Contacts of the helix formed by residues 5313 - 5334 (chain d) in PDB entry 2AXT
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 THR5313 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5067a VAL* 4.0 4.5 - - - -
5068a SER* 3.7 15.0 - - - +
5075a ASN* 3.7 23.3 - - - +
5301d GLN* 3.4 9.9 + - - +
5311d PHE* 3.4 35.7 - - + -
5312d GLU* 1.3 80.2 - - - +
5314d PHE* 1.3 57.9 + - - +
5315d TYR* 2.7 37.5 + - - +
5316d THR* 2.9 24.9 + - - +
5317d LYS* 3.2 6.0 + - - +
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Residues in contact with PHE5314 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5060a ILE* 3.7 29.4 - - + -
5067a VAL* 4.2 7.4 - - + +
5068a SER 4.9 0.6 + - - -
5069a GLY* 5.9 2.7 - - - -
5079a THR 4.4 11.3 + - - +
5081a ALA* 4.4 14.4 - - + -
5083a VAL* 3.8 27.8 - - + -
5084a PRO* 4.2 0.2 - - + -
5173a PRO* 3.8 30.7 - - + -
5177a SER* 4.2 1.3 - - - -
5178a GLY* 3.6 31.9 - - - +
5181a ASN* 3.8 25.1 - - + -
5313d THR* 1.3 72.1 - - - +
5315d TYR* 1.3 60.3 + - - +
5317d LYS* 3.6 27.0 - - + +
5318d ASN* 3.2 30.5 + - - +
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Residues in contact with TYR5315 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5079a THR* 3.8 21.2 - - + -
5177a SER* 4.1 10.4 + - - -
5190d ASN* 5.1 1.1 - - - -
5193d LEU* 4.1 20.9 - - + -
5296d TYR 4.3 2.0 - - - -
5297d ASP* 3.0 11.5 - - - +
5298d PHE* 2.9 49.3 + + - -
5301d GLN* 3.5 29.8 - - + -
5302d GLU* 2.8 27.7 + - - -
5313d THR* 2.7 12.1 + - - +
5314d PHE* 1.3 79.0 - - - +
5316d THR* 1.3 85.4 + - + +
5318d ASN* 3.3 10.4 + - - +
5319d LEU* 3.3 27.3 + - + +
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Residues in contact with THR5316 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5301d GLN* 5.0 4.7 - - + +
5302d GLU* 5.9 0.2 - - - +
5305d ALA* 4.8 15.0 - - + -
5311d PHE* 4.8 8.5 - - + +
5312d GLU* 3.7 15.9 + - - +
5313d THR* 2.9 33.1 + - + +
5315d TYR* 1.3 91.1 - - + +
5317d LYS* 1.3 75.6 + - - +
5319d LEU* 2.9 23.7 + - - +
5320d LEU* 3.3 9.9 + - - +
5185o PRO* 4.1 18.8 + - + +
5186o LYS* 5.0 9.6 + - + +
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Residues in contact with LYS5317 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5060a ILE* 4.6 7.6 - - - +
5061a ASP* 3.6 22.0 + - - -
5067a VAL* 3.7 29.2 - - + -
5181a ASN* 4.1 13.6 - - - +
5333a GLU* 4.8 13.3 + - - +
5334a ARG* 6.2 0.4 - - - +
5312d GLU* 3.7 23.0 + - - +
5313d THR 3.2 6.4 + - - +
5314d PHE* 3.6 42.0 - - + +
5316d THR* 1.3 83.4 + - - +
5318d ASN* 1.3 64.4 + - - +
5320d LEU* 3.1 24.2 + - - +
5321d LEU* 3.5 9.8 + - - +
5185o PRO 5.6 0.2 - - - -
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Residues in contact with ASN5318 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5177a SER* 3.0 36.2 + - - -
5180a PHE* 3.8 10.6 - - - +
5181a ASN* 2.9 40.9 + - - +
5184a ILE* 5.0 7.6 - - + -
5186d GLN* 4.9 2.7 + - - +
5190d ASN* 5.5 2.9 - - - +
5314d PHE 3.2 11.1 + - - +
5315d TYR 3.3 7.9 + - - +
5317d LYS* 1.3 75.2 - - - +
5319d LEU* 1.3 61.3 + - - +
5321d LEU* 3.1 23.5 + - + +
5322d ASN* 3.2 19.9 + - - +
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Residues in contact with LEU5319 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5190d ASN* 4.4 9.2 - - - +
5296d TYR* 3.3 46.2 - - + +
5297d ASP* 5.1 0.4 - - + -
5302d GLU* 3.0 29.4 - - - +
5315d TYR* 3.3 35.7 + - + +
5316d THR* 2.9 13.7 + - - +
5318d ASN* 1.3 77.8 - - - +
5320d LEU* 1.3 59.7 + - - +
5322d ASN* 3.4 12.6 + - - +
5323d GLU* 3.0 33.2 + - - +
5186o LYS* 4.2 16.2 - - - +
5199o ALA* 5.9 0.9 - - + -
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Residues in contact with LEU5320 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5331a MET* 3.7 38.7 - - + +
5334a ARG* 3.4 38.8 - - - +
5316d THR 4.1 5.6 - - - +
5317d LYS* 3.1 15.2 + - - +
5319d LEU* 1.3 75.2 - - + +
5321d LEU* 1.3 67.3 + - + +
5322d ASN 3.1 0.7 - - - -
5323d GLU* 3.3 23.1 + - - +
5324d GLY 3.1 16.5 + - - -
5185o PRO 3.7 19.1 - - - +
5186o LYS* 4.5 5.8 - - - +
5187o GLY* 4.3 21.5 - - - +
5194o TYR* 4.4 4.0 - - + -
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Residues in contact with LEU5321 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5181a ASN* 4.1 5.2 - - - +
5184a ILE* 3.5 39.0 - - + -
5185a VAL* 4.1 16.4 - - + -
5327a GLY 4.3 2.8 - - - +
5328a MET* 3.9 18.4 - - + +
5331a MET* 4.6 4.0 - - - -
5332a HIS* 3.6 38.8 - - + +
5317d LYS 3.5 9.8 + - - +
5318d ASN* 3.1 27.7 + - - +
5320d LEU* 1.3 78.5 - - + +
5322d ASN* 1.3 59.3 + - - +
5324d GLY* 3.0 3.6 + - - -
5325d ILE* 2.8 32.0 + - - +
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Residues in contact with ASN5322 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5184a ILE* 4.7 1.0 - - - +
5186d GLN* 2.6 40.1 + - - +
5187d GLY* 3.5 13.9 - - - +
5190d ASN* 3.4 28.7 + - - +
5296d TYR* 3.6 15.9 + - - +
5318d ASN* 3.3 15.5 + - - +
5319d LEU* 3.5 15.8 - - - +
5321d LEU* 1.3 75.3 - - - +
5323d GLU* 1.3 66.6 + - - +
5325d ILE* 3.6 6.8 - - - +
5326d ARG* 3.0 30.5 + - - +
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Residues in contact with GLU5323 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5331a MET* 4.9 5.2 - - + -
5365b SER* 3.7 11.5 + - - +
5296d TYR* 4.0 6.1 + - - -
5319d LEU* 3.0 27.5 + - - +
5320d LEU* 3.3 33.4 + - - +
5322d ASN* 1.3 79.6 - - - +
5324d GLY* 1.3 57.6 - - - +
5326d ARG* 3.5 28.4 + - - +
5327d ALA* 3.1 30.5 + - - +
5347d PRO* 4.2 4.0 - - + +
5186o LYS* 4.8 5.1 + - - -
5194o TYR* 3.1 32.6 + - - +
5198o ILE* 4.4 12.3 - - - +
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Residues in contact with GLY5324 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5327a GLY* 3.3 30.1 - - - -
5331a MET* 3.7 14.1 - - - +
5320d LEU 3.1 6.7 + - - -
5321d LEU 3.0 8.0 + - - -
5323d GLU* 1.3 75.6 - - - +
5325d ILE* 1.3 64.3 + - - +
5327d ALA* 3.3 1.1 + - - -
5328d TRP* 3.1 26.9 + - - -
5347d PRO* 4.7 1.6 - - - -
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Residues in contact with ILE5325 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5184a ILE* 4.3 11.4 - - + -
5324a ALA* 3.7 24.9 - - + +
5327a GLY* 4.1 1.3 - - - -
5328a MET* 3.3 46.4 - - + -
5183d LEU* 4.1 12.8 - - + +
5186d GLN* 4.5 10.1 - - + -
5187d GLY* 3.9 26.7 - - - -
5188d PHE* 5.1 1.1 - - + -
5321d LEU 2.8 18.3 + - - +
5322d ASN* 3.1 9.4 + - - +
5324d GLY* 1.3 72.4 - - - +
5326d ARG* 1.3 58.9 + - - +
5329d MET* 2.8 42.0 + - - +
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Residues in contact with ARG5326 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5363b PHE* 4.0 19.0 - - + +
5364b GLU* 4.2 15.0 - - - +
5365b SER* 3.1 39.0 + - - +
5187d GLY 3.2 27.0 + - - +
5188d PHE* 3.5 45.7 + - + +
5296d TYR* 3.0 30.1 + - - -
5322d ASN* 3.0 21.2 + - - +
5323d GLU* 3.5 28.1 + - - +
5325d ILE* 1.3 77.2 - - - +
5327d ALA* 1.3 66.6 + - - +
5330d ALA* 2.9 31.0 + - - +
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Residues in contact with ALA5327 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5363b PHE* 6.0 0.2 - - - -
5323d GLU 3.1 16.5 + - - +
5324d GLY 3.3 0.2 + - - -
5326d ARG* 1.3 82.2 - - - +
5328d TRP* 1.3 66.9 + - + +
5331d PRO* 3.4 6.8 - - - +
5341d PHE* 3.3 31.3 - - + -
5346d LEU* 4.2 6.8 - - + +
5347d PRO* 3.5 33.2 - - + -
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Residues in contact with TRP5328 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5323a ARG* 3.1 56.0 + - - +
5326a LEU* 3.9 24.0 - - + -
5327a GLY* 3.8 14.0 - - - -
5330a VAL* 3.7 26.0 - - + +
5324d GLY* 3.1 20.2 + - - +
5327d ALA* 1.3 86.8 - - + +
5329d MET* 1.3 62.6 + - - +
5331d PRO* 3.8 7.5 - - - +
5346d LEU* 3.8 21.2 - - + +
5347d PRO 3.2 19.9 + - - -
5348d ARG* 3.9 27.8 - - + -
5160v LYS* 3.7 10.3 - - + -
5161v VAL* 3.5 44.4 - - + -
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Residues in contact with MET5329 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5320a ILE* 4.1 14.1 - - + +
5321a ILE* 5.7 0.2 - - - -
5323a ARG* 4.0 9.7 + - - +
5324a ALA* 3.3 34.8 - - + -
5180d ARG* 4.2 21.5 - - + +
5183d LEU* 4.6 1.3 - - + -
5184d PHE* 4.3 17.9 - - + +
5188d PHE* 4.2 19.7 - - - -
5325d ILE* 2.8 26.7 + - - +
5328d TRP* 1.3 75.2 - - - +
5330d ALA* 1.3 68.6 + - - +
5331d PRO* 2.8 6.8 - - - +
5332d GLN* 3.1 14.7 + - - +
5333d ASP* 3.3 36.0 + - + +
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Residues in contact with ALA5330 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5363b PHE* 3.7 30.5 - - + -
5188d PHE* 4.6 3.6 - - + -
5326d ARG* 2.9 25.0 + - - +
5329d MET* 1.3 74.7 - - - +
5331d PRO* 1.3 61.6 - - + +
5333d ASP* 3.1 2.6 + - - -
5334d GLN* 2.8 43.7 + - - +
5339d PHE* 4.2 10.3 - - + -
5341d PHE* 4.4 4.7 - - + -
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Residues in contact with PRO5331 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5323a ARG* 5.9 2.0 - - - +
5327d ALA 3.4 19.3 - - - +
5328d TRP 3.8 7.2 - - - +
5329d MET 2.8 5.4 - - - +
5330d ALA* 1.3 97.0 - - + +
5332d GLN* 1.3 65.6 + - + +
5333d ASP 3.5 0.2 + - - -
5334d GLN 3.8 5.9 + - - +
5335d PRO* 3.9 12.3 - - - +
5339d PHE* 4.1 28.6 + - + +
5340d VAL* 6.3 0.2 - - - -
5341d PHE* 3.8 22.4 - - + +
5346d LEU* 6.1 0.2 - - + -
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Residues in contact with GLN5332 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5315a ASN* 2.8 28.8 - - - +
5319a ASP* 5.3 1.2 - - - +
5320a ILE* 3.5 25.3 - - + +
5323a ARG* 3.0 44.3 - - + +
5063d LEU* 6.1 0.7 - - - +
5328d TRP 5.2 0.2 + - - -
5329d MET 3.1 5.1 + - - +
5331d PRO* 1.3 79.5 - - + +
5333d ASP* 1.3 60.1 + - - +
5334d GLN 3.4 0.4 - - - -
5335d PRO* 3.7 10.5 - - - +
5163v TYR* 3.4 17.6 + - - +
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Residues in contact with ASP5333 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5317a TRP* 5.2 4.1 - - - -
5320a ILE* 2.8 32.3 - - + +
5061d HIS* 5.6 0.9 - - - -
5168d PHE* 3.4 20.8 - - - -
5180d ARG* 2.7 40.8 + - - -
5184d PHE* 5.0 1.8 - - - -
5329d MET* 3.3 35.5 + - + +
5330d ALA* 3.1 5.2 + - - +
5332d GLN* 1.3 78.1 - - - +
5334d GLN* 1.3 64.4 + - + +
5335d PRO* 3.3 4.5 - - - -
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Residues in contact with GLN5334 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5360b PRO* 5.5 1.0 - - - +
5362b PHE* 4.3 10.8 - - - -
5363b PHE* 3.7 28.0 - - - -
5169d PHE* 3.8 31.1 - - + -
5184d PHE* 4.3 5.6 - - + -
5188d PHE* 3.9 18.4 - - - -
5330d ALA* 2.8 18.6 + - - +
5331d PRO 4.1 3.9 - - - +
5333d ASP* 1.3 90.1 - - + +
5335d PRO* 1.3 58.8 - - - +
5336d HIS* 3.2 14.5 + - + -
5337d GLU* 2.8 46.3 + - + +
5338d ASN 4.2 0.5 + - - -
5339d PHE* 4.3 9.0 + - + -
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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