Contacts of the helix formed by residues 4831 - 4856 (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 ASN4831 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4829F THR 3.4 0.4 + - - -
4830F HIS* 1.3 96.1 + - + +
4832F GLY* 1.3 60.7 + - - +
4833F LYS* 3.3 3.4 - - - +
4834F GLN* 2.9 32.8 + - - +
4835F LEU* 3.9 6.8 + - - +
4933F LEU* 5.6 14.6 - - + +
4937F ALA* 5.1 5.6 - - + -
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Residues in contact with GLY4832 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4828F VAL 5.0 0.2 - - - -
4829F THR* 3.0 18.7 + - - -
4830F HIS 4.2 0.7 - - - -
4831F ASN* 1.3 74.5 - - - +
4833F LYS* 1.3 63.8 + - - +
4834F GLN 3.2 2.7 - - - -
4835F LEU* 3.1 26.2 + - - +
4836F VAL* 3.3 15.2 + - - +
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Residues in contact with LYS4833 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4831F ASN* 3.3 1.2 - - - -
4832F GLY* 1.3 78.6 - - - +
4834F GLN* 1.3 65.8 + - - +
4836F VAL* 3.3 22.2 - - - +
4837F MET* 3.8 7.4 + - - +
4820H THR* 4.7 4.4 - - - +
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Residues in contact with GLN4834 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4831F ASN* 2.9 34.2 - - - +
4833F LYS* 1.3 84.0 + - - +
4835F LEU* 1.3 63.6 + - - +
4837F MET* 3.1 3.3 + - - +
4838F THR* 3.0 26.4 + - + +
4933F LEU* 4.9 22.7 - - + +
4820H THR* 3.8 29.5 + - + +
4938H PHE* 6.1 4.0 - - + -
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Residues in contact with LEU4835 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4828F VAL* 3.6 29.4 - - + +
4830F HIS 6.0 0.2 - - - +
4831F ASN 3.9 4.5 + - - +
4832F GLY* 3.1 19.4 + - - +
4834F GLN* 1.3 78.0 - - - +
4836F VAL* 1.3 63.9 + - - +
4838F THR* 3.3 10.4 - - + +
4839F VAL* 3.1 47.5 + - + +
4930F ILE* 5.6 7.6 - - + -
4933F LEU* 6.4 3.3 - - + +
4934F ILE* 4.1 20.2 - - + -
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Residues in contact with VAL4836 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4832F GLY 3.3 9.2 + - - +
4833F LYS* 3.3 23.1 - - - +
4835F LEU* 1.3 80.5 - - - +
4837F MET* 1.3 56.9 - - + +
4839F VAL* 4.1 5.5 - - + +
4840F GLY* 3.0 23.0 + - - -
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Residues in contact with MET4837 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4833F LYS 3.9 6.7 - - - +
4834F GLN 3.1 9.7 + - - +
4836F VAL* 1.3 81.3 - - + +
4838F THR* 1.3 54.3 + - - +
4840F GLY* 3.2 3.2 + - - -
4841F LEU* 2.7 38.3 + - + +
4818H VAL* 6.1 2.2 - - + -
4820H THR* 3.7 28.0 - - + -
4821H LEU* 5.0 10.3 - - + +
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Residues in contact with THR4838 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4834F GLN* 3.0 20.1 + - + +
4835F LEU* 3.3 16.6 - - + +
4837F MET* 1.3 71.0 - - - +
4839F VAL* 1.3 53.1 + - - +
4841F LEU* 3.1 16.2 + - - +
4842F LEU* 2.5 35.0 + - - +
4926F LEU* 4.6 3.3 + - - +
4929F ILE* 4.1 29.9 - - + +
4930F ILE* 3.3 27.8 - - + +
4933F LEU* 5.9 3.4 - - + -
4824H ILE* 5.7 2.5 - - - -
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Residues in contact with VAL4839 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920D PHE* 6.2 6.1 - - + -
4835F LEU* 3.1 35.9 + - + +
4836F VAL* 4.1 6.3 - - + +
4838F THR* 1.3 77.7 - - - +
4840F GLY* 1.3 57.8 + - - +
4842F LEU* 3.1 17.6 + - + +
4843F ALA* 2.9 28.5 + - + +
4885F MET* 6.5 0.4 - - + -
4930F ILE* 4.3 14.8 - - + -
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Residues in contact with GLY4840 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4836F VAL 3.0 17.0 + - - -
4837F MET 3.2 3.8 + - - -
4839F VAL* 1.3 78.1 - - - +
4841F LEU* 1.3 59.6 + - - +
4843F ALA* 3.2 7.3 + - - +
4844F VAL* 3.2 29.0 + - - +
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Residues in contact with LEU4841 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4837F MET 2.7 20.9 + - - +
4838F THR* 3.1 15.5 + - - +
4840F GLY* 1.3 74.7 - - - +
4842F LEU* 1.3 61.1 + - - +
4844F VAL* 3.2 17.6 - - + +
4845F VAL* 3.2 21.8 - - + +
4815H ALA* 4.1 25.8 - - + +
4821H LEU* 3.6 37.7 - - + +
4824H ILE* 3.7 35.7 - - + -
4825H LEU* 6.5 1.6 - - + -
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Residues in contact with LEU4842 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920D PHE* 5.3 7.6 - - + -
4838F THR* 2.5 20.2 + - - +
4839F VAL* 3.1 17.7 + - + +
4841F LEU* 1.3 75.0 - - - +
4843F ALA* 1.3 61.5 + - + +
4844F VAL 3.4 0.2 - - - -
4845F VAL* 3.3 15.3 - - + +
4846F VAL* 3.2 22.8 - - + +
4885F MET* 3.7 35.2 - - + -
4889F VAL* 5.0 12.8 - - + -
4922F VAL* 5.4 3.4 - - + +
4926F LEU* 4.6 22.2 - - + -
4927F LEU* 4.7 15.7 - - + -
4930F ILE* 4.8 15.7 - - + -
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Residues in contact with ALA4843 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4839F VAL* 2.9 15.0 + - + +
4840F GLY* 3.2 9.3 + - - +
4842F LEU* 1.3 82.8 - - + +
4844F VAL* 1.3 62.9 + - + +
4845F VAL 3.5 0.2 - - - -
4846F VAL* 3.3 14.5 - - - +
4847F TYR* 3.4 9.4 + - - +
4881F TYR* 3.2 25.4 + - - +
4885F MET* 6.0 1.3 - - + -
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Residues in contact with VAL4844 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4840F GLY 3.2 14.5 + - - +
4841F LEU* 3.2 31.0 - - + +
4843F ALA* 1.3 80.3 - - + +
4845F VAL* 1.3 67.5 + - + +
4846F VAL 3.3 0.2 - - - -
4847F TYR* 3.1 8.9 + - + +
4848F LEU* 3.0 32.2 + - + +
4569H PHE* 6.2 4.7 - - + -
4811H LEU* 4.9 19.7 - - + +
4814H ILE* 5.7 5.2 - - + -
4815H ALA* 4.9 10.3 - - + -
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Residues in contact with VAL4845 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4841F LEU* 3.2 21.8 - - + +
4842F LEU* 3.3 17.5 - - + +
4844F VAL* 1.3 83.1 - - + +
4846F VAL* 1.3 63.7 + - + +
4848F LEU* 3.4 14.6 + - + +
4849F TYR* 3.1 35.1 + - + -
4922F VAL* 4.0 24.0 - - + -
4926F LEU* 5.8 3.6 - - + -
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Residues in contact with VAL4846 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4842F LEU* 3.2 23.8 - - + +
4843F ALA* 3.3 17.5 - - - +
4845F VAL* 1.3 75.5 - - - +
4847F TYR* 1.3 53.4 + - - +
4849F TYR* 3.4 7.9 + - - +
4850F THR* 2.3 39.7 + - - +
4881F TYR* 4.1 13.9 - - + +
4884F HIS* 5.2 14.1 + - + +
4885F MET* 4.8 19.7 - - + -
4889F VAL* 5.4 8.1 - - + -
4918F PHE* 4.5 14.8 - - + -
4922F VAL* 4.4 20.0 - - + -
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Residues in contact with TYR4847 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4843F ALA 3.4 12.5 + - - +
4844F VAL* 3.1 14.6 + - + +
4846F VAL* 1.3 81.0 - - - +
4848F LEU* 1.3 74.8 + - + +
4850F THR* 3.2 16.6 + - + -
4851F VAL* 3.3 33.0 + - + +
4881F TYR* 4.1 23.6 - + + -
4572H ASN* 3.1 49.2 + - + +
4575H LEU* 4.4 12.0 - - - +
4576H LEU* 4.8 11.2 + - + -
4808H ALA* 4.9 11.4 - - + -
4811H LEU* 4.9 7.9 - - + -
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Residues in contact with LEU4848 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4844F VAL* 3.0 17.8 + - + +
4845F VAL* 3.8 13.9 - - + +
4846F VAL 3.3 0.2 - - - -
4847F TYR* 1.3 82.2 - - + +
4849F TYR* 1.3 63.1 + - + +
4851F VAL* 3.2 11.7 - - - +
4852F VAL* 3.2 23.7 - - - +
4808H ALA* 3.3 35.7 - - + +
4811H LEU* 4.1 14.6 - - + -
4812H LEU* 4.7 18.8 - - + -
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Residues in contact with TYR4849 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4845F VAL* 3.1 30.4 + - + +
4846F VAL* 3.7 6.3 - - - +
4847F TYR 3.3 0.4 - - - -
4848F LEU* 1.3 79.6 - - + +
4850F THR* 1.3 61.4 + - - +
4851F VAL 3.5 0.2 - - - -
4852F VAL* 3.3 19.9 - - + +
4853F ALA* 3.5 11.6 + - - +
4884F HIS* 4.5 6.2 + - - +
4914F PHE* 3.5 36.9 - + + -
4917F THR* 3.6 31.5 + - + +
4918F PHE* 3.8 39.9 - + + -
4921F PHE* 4.3 12.0 - + + -
4922F VAL* 4.9 7.6 - - + -
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Residues in contact with THR4850 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4846F VAL* 2.3 27.7 + - - +
4847F TYR* 3.5 13.7 - - + -
4848F LEU 3.2 0.6 - - - -
4849F TYR* 1.3 77.0 - - - +
4851F VAL* 1.3 62.3 + - + +
4852F VAL 3.2 0.4 - - - -
4853F ALA* 3.2 3.5 + - - +
4854F PHE* 3.0 27.5 + - + +
4877F MET 4.6 5.2 - - - +
4880F CYS* 3.9 28.1 - - + +
4881F TYR* 3.9 28.2 - - + +
4884F HIS* 4.0 17.2 + - - +
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Residues in contact with VAL4851 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4847F TYR* 3.3 36.8 + - + +
4848F LEU 3.2 18.2 - - - +
4850F THR* 1.3 77.0 - - + +
4852F VAL* 1.3 62.3 + - + +
4854F PHE* 3.5 7.2 + - - +
4855F ASN* 3.2 34.3 + - - +
4575H LEU* 6.6 0.2 - - + -
4805H PHE* 3.6 25.8 - - + -
4808H ALA* 3.8 24.7 - - + -
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Residues in contact with VAL4852 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4848F LEU 3.2 13.7 - - - +
4849F TYR* 3.3 26.9 - - + +
4851F VAL* 1.3 83.3 - - + +
4853F ALA* 1.3 63.7 + - - +
4855F ASN* 3.9 2.2 - - - +
4856F PHE* 3.2 45.2 + - + +
4857F PHE* 3.9 6.8 + - + -
4910F TYR* 5.9 2.2 - - - +
4914F PHE* 4.2 20.0 - - + -
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Residues in contact with ALA4853 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4849F TYR 3.6 14.4 - - - +
4850F THR 3.2 6.1 + - - +
4852F VAL* 1.3 82.0 - - + +
4854F PHE* 1.3 60.7 + - - +
4855F ASN 3.2 0.4 - - - -
4857F PHE* 2.9 47.2 + - + +
4858F ARG* 3.7 0.7 + - - -
4861F TYR* 3.8 19.1 - - + +
4874F CYS* 5.9 0.5 - - - +
4880F CYS* 6.0 2.9 - - - -
4884F HIS* 3.7 22.7 - - + -
4914F PHE* 5.3 1.1 - - + -
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Residues in contact with PHE4854 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4850F THR* 3.0 16.6 + - + +
4851F VAL* 3.5 6.3 + - - +
4852F VAL 3.4 0.2 - - - -
4853F ALA* 1.3 77.6 - - - +
4855F ASN* 1.3 73.1 + - - +
4858F ARG* 4.8 14.1 - - + +
4874F CYS* 3.6 30.3 - - + -
4875F ASP 4.7 2.9 - - - -
4877F MET* 4.5 28.5 - - + -
4880F CYS* 4.9 12.7 - - + -
4578H TYR* 4.6 13.5 - - + -
4579H LYS* 4.4 13.2 - - - -
4580H VAL* 3.6 31.7 - - + +
4805H PHE* 4.3 17.7 - + - -
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Residues in contact with ASN4855 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4851F VAL* 3.2 19.8 + - - +
4852F VAL* 5.2 0.6 - - - +
4853F ALA 3.2 0.4 - - - -
4854F PHE* 1.3 86.4 - - - +
4856F PHE* 1.3 89.4 + - + +
4858F ARG* 5.5 2.5 - - - +
4804H ASN* 5.6 6.7 - - - +
4805H PHE* 3.2 43.2 + - - -
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Residues in contact with PHE4856 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4852F VAL* 3.2 34.4 + - + +
4855F ASN* 1.3 101.8 - - + +
4857F PHE* 1.3 73.4 + + + +
4858F ARG* 2.8 15.2 + - - +
4859F LYS* 4.6 6.6 + - - +
4860F PHE* 5.8 0.2 - - - -
4907F TYR* 4.7 32.2 - + + -
4910F TYR* 4.9 22.0 - + + -
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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