Contacts of the helix formed by residues 3909 - 3933 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3898F LEU 3.9 3.5 + - - -
3899F ARG* 3.1 31.0 + - - +
3900F THR* 5.8 0.2 - - - +
3901F GLN* 3.9 7.1 + - - +
3907F THR* 5.1 5.4 - - - +
3908F ILE* 1.3 83.0 - - - +
3910F ILE* 1.3 58.2 + - - +
3911F ILE* 2.9 22.0 - - - +
3912F ILE* 2.9 55.8 + - + +
3913F CYS* 4.0 2.4 + - - -
3974F SER* 4.4 14.2 + - - -
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Residues in contact with ILE3910 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3824F PHE* 5.5 8.3 - - + -
3827F ILE* 3.9 31.2 - - + -
3828F GLN* 6.1 0.4 - - + -
3831F MET* 5.4 2.9 - - + -
3883F LEU* 3.8 31.9 - - + -
3898F LEU* 3.7 44.4 + - + +
3901F GLN* 5.4 0.4 - - - +
3908F ILE* 3.5 12.3 - - + +
3909F ASN* 1.3 73.9 - - - +
3911F ILE* 1.3 61.8 + - + +
3912F ILE 3.2 0.2 - - - -
3913F CYS* 3.2 20.5 - - - -
3914F THR* 2.4 42.0 + - - +
3963F TYR* 5.5 1.8 - - - +
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Residues in contact with ILE3911 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3898F LEU* 4.4 14.8 - - + +
3899F ARG* 4.7 7.4 - - + -
3909F ASN* 2.9 15.3 + - - +
3910F ILE* 1.3 88.0 - - + +
3912F ILE* 1.3 63.1 + - + +
3914F THR* 3.2 5.5 + - + +
3915F VAL* 3.2 32.8 + - + +
3963F TYR* 3.7 39.5 - - + -
3971F ASN* 4.5 19.7 - - - +
3974F SER* 4.2 27.8 - - - +
3975F LEU* 5.1 5.8 - - + +
3978F SER* 5.9 0.4 - - - +
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Residues in contact with ILE3912 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3908F ILE 5.3 1.1 - - - +
3909F ASN* 2.9 41.8 + - + +
3911F ILE* 1.3 77.3 - - + +
3913F CYS* 1.3 63.2 + - + +
3915F VAL* 3.2 23.0 - - + +
3916F ASP* 3.2 10.5 + - + +
3974F SER* 5.8 3.1 - - - +
3978F SER* 6.3 1.6 - - - -
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Residues in contact with CYS3913 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3828F GLN* 4.1 33.7 - - + -
3831F MET* 3.6 26.1 - - + +
3832F GLN* 5.4 9.2 + - - +
3908F ILE 5.3 0.2 - - - -
3909F ASN 4.3 1.6 - - - -
3910F ILE* 3.2 38.8 - - - -
3912F ILE* 1.3 78.2 - - + +
3914F THR* 1.3 63.0 + - - +
3916F ASP* 3.7 15.8 + - + +
3917F TYR* 3.7 7.8 + - - +
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Residues in contact with THR3914 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831F MET* 3.7 16.4 - - + +
3880F PHE* 5.0 8.3 - - + -
3883F LEU* 5.6 2.4 - - + +
3910F ILE* 2.4 38.0 + - - +
3911F ILE* 3.4 13.2 - - - +
3912F ILE 3.2 0.2 - - - -
3913F CYS* 1.3 75.7 - - - +
3915F VAL* 1.3 67.2 + - + +
3917F TYR* 3.3 13.5 + - - +
3918F LEU* 3.3 15.5 - - + +
3956F VAL* 5.6 0.4 - - + -
3959F SER* 4.7 11.2 - - - +
3960F LEU* 5.0 10.8 - - + -
3963F TYR* 4.3 23.6 + - + +
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Residues in contact with VAL3915 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3911F ILE* 3.3 19.1 - - + +
3912F ILE* 3.2 19.1 - - + +
3914F THR* 1.3 74.1 - - + +
3916F ASP* 1.3 62.6 + - - +
3917F TYR 3.2 1.1 + - - -
3918F LEU* 3.5 12.8 + - + +
3919F LEU* 3.4 17.7 + - - +
3960F LEU* 3.7 28.7 - - + -
3975F LEU* 5.2 3.6 - - + -
3978F SER* 3.7 35.4 - - - +
3979F ARG* 5.0 6.8 - - + +
3980F LEU* 4.6 13.2 - - + +
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Residues in contact with ASP3916 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3832F GLN* 5.7 7.0 - - - +
3912F ILE* 3.2 18.3 + - + +
3913F CYS* 3.8 12.8 - - + +
3914F THR 3.2 1.0 - - - -
3915F VAL* 1.3 76.4 - - - +
3917F TYR* 1.3 63.6 + - - +
3919F LEU* 3.5 14.0 + - + +
3920F ARG* 3.4 27.4 + - - +
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Residues in contact with TYR3917 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831F MET* 4.3 10.5 - - + +
3834F CYS* 3.7 26.5 - - + +
3835F SER 5.8 0.3 + - - -
3836F VAL* 4.4 15.9 - - + +
3870F MET* 6.1 0.9 - - - +
3876F THR* 3.9 6.1 - - - +
3880F PHE* 3.6 37.7 - + + -
3913F CYS 3.7 7.7 + - - +
3914F THR 3.3 12.0 + - - +
3915F VAL 3.2 1.0 - - - -
3916F ASP* 1.3 76.4 - - - +
3918F LEU* 1.3 56.4 + - - +
3920F ARG* 3.1 24.5 + - - +
3921F LEU* 2.6 67.8 + - + +
3952F VAL* 3.5 24.1 - - + +
3956F VAL* 4.3 14.4 - - + -
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Residues in contact with LEU3918 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914F THR* 3.3 21.1 - - + +
3915F VAL* 3.6 16.6 - - + +
3916F ASP 3.5 0.2 - - - -
3917F TYR* 1.3 74.4 - - + +
3919F LEU* 1.3 60.3 + - - +
3921F LEU* 3.6 10.5 - - + -
3922F GLN* 2.8 31.9 + - - +
3956F VAL* 3.8 34.3 - - + -
3957F PHE* 3.9 34.5 - - + -
3960F LEU* 4.1 24.7 - - + -
3983F ALA* 4.7 16.1 - - + +
3987F PHE* 4.5 7.5 - - + -
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Residues in contact with LEU3919 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D SER* 6.2 0.2 - - - +
160D GLY 5.2 10.8 - - - +
161D GLU* 5.6 9.2 - - + -
3915F VAL 3.4 10.9 + - - +
3916F ASP* 3.5 16.2 - - + +
3917F TYR 3.2 0.8 - - - -
3918F LEU* 1.3 80.3 - - - +
3920F ARG* 1.3 60.5 + - + +
3922F GLN* 3.8 5.2 + - + +
3923F GLU* 3.3 25.4 + - - +
3979F ARG* 4.0 35.2 - - + +
3982F ASP* 5.2 8.1 - - + +
3983F ALA* 5.2 8.7 - - + +
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Residues in contact with ARG3920 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D SER* 5.6 9.6 - - - +
159D GLU 5.7 4.0 - - - +
3831F MET 3.3 25.1 + - - -
3832F GLN* 3.9 31.3 + - - +
3834F CYS 4.6 5.3 + - - -
3836F VAL* 3.8 28.1 - - + +
3916F ASP* 3.4 13.9 + - - +
3917F TYR* 3.1 25.3 + - - +
3919F LEU* 1.3 76.8 - - + +
3921F LEU* 1.3 64.8 + - - +
3922F GLN 3.3 0.7 - - - -
3923F GLU* 3.2 10.3 + - - +
3924F SER* 3.1 20.8 + - - -
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Residues in contact with LEU3921 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836F VAL* 4.9 9.6 - - + +
3837F LEU* 5.7 0.9 - - + +
3917F TYR* 2.6 57.9 + - + +
3918F LEU* 3.4 10.3 + - + -
3920F ARG* 1.3 71.4 - - - +
3922F GLN* 1.3 63.6 + - - +
3924F SER* 3.1 11.5 + - - +
3925F ILE* 3.1 47.5 + - + +
3949F ALA* 5.4 8.1 - - + +
3952F VAL* 4.9 3.8 - - + +
3953F ALA* 4.1 31.4 - - + +
3956F VAL* 4.3 8.1 - - + -
3957F PHE* 6.3 0.2 - - + -
3987F PHE* 5.1 6.1 - - + -
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Residues in contact with GLN3922 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918F LEU 2.8 22.9 + - - +
3919F LEU* 4.0 7.4 - - + +
3921F LEU* 1.3 73.1 - - - +
3923F GLU* 1.3 52.9 + - + +
3925F ILE* 4.1 1.1 - - - +
3926F SER* 2.6 36.6 + - - -
3983F ALA* 5.1 9.4 - - + +
3986F GLY* 5.8 4.0 - - - -
3987F PHE* 3.6 33.6 - - + +
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Residues in contact with GLU3923 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D GLU 4.7 4.9 - - - +
160D GLY* 3.4 38.8 - - - +
3919F LEU* 3.3 18.0 + - - +
3920F ARG* 3.2 11.1 + - - +
3921F LEU 3.2 0.6 - - - -
3922F GLN* 1.3 79.4 - - - +
3924F SER* 1.3 60.9 + - - +
3926F SER* 3.0 22.0 + - - -
3927F ASP* 3.2 27.7 - - - +
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Residues in contact with SER3924 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836F VAL* 3.8 15.9 - - - -
3837F LEU* 3.3 53.0 - - - +
3920F ARG 3.1 8.0 + - - -
3921F LEU* 3.1 14.3 + - - -
3923F GLU* 1.3 77.3 - - - +
3925F ILE* 1.3 62.9 + - - +
3926F SER 3.6 0.2 + - - -
3927F ASP* 3.9 5.3 + - - +
3928F PHE* 3.8 14.0 + - - +
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Residues in contact with ILE3925 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837F LEU* 5.5 2.7 - - + -
3921F LEU* 3.1 38.9 + - + +
3922F GLN* 4.4 2.5 - - - +
3924F SER* 1.3 76.4 - - - +
3926F SER* 1.3 65.2 + - - +
3928F PHE* 3.3 8.9 + - + +
3929F TYR* 3.3 17.0 + - - +
3946F PHE* 3.7 32.8 - - + -
3949F ALA* 5.1 13.2 - - + +
3950F MET* 6.3 0.2 - - - -
3953F ALA* 4.4 18.4 - - + -
3987F PHE* 4.3 18.6 - - + -
3990F VAL* 5.5 10.8 - - + +
3991F PHE* 5.5 7.0 - - + -
3994F MET* 5.3 5.5 - - + +
4014F LEU* 5.8 3.8 - - + -
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Residues in contact with SER3926 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3922F GLN 2.6 25.3 + - - -
3923F GLU* 3.0 24.8 + - - -
3925F ILE* 1.3 74.1 - - - +
3927F ASP* 1.3 59.6 + - - +
3929F TYR* 2.8 23.6 + - - +
3930F TRP* 3.1 41.6 + - - -
3990F VAL* 4.5 12.8 - - - -
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Residues in contact with ASP3927 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 5.3 6.9 - - - +
3837F LEU 6.1 0.4 - - - +
3839F LEU* 4.7 21.7 - - + +
3923F GLU* 3.2 22.3 + - - +
3924F SER* 3.9 5.8 + - - +
3925F ILE 3.4 0.6 - - - -
3926F SER* 1.3 79.8 + - - +
3928F PHE* 1.3 60.5 + - - +
3929F TYR 3.5 0.3 + - - -
3930F TRP* 4.0 8.7 + - - +
3931F TYR* 3.5 22.3 + - - +
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Residues in contact with PHE3928 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837F LEU* 5.8 4.9 - - + -
3839F LEU* 5.7 2.0 - - - +
3842F PHE* 4.7 18.2 - + - -
3924F SER 3.8 10.6 + - - +
3925F ILE* 3.3 13.0 + - + +
3926F SER 3.1 0.8 - - - -
3927F ASP* 1.3 77.0 - - - +
3929F TYR* 1.3 63.8 + - - +
3931F TYR* 3.9 8.2 + + + +
3932F TYR* 3.8 48.4 + + + +
3938F ILE* 5.6 3.6 - - + -
3942F GLY* 3.5 30.3 - - - -
3945F ASN* 5.8 1.8 - - + -
3946F PHE* 3.9 36.3 - + + -
3994F MET* 5.6 4.5 - - + -
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Residues in contact with TYR3929 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925F ILE 3.3 10.2 + - - +
3926F SER* 2.8 15.3 + - - +
3928F PHE* 1.3 76.4 - - - +
3930F TRP* 1.3 60.4 + - + +
3931F TYR 3.1 1.6 - - - -
3932F TYR* 3.2 5.8 + - - +
3933F SER* 2.4 35.5 + - - +
3990F VAL* 4.5 20.2 - - + +
3994F MET* 5.4 14.6 - - + -
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Residues in contact with TRP3930 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74D SER* 5.2 14.4 - - - -
76D ARG* 4.0 24.6 - - + +
77D ALA* 3.6 35.1 - - + +
80D GLU* 4.9 13.1 - - + +
3926F SER* 3.1 53.2 + - - +
3927F ASP* 4.7 7.4 - - - +
3929F TYR* 1.3 81.3 - - + +
3931F TYR* 1.3 60.6 + - - +
3932F TYR 3.3 0.4 + - - -
3933F SER* 3.2 22.5 + - - -
3934F GLY 4.6 2.9 + - - -
3989F HIS* 4.1 30.4 + + - -
3990F VAL* 4.5 10.1 - - + -
3993F HIS* 5.7 6.6 + - - -
----------------------------------------------------------
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Residues in contact with TYR3931 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D ARG* 5.4 1.5 - - - +
3839F LEU* 5.4 15.5 - - + -
3842F PHE* 5.1 14.3 - + - -
3843F GLU* 5.1 12.6 - - + +
3927F ASP 3.5 19.7 + - - +
3928F PHE* 4.1 10.1 - + + +
3929F TYR 3.1 1.0 - - - -
3930F TRP* 1.3 80.2 - - - +
3932F TYR* 1.3 94.7 + + - +
3933F SER 3.6 0.2 - - - -
3934F GLY* 4.9 2.3 + - - -
3935F LYS* 5.1 3.5 + - - +
----------------------------------------------------------
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Residues in contact with TYR3932 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842F PHE* 3.7 19.0 - + - -
3846F ASN* 4.8 2.6 + - - -
3928F PHE* 3.8 48.6 + + + +
3929F TYR 3.2 5.1 + - - +
3931F TYR* 1.3 108.1 - + - +
3933F SER* 1.3 59.9 + - - +
3934F GLY 3.4 2.0 - - - -
3935F LYS* 2.9 36.8 - - + +
3937F VAL 5.0 3.4 - - - -
3938F ILE* 3.9 26.5 - - + +
3939F GLU* 3.5 32.8 - - + +
3942F GLY* 4.6 6.3 - - - -
3997F LYS* 3.4 11.0 - - - -
----------------------------------------------------------
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Residues in contact with SER3933 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3929F TYR* 2.4 33.2 + - - +
3930F TRP* 3.2 19.7 + - - -
3931F TYR 3.6 1.0 - - - -
3932F TYR* 1.3 76.5 - - - +
3934F GLY* 1.3 65.9 + - - +
3935F LYS 4.4 0.2 - - - -
3993F HIS* 6.0 2.5 - - - +
3997F LYS* 3.8 25.4 + - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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