Contacts of the helix formed by residues 3939 - 3964 (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 GLU3939 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3846B ASN* 5.8 3.4 - - - +
3932B TYR* 3.6 28.7 - - + +
3937B VAL* 4.2 1.4 + - - +
3938B ILE* 1.3 83.1 - - - +
3940B GLU* 1.3 65.2 + - - +
3941B GLN* 4.3 5.2 - - + +
3942B GLY 3.4 7.9 + - - +
3943B LYS* 3.3 17.5 + - - +
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Residues in contact with GLU3940 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938B ILE 3.7 2.0 + - - -
3939B GLU* 1.3 71.7 - - - +
3941B GLN* 1.3 70.0 + - + +
3943B LYS* 3.3 16.0 + - - +
3944B ARG* 3.5 11.4 + - - +
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Residues in contact with GLN3941 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842B PHE* 4.5 2.2 - - + -
3846B ASN* 3.9 26.7 - - - +
3939B GLU* 3.3 4.1 - - + +
3940B GLU* 1.3 81.6 - - + +
3942B GLY* 1.3 62.4 + - - +
3944B ARG* 3.4 37.7 + - - +
3945B ASN* 3.1 21.5 + - - +
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Residues in contact with GLY3942 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842B PHE* 3.8 23.6 - - - -
3928B PHE* 3.5 20.2 - - - -
3932B TYR* 4.6 5.8 - - - -
3938B ILE* 5.4 1.8 - - - -
3939B GLU* 3.4 10.5 + - - +
3940B GLU 3.3 0.8 - - - -
3941B GLN* 1.3 76.1 - - - +
3943B LYS* 1.3 60.7 + - - +
3945B ASN* 3.6 1.1 + - - +
3946B PHE* 3.1 28.8 + - - +
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Residues in contact with LYS3943 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938B ILE* 4.9 5.3 - - + +
3939B GLU 3.3 13.2 + - - +
3940B GLU* 3.6 11.9 - - - +
3941B GLN 3.2 0.4 - - - -
3942B GLY* 1.3 76.1 - - - +
3944B ARG* 1.3 57.6 + - - +
3946B PHE* 3.6 2.5 + - - +
3947B SER* 3.1 28.1 + - - -
4004B GLN* 6.5 0.9 - - + -
4007B LEU* 3.8 29.8 - - + +
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Residues in contact with ARG3944 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3867B GLU* 4.9 17.4 - - - +
3869B VAL* 5.1 4.4 - - - +
3940B GLU 3.5 7.6 + - - +
3941B GLN* 3.4 28.0 + - - +
3942B GLY 3.3 0.6 - - - -
3943B LYS* 1.3 77.4 - - - +
3945B ASN* 1.3 91.1 + - - +
3947B SER* 3.4 7.0 + - - -
3948B LYS* 3.2 21.0 + - + +
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Residues in contact with ASN3945 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842B PHE* 3.2 22.7 - - + -
3867B GLU* 6.1 1.0 - - - +
3869B VAL* 3.4 42.8 - - + +
3870B MET* 4.8 11.0 - - + +
3928B PHE* 5.8 2.9 - - + -
3941B GLN* 3.1 18.2 + - - +
3942B GLY 4.1 4.7 - - - +
3943B LYS 3.4 0.2 - - - -
3944B ARG* 1.3 102.3 + - - +
3946B PHE* 1.3 59.1 + - - +
3948B LYS* 3.5 7.2 + - - +
3949B ALA* 3.1 26.0 + - - +
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Residues in contact with PHE3946 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925B ILE* 3.7 29.4 - - + -
3928B PHE* 3.9 28.8 - + + -
3942B GLY 3.1 18.9 + - - +
3943B LYS* 4.0 5.8 - - - +
3944B ARG 3.3 0.2 - - - -
3945B ASN* 1.3 76.8 - - - +
3947B SER* 1.3 60.8 + - - +
3949B ALA* 3.3 9.0 + - + +
3950B MET* 2.8 40.0 + - + +
3991B PHE* 5.4 4.0 - + - -
3994B MET* 3.5 26.9 - - + -
4007B LEU* 4.0 24.2 - - + -
4011B LEU* 3.5 28.3 - - + -
4014B LEU* 6.2 3.4 - - + -
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Residues in contact with SER3947 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3943B LYS 3.1 19.0 + - - -
3944B ARG* 3.7 6.3 - - - -
3946B PHE* 1.3 80.1 - - - +
3948B LYS* 1.3 59.2 + - - +
3950B MET* 3.4 7.9 + - - +
3951B SER* 3.0 26.9 + - - -
4007B LEU* 6.1 3.1 - - - -
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Residues in contact with LYS3948 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870B MET* 4.8 13.9 - - + -
3873B ASP* 5.6 10.3 - - + -
3944B ARG 3.2 13.2 + - - +
3945B ASN* 3.8 10.8 - - - +
3946B PHE 3.3 0.4 - - - -
3947B SER* 1.3 77.2 + - - +
3949B ALA* 1.3 62.1 + - - +
3951B SER* 3.3 16.2 + - - -
3952B VAL* 3.3 17.7 + - - +
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Residues in contact with ALA3949 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837B LEU* 5.3 9.0 - - + -
3870B MET* 4.7 18.1 - - + +
3921B LEU* 5.4 6.4 - - + +
3925B ILE* 5.1 14.6 - - + +
3945B ASN 3.1 17.9 + - - +
3946B PHE* 3.8 11.2 - - + +
3948B LYS* 1.3 74.9 - - - +
3950B MET* 1.3 59.9 + - - +
3952B VAL* 3.3 10.1 + - - +
3953B ALA* 2.9 28.4 + - - +
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Residues in contact with MET3950 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925B ILE* 6.3 0.4 - - - -
3946B PHE* 2.8 31.6 + - + +
3947B SER* 3.6 10.1 - - - +
3948B LYS 3.2 0.2 - - - -
3949B ALA* 1.3 75.2 - - - +
3951B SER* 1.3 59.3 + - - +
3953B ALA* 3.3 6.8 + - - +
3954B LYS* 2.9 30.0 + - - +
4010B GLU* 5.3 15.7 - - + +
4011B LEU* 5.9 2.0 - - - -
4014B LEU* 5.2 13.0 - - + +
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Residues in contact with SER3951 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3947B SER* 3.0 14.9 + - - -
3948B LYS* 3.3 10.4 + - - -
3949B ALA 3.3 0.6 - - - -
3950B MET* 1.3 78.5 - - - +
3952B VAL* 1.3 62.2 + - - +
3954B LYS* 3.4 9.4 + - - +
3955B GLN* 3.3 28.2 + - - +
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Residues in contact with VAL3952 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870B MET* 4.9 13.9 - - + -
3872B ASP 5.9 1.6 - - - +
3873B ASP* 6.0 5.4 - - - -
3876B THR* 3.7 29.6 - - + +
3877B GLN* 5.6 8.1 - - + +
3880B PHE* 5.3 3.4 - - + -
3917B TYR* 3.5 28.7 - - + +
3921B LEU* 4.9 4.9 - - + -
3948B LYS 3.3 16.4 - - - +
3949B ALA* 3.3 10.7 + - - +
3950B MET 3.3 0.4 - - - -
3951B SER* 1.3 76.0 - - - +
3953B ALA* 1.3 61.9 + - - +
3954B LYS 3.4 0.5 + - - -
3955B GLN* 3.5 3.5 + - - +
3956B VAL* 3.3 22.9 + - - +
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Residues in contact with ALA3953 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3921B LEU* 4.1 17.0 - - + +
3925B ILE* 4.4 13.0 - - + -
3949B ALA 2.9 16.3 + - - +
3950B MET* 3.3 6.3 + - - +
3952B VAL* 1.3 75.9 - - - +
3954B LYS* 1.3 57.7 + - - +
3956B VAL* 3.3 11.8 - - + +
3957B PHE* 3.1 32.0 - - + -
3987B PHE* 5.8 2.0 - - + -
4014B LEU* 3.4 22.6 - - + +
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Residues in contact with LYS3954 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3950B MET 2.9 16.7 + - - +
3951B SER* 3.7 10.1 - - - +
3952B VAL 3.2 0.4 - - - -
3953B ALA* 1.3 78.0 - - - +
3955B GLN* 1.3 70.4 + - + +
3957B PHE* 3.6 5.3 + - - +
3958B ASN* 3.0 36.3 + - - +
4013B ASP* 5.2 14.4 - - + +
4014B LEU* 4.2 13.5 - - + -
4016B LYS* 5.6 3.8 - - - +
4017B ASP* 3.5 27.7 - - - +
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Residues in contact with GLN3955 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3876B THR 6.2 0.2 - - - +
3877B GLN* 5.0 18.6 - - + +
3880B PHE* 4.6 14.7 - - + +
3881B ARG* 3.6 36.0 + - - +
3884B GLN* 5.4 1.6 - - - +
3951B SER 3.3 15.2 + - - +
3952B VAL* 3.5 4.4 + - - +
3954B LYS* 1.3 87.4 - - + +
3956B VAL* 1.3 63.6 + - - +
3958B ASN* 2.8 42.1 + - - +
3959B SER* 3.5 11.4 + - - -
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Residues in contact with VAL3956 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880B PHE* 4.4 21.9 - - + +
3914B THR* 5.2 2.2 - - + +
3917B TYR* 4.3 16.6 - - + -
3918B LEU* 3.8 34.3 - - + -
3921B LEU* 4.3 9.6 - - + -
3952B VAL 3.3 15.4 + - - +
3953B ALA* 3.3 22.7 - - - +
3955B GLN* 1.3 76.9 - - - +
3957B PHE* 1.3 70.3 + - + +
3959B SER* 2.3 38.3 + - - +
3960B LEU* 3.1 8.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE3957 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918B LEU* 3.9 18.6 - - + -
3921B LEU* 6.3 0.2 - - + -
3953B ALA* 3.1 24.9 - - + +
3954B LYS 3.6 7.1 + - - +
3955B GLN 3.4 0.6 - - - -
3956B VAL* 1.3 85.7 - - + +
3958B ASN* 1.3 61.5 + - - +
3959B SER 3.1 0.9 + - - -
3960B LEU* 3.6 13.1 + - + +
3961B THR* 3.3 22.6 + - - +
3983B ALA* 5.7 2.0 - - + -
3984B VAL* 4.6 13.0 - - + -
3987B PHE* 3.6 39.5 - + - -
4014B LEU* 3.9 16.8 - - + -
4017B ASP* 4.3 20.0 - - + +
4018B MET* 3.7 31.4 - - + -
4021B MET* 5.3 9.6 - - + +
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Residues in contact with ASN3958 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3881B ARG* 5.3 3.7 - - - +
3884B GLN* 4.3 7.0 - - + +
3954B LYS* 3.0 28.6 + - - +
3955B GLN* 2.8 37.5 + - - +
3956B VAL 3.1 0.6 - - - -
3957B PHE* 1.3 77.4 - - - +
3959B SER* 1.3 56.2 + - - +
3961B THR* 3.3 13.4 - - + +
3962B GLU* 3.2 26.5 - - - +
4017B ASP* 4.1 18.9 - - - +
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Residues in contact with SER3959 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880B PHE* 4.5 16.3 - - - -
3883B LEU* 5.8 0.4 - - - -
3884B GLN* 4.1 19.1 - - - -
3914B THR* 4.7 5.7 - - - +
3955B GLN 3.5 7.2 + - - -
3956B VAL* 2.3 33.8 + - - +
3958B ASN* 1.3 79.3 - - - +
3960B LEU* 1.3 67.4 + - - +
3961B THR 3.3 0.2 - - - -
3962B GLU* 3.5 2.3 + - - +
3963B TYR* 3.2 44.4 + - - -
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Residues in contact with LEU3960 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914B THR* 5.0 8.1 - - + -
3915B VAL* 3.7 30.3 - - + -
3918B LEU* 4.1 27.6 - - + -
3956B VAL* 3.1 28.9 + - + +
3957B PHE* 3.6 18.6 + - + +
3959B SER* 1.3 83.9 + - - +
3961B THR* 1.3 61.9 + - - +
3963B TYR* 3.3 21.2 + - + +
3964B ILE* 3.5 12.6 + - - +
3975B LEU* 4.1 25.9 - - + +
3980B LEU* 4.9 6.7 - - + -
4021B MET* 5.9 4.9 - - + -
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Residues in contact with THR3961 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957B PHE 3.3 18.9 + - - +
3958B ASN* 3.3 20.2 - - + +
3960B LEU* 1.3 78.3 - - - +
3962B GLU* 1.3 65.4 + - + +
3964B ILE* 3.1 4.9 + - - +
3965B GLN* 2.8 49.7 + - - +
4017B ASP 5.5 3.1 - - - +
4020B VAL* 4.9 10.6 + - + +
4021B MET* 4.7 16.8 - - - +
4024B SER* 3.5 17.4 + - - -
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Residues in contact with GLU3962 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884B GLN* 4.0 26.0 - - + +
3887B CYS* 3.2 35.2 - - + +
3888B GLU* 3.9 10.4 - - - +
3890B HIS* 4.0 7.4 + - - -
3895B GLN* 6.0 0.7 - - - +
3958B ASN 3.2 19.5 - - - +
3959B SER* 3.5 7.3 + - - +
3960B LEU 3.3 0.4 - - - -
3961B THR* 1.3 81.1 - - + +
3963B TYR* 1.3 63.2 + - + +
3964B ILE 3.5 0.3 + - - -
3965B GLN* 3.6 32.4 + - - +
4999B THR* 4.6 14.4 + - - +
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Residues in contact with TYR3963 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3883B LEU* 3.4 47.3 + - - +
3884B GLN* 5.0 2.7 - - - -
3887B CYS* 5.1 12.1 - - + -
3895B GLN* 4.8 9.2 - - + +
3898B LEU* 4.2 23.8 - - + +
3910B ILE* 5.5 1.8 - - + +
3911B ILE* 3.7 24.5 - - + -
3914B THR* 4.3 21.0 + - + +
3959B SER* 3.2 30.4 - - - -
3960B LEU* 3.3 13.4 + - + +
3961B THR 3.2 0.8 - - - -
3962B GLU* 1.3 81.2 - - + +
3964B ILE* 1.3 57.7 + - + +
3965B GLN 3.6 0.6 + - - -
3968B CYS* 3.7 4.5 - - - +
3971B ASN* 3.1 40.4 - - + +
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Residues in contact with ILE3964 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960B LEU 3.5 9.5 + - - +
3961B THR* 3.1 9.1 + - - +
3963B TYR* 1.3 78.7 - - - +
3965B GLN* 1.3 66.0 + - - +
3966B GLY 3.6 5.2 - - - +
3968B CYS* 3.6 17.1 - - - -
3971B ASN* 4.6 7.6 - - + +
3972B GLN* 5.2 6.3 - - + -
3975B LEU* 5.5 8.3 - - + -
4021B MET 6.0 0.7 - - - +
4024B SER* 3.2 25.9 - - - +
4025B LEU* 5.1 9.2 - - + -
----------------------------------------------------------
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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