3 57.1 + - - +
859A LEU* 3.5 5.0 + - - +
860A LEU* 3.0 29.2 + - + +
911A TYR* 3.4 45.8 + - + +
912A GLN* 4.3 9.3 + - - +
913A ALA 3.8 21.0 + - - -
914A ARG* 4.5 9.1 - - - +
4X A 6.0 0.2 + - - -
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Residues in contact with ARG 857 (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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221A TYR* 3.3 36.4 + - - +
224A GLU* 2.8 40.6 + - - +
225A ASP 5.4 1.2 - - - +
228A MET* 6.0 3.6 - - - -
499A LYS* 3.5 53.4 + - + +
500A ILE* 4.3 6.7 - - + +
502A GLU* 4.3 0.2 - - - +
853A LYS* 3.3 14.2 + - - +
854A LYS* 3.1 15.5 - - - +
856A ARG* 1.3 76.7 - - - +
858A GLU* 1.3 56.6 + - + +
860A LEU* 3.9 8.8 - - - +
861A SER* 2.6 32.1 + - - -
911A TYR* 4.2 20.6 - - + -
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Residues in contact with GLU 858 (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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221A TYR* 4.9 1.2 + - - -
445A ARG* 2.9 43.5 + - - +
502A GLU* 3.8 12.5 - - - +
825A ASP* 4.8 2.1 - - - +
826A LYS* 4.3 18.0 + - - +
854A LYS* 3.0 54.6 + - + +
855A MET* 3.9 9.2 - - + +
857A ARG* 1.3 82.0 - - + +
859A LEU* 1.3 64.2 + - - +
860A LEU 3.2 1.3 - - - -
861A SER* 3.3 1.0 + - - -
862A GLU* 3.2 13.7 + - - +
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Residues in contact with LEU 859 (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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445A ARG* 6.5 1.1 - - + -
446A PHE* 6.4 1.8 - - + -
814A ASN 3.8 15.3 - - - +
815A MET* 3.7 31.2 - - + -
817A ASP* 5.0 13.7 - - + +
818A LEU* 5.4 4.9 - - + -
855A MET* 2.8 38.9 + - + +
856A ARG* 3.7 5.8 - - - +
858A GLU* 1.3 76.4 - - - +
860A LEU* 1.3 62.4 + - - +
862A GLU* 3.4 11.8 - - + +
863A GLU* 3.2 34.8 + - + +
45X T 6.2 0.9 - - - +
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Residues in contact with LEU 860 (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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500A ILE* 3.7 24.1 - - + +
813A PHE* 3.7 25.6 - - + -
815A MET* 3.5 29.8 - - + -
856A ARG* 3.0 19.6 + - - +
857A ARG* 4.1 2.0 - - - +
858A GLU 3.2 0.2 - - - -
859A LEU* 1.3 76.2 - - - +
861A SER* 1.3 64.0 + - - +
863A GLU* 3.3 4.5 + - + +
864A LEU* 3.2 21.1 + - - +
910A ARG 3.5 14.8 - - - +
911A TYR* 3.2 31.6 - - + +
913A ALA 4.1 8.1 - - - +
919A PHE* 4.0 13.8 - - + -
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Residues in contact with SER 861 (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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499A LYS 3.5 0.2 + - - -
500A ILE 2.5 28.4 + - - -
501A GLY* 4.7 1.1 - - - -
502A GLU* 2.8 37.6 + - - +
857A ARG 2.6 21.2 + - - -
858A GLU 3.3 4.5 + - - -
860A LEU* 1.3 80.2 - - - +
862A GLU* 1.3 60.3 + - - +
864A LEU* 3.1 13.9 + - - +
865A ARG* 3.2 27.2 + - - +
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Residues in contact with GLU 862 (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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442A SER* 3.5 8.1 + - - +
443A ILE 2.8 26.8 - - - +
444A TYR 3.2 1.2 + - - -
445A ARG* 2.7 52.2 + - + +
446A PHE* 5.8 3.1 - - + +
590A ARG* 5.9 1.1 - - - +
794A HIS* 5.6 0.4 - - + +
858A GLU 3.2 8.0 + - - +
859A LEU* 3.4 17.3 - - + +
861A SER* 1.3 79.8 - - - +
863A GLU* 1.3 62.8 + - - +
865A ARG* 2.9 33.6 + - - +
866A VAL* 2.9 35.6 + - + +
46X T 6.0 0.7 - - - +
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Residues in contact with GLU 863 (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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590A ARG* 2.5 49.6 + - - -
813A PHE* 3.9 47.2 - - + -
815A MET* 6.0 0.7 - - + -
859A LEU* 3.2 26.3 + - + +
860A LEU* 3.7 7.2 - - + +
861A SER 3.3 0.4 - - - -
862A GLU* 1.3 83.1 - - - +
864A LEU* 1.3 58.2 + - - +
866A VAL* 3.3 2.3 + - - +
867A LEU 2.9 23.6 + - - -
916A TYR* 3.1 18.9 + - + -
919A PHE* 4.8 1.1 - - + -
45X T 5.5 0.2 - - - +
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Residues in contact with LEU 864 (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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492A PHE* 3.0 42.7 - - + -
495A LEU* 3.6 30.7 - - + +
496A MET* 3.5 43.4 - - + +
500A ILE* 3.8 16.6 - - + -
501A GLY* 4.6 3.1 - - - -
860A LEU 3.2 11.8 + - - +
861A SER* 3.1 11.5 + - - +
863A GLU* 1.3 76.9 - - - +
865A ARG* 1.3 57.9 + - - +
867A LEU* 3.8 6.0 + - + +
868A TYR* 3.2 5.9 + - - +
919A PHE* 3.9 28.7 - - + -
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Residues in contact with ARG 865 (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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439A VAL* 3.1 41.0 + - - +
440A LYS* 3.3 18.7 - - - +
442A SER* 3.2 16.1 + - - +
443A ILE* 3.8 4.3 - - + -
445A ARG* 4.1 8.5 - - - +
451A PRO* 4.8 8.0 - - - +
496A MET* 4.6 11.1 - - + +
501A GLY* 3.4 18.9 + - - +
502A GLU* 3.1 37.0 + - - +
503A VAL* 5.6 0.4 - - - +
861A SER* 3.2 18.7 - - - +
862A GLU* 2.9 39.3 + - - +
864A LEU* 1.3 76.1 - - - +
866A VAL* 1.3 61.5 + - - +
867A LEU 3.2 1.1 - - - -
868A TYR* 2.9 17.6 + - - +
869A VAL* 2.9 20.6 + - - +
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Residues in contact with VAL 866 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ILE* 3.6 24.0 - - + +
590A ARG* 3.7 17.9 - - - +
793A ILE* 3.1 29.6 - - + +
794A HIS* 3.6 25.1 - - + +
862A GLU* 2.9 25.0 + - + +
863A GLU* 3.3 9.4 + - - +
865A ARG* 1.3 75.6 - - - +
867A LEU* 1.3 58.9 + - - +
869A VAL* 3.0 22.5 - - + +
870A ALA 3.3 0.9 + - - -
916A TYR* 3.3 20.2 - - - +
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Residues in contact with LEU 867 (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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492A PHE* 3.6 17.4 - - + -
495A LEU* 5.2 1.8 - - + -
793A ILE* 5.3 2.0 - - + -
806A VAL* 5.4 3.1 - - + -
809A LEU* 4.9 10.5 - - + -
863A GLU 2.9 17.0 + - - +
864A LEU* 3.9 15.7 - - + +
866A VAL* 1.3 77.0 - - - +
868A TYR* 1.3 59.2 - - - +
869A VAL 3.4 0.2 - - - -
870A ALA* 3.7 7.8 - - + +
871A LEU* 3.2 41.3 + - + +
880A LEU* 5.4 1.1 - - + -
916A TYR* 3.7 36.3 - - + -
919A PHE* 4.7 5.4 - - + -
920A ILE* 3.6 32.3 - - + -
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Residues in contact with TYR 868 (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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31A ALA* 4.9 1.7 - - - +
32A ALA* 4.9 0.6 + - + -
438A ASP* 4.5 1.0 + - - -
440A LYS* 3.4 53.7 - - + +
441A GLN* 4.0 22.1 + - + -
488A THR* 3.7 19.5 - - + -
492A PHE* 3.3 29.4 - + + -
496A MET* 4.4 7.2 - - + -
505A TYR* 4.5 13.8 + + - -
509A ALA 5.1 0.9 + - - -
511A LEU* 3.8 25.8 - - - +
864A LEU 3.2 15.9 + - - +
865A ARG* 2.9 14.4 + - - +
867A LEU* 1.3 77.4 - - - +
869A VAL* 1.3 54.6 + - - +
871A LEU* 4.5 0.7 - - - +
872A THR* 2.7 44.4 + - + +
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Residues in contact with VAL 869 (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 GLN* 3.9 36.1 - - + +
443A ILE* 4.0 20.0 - - + -
793A ILE* 3.4 24.7 - - + +
796A SER* 5.3 1.8 - - - -
797A LYS* 5.8 3.1 - - - +
865A ARG 2.9 12.2 + - - +
866A VAL* 3.0 24.9 - - - +
868A TYR* 1.3 75.0 - - - +
870A ALA* 1.3 64.0 + - - +
872A THR* 3.0 13.5 + - - -
873A ARG* 2.8 35.6 + - + +
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Residues in contact with ALA 870 (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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588A LEU* 4.3 7.4 - - + +
793A ILE* 3.6 29.8 - - + -
804A VAL* 4.1 15.1 - - - +
806A VAL* 3.9 25.4 - - + -
866A VAL 3.3 2.7 + - - +
867A LEU* 3.7 13.5 - - + +
868A TYR 3.3 0.2 - - - -
869A VAL* 1.3 84.8 - - - +
871A LEU* 1.3 65.6 + - + +
873A ARG* 3.3 13.3 + - - +
874A ALA 4.3 0.9 + - - -
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Residues in contact with LEU 871 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484A ILE* 3.6 17.8 - - - +
487A SER* 5.1 1.3 - - - -
488A THR* 3.3 26.2 - - + +
491A LEU* 3.9 27.4 - - + -
492A PHE* 4.0 14.8 - - + -
525A THR* 6.3 0.2 - - + -
804A VAL* 6.0 0.2 - - - -
806A VAL* 4.8 3.6 - - + -
867A LEU* 3.2 38.6 + - + +
868A TYR 4.5 2.7 - - - +
869A VAL 3.4 0.2 - - - -
870A ALA* 1.3 83.8 - - + +
872A THR* 1.3 60.6 + - - +
873A ARG 3.5 0.5 + - - -
874A ALA* 3.5 12.3 + - - +
878A LEU* 3.9 24.9 - - + +
880A LEU* 4.1 20.6 - - + -
920A ILE* 5.5 1.3 - - + -
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Residues in contact with THR 872 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ALA* 3.7 20.9 - - + +
477A ASN* 5.3 5.1 + - - -
480A SER* 5.3 1.9 + - - -
484A ILE* 5.1 3.1 - - - -
485A LEU* 6.5 0.7 - - - -
488A THR* 4.2 7.4 - - + +
511A LEU* 4.1 20.0 - - + -
868A TYR* 2.7 51.3 + - + +
869A VAL* 3.0 13.0 + - - -
871A LEU* 1.3 73.6 - - - +
873A ARG* 1.3 75.3 + - - +
874A ALA 3.0 16.7 + - - +
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Residues in contact with ARG 873 (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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32A ALA* 3.2 27.0 - - - +
33A GLY 5.6 1.6 - - - +
441A GLN* 3.5 21.3 + - - +
588A LEU* 4.8 7.4 - - + -
796A SER* 3.7 24.0 - - - -
797A LYS 2.9 34.5 + - - +
798A GLY* 3.9 9.5 + - - -
799A LEU 3.2 14.1 + - - +
800A GLU* 3.3 6.9 - - - +
801A PHE* 2.9 29.2 + - + -
804A VAL* 4.2 5.6 - - + +
869A VAL* 2.8 35.5 + - + +
870A ALA* 3.6 9.0 - - - +
871A LEU 3.3 0.8 - - - -
872A THR* 1.3 96.7 + - - +
874A ALA* 1.3 58.4 + - - +
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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) + - + + + + + -
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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