Contacts of the helix formed by residues 688 - 720 (chain A) in PDB entry 5KZX
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 SER 688 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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655A GLU* 2.6 37.6 + - - -
687A PHE* 1.3 75.9 - - - +
689A GLU* 1.3 60.3 + - - +
690A PRO* 3.4 16.8 - - - +
691A ALA* 3.2 3.6 + - - +
692A GLN* 2.9 25.5 + - - +
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Residues in contact with GLU 689 (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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687A PHE 3.9 0.6 + - - -
688A SER* 1.3 70.3 - - - +
690A PRO* 1.3 72.2 - - + +
692A GLN* 3.3 20.7 + - - +
693A GLN* 3.0 53.0 + - - +
696A ARG* 5.1 7.1 + - - -
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Residues in contact with PRO 690 (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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655A GLU* 5.7 0.2 - - - +
688A SER* 3.4 15.3 - - - +
689A GLU* 1.3 95.7 - - + +
691A ALA* 1.3 60.7 + - - +
693A GLN* 3.3 14.3 + - + +
694A ALA* 3.2 21.5 + - - +
811A LEU* 6.5 0.9 - - + -
812A ASP* 6.0 0.5 - - - +
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Residues in contact with ALA 691 (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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655A GLU* 3.4 41.3 + - + +
659A VAL* 3.7 18.2 - - + -
687A PHE* 3.8 8.3 - - + -
688A SER* 3.2 8.4 + - - +
690A PRO* 1.3 79.3 - - - +
692A GLN* 1.3 56.8 + - - +
694A ALA* 3.2 4.4 + - - +
695A MET* 2.9 35.9 + - + +
811A LEU* 6.3 1.6 - - + -
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Residues in contact with GLN 692 (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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394A ALA* 3.8 9.5 - - - +
396A PHE* 3.4 26.8 - - + -
684A PRO 3.3 23.1 - - - +
685A TYR* 3.4 16.6 + - - +
687A PHE* 2.9 20.6 + - - +
688A SER 2.9 16.2 + - - +
689A GLU* 3.5 21.7 + - - +
691A ALA* 1.3 75.9 - - - +
693A GLN* 1.3 57.3 + - - +
695A MET* 4.4 2.0 - - - -
696A ARG* 2.8 47.4 + - - +
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Residues in contact with GLN 693 (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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689A GLU* 3.0 45.6 + - - +
690A PRO* 3.5 13.5 - - - +
691A ALA 3.3 0.2 - - - -
692A GLN* 1.3 74.6 - - - +
694A ALA* 1.3 58.6 + - - +
696A ARG* 3.3 21.1 + - - +
697A LYS* 2.9 30.2 + - - +
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Residues in contact with ALA 694 (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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659A VAL* 3.9 25.1 - - + -
663A GLN* 4.3 9.0 + - - +
690A PRO 3.2 10.4 + - - +
691A ALA* 3.6 7.9 - - - +
693A GLN* 1.3 80.4 - - - +
695A MET* 1.3 57.0 + - - +
697A LYS* 3.5 8.5 + - - +
698A ALA* 3.1 26.0 + - - +
811A LEU* 5.1 1.1 - - + -
812A ASP* 4.2 27.3 - - + +
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Residues in contact with MET 695 (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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396A PHE* 4.2 9.4 - - + -
655A GLU 4.4 1.3 - - - +
658A CYS* 3.8 9.2 - - + -
659A VAL* 3.7 39.7 - - + +
662A THR* 3.9 30.8 - - + +
663A GLN* 6.2 0.4 - - - -
684A PRO* 3.8 24.9 - - + +
687A PHE* 3.5 43.1 - - + -
691A ALA* 2.9 20.7 + - + +
692A GLN 3.7 3.6 - - - +
694A ALA* 1.3 74.3 - - - +
696A ARG* 1.3 64.0 + - - +
698A ALA* 3.2 5.2 + - - +
699A LEU* 3.0 27.2 + - + +
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Residues in contact with ARG 696 (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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394A ALA* 2.8 32.2 + - - +
395A HIS* 3.4 32.9 + - - +
396A PHE* 3.5 20.0 - - + -
397A PRO* 5.1 1.3 - - + +
689A GLU* 5.1 7.9 + - - -
692A GLN* 2.8 44.2 + - - +
693A GLN* 3.6 31.2 - - - +
695A MET* 1.3 73.2 - - - +
697A LYS* 1.3 54.5 + - - +
699A LEU* 3.3 4.6 + - - +
700A THR* 2.8 44.1 + - - +
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Residues in contact with LYS 697 (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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693A GLN 2.9 16.5 + - - +
694A ALA* 3.6 8.1 - - - +
695A MET 3.3 0.2 - - - -
696A ARG* 1.3 75.5 - - - +
698A ALA* 1.3 58.0 + - - +
700A THR* 3.3 7.2 + - - -
701A LEU* 3.0 38.9 + - + +
776A GLN* 3.9 34.1 + - - +
812A ASP* 4.1 23.7 + - + +
813A THR* 5.0 4.4 + - - +
814A ILE 5.5 1.6 + - - +
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Residues in contact with ALA 698 (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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662A THR* 3.9 28.3 - - + +
663A GLN* 4.1 16.8 - - + -
666A ALA* 3.6 17.6 - - + +
667A PHE* 6.1 0.2 - - - -
694A ALA 3.1 11.1 + - - +
695A MET 3.2 9.2 + - - +
697A LYS* 1.3 81.1 - - - +
699A LEU* 1.3 55.3 + - - +
701A LEU* 3.5 6.6 + - - +
702A ARG* 3.1 22.7 + - - +
814A ILE* 6.0 3.4 - - + -
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Residues in contact with LEU 699 (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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371A PHE* 3.6 43.7 - - + -
396A PHE* 3.9 25.1 - - + -
397A PRO* 4.0 28.7 - - + +
662A THR* 4.9 4.5 - - + -
671A MET* 3.7 27.1 - - + -
684A PRO* 4.5 7.4 - - + -
695A MET 3.0 20.2 + - - +
696A ARG 3.8 3.8 - - - +
698A ALA* 1.3 73.9 - - - +
700A THR* 1.3 58.9 + - - +
702A ARG* 3.4 4.7 + - - +
703A TYR* 3.0 39.1 + - + -
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Residues in contact with THR 700 (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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397A PRO* 4.8 8.5 - - - +
696A ARG* 2.8 34.2 + - - +
697A LYS* 3.3 8.2 + - - -
699A LEU* 1.3 71.6 - - - +
701A LEU* 1.3 60.0 + - - +
703A TYR* 3.4 7.3 + - - +
704A ALA* 2.9 27.6 + - + +
780A ILE* 4.6 8.5 - - + -
781A GLU 3.7 28.7 - - - +
829A PRO* 5.4 6.7 - - + -
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Residues in contact with LEU 701 (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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667A PHE* 4.1 24.5 - - + -
697A LYS* 3.0 26.2 + - + +
698A ALA* 3.8 6.5 - - - +
700A THR* 1.3 74.4 - - - +
702A ARG* 1.3 64.4 + - - +
704A ALA* 3.2 4.6 + - + +
705A LEU* 3.0 40.5 + - + +
775A LEU* 4.1 15.3 - - + -
780A ILE* 3.8 30.7 - - + -
814A ILE* 5.5 5.6 - - + -
816A VAL* 4.5 11.7 - - + -
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Residues in contact with ARG 702 (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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369A LEU* 2.9 30.6 + - - +
370A GLY 4.5 2.7 + - - -
666A ALA* 2.8 40.1 + - + +
667A PHE* 6.0 1.7 - - - -
668A TYR 2.6 22.8 + - - -
669A PRO 3.0 26.5 + - - -
671A MET* 3.6 40.4 - - - +
698A ALA 3.1 15.1 + - - +
699A LEU* 3.5 9.4 - - - +
700A THR 3.3 0.2 - - - -
701A LEU* 1.3 77.3 - - - +
703A TYR* 1.3 74.0 + - - +
705A LEU* 3.1 20.5 + - - +
706A LEU* 3.1 19.1 + - + +
709A LEU* 3.7 11.6 - - - +
746A TRP* 4.1 12.5 - - + -
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Residues in contact with TYR 703 (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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370A GLY* 3.8 5.8 - - - -
371A PHE* 2.9 35.7 + - + +
397A PRO* 3.5 25.8 - - + -
398A LEU 4.0 2.3 + - - -
399A ASP* 2.5 38.8 + - - -
699A LEU* 3.0 28.8 + - + +
700A THR* 3.9 6.5 - - - +
701A LEU 3.3 0.2 - - - -
702A ARG* 1.3 82.4 - - + +
704A ALA* 1.3 63.2 + - - +
706A LEU* 3.2 31.3 + - + +
707A PRO* 4.2 2.8 - - - +
827A GLN* 4.3 5.3 - - - +
828A GLY 5.0 3.3 - - - +
829A PRO* 5.6 3.6 - - + -
830A GLY 3.8 21.3 - - - +
832A THR* 4.0 9.2 - - - -
833A THR* 4.0 9.2 - - + -
836A SER* 4.4 16.2 + - - -
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Residues in contact with ALA 704 (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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700A THR* 2.9 15.4 + - + +
701A LEU* 3.2 10.5 + - + +
703A TYR* 1.3 75.0 - - - +
705A LEU* 1.3 59.8 + - - +
706A LEU 3.5 0.7 + - - -
707A PRO* 3.5 1.0 - - - +
780A ILE* 4.1 32.8 - - + -
826A LEU* 3.2 16.9 - - + -
827A GLN 3.0 41.8 + - - +
828A GLY 5.7 0.2 - - - -
829A PRO* 6.1 0.8 - - - +
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Residues in contact with LEU 705 (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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667A PHE* 3.9 28.7 - - + -
701A LEU* 3.0 43.4 + - + +
702A ARG* 3.1 6.9 + - - +
704A ALA* 1.3 74.9 - - - +
706A LEU* 1.3 64.8 + - - +
707A PRO* 3.3 2.9 - - - -
708A HIS* 3.0 11.2 + - + +
709A LEU* 2.9 19.4 + - - +
746A TRP* 4.1 16.2 - - + -
750A LEU* 4.0 23.1 - - + -
775A LEU* 4.8 10.5 - - + -
824A ILE* 4.1 11.2 - - + -
825A PRO 4.9 0.2 - - - -
826A LEU* 3.7 23.1 - - + -
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Residues in contact with LEU 706 (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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366A TYR* 3.3 21.0 - - + +
369A LEU* 3.5 41.3 - - + +
702A ARG* 3.1 24.0 + - + +
703A TYR* 3.2 34.0 + - + +
705A LEU* 1.3 77.2 - - - +
707A PRO* 1.3 59.8 - - - +
709A LEU* 3.8 15.6 - - + +
710A TYR* 2.8 32.6 + - - +
746A TRP* 5.9 0.2 - - + -
833A THR* 3.7 30.1 - - + -
836A SER* 4.8 1.8 - - - +
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Residues in contact with PRO 707 (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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366A TYR* 3.4 20.4 - - + +
703A TYR 4.2 1.3 - - - +
704A ALA 3.5 11.2 - - - +
705A LEU 3.5 3.6 - - - -
706A LEU* 1.3 89.2 - - + +
708A HIS* 1.3 55.7 + - - +
710A TYR* 3.6 2.6 + - - +
711A THR* 2.8 31.8 + - - -
825A PRO* 4.1 13.0 - - + +
826A LEU* 4.0 1.6 - - - -
827A GLN* 3.5 32.1 - - + +
841A MET* 3.8 22.9 - - + -
857A LEU* 4.1 12.7 - - + +
858A PHE 4.7 0.7 - - - +
859A TRP* 4.3 3.6 - - + -
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Residues in contact with HIS 708 (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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705A LEU* 3.0 10.7 + - + +
707A PRO* 1.3 77.2 - - - +
709A LEU* 1.3 60.9 + - - +
711A THR* 3.0 8.3 + - + +
712A LEU* 2.8 67.0 + - + +
746A TRP* 4.6 9.4 + + - -
748A GLU 6.4 0.2 - - - -
749A ALA* 5.6 3.2 + - + +
750A LEU* 3.9 27.4 - - + +
823A ILE 5.3 0.9 - - - -
824A ILE* 3.4 34.6 - - + +
825A PRO* 3.6 34.0 + - + +
856A GLU 5.1 2.8 + - - -
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Residues in contact with LEU 709 (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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369A LEU* 4.0 15.5 - - + -
669A PRO* 4.2 9.0 - - + +
702A ARG* 3.7 26.5 - - - +
705A LEU 2.9 11.9 + - - +
706A LEU* 3.8 23.3 - - + +
708A HIS* 1.3 75.2 - - - +
710A TYR* 1.3 57.7 + - - +
712A LEU* 3.1 10.9 + - + +
713A PHE* 2.9 33.5 + - + -
723A VAL* 3.6 31.0 - - + -
746A TRP* 3.8 42.8 - - + -
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Residues in contact with TYR 710 (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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363A MET* 3.5 27.1 - - + +
364A PRO* 3.7 7.0 - - + -
365A PRO 4.3 0.2 - - - -
366A TYR* 3.4 53.6 - + + -
369A LEU* 3.9 19.9 - - + +
594A ARG* 2.7 21.3 + - - -
706A LEU 2.8 21.4 + - - +
707A PRO 3.7 4.3 - - - +
709A LEU* 1.3 72.4 - - - +
711A THR* 1.3 57.3 + - - +
713A PHE* 3.2 6.1 + - + +
714A HIS* 2.9 23.6 + - - +
837A ARG* 5.1 1.8 - - - -
858A PHE* 3.9 27.8 - + - -
859A TRP* 5.0 2.2 - + - -
860A ASP* 2.5 33.8 + - - -
862A GLY* 3.5 4.0 - - - -
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Residues in contact with THR 711 (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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707A PRO 2.8 15.8 + - - -
708A HIS* 3.0 14.3 + - - +
710A TYR* 1.3 72.3 - - - +
712A LEU* 1.3 63.4 + - + +
714A HIS* 3.3 8.9 + - - +
715A GLN* 3.0 30.3 + - + +
856A GLU* 3.9 39.6 + - + +
857A LEU* 3.8 5.2 - - - +
858A PHE* 3.0 40.4 + - + +
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Residues in contact with LEU 712 (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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708A HIS* 2.8 49.2 + - + +
709A LEU* 3.4 13.0 - - - +
711A THR* 1.3 78.8 - - + +
713A PHE* 1.3 57.1 + - - +
715A GLN* 3.2 12.5 + - + +
716A ALA* 3.0 26.0 + - - +
722A THR 4.9 4.4 - - - +
723A VAL* 3.8 25.3 - - + +
725A ARG* 5.6 1.6 - - - +
746A TRP* 3.8 17.0 - - + -
747A GLY* 3.6 38.6 - - - +
748A GLU 5.2 0.7 - - - +
856A GLU* 6.1 0.4 - - - +
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Residues in contact with PHE 713 (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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361A PRO* 5.7 0.4 - - + +
362A PHE 4.9 4.1 - - - +
363A MET* 3.7 6.4 - - + +
364A PRO* 3.6 32.8 - - + -
369A LEU* 3.4 34.5 - - + -
640A PRO* 4.0 17.3 - - + -
641A LEU* 3.8 31.4 - - + -
669A PRO* 3.6 31.0 - - + -
709A LEU* 2.9 33.2 + - + -
710A TYR* 3.2 9.1 + - - +
712A LEU* 1.3 71.5 - - - +
714A HIS* 1.3 60.7 + - - +
716A ALA* 3.2 4.2 + - + +
717A HIS* 2.9 30.0 + - - +
723A VAL* 4.1 12.8 - - + -
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Residues in contact with HIS 714 (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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363A MET* 3.6 14.2 - - + -
710A TYR 2.9 9.6 + - - +
711A THR 3.4 7.4 - - - +
713A PHE* 1.3 76.5 - - - +
715A GLN* 1.3 81.2 + - - +
717A HIS* 3.2 2.2 + - - -
718A VAL* 2.9 60.8 + - + +
858A PHE* 3.4 65.2 - + + -
868A LEU* 3.8 11.6 - - + +
873A TYR* 5.5 1.8 - + - -
875A GLN* 3.7 14.5 + - - -
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Residues in contact with GLN 715 (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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711A THR* 3.0 18.3 + - - +
712A LEU* 3.2 15.4 + - + +
714A HIS* 1.3 97.0 + - - +
716A ALA* 1.3 60.6 + - - +
718A VAL* 4.2 10.1 - - - +
719A ALA* 2.9 39.2 + - - +
720A GLY 3.5 1.4 + - - -
721A GLU* 3.6 19.5 + - + +
856A GLU* 3.1 37.4 + - - +
875A GLN* 4.3 5.3 + - - -
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Residues in contact with ALA 716 (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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360A TYR* 3.9 0.3 - - - +
361A PRO* 3.4 26.7 - - + +
640A PRO* 4.4 4.3 - - + -
712A LEU 3.0 13.1 + - - +
713A PHE* 3.5 10.3 - - + +
715A GLN* 1.3 75.6 - - - +
717A HIS* 1.3 59.5 + - - +
720A GLY* 2.9 26.2 + - - -
721A GLU* 3.2 28.2 - - - +
723A VAL* 4.0 15.9 - - + -
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Residues in contact with HIS 717 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A TYR* 3.4 22.3 + - + +
361A PRO 2.7 29.6 + - - +
362A PHE* 4.5 3.8 - - - +
363A MET* 3.7 40.0 + - + +
713A PHE 2.9 17.5 + - - +
714A HIS* 3.2 4.5 + - - +
716A ALA* 1.3 78.3 - - - +
718A VAL* 1.3 55.5 + - + +
868A LEU* 3.7 19.0 - - + +
1025A SO4 2.8 34.8 + - - -
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Residues in contact with VAL 718 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A TYR* 3.3 14.4 - - - -
714A HIS* 2.9 43.1 + - + +
715A GLN* 4.2 13.5 - - - +
717A HIS* 1.3 80.6 - - + +
719A ALA* 1.3 67.1 + - + +
868A LEU* 3.2 35.7 - - + -
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Residues in contact with ALA 719 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLN* 3.2 21.0 - - - +
360A TYR* 3.8 9.9 - - - -
715A GLN* 2.9 19.3 + - - +
718A VAL* 1.3 85.0 - - + +
720A GLY* 1.3 64.2 + - - +
721A GLU* 3.2 16.9 + - + +
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Residues in contact with GLY 720 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A LYS 4.8 1.0 - - - +
351A VAL* 3.9 6.8 - - - +
352A GLN* 3.7 16.7 - - - +
355A LEU* 3.6 23.1 - - - +
360A TYR* 3.8 24.8 - - - -
716A ALA 2.9 15.8 + - - -
719A ALA* 1.3 77.3 - - - +
721A GLU* 1.3 64.8 + - - +
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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