Contacts of the helix formed by residues 3909 - 3933 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3898D LEU 3.9 4.0 + - - -
3899D ARG* 3.1 31.1 + - - +
3901D GLN* 3.9 6.5 + - - +
3907D THR* 4.8 5.6 - - - +
3908D ILE* 1.3 83.1 - - - +
3910D ILE* 1.3 57.8 - - - +
3911D ILE* 2.9 22.7 - - - +
3912D ILE* 2.9 56.0 + - + +
3913D CYS* 4.0 2.3 + - - -
3974D SER* 4.4 13.4 + - - -
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Residues in contact with ILE3910 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3824D PHE* 5.5 8.3 - - + -
3827D ILE* 3.9 31.2 - - + -
3828D GLN* 6.1 0.9 - - + -
3831D MET* 5.4 2.5 - - + -
3883D LEU* 3.8 31.9 - - + -
3898D LEU* 3.7 45.0 + - + +
3901D GLN* 5.4 0.4 - - - +
3908D ILE* 3.5 11.7 - - + +
3909D ASN* 1.3 73.2 - - - +
3911D ILE* 1.3 60.8 + - + +
3912D ILE 3.2 0.2 - - - -
3913D CYS* 3.2 19.4 - - - -
3914D THR* 2.4 42.6 + - - +
3963D TYR* 5.5 1.8 - - - +
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Residues in contact with ILE3911 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3898D LEU* 4.4 15.5 - - + +
3899D ARG* 4.7 7.0 - - + -
3909D ASN* 2.9 13.9 + - - +
3910D ILE* 1.3 89.0 - - + +
3912D ILE* 1.3 62.3 + - + +
3914D THR* 3.2 5.1 + - - +
3915D VAL* 3.2 32.9 + - + +
3963D TYR* 3.7 39.7 - - + -
3971D ASN* 4.5 18.8 - - - +
3974D SER* 4.2 27.8 - - - +
3975D LEU* 5.1 5.8 - - + +
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Residues in contact with ILE3912 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3908D ILE 5.3 1.3 - - - +
3909D ASN* 2.9 41.6 + - + +
3911D ILE* 1.3 78.7 - - + +
3913D CYS* 1.3 63.0 + - + +
3915D VAL* 3.2 21.7 - - + +
3916D ASP* 3.2 10.7 + - + +
3974D SER* 5.8 3.1 - - - +
3978D SER* 6.0 3.1 - - - -
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Residues in contact with CYS3913 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3827D ILE* 6.2 0.2 - - - -
3828D GLN* 4.1 33.0 - - + -
3831D MET* 3.6 24.5 - - + +
3832D GLN* 5.4 9.4 + - - +
3908D ILE 5.3 0.4 - - - -
3909D ASN 4.3 2.0 - - - -
3910D ILE* 3.2 39.0 - - - -
3912D ILE* 1.3 78.2 - - + +
3914D THR* 1.3 63.3 + - - +
3916D ASP* 3.7 14.8 + - + +
3917D TYR* 3.7 7.8 + - - +
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Residues in contact with THR3914 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831D MET* 3.7 15.9 - - + +
3880D PHE* 5.0 8.8 - - + -
3883D LEU* 5.6 2.4 - - + +
3910D ILE* 2.4 37.3 + - - +
3911D ILE* 3.4 14.4 - - - +
3912D ILE 3.2 0.4 - - - -
3913D CYS* 1.3 76.4 - - - +
3915D VAL* 1.3 66.9 + - + +
3917D TYR* 3.3 13.7 + - - +
3918D LEU* 3.3 15.5 - - + +
3956D VAL* 5.6 0.7 - - + -
3959D SER* 4.7 11.7 - - - +
3960D LEU* 5.0 10.3 - - + -
3963D TYR* 4.3 23.7 + - + +
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Residues in contact with VAL3915 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3911D ILE* 3.3 19.3 - - + +
3912D ILE* 3.2 19.7 - - - +
3914D THR* 1.3 73.8 - - - +
3916D ASP* 1.3 63.4 + - - +
3917D TYR 3.2 0.6 + - - -
3918D LEU* 3.5 12.8 + - + +
3919D LEU* 3.4 18.2 + - - +
3960D LEU* 3.7 28.3 - - + -
3975D LEU* 5.2 4.5 - - + -
3978D SER* 3.7 34.5 - - - +
3979D ARG* 5.0 6.8 - - + +
3980D LEU* 4.6 14.1 - - + +
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Residues in contact with ASP3916 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3832D GLN* 5.7 6.7 - - - +
3912D ILE* 3.2 18.5 + - + +
3913D CYS* 3.8 13.5 - - + +
3914D THR 3.2 0.6 - - - -
3915D VAL* 1.3 77.1 - - - +
3917D TYR* 1.3 63.5 + - - +
3918D LEU 3.5 0.2 - - - -
3919D LEU* 3.5 12.7 + - + +
3920D ARG* 3.4 27.1 + - - +
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Residues in contact with TYR3917 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3831D MET* 4.3 10.3 - - + +
3834D CYS* 3.7 25.6 - - + +
3835D SER 5.8 0.7 + - - -
3836D VAL* 4.4 15.8 - - + +
3870D MET* 6.1 0.7 - - - +
3876D THR* 3.9 5.9 - - - +
3880D PHE* 3.6 38.6 - + + -
3913D CYS 3.7 8.2 + - - +
3914D THR 3.3 11.3 + - - +
3915D VAL 3.2 1.2 - - - -
3916D ASP* 1.3 76.4 - - - +
3918D LEU* 1.3 55.1 + - - +
3920D ARG* 3.1 23.7 + - - +
3921D LEU* 2.6 68.1 + - + +
3952D VAL* 3.5 24.5 - - + +
3956D VAL* 4.3 13.9 - - + -
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Residues in contact with LEU3918 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914D THR* 3.3 21.3 - - + +
3915D VAL* 3.6 15.0 - - + +
3917D TYR* 1.3 73.9 - - + +
3919D LEU* 1.3 60.6 + - - +
3921D LEU* 3.6 10.8 - - + -
3922D GLN* 2.8 31.2 + - - +
3956D VAL* 3.8 34.1 - - + -
3957D PHE* 3.9 34.8 - - + -
3960D LEU* 4.1 24.5 - - + -
3983D ALA* 4.7 17.8 - - + +
3987D PHE* 4.5 6.6 - - + -
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Residues in contact with LEU3919 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B GLY 5.2 11.0 - - - +
161B GLU* 5.6 10.3 - - + -
3915D VAL 3.4 9.8 + - - +
3916D ASP* 3.5 16.4 - - + +
3917D TYR 3.2 0.2 - - - -
3918D LEU* 1.3 81.6 - - - +
3920D ARG* 1.3 60.3 + - + +
3922D GLN* 4.0 5.2 - - + +
3923D GLU* 3.3 25.3 + - - +
3979D ARG* 4.0 35.0 - - + +
3982D ASP* 5.2 8.3 - - + +
3983D ALA* 5.2 8.7 - - + +
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Residues in contact with ARG3920 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B SER* 5.6 9.4 - - - +
159B GLU 5.7 4.5 - - - +
3831D MET 3.3 24.9 + - - -
3832D GLN* 3.9 32.5 + - - +
3834D CYS 4.6 5.9 + - - -
3836D VAL* 3.8 28.0 - - + +
3916D ASP* 3.4 14.5 + - - +
3917D TYR* 3.1 26.1 + - - +
3919D LEU* 1.3 76.9 - - + +
3921D LEU* 1.3 65.4 + - - +
3922D GLN 3.3 0.4 - - - -
3923D GLU* 3.2 10.5 + - - +
3924D SER* 3.1 20.4 + - - -
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Residues in contact with LEU3921 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836D VAL* 4.9 10.5 - - + +
3837D LEU* 5.7 0.9 - - + +
3917D TYR* 2.6 56.4 + - + +
3918D LEU* 3.8 10.3 - - + +
3920D ARG* 1.3 72.1 - - - +
3922D GLN* 1.3 63.0 + - - +
3924D SER* 3.1 10.6 + - - +
3925D ILE* 3.1 47.9 + - + +
3949D ALA* 5.4 8.1 - - + +
3952D VAL* 4.9 3.4 - - + -
3953D ALA* 4.1 31.4 - - + +
3956D VAL* 4.3 8.7 - - + -
3957D PHE* 6.3 0.4 - - + -
3987D PHE* 4.9 6.5 - - + -
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Residues in contact with GLN3922 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918D LEU 2.8 21.9 + - - +
3919D LEU* 4.0 7.6 - - + +
3920D ARG 3.3 0.2 - - - -
3921D LEU* 1.3 73.4 - - - +
3923D GLU* 1.3 52.6 + - + +
3925D ILE* 4.1 0.9 - - - +
3926D SER* 2.6 37.3 + - - -
3983D ALA* 5.1 9.6 - - + +
3986D GLY* 5.8 3.6 - - - -
3987D PHE* 3.6 32.5 - - + +
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Residues in contact with GLU3923 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B GLU 4.7 5.2 - - - +
160B GLY* 3.4 38.8 - - - +
3919D LEU* 3.3 17.0 - - - +
3920D ARG* 3.2 12.4 + - - +
3921D LEU 3.2 0.6 - - - -
3922D GLN* 1.3 78.4 - - - +
3924D SER* 1.3 61.5 + - - +
3926D SER* 3.0 23.0 + - - -
3927D ASP* 3.2 28.9 - - - +
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Residues in contact with SER3924 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3836D VAL* 3.8 16.6 - - - -
3837D LEU* 3.3 52.5 - - - +
3920D ARG 3.1 8.8 + - - -
3921D LEU* 3.1 14.1 + - - -
3923D GLU* 1.3 78.6 - - - +
3925D ILE* 1.3 64.2 + - - +
3927D ASP* 3.9 4.3 + - - +
3928D PHE* 3.8 13.7 + - - +
----------------------------------------------------------
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Residues in contact with ILE3925 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837D LEU* 5.5 2.9 - - + -
3921D LEU* 3.1 38.9 + - + +
3922D GLN* 4.4 2.9 - - - +
3924D SER* 1.3 76.0 - - - +
3926D SER* 1.3 65.0 + - - +
3928D PHE* 3.3 9.0 + - - +
3929D TYR* 3.3 17.5 + - - +
3946D PHE* 3.7 32.8 - - + -
3949D ALA* 5.1 13.9 - - + +
3950D MET* 6.3 0.4 - - - -
3953D ALA* 4.4 17.3 - - + -
3987D PHE* 4.3 17.9 - - + -
3990D VAL* 5.5 10.3 - - + +
3991D PHE* 5.5 6.7 - - + -
3994D MET* 5.3 4.8 - - + +
4014D LEU* 5.8 4.0 - - + -
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Residues in contact with SER3926 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3922D GLN 2.6 25.3 + - - -
3923D GLU* 3.0 25.3 + - - -
3925D ILE* 1.3 74.2 - - - +
3927D ASP* 1.3 59.4 + - - +
3929D TYR* 2.8 23.0 + - - +
3930D TRP* 3.1 43.0 + - - -
3990D VAL* 4.5 13.4 - - - +
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Residues in contact with ASP3927 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 5.3 7.1 - - - +
3837D LEU 6.1 0.2 - - - +
3839D LEU* 4.7 22.1 - - + +
3923D GLU* 3.2 23.9 + - - +
3924D SER* 4.3 4.8 - - - +
3925D ILE 3.4 0.4 - - - -
3926D SER* 1.3 81.1 + - - +
3928D PHE* 1.3 60.8 + - - +
3929D TYR 3.5 0.2 + - - -
3930D TRP* 4.4 9.4 - - - +
3931D TYR* 3.5 22.2 + - - +
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Residues in contact with PHE3928 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837D LEU* 5.8 5.6 - - + -
3839D LEU* 6.0 1.6 - - - -
3842D PHE* 4.7 17.9 - + - -
3924D SER 3.8 10.0 + - - +
3925D ILE* 3.3 13.4 + - - +
3926D SER 3.1 0.8 - - - -
3927D ASP* 1.3 76.8 - - - +
3929D TYR* 1.3 65.1 + - - +
3931D TYR* 4.0 8.7 - + + +
3932D TYR* 3.8 49.1 + + + +
3938D ILE* 5.6 4.0 - - + -
3942D GLY* 3.5 30.7 - - - -
3945D ASN* 5.8 2.2 - - + -
3946D PHE* 3.9 36.3 - + + -
3994D MET* 5.6 4.7 - - + -
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Residues in contact with TYR3929 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925D ILE 3.3 9.1 + - - +
3926D SER* 2.8 16.2 + - - +
3928D PHE* 1.3 76.5 - - - +
3930D TRP* 1.3 60.6 + - + +
3931D TYR 3.1 1.6 - - - -
3932D TYR* 3.2 5.6 + - - +
3933D SER* 2.4 35.9 + - - +
3990D VAL* 4.5 20.6 - - + +
3994D MET* 5.4 13.5 - - + -
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Residues in contact with TRP3930 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B SER* 5.2 13.5 - - - -
76B ARG* 4.0 25.1 - - + +
77B ALA* 3.5 35.9 - - + +
80B GLU* 4.9 13.6 - - + +
3926D SER* 3.1 53.0 + - - +
3927D ASP* 4.5 8.1 - - - +
3929D TYR* 1.3 81.7 - - + +
3931D TYR* 1.3 61.2 + - - +
3932D TYR 3.3 0.2 - - - -
3933D SER* 3.2 22.9 + - - -
3934D GLY 4.6 2.8 + - - -
3989D HIS* 4.1 30.8 + + - -
3990D VAL* 4.5 10.5 - - + -
3993D HIS* 5.7 6.9 + - - -
----------------------------------------------------------
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Residues in contact with TYR3931 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B ARG* 5.4 1.5 - - - +
3839D LEU* 5.4 15.7 - - + -
3842D PHE* 5.1 14.7 - + - -
3843D GLU* 5.1 12.8 - - + +
3927D ASP 3.5 18.2 + - - +
3928D PHE* 4.1 11.4 - + + +
3929D TYR 3.1 1.0 - - - -
3930D TRP* 1.3 80.6 - - - +
3932D TYR* 1.3 95.3 + + - +
3933D SER 3.6 0.4 - - - -
3934D GLY 4.9 2.5 + - - -
3935D LYS* 5.1 3.5 + - - +
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Residues in contact with TYR3932 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842D PHE* 3.7 19.0 - + - -
3846D ASN* 4.8 2.6 + - - -
3928D PHE* 3.8 48.4 + + - +
3929D TYR* 3.2 5.9 + - - +
3931D TYR* 1.3 108.7 - + - +
3933D SER* 1.3 58.5 + - - +
3934D GLY 3.4 2.0 - - - -
3935D LYS* 2.9 36.3 - - + +
3937D VAL 5.0 3.8 - - - -
3938D ILE* 3.9 26.3 - - + +
3939D GLU* 3.6 33.4 - - + +
3942D GLY* 4.6 5.6 - - - -
3997D LYS* 3.4 10.5 - - - -
----------------------------------------------------------
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Residues in contact with SER3933 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3929D TYR* 2.4 33.0 + - - +
3930D TRP* 3.2 20.2 + - - -
3931D TYR 3.6 1.0 - - - -
3932D TYR* 1.3 77.2 - - - +
3934D GLY* 1.3 65.5 + - - +
3993D HIS* 6.0 2.2 - - - +
3997D LYS* 3.8 24.9 + - - +
----------------------------------------------------------
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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