Contacts of the helix formed by residues 5446 - 5474 (chain b) 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 SER5446 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5056b TRP* 4.4 1.8 - - - -
5269b GLY* 4.2 12.8 - - - -
5317b ASN 5.3 0.7 - - - -
5319b PRO* 3.5 25.5 - - - +
5330b MET* 3.6 29.0 - - - +
5445b THR* 1.3 80.5 + - - +
5447b PRO* 1.4 68.7 - - - +
5448b ARG* 3.6 11.6 + - - +
5449b GLY* 2.7 19.6 + - - -
5450b TRP* 3.0 15.4 + - - -
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Residues in contact with PRO5447 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5056b TRP* 3.5 32.8 - - + +
5059b GLY* 4.7 2.0 - - - -
5060b MET 3.2 28.9 - - - +
5061b PHE* 5.1 8.0 - - + -
5064b PRO* 5.5 0.9 - - + -
5267b LEU 5.4 0.7 - - - +
5268b PHE* 4.7 17.3 - - + -
5269b GLY 4.8 0.7 - - - +
5446b SER* 1.4 87.1 - - - +
5448b ARG* 1.3 66.5 + - - +
5449b GLY 3.0 0.3 + - - -
5450b TRP* 4.4 1.1 - - + +
5451b PHE* 2.8 30.9 + - + +
5517b CLA 4.1 23.3 - - + -
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Residues in contact with ARG5448 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5256b MET* 2.4 57.7 + - - +
5257b TRP* 4.1 10.4 - - + -
5258b TYR 3.6 9.5 + - - -
5259b GLY* 5.2 0.8 - - - -
5263b THR* 2.6 45.6 + - - +
5264b PRO 3.8 1.0 + - - -
5265b ILE* 3.7 8.6 - - - +
5268b PHE* 3.6 14.1 - - + +
5269b GLY 2.9 33.2 + - - +
5270b PRO 3.2 17.0 + - - -
5271b THR* 4.0 16.5 + - - +
5272b ARG 5.1 0.4 - - - +
5319b PRO* 4.0 8.5 - - + -
5446b SER* 3.6 10.2 + - - +
5447b PRO* 1.3 79.0 - - - +
5449b GLY* 1.3 58.8 + - - +
5452b THR* 2.7 30.3 + - - -
5062h TRP* 5.0 0.4 - - - -
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Residues in contact with GLY5449 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5257b TRP* 3.7 17.9 - - - -
5319b PRO* 4.4 1.3 - - - +
5445b THR* 3.3 17.7 - - - -
5446b SER* 2.7 13.0 + - - -
5448b ARG* 1.3 80.9 - - - +
5450b TRP* 1.3 64.8 + - - -
5452b THR* 3.2 3.5 + - - -
5453b PHE* 3.0 20.0 + - - +
5291d LEU* 4.0 5.1 - - - +
5293d LEU* 5.3 2.5 - - - -
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Residues in contact with TRP5450 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5323b GLY 4.2 8.5 - - - -
5324b LEU* 3.2 29.6 - - + -
5326b ARG 4.3 12.0 + - - -
5328b GLY 4.8 2.2 + - - -
5444b ARG* 6.1 0.4 - - - +
5445b THR* 3.2 39.6 + - + +
5446b SER 3.0 14.5 + - - -
5447b PRO 4.0 3.4 - - - +
5449b GLY* 1.3 70.8 - - - +
5451b PHE* 1.3 59.7 + - - +
5453b PHE* 2.6 49.5 + + - +
5454b ALA* 2.8 12.8 + - - +
5517b CLA 3.0 91.2 - + + +
5530b MGE 4.1 12.8 - - + -
5293d LEU* 4.2 14.1 - - + -
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Residues in contact with PHE5451 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5061b PHE* 3.6 24.4 - + + -
5065b PHE* 3.7 22.4 - + - -
5252b VAL* 3.8 23.3 - - + -
5256b MET* 3.6 27.4 - - + -
5268b PHE* 5.9 0.7 - - + -
5447b PRO 2.8 19.6 + - - +
5450b TRP* 1.3 75.0 - - - +
5452b THR* 1.3 68.0 + - - +
5454b ALA* 3.3 0.3 + - - +
5455b HIS* 3.0 68.4 + + + +
5514b CLA 3.0 36.8 - + + -
5517b CLA 3.4 12.4 - - - +
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Residues in contact with THR5452 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5253b ALA* 3.5 25.2 - - + +
5256b MET* 3.1 19.6 - - - +
5257b TRP* 3.5 25.3 + - + -
5448b ARG 2.7 22.9 + - - -
5449b GLY 3.2 4.9 + - - -
5450b TRP 3.0 0.4 - - - -
5451b PHE* 1.3 85.0 - - - +
5453b PHE* 1.3 62.1 + - - +
5455b HIS 4.0 0.3 - - - -
5456b ALA* 3.0 26.0 + - + +
5291d LEU* 3.9 16.6 - - + -
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Residues in contact with PHE5453 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5324b LEU* 4.2 26.2 - - + -
5449b GLY 3.0 6.8 + - - +
5450b TRP* 2.6 27.5 + + - +
5452b THR* 1.3 70.0 - - - +
5454b ALA* 1.3 69.9 + - + +
5456b ALA* 3.4 2.7 + - - +
5457b VAL* 3.3 39.1 + - + +
5517b CLA 5.3 2.2 - - + -
5530b MGE 3.5 33.9 - - + -
5196d PHE* 5.7 4.3 - + - -
5284d ILE* 4.7 9.4 - - + -
5287d VAL 4.6 1.1 - - - -
5288d GLY* 3.7 29.6 - - - -
5291d LEU* 3.4 15.5 - - + +
5293d LEU* 3.4 32.5 - - + -
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Residues in contact with ALA5454 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5450b TRP 2.8 9.4 + - - +
5451b PHE 3.8 6.7 - - - +
5453b PHE* 1.3 83.7 - - - +
5455b HIS* 1.3 59.5 + - - +
5457b VAL* 3.2 4.4 + - - +
5458b PHE* 2.9 38.4 + - + -
5517b CLA 3.9 35.4 - - + -
5530b MGE 4.1 21.0 - - + +
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Residues in contact with HIS5455 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5249b ALA* 4.1 6.5 - - + +
5252b VAL* 4.2 8.1 - - + -
5253b ALA* 4.2 17.6 - - + +
5451b PHE* 3.0 59.2 + + + +
5454b ALA* 1.3 80.3 - - + +
5456b ALA* 1.3 60.4 + - - +
5457b VAL 3.2 0.2 - - - -
5458b PHE* 4.0 5.8 - + - +
5459b ALA* 3.1 26.9 + - - +
5514b CLA 2.2 69.0 + + + -
5517b CLA 3.7 25.8 - - + -
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Residues in contact with ALA5456 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5250b PHE* 4.1 11.3 - - + -
5253b ALA* 4.1 12.3 - - + +
5452b THR* 3.0 22.6 + - + +
5453b PHE* 3.9 3.4 - - - +
5454b ALA 3.2 0.2 - - - -
5455b HIS* 1.3 78.7 - - - +
5457b VAL* 1.3 61.3 + - - +
5459b ALA* 3.7 5.6 - - - +
5460b LEU* 3.5 19.1 + - - +
5159d ILE* 4.7 8.3 - - + +
5287d VAL* 3.7 23.7 - - + +
5291d LEU* 5.6 1.6 - - + -
5208h DGD 6.3 2.2 - - + -
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Residues in contact with VAL5457 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5453b PHE* 3.3 35.6 + - + +
5454b ALA 3.2 3.9 + - - +
5456b ALA* 1.3 77.5 - - - +
5458b PHE* 1.3 65.1 + - - +
5459b ALA 3.1 1.3 - - - -
5460b LEU* 3.4 5.7 + - - +
5461b LEU* 3.0 36.3 + - + +
5530b MGE 4.3 19.1 - - + -
5284d ILE* 3.7 30.3 - - + -
5287d VAL* 3.6 26.2 - - + -
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Residues in contact with PHE5458 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5454b ALA* 2.9 34.7 + - + +
5455b HIS* 4.5 5.6 - + - +
5457b VAL* 1.3 73.2 - - - +
5459b ALA* 1.3 56.8 + - - +
5461b LEU* 3.5 8.2 - - + -
5462b PHE* 2.8 39.9 + - + -
5514b CLA 3.5 81.0 - + + -
5517b CLA 4.8 1.1 - - + -
5521b CLA 4.8 5.2 - - + -
5523b CLA 4.0 33.0 - - + -
5528b BCR 4.7 7.9 - - + -
5530b MGE 4.2 31.0 - - + -
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Residues in contact with ALA5459 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5246b PHE* 3.7 12.2 - - - +
5249b ALA* 3.8 11.7 - - + -
5250b PHE* 3.6 36.2 - - + -
5455b HIS 3.1 19.6 + - - +
5456b ALA 3.7 6.3 - - - +
5458b PHE* 1.3 81.8 - - - +
5460b LEU* 1.3 62.4 + - - +
5462b PHE 3.2 6.8 + - - -
5463b PHE* 3.2 11.8 + - - +
5514b CLA 3.8 9.8 - - - +
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Residues in contact with LEU5460 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5250b PHE* 3.8 20.8 - - + -
5456b ALA 3.5 9.9 + - - +
5457b VAL* 3.4 9.5 + - + +
5458b PHE 3.3 0.4 - - - -
5459b ALA* 1.3 78.2 - - - +
5461b LEU* 1.3 61.7 + - + +
5463b PHE* 3.5 12.0 + - + +
5151d ALA* 4.5 8.5 - - + -
5154d VAL* 4.6 16.8 - - + -
5155d SER* 4.3 7.4 - - - -
5159d ILE* 3.9 12.1 - - + -
5280d TRP* 3.1 40.5 - - + -
5283d ALA* 4.2 22.0 - - + -
5284d ILE* 5.0 4.9 - - + +
5287d VAL* 4.0 22.7 - - + -
5208h DGD 4.7 9.2 - - + -
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Residues in contact with LEU5461 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5457b VAL* 3.0 31.2 + - + +
5458b PHE* 3.1 12.8 + - + +
5460b LEU* 1.3 77.3 - - - +
5462b PHE* 1.3 61.6 + - + +
5463b PHE 3.3 0.6 + - - -
5464b PHE* 3.6 7.2 + - + +
5521b CLA 3.4 28.3 - - + +
5523b CLA 3.9 40.4 - - + -
5530b MGE 5.5 4.3 - - + -
5280d TRP* 4.5 15.9 - - + -
5284d ILE* 4.0 26.5 - - + -
5360d MGE 4.2 28.9 - - + -
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Residues in contact with PHE5462 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5242b ILE* 3.0 24.0 - - + +
5245b VAL* 3.8 17.5 - - + -
5246b PHE* 3.8 15.4 - - + -
5458b PHE 2.8 25.1 + - - +
5459b ALA 3.7 4.5 - - - +
5461b LEU* 1.3 76.5 - - - +
5463b PHE* 1.3 63.7 + - - +
5464b PHE 3.2 0.9 - - - -
5465b GLY 3.5 0.9 - - - -
5466b HIS* 3.0 17.5 + - - +
5514b CLA 3.7 26.0 - - + -
5521b CLA 3.4 39.3 - - + -
5523b CLA 3.4 67.5 - + + -
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Residues in contact with PHE5463 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5246b PHE* 3.8 26.9 - + + -
5250b PHE* 5.6 0.4 - - + -
5459b ALA 3.2 10.8 + - - +
5460b LEU* 3.5 13.5 - - + +
5461b LEU 3.3 0.4 - - - -
5462b PHE* 1.3 76.6 - - - +
5464b PHE* 1.3 62.8 + - - +
5466b HIS* 3.1 6.2 + + - +
5467b ILE* 2.9 60.3 + - + +
5518b CLA 3.3 35.4 - + + -
5147d SER* 4.5 9.9 - - - -
5150d ILE* 4.0 21.8 - - + -
5151d ALA* 5.6 1.1 - - - -
5280d TRP* 4.2 14.8 - + - -
5208h DGD 3.4 33.7 - - + -
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Residues in contact with PHE5464 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5460b LEU 3.9 1.2 + - - -
5461b LEU* 3.6 10.7 + - + +
5462b PHE 3.2 0.2 - - - -
5463b PHE* 1.3 83.3 - - - +
5465b GLY* 1.3 63.6 + - - +
5467b ILE* 4.0 6.2 - - + +
5468b TRP* 3.1 30.0 + - + +
5521b CLA 3.6 34.8 - - + -
5144d ILE* 3.9 24.9 - - + -
5147d SER* 3.4 28.5 - - - -
5276d VAL* 5.3 1.1 - - + -
5280d TRP* 3.9 24.0 - + + -
5360d MGE 3.4 52.5 - - + -
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Residues in contact with GLY5465 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5242b ILE* 3.9 7.2 - - - -
5462b PHE 3.3 6.4 + - - -
5463b PHE 3.1 0.6 - - - -
5464b PHE* 1.3 81.8 - - - +
5466b HIS* 1.3 62.1 + - - +
5468b TRP* 3.2 1.5 + - - +
5469b HIS* 3.0 29.5 + - - +
5521b CLA 3.3 43.1 - - - +
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Residues in contact with HIS5466 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5239b SER* 2.8 28.8 + - - +
5242b ILE* 3.2 21.2 - - + +
5243b ALA* 3.5 6.2 - - + +
5246b PHE* 4.1 17.9 - + + -
5462b PHE 3.0 8.2 + - - +
5463b PHE* 3.3 8.7 - + - +
5465b GLY* 1.3 76.7 - - - +
5467b ILE* 1.3 67.3 + - + +
5470b GLY* 2.8 30.8 + - - -
5518b CLA 2.4 84.9 + + + -
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Residues in contact with ILE5467 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5463b PHE* 2.9 48.9 + - + +
5464b PHE* 4.3 9.0 - - + +
5466b HIS* 1.3 80.6 - - + +
5468b TRP* 1.3 58.1 + - + +
5471b ALA* 3.3 24.3 + - - +
5518b CLA 3.9 29.4 - - + -
5126d MET* 3.1 31.9 - - + -
5130d PHE* 3.7 7.8 - - + -
5143d ALA 4.4 13.2 - - - +
5144d ILE* 4.3 13.9 - - + +
5147d SER* 4.6 9.4 - - - -
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Residues in contact with TRP5468 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5464b PHE* 3.1 28.6 + + + +
5465b GLY* 3.6 1.1 - - - +
5466b HIS 3.0 1.0 - - - -
5467b ILE* 1.3 78.1 - - + +
5469b HIS* 1.3 95.0 + + - +
5470b GLY 3.2 0.9 - - - -
5471b ALA* 3.2 4.6 + - - +
5472b ARG* 2.8 39.8 + - + +
5479b PHE* 4.9 5.4 - + - -
5521b CLA 3.3 69.1 + + + -
5141d TYR* 4.5 7.9 - + - -
5144d ILE* 3.5 33.7 - - + +
5360d MGE 3.1 59.7 - - - -
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Residues in contact with HIS5469 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5235b GLU* 3.4 19.4 + - + +
5238b LEU* 3.5 30.1 - - + +
5239b SER* 2.9 17.5 - - - +
5242b ILE* 4.1 6.1 - - + -
5465b GLY 3.0 17.9 + - - +
5468b TRP* 1.3 91.1 + + - +
5470b GLY* 1.3 68.6 + - - +
5472b ARG* 2.9 5.8 + - - +
5473b THR* 2.9 26.0 + - - -
5521b CLA 2.3 77.6 + + + -
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Residues in contact with GLY5470 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5239b SER* 2.7 21.7 + - - -
5466b HIS* 2.8 17.0 + - - -
5469b HIS* 1.3 74.9 - - - +
5471b ALA* 1.3 57.3 + - - +
5473b THR* 2.9 21.2 + - - -
5474b LEU* 3.2 16.1 + - - +
5518b CLA 3.9 22.7 - - - -
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Residues in contact with ALA5471 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5467b ILE 3.3 13.9 + - - +
5468b TRP 3.2 3.9 + - - +
5470b GLY* 1.3 75.0 - - - +
5472b ARG* 1.3 59.3 + - - +
5473b THR 3.4 0.3 + - - -
5474b LEU* 4.8 1.8 - - - +
5475b PHE* 3.0 36.3 + - - +
5518b CLA 4.0 5.6 - - - +
5130d PHE* 3.1 42.0 - - + -
5140d PRO* 4.0 11.6 - - + +
5144d ILE* 4.5 7.4 - - + -
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Residues in contact with ARG5472 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5229a GLU* 5.3 3.0 + - - +
5010b THR* 5.1 8.5 - - - +
5013b ILE* 4.7 8.3 - - - +
5235b GLU* 2.5 47.4 + - - +
5468b TRP* 2.8 29.1 + - + +
5469b HIS* 2.9 3.5 + - - +
5471b ALA* 1.3 77.4 - - - +
5473b THR* 1.3 62.1 + - - +
5475b PHE* 4.1 3.1 - - - -
5476b ARG* 3.6 21.1 + - - +
5479b PHE* 3.0 64.9 - - + -
5521b CLA 3.3 34.7 + - - +
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Residues in contact with THR5473 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5230b ARG* 3.8 23.9 + - + +
5233b ASN* 3.8 18.6 - - - +
5235b GLU* 2.5 31.1 + - - +
5236b THR* 3.5 29.9 - - - +
5239b SER* 3.8 1.4 + - - -
5469b HIS 2.9 10.7 + - - -
5470b GLY 2.9 7.8 + - - -
5472b ARG* 1.3 76.1 - - - +
5474b LEU* 1.3 55.7 + - - +
5475b PHE 2.7 15.3 + - - -
5476b ARG* 3.4 16.8 + - - +
5518b CLA 4.1 8.5 - - - -
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Residues in contact with LEU5474 (chain b).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5228b ALA 3.9 5.4 - - - +
5229b LEU* 4.8 0.2 - - - -
5230b ARG* 3.0 49.6 - - + +
5470b GLY 3.2 7.2 + - - +
5471b ALA* 5.1 0.7 - - - -
5473b THR* 1.3 72.7 - - - +
5475b PHE* 1.3 79.3 + - + +
5518b CLA 3.4 63.7 - - + -
5481c UNK 4.8 11.2 - - + -
5482c UNK 4.2 12.6 - - + -
5490c UNK 5.1 2.2 - - + -
5134d ARG* 3.3 19.7 + - - -
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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