Contacts of the helix formed by residues 4004 - 4026 (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 GLN4004 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3937F VAL* 6.0 0.8 - - - +
3938F ILE* 3.7 38.2 + - - +
3997F LYS 3.8 5.3 + - - -
3998F LEU* 3.4 46.8 - - + +
4001F ASP* 3.6 34.8 - - + +
4002F SER 3.3 0.4 - - - -
4003F SER* 1.3 79.1 - - - +
4005F ILE* 1.3 62.1 + - - +
4006F GLU* 3.2 4.3 - - - +
4007F LEU* 3.4 15.0 + - + +
4008F LEU 3.7 6.4 + - - -
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Residues in contact with ILE4005 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3998F LEU 4.9 4.5 - - - +
3999F ALA* 5.6 5.6 - - + -
4001F ASP 4.1 3.7 + - - +
4002F SER* 3.9 19.0 + - - +
4003F SER 3.6 1.3 - - - -
4004F GLN* 1.3 75.7 - - - +
4006F GLU* 1.3 64.0 + - + +
4008F LEU* 3.2 17.5 + - + +
4009F LYS* 2.9 32.9 + - + +
4126F ARG* 5.3 7.9 - - + +
4127F PHE* 4.8 21.8 - - + -
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Residues in contact with GLU4006 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4003F SER 5.1 2.0 + - - +
4004F GLN* 3.2 3.0 - - - +
4005F ILE* 1.3 84.8 - - + +
4007F LEU* 1.3 59.2 + - - +
4009F LYS* 3.6 6.6 + - - +
4010F GLU* 3.4 21.0 + - - +
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Residues in contact with LEU4007 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3938F ILE* 5.4 6.1 - - + -
3943F LYS* 3.8 38.1 - - + +
3946F PHE* 4.0 24.0 - - + -
3947F SER* 6.0 2.7 - - - +
3994F MET* 5.8 0.4 - - + -
3998F LEU* 3.6 33.4 - - + -
4004F GLN* 3.4 15.0 + - + +
4005F ILE 3.2 0.6 - - - -
4006F GLU* 1.3 78.5 - - - +
4008F LEU* 1.3 59.4 + - - +
4010F GLU* 3.4 5.1 + - - +
4011F LEU* 2.8 49.5 + - + +
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Residues in contact with LEU4008 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3995F MET* 5.8 4.0 - - - +
3998F LEU* 4.0 24.7 - - + +
3999F ALA* 5.3 2.0 - - + +
4004F GLN 3.7 4.0 + - - +
4005F ILE* 3.2 24.1 + - + +
4007F LEU* 1.3 81.9 - - - +
4009F LYS* 1.3 61.7 + - - +
4011F LEU* 3.8 8.3 - - - +
4012F LEU* 3.1 25.3 + - - +
4130F PRO* 5.7 0.2 - - - +
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Residues in contact with LYS4009 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4005F ILE* 2.9 22.3 + - + +
4006F GLU* 3.8 9.0 - - - +
4007F LEU 3.2 0.2 - - - -
4008F LEU* 1.3 77.6 - - - +
4010F GLU* 1.3 58.9 + - - +
4012F LEU* 3.6 3.2 + - - +
4013F ASP* 2.9 30.0 + - - +
4130F PRO* 4.8 21.6 - - + +
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Residues in contact with GLU4010 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3947F SER* 5.9 5.4 - - - +
3950F MET* 5.3 12.5 - - + +
4006F GLU 3.4 13.1 + - - +
4007F LEU* 3.4 5.7 + - - +
4009F LYS* 1.3 75.6 - - - +
4011F LEU* 1.3 65.9 + - - +
4013F ASP* 3.4 22.3 + - - +
4014F LEU* 3.7 5.9 + - - +
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Residues in contact with LEU4011 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3946F PHE* 3.5 38.8 - - + -
3950F MET* 5.9 3.4 - - - -
3991F PHE* 4.1 18.6 - - + +
3994F MET* 3.7 27.4 - - + -
3995F MET* 5.5 8.1 - - + +
3998F LEU* 5.5 2.2 - - + -
4007F LEU* 2.8 27.2 + - + +
4008F LEU* 3.8 8.3 - - - +
4009F LYS 3.3 0.2 - - - -
4010F GLU* 1.3 76.2 - - - +
4012F LEU* 1.3 59.0 + - - +
4014F LEU* 2.9 24.4 + - + +
4015F GLN* 3.0 49.7 + - - +
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Residues in contact with LEU4012 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4008F LEU 3.1 17.6 + - - +
4009F LYS 4.0 4.0 - - - +
4011F LEU* 1.3 77.3 - - - +
4013F ASP* 1.3 61.9 + - - +
4014F LEU 3.3 0.5 + - - -
4015F GLN* 3.3 19.4 + - + +
4016F LYS* 3.4 18.6 + - + +
4057F PHE* 4.3 15.3 - - + -
4130F PRO* 3.5 43.1 - - + +
4131F ALA* 4.0 4.3 - - + +
4134F ILE* 3.7 33.2 - - + -
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Residues in contact with ASP4013 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954F LYS* 5.3 12.6 - - + +
4009F LYS* 2.9 19.7 - - - +
4010F GLU* 3.5 17.0 - - - +
4011F LEU 3.1 0.6 - - - -
4012F LEU* 1.3 78.9 - - - +
4014F LEU* 1.3 57.0 - - - +
4016F LYS* 3.2 32.2 - - - +
4017F ASP* 2.8 30.3 - - - +
4130F PRO* 5.2 6.6 - - - +
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Residues in contact with LEU4014 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3925F ILE* 5.8 3.8 - - + -
3946F PHE* 6.2 2.9 - - + -
3950F MET* 5.2 14.6 - - + +
3953F ALA* 3.4 45.5 - - + +
3954F LYS* 4.2 9.0 - - + -
3957F PHE* 3.9 19.1 - - + -
3987F PHE* 6.3 1.8 - - + -
3991F PHE* 3.7 30.3 - - + -
4010F GLU 3.7 5.2 + - - +
4011F LEU* 2.9 16.9 + - + +
4013F ASP* 1.3 77.9 - - - +
4015F GLN* 1.3 70.2 + - - +
4017F ASP* 3.3 7.9 + - + +
4018F MET* 3.3 17.3 + - + +
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Residues in contact with GLN4015 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3988F LEU* 4.8 11.4 - - + -
3991F PHE* 3.1 50.9 - - + +
4011F LEU* 3.0 41.8 + - - +
4012F LEU* 3.3 28.8 + - + +
4014F LEU* 1.3 80.7 - - - +
4016F LYS* 1.3 58.2 + - - +
4018F MET* 3.2 7.0 + - - +
4019F VAL* 2.9 31.8 + - - +
4134F ILE* 4.7 9.3 - - + +
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Residues in contact with LYS4016 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954F LYS* 5.6 4.2 - - - +
4012F LEU* 3.4 8.7 + - + +
4013F ASP* 3.2 46.8 + - - +
4015F GLN* 1.3 78.9 - - - +
4017F ASP* 1.3 84.0 + - - +
4018F MET 3.7 0.2 + - - -
4020F VAL* 3.7 11.3 + - - +
4130F PRO 6.0 0.9 - - - +
4133F ASP* 3.7 40.1 + - + +
4134F ILE* 4.5 16.0 - - + +
4137F ASN* 3.3 23.7 + - - +
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Residues in contact with ASP4017 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3954F LYS* 3.5 34.3 - - - +
3957F PHE* 4.3 19.6 - - + +
3958F ASN* 4.1 18.7 - - - +
3961F THR* 5.5 1.6 - - - +
4013F ASP 2.8 17.9 - - - +
4014F LEU* 3.3 7.8 + - + +
4015F GLN 3.2 0.6 - - - -
4016F LYS* 1.3 101.9 + - - +
4018F MET* 1.3 58.0 + - - +
4019F VAL 3.6 0.2 - - - -
4020F VAL* 3.3 22.1 - - + +
4021F MET* 4.2 4.9 + - - +
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Residues in contact with MET4018 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957F PHE* 3.7 36.8 - - + -
3984F VAL* 5.1 10.7 - - + +
4014F LEU* 3.3 11.8 + - + +
4015F GLN* 3.2 11.3 + - - +
4017F ASP* 1.3 76.7 - - - +
4019F VAL* 1.3 62.8 + - - +
4020F VAL 3.2 1.8 - - - -
4021F MET* 3.3 13.2 + - - +
4022F LEU* 3.3 15.2 - - - +
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Residues in contact with VAL4019 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4015F GLN 2.9 16.5 + - - +
4017F ASP 3.6 0.2 - - - -
4018F MET* 1.3 75.4 - - - +
4020F VAL* 1.3 63.4 + - - +
4021F MET 3.3 0.5 + - - -
4022F LEU* 3.4 23.3 + - + +
4023F LEU* 3.5 14.1 + - - +
4134F ILE* 4.6 10.1 - - + -
4137F ASN* 4.1 21.7 - - - +
4138F VAL* 6.0 0.4 - - + -
4141F LEU* 4.3 18.0 - - + +
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Residues in contact with VAL4020 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3961F THR* 4.9 11.2 + - + +
4016F LYS 3.7 11.2 + - - +
4017F ASP* 3.3 24.7 - - - +
4019F VAL* 1.3 76.3 - - - +
4021F MET* 1.3 68.0 + - - +
4022F LEU 3.3 0.2 - - - -
4023F LEU* 3.2 32.8 + - + +
4024F SER* 3.2 14.6 + - - -
4137F ASN* 4.3 6.0 - - - +
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Residues in contact with MET4021 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3957F PHE* 5.3 9.2 - - + +
3960F LEU* 5.9 4.7 - - + -
3961F THR* 4.7 17.7 - - - +
3964F ILE* 6.0 0.7 - - - +
4017F ASP 4.6 5.6 - - - +
4018F MET* 3.3 16.7 + - - +
4019F VAL 3.2 1.0 - - - -
4020F VAL* 1.3 83.8 - - - +
4022F LEU* 1.3 58.7 + - + +
4024F SER* 3.2 9.2 + - - -
4025F LEU* 3.1 26.5 + - - +
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Residues in contact with LEU4022 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3984F VAL* 5.7 14.6 - - + -
4018F MET 3.3 21.1 - - - +
4019F VAL* 3.4 16.8 - - + +
4020F VAL 3.3 0.2 - - - -
4021F MET* 1.3 75.4 - - + +
4023F LEU* 1.3 67.5 + - + +
4025F LEU* 3.3 20.5 + - + +
4026F LEU* 3.4 15.4 + - - +
4039F MET* 4.0 30.7 - - + +
4042F MET* 6.5 1.1 - - + -
4141F LEU* 5.6 7.2 - - + -
4144F ASN* 5.9 0.3 + - - -
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Residues in contact with LEU4023 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4019F VAL 3.5 12.1 - - - +
4020F VAL* 3.2 25.3 + - + +
4022F LEU* 1.3 79.9 - - + +
4024F SER* 1.3 60.6 + - - +
4025F LEU 3.3 0.5 + - - -
4026F LEU* 3.4 11.8 + - - +
4027F GLU* 3.4 12.1 + - - +
4137F ASN* 3.3 24.5 - - - +
4140F VAL* 4.3 12.8 - - + +
4141F LEU* 3.7 36.1 - - + +
4144F ASN* 5.7 7.9 - - + +
4189F TYR 5.9 2.2 - - - +
5002F THR* 5.7 0.4 - - - -
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Residues in contact with SER4024 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3961F THR* 3.5 22.1 + - - -
3964F ILE* 3.2 27.7 + - - +
3965F GLN* 4.5 12.0 - - - +
3966F GLY 5.4 0.5 - - - +
3972F GLN* 5.3 2.4 - - - +
4020F VAL* 3.2 11.2 + - - +
4021F MET* 3.2 12.5 + - - -
4023F LEU* 1.3 76.1 - - - +
4025F LEU* 1.3 62.3 + - - +
4026F LEU 3.3 0.2 - - - -
4027F GLU* 3.8 14.1 + - - +
5002F THR* 4.4 20.2 - - - -
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Residues in contact with LEU4025 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3964F ILE* 5.1 9.9 - - + -
3972F GLN* 4.0 32.0 + - + +
3975F LEU* 3.7 31.0 - - + -
3976F ALA* 6.0 3.4 - - + +
4021F MET 3.1 18.7 + - - +
4022F LEU* 3.5 12.8 - - + +
4023F LEU 3.1 0.4 - - - -
4024F SER* 1.3 79.7 - - - +
4026F LEU* 1.3 62.9 + - + +
4027F GLU 3.8 0.5 + - - -
4035F ILE* 4.2 18.2 - - + +
4039F MET* 3.7 38.4 - - + -
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Residues in contact with LEU4026 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4022F LEU 3.4 11.9 + - - +
4023F LEU 3.6 5.4 - - - +
4024F SER 3.3 0.2 - - - -
4025F LEU* 1.3 84.4 - - + +
4027F GLU* 1.3 65.0 + - - +
4028F GLY* 3.6 1.3 - - - -
4029F ASN* 3.7 30.4 + - + +
4030F VAL 5.0 1.1 - - - +
4035F ILE* 4.9 6.3 - - + -
4036F ALA* 4.1 26.7 - - + +
4039F MET* 3.7 24.0 - - + -
4144F ASN* 4.1 18.0 + - - +
4145F LEU* 5.5 6.5 - - + -
4148F HIS* 3.5 38.2 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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