Contacts of the helix formed by residues 3939 - 3964 (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 GLU3939 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3846F ASN* 5.8 2.7 - - - +
3932F TYR* 3.5 29.6 - - + +
3937F VAL 4.2 0.8 + - - -
3938F ILE* 1.3 83.0 - - - +
3940F GLU* 1.3 64.8 + - - +
3941F GLN* 3.3 5.2 - - + +
3942F GLY* 3.4 8.5 + - - +
3943F LYS* 3.3 18.0 + - - +
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Residues in contact with GLU3940 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938F ILE 3.7 2.0 + - - -
3939F GLU* 1.3 71.3 - - - +
3941F GLN* 1.3 69.9 + - + +
3943F LYS* 3.3 15.9 + - - +
3944F ARG* 3.5 11.4 + - - +
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Residues in contact with GLN3941 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842F PHE* 4.5 1.8 - - + -
3846F ASN* 3.9 26.9 - - - +
3939F GLU* 3.3 4.6 - - + +
3940F GLU* 1.3 81.2 - - + +
3942F GLY* 1.3 61.4 + - - +
3944F ARG* 3.4 37.4 + - - +
3945F ASN* 3.1 22.0 + - - +
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Residues in contact with GLY3942 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842F PHE* 3.8 23.9 - - - -
3928F PHE* 3.5 21.0 - - - -
3932F TYR* 4.6 5.6 - - - -
3938F ILE* 5.4 1.3 - - - -
3939F GLU* 3.4 10.9 + - - +
3940F GLU 3.3 0.6 - - - -
3941F GLN* 1.3 75.6 - - - +
3943F LYS* 1.3 60.4 + - - +
3945F ASN* 3.6 1.7 + - - +
3946F PHE* 3.1 29.1 + - - +
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Residues in contact with LYS3943 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3938F ILE* 4.9 6.0 - - + +
3939F GLU 3.3 11.9 + - - +
3940F GLU* 3.6 12.1 - - - +
3941F GLN 3.2 0.8 - - - -
3942F GLY* 1.3 77.6 - - - +
3944F ARG* 1.3 57.5 + - - +
3946F PHE* 4.0 1.5 - - - +
3947F SER* 3.1 28.2 + - - -
4004F GLN* 6.5 1.3 - - + -
4007F LEU* 3.8 29.3 - - + +
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Residues in contact with ARG3944 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3867F GLU* 4.9 17.8 - - - +
3869F VAL* 5.1 4.0 - - - +
3940F GLU 3.5 8.2 + - - +
3941F GLN* 3.4 29.2 + - - +
3942F GLY 3.3 0.6 - - - -
3943F LYS* 1.3 77.0 - - - +
3945F ASN* 1.3 91.9 + - - +
3947F SER* 3.4 7.0 + - - -
3948F LYS* 3.2 21.7 + - + +
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Residues in contact with ASN3945 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3842F PHE* 3.2 22.1 - - + -
3867F GLU* 6.1 1.0 - - - +
3869F VAL* 3.4 44.9 - - + +
3870F MET* 4.8 10.1 - - + +
3928F PHE* 5.8 2.7 - - + -
3941F GLN* 3.1 18.1 + - - +
3942F GLY 3.6 4.7 + - - +
3944F ARG* 1.3 102.6 + - - +
3946F PHE* 1.3 58.2 + - - +
3948F LYS* 3.5 7.2 + - - +
3949F ALA* 3.1 26.3 + - - +
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Residues in contact with PHE3946 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925F ILE* 3.7 30.3 - - + -
3928F PHE* 3.9 29.1 - + + -
3942F GLY 3.1 19.0 + - - +
3943F LYS* 4.0 5.8 - - - +
3944F ARG 3.3 0.2 - - - -
3945F ASN* 1.3 75.5 - - - +
3947F SER* 1.3 62.0 + - - +
3949F ALA* 3.3 9.4 + - + +
3950F MET* 2.8 40.2 + - + +
3991F PHE* 5.4 4.3 - + - -
3994F MET* 3.5 26.7 - - + -
4007F LEU* 4.0 24.7 - - + -
4011F LEU* 3.5 27.8 - - + -
4014F LEU* 6.2 2.7 - - + -
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Residues in contact with SER3947 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3943F LYS 3.1 18.3 + - - -
3944F ARG* 3.7 6.7 - - - -
3945F ASN 3.4 0.4 - - - -
3946F PHE* 1.3 80.0 - - - +
3948F LYS* 1.3 58.9 + - - +
3950F MET* 3.4 8.3 + - - +
3951F SER* 3.0 26.2 + - - -
4007F LEU* 6.1 2.9 - - - -
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Residues in contact with LYS3948 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870F MET* 4.8 13.7 - - + -
3873F ASP* 5.6 10.5 - - + -
3944F ARG* 3.2 13.4 + - + +
3945F ASN* 3.8 10.5 - - - +
3946F PHE 3.3 0.2 - - - -
3947F SER* 1.3 77.2 + - - +
3949F ALA* 1.3 61.0 + - - +
3951F SER* 3.3 16.2 + - - -
3952F VAL* 3.3 17.9 + - - +
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Residues in contact with ALA3949 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3837F LEU* 5.3 9.0 - - + -
3870F MET* 4.7 18.3 - - + +
3921F LEU* 5.4 6.7 - - + +
3925F ILE* 5.1 14.3 - - + +
3945F ASN 3.1 17.6 + - - +
3946F PHE* 3.3 12.3 + - + +
3948F LYS* 1.3 74.7 - - - +
3950F MET* 1.3 59.9 + - - +
3952F VAL* 3.3 10.1 + - - +
3953F ALA* 2.9 27.5 + - - +
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Residues in contact with MET3950 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3925F ILE* 6.3 0.4 - - - -
3946F PHE* 2.8 31.3 + - + +
3947F SER* 3.6 10.3 - - - +
3948F LYS 3.2 0.2 - - - -
3949F ALA* 1.3 75.8 - - - +
3951F SER* 1.3 59.8 + - - +
3953F ALA* 3.3 7.1 + - - +
3954F LYS* 2.9 29.8 + - - +
4010F GLU* 5.3 15.9 - - + +
4011F LEU* 5.9 2.2 - - - -
4014F LEU* 5.2 13.5 - - + +
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Residues in contact with SER3951 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3947F SER* 3.0 14.4 + - - -
3948F LYS* 3.3 10.4 + - - -
3949F ALA 3.3 0.4 - - - -
3950F MET* 1.3 79.7 - - - +
3952F VAL* 1.3 61.7 + - - +
3954F LYS* 3.4 9.6 + - - +
3955F GLN* 3.3 27.0 + - - +
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Residues in contact with VAL3952 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3870F MET* 4.9 13.7 - - + -
3872F ASP 5.9 1.3 - - - +
3873F ASP* 6.0 5.4 - - - -
3876F THR* 3.7 28.5 - - + +
3877F GLN* 5.6 9.2 - - + +
3880F PHE* 5.3 3.6 - - + -
3917F TYR* 3.5 27.8 - - + +
3921F LEU* 4.9 5.2 - - + -
3948F LYS 3.3 16.6 - - - +
3949F ALA* 3.3 9.8 + - - +
3950F MET 3.3 0.6 - - - -
3951F SER* 1.3 78.1 - - - +
3953F ALA* 1.3 62.4 + - - +
3954F LYS 3.4 0.5 + - - -
3955F GLN* 3.5 4.1 + - - +
3956F VAL* 3.3 22.7 + - - +
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Residues in contact with ALA3953 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3921F LEU* 4.1 16.8 - - + +
3925F ILE* 4.4 12.6 - - + -
3949F ALA 2.9 17.7 + - - +
3950F MET* 3.3 6.3 + - - +
3952F VAL* 1.3 76.3 - - - +
3954F LYS* 1.3 57.6 + - - +
3956F VAL* 3.3 11.5 - - - +
3957F PHE* 3.1 31.8 - - + -
3987F PHE* 5.8 1.8 - - + -
4014F LEU* 3.4 23.4 - - + +
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Residues in contact with LYS3954 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3950F MET 2.9 16.3 + - - +
3951F SER* 3.7 10.1 - - - +
3952F VAL 3.2 0.4 - - - -
3953F ALA* 1.3 77.4 - - - +
3955F GLN* 1.3 71.4 + - + +
3957F PHE* 3.6 5.4 + - - +
3958F ASN* 3.0 35.5 + - - +
4013F ASP* 5.2 14.0 - - + +
4014F LEU* 4.2 12.3 - - + -
4016F LYS* 5.6 3.4 - - - +
4017F ASP* 3.5 27.5 - - - +
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Residues in contact with GLN3955 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3877F GLN* 5.0 18.8 - - + +
3880F PHE* 4.6 14.5 - - + +
3881F ARG* 3.6 36.6 + - - +
3884F GLN* 5.4 1.6 - - - +
3951F SER 3.3 15.2 + - - +
3952F VAL* 3.5 4.7 + - - +
3954F LYS* 1.3 87.3 - - + +
3956F VAL* 1.3 63.5 + - - +
3958F ASN* 2.8 41.6 + - - +
3959F SER* 3.5 10.9 + - - -
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Residues in contact with VAL3956 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880F PHE* 4.4 20.6 - - + +
3914F THR* 5.2 2.2 - - + +
3917F TYR* 4.3 16.4 - - + -
3918F LEU* 3.8 34.8 - - + -
3921F LEU* 4.3 9.6 - - + -
3952F VAL 3.3 15.6 + - - +
3953F ALA* 3.3 23.1 - - - +
3955F GLN* 1.3 77.2 - - - +
3957F PHE* 1.3 70.2 + - + +
3959F SER* 2.3 37.6 + - - +
3960F LEU* 3.1 9.3 - - + +
----------------------------------------------------------
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Residues in contact with PHE3957 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3918F LEU* 3.9 19.7 - - + -
3921F LEU* 6.3 0.2 - - + -
3953F ALA* 3.1 24.7 - - + -
3954F LYS 3.6 7.3 + - - +
3955F GLN 3.4 0.2 - - - -
3956F VAL* 1.3 85.0 - - + +
3958F ASN* 1.3 61.3 + - - +
3959F SER 3.1 1.3 + - - -
3960F LEU* 3.6 12.4 + - + +
3961F THR* 3.3 22.5 + - - +
3983F ALA* 5.7 1.8 - - + -
3984F VAL* 4.6 13.7 - - + -
3987F PHE* 3.6 39.3 - + - -
4014F LEU* 3.9 17.5 - - + -
4017F ASP* 4.3 19.9 - - + +
4018F MET* 3.7 30.7 - - + -
4021F MET* 5.3 9.0 - - + +
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Residues in contact with ASN3958 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3881F ARG* 5.3 3.5 - - - +
3884F GLN* 4.3 6.4 - - + +
3954F LYS* 3.0 27.9 + - - +
3955F GLN* 2.8 37.4 + - - +
3956F VAL 3.1 1.0 - - - -
3957F PHE* 1.3 77.8 - - - +
3959F SER* 1.3 56.4 + - - +
3961F THR* 3.3 14.1 - - + +
3962F GLU* 3.2 26.5 - - - +
4017F ASP* 4.1 18.4 - - - +
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Residues in contact with SER3959 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3880F PHE* 4.5 16.4 - - - -
3883F LEU* 5.8 0.4 - - - -
3884F GLN* 4.1 18.4 - - - -
3914F THR* 4.7 5.6 - - - +
3955F GLN 3.5 8.1 + - - -
3956F VAL* 2.3 33.3 + - - +
3958F ASN* 1.3 78.2 - - - +
3960F LEU* 1.3 68.0 + - - +
3961F THR 3.3 0.4 - - - -
3962F GLU* 3.5 1.7 + - - +
3963F TYR* 3.2 45.4 + - - -
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Residues in contact with LEU3960 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3914F THR* 5.0 8.5 - - + -
3915F VAL* 3.7 30.1 - - + -
3918F LEU* 4.1 28.3 - - + -
3956F VAL* 3.1 29.6 - - + +
3957F PHE* 3.6 19.7 + - + +
3959F SER* 1.3 84.0 + - - +
3961F THR* 1.3 62.6 + - - +
3963F TYR* 3.3 20.8 + - + +
3964F ILE* 3.5 13.3 + - - +
3975F LEU* 4.1 27.5 - - + +
3980F LEU* 4.9 6.5 - - + -
4021F MET* 5.9 6.1 - - + -
----------------------------------------------------------
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Residues in contact with THR3961 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3957F PHE 3.3 18.9 + - - +
3958F ASN* 3.3 19.1 - - - +
3960F LEU* 1.3 78.4 - - - +
3962F GLU* 1.3 65.5 + - + +
3964F ILE* 3.1 5.5 + - - -
3965F GLN* 2.8 49.6 + - - +
4017F ASP 5.5 2.9 - - - +
4020F VAL* 4.9 10.4 + - + +
4021F MET* 4.7 17.0 - - - +
4024F SER* 3.5 17.5 + - - -
----------------------------------------------------------
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Residues in contact with GLU3962 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3884F GLN* 4.0 25.4 - - + +
3887F CYS* 3.2 35.6 - - + +
3888F GLU* 3.9 10.4 - - - +
3890F HIS* 4.0 7.2 + - - -
3895F GLN* 6.0 0.3 - - - +
3958F ASN 3.2 19.7 - - - +
3959F SER* 3.5 7.1 + - - +
3960F LEU 3.3 0.4 - - - -
3961F THR* 1.3 80.7 - - + +
3963F TYR* 1.3 65.1 + - + +
3964F ILE 3.5 0.2 + - - -
3965F GLN* 3.6 33.2 + - - +
4999F THR* 4.6 13.7 + - - +
----------------------------------------------------------
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Residues in contact with TYR3963 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3883F LEU* 3.4 46.9 + - - +
3884F GLN* 5.0 2.5 - - - -
3887F CYS* 5.1 12.8 - - + -
3895F GLN* 4.8 9.5 - - + +
3898F LEU* 4.2 24.4 - - + +
3910F ILE* 5.5 1.4 - - + +
3911F ILE* 3.7 24.2 - - + -
3914F THR* 4.3 21.2 + - + +
3959F SER* 3.2 30.2 - - - -
3960F LEU* 3.3 12.3 + - + +
3961F THR 3.2 0.6 - - - -
3962F GLU* 1.3 80.5 - - + +
3964F ILE* 1.3 59.2 + - + +
3965F GLN 3.6 0.2 - - - -
3968F CYS* 3.7 5.0 - - - +
3971F ASN* 3.1 39.9 + - + +
----------------------------------------------------------
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Residues in contact with ILE3964 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3960F LEU 3.5 10.0 + - - +
3961F THR* 3.1 7.7 + - - +
3963F TYR* 1.3 78.0 - - + +
3965F GLN* 1.3 66.5 + - - +
3966F GLY 3.6 5.7 - - - +
3968F CYS* 3.6 17.8 - - - -
3971F ASN* 4.6 8.3 - - + +
3972F GLN* 5.2 6.1 - - + +
3975F LEU* 5.5 8.3 - - + -
4021F MET 6.0 0.4 - - - +
4024F SER* 3.2 26.0 - - - +
4025F LEU* 5.1 9.6 - - + -
----------------------------------------------------------
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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