Contacts of the helix formed by residues 4831 - 4856 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4829H THR 3.4 0.2 + - - -
4830H HIS* 1.3 94.9 + - + +
4832H GLY* 1.3 59.9 + - - +
4833H LYS 3.3 3.6 - - - +
4834H GLN* 2.9 32.0 + - - +
4835H LEU* 3.9 7.4 + - - +
4933H LEU* 5.6 14.4 - - + +
4937H ALA* 5.1 5.8 - - + -
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Residues in contact with GLY4832 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4828H VAL 5.0 0.2 - - - -
4829H THR* 3.0 19.7 + - - -
4830H HIS 4.2 0.7 - - - -
4831H ASN* 1.3 74.1 - - - +
4833H LYS* 1.3 64.1 + - - +
4834H GLN 3.2 2.5 - - - -
4835H LEU* 3.1 25.8 + - - +
4836H VAL* 3.3 15.4 + - - +
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Residues in contact with LYS4833 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4820B THR* 4.7 4.0 + - - +
4831H ASN 3.3 1.4 - - - -
4832H GLY* 1.3 77.4 - - - +
4834H GLN* 1.3 65.8 + - + +
4836H VAL* 3.3 23.0 - - - +
4837H MET* 3.8 7.8 + - - +
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Residues in contact with GLN4834 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4820B THR* 3.8 30.9 + - + +
4938B PHE* 6.1 4.5 - - + -
4831H ASN* 2.9 33.6 - - - +
4833H LYS* 1.3 82.1 + - + +
4835H LEU* 1.3 63.1 + - - +
4837H MET* 3.1 3.1 + - - +
4838H THR* 3.0 27.2 + - + +
4933H LEU* 4.9 21.6 - - + +
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Residues in contact with LEU4835 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4828H VAL* 3.6 28.3 - - + +
4830H HIS 6.0 0.2 - - - +
4831H ASN 3.9 3.6 + - - +
4832H GLY* 3.1 20.3 + - - +
4834H GLN* 1.3 78.8 - - - +
4836H VAL* 1.3 63.1 + - - +
4838H THR* 3.3 9.1 - - + +
4839H VAL* 3.1 47.9 + - + +
4930H ILE* 5.6 7.2 - - + -
4933H LEU* 6.2 3.1 - - + +
4934H ILE* 4.1 21.1 - - + -
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Residues in contact with VAL4836 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4832H GLY 3.3 9.0 + - - +
4833H LYS* 3.3 22.7 - - - +
4835H LEU* 1.3 80.6 - - - +
4837H MET* 1.3 56.8 + - - +
4839H VAL* 4.1 5.5 - - + +
4840H GLY* 3.0 23.4 + - - -
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Residues in contact with MET4837 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4818B VAL* 6.1 2.0 - - + -
4820B THR* 3.7 27.1 - - + -
4821B LEU* 5.0 11.0 - - + +
4833H LYS 3.9 7.0 - - - +
4834H GLN 3.1 10.6 + - - +
4836H VAL* 1.3 80.6 - - + +
4838H THR* 1.3 55.0 + - - +
4840H GLY* 3.2 2.8 + - - -
4841H LEU* 2.7 39.4 + - + +
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Residues in contact with THR4838 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4824B ILE* 5.7 2.7 - - - -
4834H GLN* 3.0 18.8 + - + +
4835H LEU* 3.3 16.4 - - + +
4837H MET* 1.3 71.0 - - - +
4839H VAL* 1.3 53.3 + - - +
4841H LEU* 3.1 16.6 + - - +
4842H LEU* 2.5 35.0 + - - +
4926H LEU* 4.6 3.1 + - - +
4929H ILE* 4.1 30.3 - - + +
4930H ILE* 3.3 28.1 - - + +
4933H LEU* 5.9 3.6 - - + -
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Residues in contact with VAL4839 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920F PHE* 6.2 5.4 - - + -
4835H LEU* 3.1 36.7 + - + +
4836H VAL* 4.1 6.3 - - + +
4838H THR* 1.3 75.8 - - - +
4840H GLY* 1.3 57.8 + - - +
4842H LEU* 3.1 17.4 + - + +
4843H ALA* 2.9 28.6 + - + +
4885H MET* 6.5 0.4 - - + -
4930H ILE* 4.3 15.0 - - + -
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Residues in contact with GLY4840 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4836H VAL 3.0 17.2 + - - -
4837H MET 3.5 4.3 - - - -
4839H VAL* 1.3 77.7 - - - +
4841H LEU* 1.3 60.8 + - - +
4843H ALA* 3.2 8.0 + - - +
4844H VAL* 3.2 29.7 + - - +
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Residues in contact with LEU4841 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4815B ALA* 4.1 25.6 - - + +
4821B LEU* 3.6 37.2 - - + +
4824B ILE* 3.7 35.9 - - + -
4825B LEU* 6.5 1.8 - - + -
4837H MET* 2.7 21.8 + - + +
4838H THR* 3.3 15.0 - - - +
4840H GLY* 1.3 74.4 - - - +
4842H LEU* 1.3 60.9 + - - +
4844H VAL* 3.2 16.7 - - + +
4845H VAL* 3.2 22.1 - - + +
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Residues in contact with LEU4842 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4920F PHE* 5.3 7.9 - - + -
4838H THR* 2.5 20.0 + - - +
4839H VAL* 3.1 18.6 + - + +
4841H LEU* 1.3 73.9 - - - +
4843H ALA* 1.3 61.3 + - + +
4845H VAL* 3.3 16.7 - - + +
4846H VAL* 3.2 21.8 - - + +
4885H MET* 3.7 34.8 - - + -
4889H VAL* 5.0 13.2 - - + -
4922H VAL* 5.4 3.6 - - + +
4926H LEU* 4.6 22.9 - - + -
4927H LEU* 4.7 15.3 - - + -
4930H ILE* 4.8 15.9 - - + -
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Residues in contact with ALA4843 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4839H VAL* 2.9 15.0 + - + +
4840H GLY* 3.2 10.2 + - - +
4842H LEU* 1.3 81.5 - - + +
4844H VAL* 1.3 60.9 + - + +
4846H VAL* 3.3 15.8 - - - +
4847H TYR* 3.4 9.4 + - - +
4881H TYR* 3.2 25.6 + - - +
4885H MET* 6.0 1.6 - - + -
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Residues in contact with VAL4844 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4569B PHE* 6.2 4.3 - - + -
4811B LEU* 4.9 21.1 - - + +
4814B ILE* 5.7 4.7 - - + -
4815B ALA* 4.9 10.1 - - + -
4840H GLY 3.2 14.6 + - - +
4841H LEU* 3.2 31.2 - - + +
4843H ALA* 1.3 80.1 - - + +
4845H VAL* 1.3 66.5 + - + +
4847H TYR* 3.1 9.6 + - + +
4848H LEU* 3.0 31.5 + - + +
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Residues in contact with VAL4845 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4841H LEU* 3.2 21.3 - - + +
4842H LEU* 3.3 17.7 - - + +
4844H VAL* 1.3 81.7 - - + +
4846H VAL* 1.3 63.4 + - - +
4848H LEU* 3.4 13.4 + - + +
4849H TYR* 3.1 34.7 + - + -
4921H PHE* 6.6 0.2 - - + -
4922H VAL* 4.0 24.2 - - + -
4926H LEU* 5.8 3.4 - - + -
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Residues in contact with VAL4846 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4842H LEU* 3.2 23.1 - - + +
4843H ALA* 3.3 17.0 - - - +
4845H VAL* 1.3 74.7 - - - +
4847H TYR* 1.3 54.0 + - - +
4848H LEU 3.3 0.2 - - - -
4849H TYR* 3.4 8.2 + - - +
4850H THR* 2.3 38.5 + - - +
4881H TYR* 4.1 14.4 - - + +
4884H HIS* 5.2 13.4 + - + +
4885H MET* 4.8 20.2 - - + -
4889H VAL* 5.4 8.5 - - + -
4918H PHE* 4.5 14.4 - - + -
4922H VAL* 4.4 20.4 - - + -
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Residues in contact with TYR4847 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4572B ASN* 3.1 50.7 + - + +
4575B LEU* 4.4 11.6 - - - +
4576B LEU* 4.8 11.7 + - + -
4808B ALA* 4.9 11.7 - - + -
4811B LEU* 4.9 7.4 - - + -
4843H ALA 3.4 12.5 + - - +
4844H VAL* 3.1 14.6 + - + +
4846H VAL* 1.3 79.6 - - - +
4848H LEU* 1.3 74.7 - - + +
4850H THR* 3.2 17.6 + - + -
4851H VAL* 3.3 30.6 + - + +
4881H TYR* 4.1 22.9 - + + -
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Residues in contact with LEU4848 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4808B ALA* 3.3 34.5 - - + +
4809B ALA* 6.4 0.2 - - - -
4811B LEU* 4.1 15.3 - - + -
4812B LEU* 4.7 18.6 - - + -
4844H VAL* 3.0 17.8 + - + +
4845H VAL* 3.8 14.1 - - + +
4846H VAL 3.3 0.2 - - - -
4847H TYR* 1.3 82.4 - - + +
4849H TYR* 1.3 62.8 + - + +
4851H VAL* 3.2 11.4 - - - +
4852H VAL* 3.2 23.9 - - - +
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Residues in contact with TYR4849 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4845H VAL* 3.1 30.9 + - + +
4846H VAL* 3.7 6.1 - - - +
4847H TYR 3.3 0.2 - - - -
4848H LEU* 1.3 77.6 - - + +
4850H THR* 1.3 60.3 + - - +
4852H VAL* 3.3 22.4 - - + +
4853H ALA* 3.5 11.6 + - - +
4884H HIS* 4.5 6.1 + - - +
4914H PHE* 3.5 36.7 - + + -
4917H THR* 3.6 30.2 + - + +
4918H PHE* 3.8 38.6 - + + -
4921H PHE* 4.3 11.6 - - + -
4922H VAL* 4.9 8.7 - - + -
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Residues in contact with THR4850 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4846H VAL* 2.3 27.5 + - - +
4847H TYR* 3.5 12.9 - - + -
4848H LEU 3.2 0.8 - - - -
4849H TYR* 1.3 77.2 - - - +
4851H VAL* 1.3 63.3 + - + +
4852H VAL 3.2 0.2 - - - -
4853H ALA* 3.2 3.5 + - - +
4854H PHE* 3.0 27.1 + - + +
4877H MET 4.6 4.7 - - - +
4880H CYS* 3.9 28.3 - - + +
4881H TYR* 3.9 27.6 - - + +
4884H HIS* 4.0 16.7 + - - +
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Residues in contact with VAL4851 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4575B LEU* 6.6 0.2 - - + -
4805B PHE* 3.7 26.4 - - + -
4808B ALA* 3.8 25.1 - - + -
4847H TYR* 3.3 36.1 + - + +
4848H LEU* 3.2 17.3 - - - +
4850H THR* 1.3 78.6 - - + +
4852H VAL* 1.3 63.0 + - + +
4854H PHE* 3.5 6.4 + - - +
4855H ASN* 3.2 34.3 + - - +
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Residues in contact with VAL4852 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4848H LEU 3.2 13.5 - - - +
4849H TYR* 3.3 26.5 - - + +
4851H VAL* 1.3 82.6 - - + +
4853H ALA* 1.3 64.2 + - - +
4855H ASN* 4.5 1.8 - - - +
4856H PHE* 3.2 45.0 + - + +
4857H PHE* 3.9 7.0 + - + -
4910H TYR* 5.9 1.8 - - - +
4914H PHE* 4.2 20.0 - - + -
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Residues in contact with ALA4853 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4849H TYR 3.5 13.9 + - - +
4850H THR 3.2 6.3 + - - +
4852H VAL* 1.3 80.1 - - + +
4854H PHE* 1.3 60.5 + - - +
4855H ASN 3.2 0.4 - - - -
4857H PHE* 2.9 48.1 + - + +
4858H ARG* 3.7 0.7 + - - -
4861H TYR* 3.8 18.6 - - + +
4874H CYS* 5.9 0.5 - - - +
4880H CYS* 6.0 3.1 - - - -
4884H HIS* 3.7 22.7 - - + -
4914H PHE* 5.3 1.3 - - + -
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Residues in contact with PHE4854 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4578B TYR* 4.6 13.2 - - + -
4579B LYS* 4.4 13.2 - - - -
4580B VAL* 3.6 31.4 - - + +
4805B PHE* 4.3 17.7 - + - -
4850H THR* 3.0 15.3 + - + +
4851H VAL* 4.0 7.2 - - - +
4852H VAL 3.4 0.2 - - - -
4853H ALA* 1.3 77.2 - - - +
4855H ASN* 1.3 70.8 - - - +
4858H ARG* 4.8 14.7 - - + +
4874H CYS* 3.6 29.4 - - + -
4875H ASP 4.7 2.7 - - - -
4877H MET* 4.5 28.5 - - + -
4880H CYS* 4.9 13.6 - - + -
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Residues in contact with ASN4855 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4804B ASN* 5.6 6.5 - - - +
4805B PHE* 3.2 42.2 + - - -
4851H VAL* 3.2 19.0 + - - +
4852H VAL* 3.7 0.8 + - - +
4854H PHE* 1.3 86.3 - - - +
4856H PHE* 1.3 87.1 + - + +
4858H ARG* 5.5 2.5 - - - +
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Residues in contact with PHE4856 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4852H VAL* 3.2 33.6 + - + +
4855H ASN* 1.3 101.2 - - + +
4857H PHE* 1.3 72.0 + + + +
4858H ARG* 2.8 15.5 + - - +
4859H LYS* 4.6 5.7 + - - +
4860H PHE* 5.8 0.3 - - - -
4907H TYR* 4.7 32.3 - + + -
4910H 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