Contacts of the helix formed by residues 3909 - 3933 (chain B) in PDB entry 6X34
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 ASN3909 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3898B LEU 3.9 3.7 + - - -
3899B ARG* 3.1 31.2 + - - +
3901B GLN* 3.9 6.9 + - - +
3907B THR* 5.1 5.4 - - - -
3908B ILE* 1.3 82.7 - - - +
3910B ILE* 1.3 58.7 + - - +
3911B ILE* 2.9 22.3 - - - +
3912B ILE* 2.9 56.2 + - + +
3913B CYS* 4.0 2.3 + - - -
3974B SER* 4.4 14.1 + - - -
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Residues in contact with ILE3910 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3824B PHE* 5.5 8.5 - - + -
3827B ILE* 3.9 31.0 - - + -
3828B GLN* 6.1 0.7 - - + -
3831B MET* 5.4 2.5 - - + -
3883B LEU* 3.8 32.5 - - + -
3898B LEU* 3.7 45.1 + - + +
3901B GLN* 5.4 0.2 - - - +
3908B ILE* 3.5 11.3 - - + +
3909B ASN* 1.3 73.8 - - - +
3911B ILE* 1.3 59.7 + - + +
3912B ILE 3.2 0.2 - - - -
3913B CYS* 3.2 19.9 - - - -
3914B THR* 2.4 43.6 + - - +
3963B TYR* 5.5 1.6 - - - +
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Residues in contact with ILE3911 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3898B LEU* 4.4 15.0 - - + +
3899B ARG* 4.7 7.6 - - + -
3909B ASN* 2.9 14.6 + - - +
3910B ILE* 1.3 89.0 - - + +
3912B ILE* 1.3 63.1 + - + +
3914B THR* 3.2 5.5 + - - +
3915B VAL* 3.2 32.2 + - + +
3963B TYR* 3.7 40.2 - - + -
3970B GLY 6.1 0.2 - - - +
3971B ASN* 4.5 19.5 - - - +
3974B SER* 4.2 28.0 - - - +
3975B LEU* 5.1 5.4 - - + +
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Residues in contact with ILE3912 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3908B ILE 5.3 1.3 - - - +
3909B ASN* 2.9 41.8 + - + +
3911B ILE* 1.3 78.9 - - + +
3913B CYS* 1.3 62.3 + - + +
3915B VAL* 3.2 21.7 - - + +
3916B ASP* 3.2 11.5 + - + +
3974B SER* 5.8 2.9 - - - +
3978B SER* 6.0 2.0 - - - -
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Residues in contact with CYS3913 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3827B ILE* 6.2 0.4 - - - -
3828B GLN* 4.1 33.4 - - + -
3831B MET* 3.6 25.0 - - + +
3832B GLN* 5.4 9.4 + - - +
3908B ILE 5.3 0.4 - - - -
3909B ASN 4.3 2.0 - - - -
3910B ILE* 3.2 38.8 - - - -
3912B ILE* 1.3 78.1 - - + +
3914B THR* 1.3 64.4 + - - +
3916B ASP* 3.7 15.0 + - + +
3917B TYR* 3.7 7.6 + - - +
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Residues in contact with THR3914 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831B MET* 3.7 15.5 - - + +
3880B PHE* 5.0 8.2 - - + -
3883B LEU* 5.6 1.9 - - + +
3910B ILE* 2.4 38.3 + - - +
3911B ILE* 3.4 13.9 - - + +
3912B ILE 3.2 0.6 - - - -
3913B CYS* 1.3 76.3 - - - +
3915B VAL* 1.3 65.0 + - + +
3917B TYR* 3.3 13.7 + - - +
3918B LEU* 3.3 16.6 - - + +
3956B VAL* 5.6 0.9 - - + -
3959B SER* 4.7 11.2 - - - +
3960B LEU* 5.0 10.5 - - + -
3963B TYR* 4.3 24.4 + - + +
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Residues in contact with VAL3915 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3911B ILE* 3.3 19.7 - - + +
3912B ILE* 3.2 19.1 - - + +
3914B THR* 1.3 74.9 - - + +
3916B ASP* 1.3 64.4 + - - +
3917B TYR 3.2 0.7 + - - -
3918B LEU* 3.5 13.2 + - + +
3919B LEU* 3.4 17.5 + - - +
3960B LEU* 3.7 27.8 - - + -
3975B LEU* 5.2 3.6 - - + -
3978B SER* 3.7 36.8 - - - +
3979B ARG* 5.0 7.6 - - + +
3980B LEU* 4.6 14.6 - - + +
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Residues in contact with ASP3916 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3832B GLN* 5.7 6.7 - - - +
3912B ILE* 3.2 18.5 + - + +
3913B CYS* 3.8 12.6 - - - +
3914B THR 3.2 0.8 - - - -
3915B VAL* 1.3 76.4 - - - +
3917B TYR* 1.3 62.7 + - - +
3919B LEU* 3.5 14.0 + - + +
3920B ARG* 3.4 27.0 + - - +
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Residues in contact with TYR3917 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831B MET* 4.3 10.5 - - + +
3834B CYS* 3.7 25.6 - - + +
3835B SER 5.8 0.5 + - - -
3836B VAL* 4.4 16.4 - - + +
3870B MET* 6.1 0.5 - - - +
3876B THR* 3.9 6.1 - - - +
3880B PHE* 3.6 38.6 - + + -
3913B CYS 3.7 7.8 + - - +
3914B THR 3.3 12.4 + - - +
3915B VAL 3.2 0.6 - - - -
3916B ASP* 1.3 76.8 - - - +
3918B LEU* 1.3 55.4 + - - +
3920B ARG* 3.1 24.7 + - - +
3921B LEU* 2.6 69.0 + - + +
3952B VAL* 3.5 23.7 - - + +
3956B VAL* 4.3 14.6 - - + -
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Residues in contact with LEU3918 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914B THR* 3.3 20.9 - - + +
3915B VAL* 3.6 16.4 - - + +
3916B ASP 3.5 0.2 - - - -
3917B TYR* 1.3 73.7 - - + +
3919B LEU* 1.3 59.4 + - - +
3921B LEU* 3.8 11.4 - - + +
3922B GLN* 2.8 31.5 + - - +
3956B VAL* 3.8 33.9 - - + -
3957B PHE* 3.9 35.4 - - + -
3960B LEU* 4.1 24.5 - - + -
3983B ALA* 4.7 16.7 - - + +
3987B PHE* 4.5 6.6 - - + -
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Residues in contact with LEU3919 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3915B VAL 3.4 10.3 + - - +
3916B ASP* 3.5 15.7 - - + +
3917B TYR 3.2 0.6 - - - -
3918B LEU* 1.3 79.9 - - - +
3920B ARG* 1.3 60.0 + - + +
3922B GLN* 4.0 5.0 - - + +
3923B GLU* 3.3 25.9 + - - +
3979B ARG* 4.0 34.8 - - + +
3982B ASP* 5.2 9.2 - - + +
3983B ALA* 5.2 7.8 - - + +
158H SER* 6.2 0.2 - - - +
160H GLY 5.2 12.5 - - - +
161H GLU* 5.6 9.2 - - + -
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Residues in contact with ARG3920 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831B MET 3.3 25.1 + - - -
3832B GLN* 3.9 32.5 + - - +
3834B CYS 4.6 5.3 + - - -
3836B VAL* 3.8 28.9 - - + +
3916B ASP* 3.4 13.2 + - - +
3917B TYR* 3.1 24.8 + - - +
3919B LEU* 1.3 77.3 - - + +
3921B LEU* 1.3 64.6 + - - +
3922B GLN 3.3 0.2 - - - -
3923B GLU* 3.2 10.5 + - - +
3924B SER* 3.1 21.1 + - - -
158H SER* 5.6 9.0 - - - +
159H GLU 5.7 4.0 - - - +
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Residues in contact with LEU3921 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836B VAL* 4.9 9.6 - - + +
3837B LEU* 5.7 1.6 - - + +
3917B TYR* 2.6 57.7 + - + +
3918B LEU* 3.4 10.3 + - + -
3920B ARG* 1.3 71.3 - - - +
3922B GLN* 1.3 64.5 + - - +
3924B SER* 3.1 10.6 + - - +
3925B ILE* 3.1 47.8 + - + +
3949B ALA* 5.4 8.5 - - + +
3952B VAL* 4.9 3.4 - - + +
3953B ALA* 4.1 31.4 - - + +
3956B VAL* 4.3 8.1 - - + -
3957B PHE* 6.3 0.2 - - + -
3987B PHE* 5.1 5.8 - - + -
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Residues in contact with GLN3922 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918B LEU 2.8 22.1 + - - +
3919B LEU* 4.0 7.4 - - + +
3920B ARG 3.3 0.2 - - - -
3921B LEU* 1.3 73.6 - - - +
3923B GLU* 1.3 53.2 + - + +
3925B ILE* 4.3 0.7 - - - +
3926B SER* 2.6 37.1 + - - -
3983B ALA* 5.1 10.3 - - + +
3986B GLY* 5.8 3.6 - - - -
3987B PHE* 3.6 33.3 - - + +
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Residues in contact with GLU3923 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3919B LEU* 3.3 18.1 + - - +
3920B ARG* 3.2 11.6 + - - +
3921B LEU 3.2 0.6 - - - -
3922B GLN* 1.3 80.0 - - - +
3924B SER* 1.3 61.6 + - - +
3926B SER* 3.0 22.0 + - - -
3927B ASP* 3.2 28.1 - - - +
159H GLU 4.7 5.6 - - - +
160H GLY* 3.4 37.8 - - - +
----------------------------------------------------------
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Residues in contact with SER3924 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836B VAL* 3.8 16.2 - - - -
3837B LEU* 3.3 53.5 - - - +
3920B ARG 3.1 9.6 + - - -
3921B LEU* 3.1 13.9 + - - -
3923B GLU* 1.3 76.6 - - - +
3925B ILE* 1.3 64.7 + - - +
3927B ASP* 3.9 4.7 + - - +
3928B PHE* 3.8 13.9 + - - +
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Residues in contact with ILE3925 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837B LEU* 5.5 2.2 - - + -
3921B LEU* 3.1 38.8 + - + +
3922B GLN* 4.4 2.7 - - - +
3924B SER* 1.3 75.1 - - - +
3926B SER* 1.3 64.7 + - - +
3928B PHE* 3.3 8.8 + - + +
3929B TYR* 3.3 17.5 + - - +
3946B PHE* 3.7 33.2 - - + -
3949B ALA* 5.1 13.7 - - + +
3950B MET* 6.3 0.2 - - - -
3953B ALA* 4.4 18.2 - - + -
3987B PHE* 4.3 18.2 - - + -
3990B VAL* 5.5 10.7 - - + +
3991B PHE* 5.5 6.7 - - + -
3994B MET* 5.3 4.6 - - + +
4014B LEU* 5.7 3.8 - - + -
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Residues in contact with SER3926 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3922B GLN 2.6 25.4 + - - -
3923B GLU* 3.0 25.1 + - - -
3925B ILE* 1.3 73.4 - - - +
3927B ASP* 1.3 61.1 + - - +
3929B TYR* 2.8 23.1 + - - +
3930B TRP* 3.1 42.2 + - - -
3990B VAL* 4.5 14.1 - - - +
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Residues in contact with ASP3927 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837B LEU 6.1 0.4 - - - +
3839B LEU* 4.7 22.6 - - + +
3923B GLU* 3.2 21.9 + - - +
3924B SER* 4.3 5.4 - - - +
3925B ILE 3.4 0.6 - - - -
3926B SER* 1.3 79.1 + - - +
3928B PHE* 1.3 59.1 + - - +
3929B TYR 3.5 0.2 + - - -
3930B TRP* 4.0 9.1 + - - +
3931B TYR* 3.5 22.3 + - - +
76H ARG* 5.3 6.8 - - - +
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Residues in contact with PHE3928 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837B LEU* 5.8 5.2 - - + -
3839B LEU* 6.0 1.6 - - - -
3842B PHE* 4.7 17.9 - + - -
3924B SER 3.8 10.6 + - - +
3925B ILE* 3.3 12.7 + - - +
3926B SER 3.1 0.8 - - - -
3927B ASP* 1.3 77.0 - - - +
3929B TYR* 1.3 64.0 + - - +
3931B TYR* 3.9 8.4 + + + +
3932B TYR* 3.8 48.7 + + + +
3938B ILE* 5.6 4.0 - - + -
3942B GLY* 3.5 30.7 - - - -
3945B ASN* 5.8 2.7 - - + -
3946B PHE* 3.9 35.4 - + + -
3994B MET* 5.6 5.2 - - + -
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Residues in contact with TYR3929 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925B ILE 3.3 10.4 + - - +
3926B SER* 2.8 15.9 + - - +
3928B PHE* 1.3 76.7 - - - +
3930B TRP* 1.3 60.4 + - + +
3931B TYR 3.1 1.6 - - - -
3932B TYR* 3.2 5.6 + - - +
3933B SER* 2.4 36.3 + - - +
3990B VAL* 4.5 20.6 - - + +
3994B MET* 5.4 12.8 - - + -
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Residues in contact with TRP3930 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3926B SER* 3.1 52.9 + - - +
3927B ASP* 4.5 7.4 - - - +
3929B TYR* 1.3 81.3 - - + +
3931B TYR* 1.3 61.8 + - - +
3932B TYR 3.3 0.2 - - - -
3933B SER* 3.2 24.0 + - - -
3934B GLY 4.6 2.8 + - - -
3989B HIS* 4.1 30.9 + + - -
3990B VAL* 4.5 9.6 - - + -
3993B HIS* 5.7 6.5 + - - -
74H SER* 5.2 13.7 - - - -
76H ARG* 4.0 24.5 - - + +
77H ALA* 3.5 35.0 - - + +
80H GLU* 4.9 13.5 - - + +
----------------------------------------------------------
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Residues in contact with TYR3931 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3839B LEU* 5.4 16.4 - - + -
3842B PHE* 5.1 13.9 - + - -
3843B GLU* 5.1 12.3 - - + +
3927B ASP 3.5 18.6 + - - +
3928B PHE* 4.1 9.9 - + - +
3929B TYR 3.1 1.2 - - - -
3930B TRP* 1.3 80.4 - - - +
3932B TYR* 1.3 95.5 + + - +
3933B SER 3.6 0.4 + - - -
3934B GLY 4.9 2.1 + - - -
3935B LYS* 5.1 2.8 + - - +
76H ARG* 5.4 1.8 - - - +
----------------------------------------------------------
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Residues in contact with TYR3932 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842B PHE* 3.7 19.8 - + - -
3846B ASN* 4.8 2.6 + - - -
3928B PHE* 3.8 48.4 + + + +
3929B TYR* 3.2 5.7 + - - +
3931B TYR* 1.3 108.6 - + - +
3933B SER* 1.3 59.4 + - - +
3934B GLY 3.4 2.2 - - - +
3935B LYS* 2.9 37.0 - - + +
3937B VAL 5.0 2.9 - - - -
3938B ILE* 3.9 27.0 - - + +
3939B GLU* 3.6 33.4 - - + +
3942B GLY* 4.6 6.1 - - - -
3997B LYS* 3.4 10.3 - - - -
----------------------------------------------------------
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Residues in contact with SER3933 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3929B TYR* 2.4 32.8 + - - +
3930B TRP* 3.2 20.1 - - - -
3931B TYR 3.6 1.2 - - - -
3932B TYR* 1.3 76.7 - - - +
3934B GLY* 1.3 65.7 + - - +
3993B HIS* 6.0 2.5 - - - +
3997B LYS* 3.8 25.3 + - - +
----------------------------------------------------------
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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