Contacts of the helix formed by residues 5108 - 5137 (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 GLY5108 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5060d THR* 4.9 3.8 - - - -
5079d SER 4.7 8.3 - - - -
5081d PRO* 3.9 14.0 - - - +
5090d LEU* 3.4 11.9 - - - +
5104d TRP 3.4 1.2 + - - -
5105d CYS 3.6 6.7 + - - -
5106d GLN 3.1 6.0 + - - -
5107d LEU* 1.3 80.2 - - - +
5109d GLY* 1.3 66.0 + - - +
5110d LEU* 3.2 3.4 - - - -
5111d TRP* 3.1 20.8 + - - +
5112d THR 4.1 0.7 + - - -
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Residues in contact with GLY5109 (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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5090d LEU* 3.5 16.8 - - - +
5104d TRP* 2.8 44.8 + - - -
5108d GLY* 1.3 72.7 - - - +
5110d LEU* 1.3 58.7 + - - +
5111d TRP 2.8 11.6 + - - -
5112d THR* 3.2 5.5 + - - -
5113d PHE* 3.1 21.3 + - - +
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Residues in contact with LEU5110 (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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5047d GLY* 4.1 18.8 - - - +
5050d THR* 5.0 2.9 - - + -
5051d GLY* 3.9 20.0 - - - +
5055d VAL* 3.4 37.0 - - + -
5078d VAL* 3.9 13.7 - - + -
5101d PHE* 6.1 0.2 - - + -
5104d TRP* 4.3 9.2 + - + -
5105d CYS* 4.2 19.7 - - - +
5108d GLY* 3.2 2.0 - - - -
5109d GLY* 1.3 75.5 - - - +
5111d TRP* 1.3 56.0 + - - +
5113d PHE* 3.8 11.2 - - + +
5114d ILE* 2.9 34.5 + - - +
5357d BCR 4.2 28.5 - - + -
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Residues in contact with TRP5111 (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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5078d VAL* 3.4 28.6 - - + +
5079d SER 4.3 4.9 - - - +
5080d THR* 3.5 20.5 - - + +
5081d PRO* 3.8 16.6 - - + -
5108d GLY 3.1 12.6 + - - +
5109d GLY 2.8 3.8 + - - -
5110d LEU* 1.3 76.1 - - - +
5112d THR* 1.3 74.0 + - + +
5113d PHE 3.1 1.3 - - - -
5114d ILE* 3.2 3.1 + - - +
5115d ALA* 2.8 43.0 + - + +
5157d PHE* 3.5 29.2 - + - -
5167d TRP* 3.3 33.7 - + + -
5170d ALA* 3.5 24.0 - - + -
5171d PRO 3.2 19.6 + - - -
5173d PHE* 3.3 23.3 - + - -
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Residues in contact with THR5112 (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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5081d PRO* 5.0 2.5 - - + -
5088d SER 3.7 16.2 - - - +
5089d LEU* 2.7 30.6 + - - +
5090d LEU* 3.3 15.6 - - + +
5108d GLY 4.1 0.6 + - - -
5109d GLY* 3.2 12.1 + - - -
5111d TRP* 1.3 96.4 - - + +
5113d PHE* 1.3 58.9 + - - +
5115d ALA* 4.2 2.7 - - - -
5116d LEU* 2.9 45.6 + - + +
5167d TRP* 4.0 17.3 - - + +
5355d CLA 3.6 2.6 - - - -
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Residues in contact with PHE5113 (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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5043d LEU* 3.0 39.7 - - + -
5047d GLY* 4.4 4.9 - - - -
5104d TRP* 3.3 28.0 - + + -
5109d GLY 3.1 17.7 + - - +
5110d LEU* 3.8 11.2 - - + +
5112d THR* 1.3 80.3 + - - +
5114d ILE* 1.3 74.4 + - + +
5116d LEU* 4.3 0.2 - - - +
5117d HIS* 3.1 51.7 + + - +
5355d CLA 3.1 47.3 - + - +
5357d BCR 3.7 29.8 - - + -
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Residues in contact with ILE5114 (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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5562a PHO 3.8 28.2 - - + +
5044d ALA* 4.3 15.4 - - + +
5047d GLY* 3.8 5.4 - - - -
5048d TRP* 3.5 38.6 - - + +
5078d VAL* 3.6 24.5 - - + -
5110d LEU* 2.9 24.0 + - + +
5111d TRP 3.2 3.6 + - - +
5113d PHE* 1.3 83.7 - - + +
5115d ALA* 1.3 65.6 + - - +
5118d GLY* 2.8 23.7 + - - -
5173d PHE* 3.8 19.1 - - + -
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Residues in contact with ALA5115 (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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5111d TRP* 2.8 52.0 + - + +
5112d THR* 3.9 2.9 - - - +
5114d ILE* 1.3 74.9 - - - +
5116d LEU* 1.3 61.0 + - + +
5119d ALA* 2.9 27.9 + - - +
5153d PHE* 3.7 14.8 - - + -
5157d PHE* 5.2 1.3 - - + +
5158d LEU* 5.0 10.5 - - + +
5173d PHE* 4.2 12.3 - - + -
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Residues in contact with LEU5116 (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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5518b CLA 4.0 24.5 - - + -
5089d LEU* 4.3 27.1 - - + +
5091d LEU* 5.5 1.1 - - + -
5112d THR* 2.9 39.0 + - + +
5113d PHE* 4.3 1.6 - - - +
5115d ALA* 1.3 77.1 - - + +
5117d HIS* 1.3 61.1 + - + +
5119d ALA* 3.2 6.2 - - + +
5120d PHE* 3.1 28.9 + - + -
5158d LEU* 4.9 11.7 - - + -
5167d TRP* 6.0 4.9 - - + -
5355d CLA 4.1 26.0 - - + +
5208h DGD 4.1 26.5 - - + -
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Residues in contact with HIS5117 (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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5040d CYS* 3.4 25.9 - - + +
5043d LEU* 3.6 15.3 - - + +
5044d ALA* 4.1 17.3 - - + +
5113d PHE* 3.1 64.7 + + - +
5116d LEU* 1.3 71.6 - - + +
5118d GLY* 1.3 60.9 + - - +
5119d ALA 3.0 1.3 - - - -
5120d PHE* 3.4 1.3 + - - -
5121d GLY* 2.8 23.6 + - - -
5355d CLA 2.5 70.6 + + + -
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Residues in contact with GLY5118 (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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5562a PHO 3.7 31.4 - - - -
5044d ALA* 3.8 9.8 - - - +
5114d ILE 2.8 17.7 + - - -
5117d HIS* 1.3 77.9 - - - +
5119d ALA* 1.3 60.3 + - - +
5121d GLY* 3.0 2.8 + - - -
5122d LEU* 2.9 31.4 + - - +
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Residues in contact with ALA5119 (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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5115d ALA 2.9 16.1 + - - +
5116d LEU* 3.2 16.6 - - + +
5117d HIS 3.0 0.4 - - - -
5118d GLY* 1.3 76.5 - - - +
5120d PHE* 1.3 63.3 + - + +
5122d LEU* 3.0 16.2 + - - +
5123d ILE* 3.2 16.6 + - - +
5153d PHE* 3.9 19.5 - - + -
5154d VAL* 6.3 1.3 - - + -
5158d LEU* 4.5 14.6 - - + -
5208h DGD 4.9 15.4 - - + +
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Residues in contact with PHE5120 (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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5518b CLA 3.8 59.5 - - + -
5519b CLA 3.8 28.9 - - + -
5036d LEU* 4.0 14.7 - - + +
5040d CYS* 3.9 20.9 - - - -
5116d LEU* 3.1 21.7 + - + +
5117d HIS* 5.1 0.7 - - - -
5119d ALA* 1.3 79.7 - - + +
5121d GLY* 1.3 56.8 + - - +
5123d ILE* 3.3 21.6 - - + +
5124d GLY* 2.8 25.1 + - - -
5355d CLA 3.6 34.8 - - + -
5208h DGD 4.4 17.5 - - + -
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Residues in contact with GLY5121 (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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5562a PHO 4.0 7.7 - - - +
5037d LEU* 3.2 16.0 - - - +
5040d CYS* 4.0 12.3 - - - +
5041d ALA 4.3 8.1 - - - -
5117d HIS 2.8 15.1 + - - -
5118d GLY* 3.4 6.3 - - - -
5119d ALA 2.9 0.8 - - - -
5120d PHE* 1.3 79.5 - - - +
5122d LEU* 1.3 58.6 + - - +
5124d GLY* 4.9 0.4 - - - -
5125d PHE* 2.9 24.8 + - - +
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Residues in contact with LEU5122 (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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5562a PHO 3.5 36.8 - - + +
5118d GLY 2.9 29.9 + - - +
5119d ALA* 3.0 7.6 + - - +
5121d GLY* 1.3 75.4 - - - +
5123d ILE* 1.3 64.9 + - - +
5125d PHE* 4.4 4.9 - - - +
5126d MET* 3.1 23.6 + - - +
5146d PHE* 3.9 10.3 - - + -
5149d PRO 4.6 1.6 - - - +
5150d ILE* 3.4 35.5 - - + +
5153d PHE* 4.2 28.7 - - + -
5154d VAL* 5.9 0.7 - - + -
5354d CLA 3.7 26.9 - - + -
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Residues in contact with ILE5123 (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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5518b CLA 3.4 63.8 - - + +
5519b CLA 4.6 6.1 - - + -
5036d LEU* 4.6 5.2 - - + -
5119d ALA 3.2 10.5 + - - +
5120d PHE* 3.3 41.7 - - + +
5122d LEU* 1.3 76.8 - - + +
5124d GLY* 1.3 65.4 + - - +
5126d MET* 3.3 3.1 + - - +
5127d LEU* 3.1 29.7 + - + +
5150d ILE* 5.6 1.1 - - + -
5208h DGD 3.6 32.1 - - + -
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Residues in contact with GLY5124 (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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5033d SER* 4.0 5.0 - - - -
5036d LEU* 4.0 15.7 - - - +
5037d LEU* 4.0 19.7 - - - -
5120d PHE 2.8 16.5 + - - -
5121d GLY 3.7 1.8 - - - -
5123d ILE* 1.3 77.4 - - - +
5125d PHE* 1.3 60.4 + - - +
5127d LEU* 2.9 20.7 + - - +
5128d ARG* 3.0 11.3 + - - +
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Residues in contact with PHE5125 (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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5258a LEU* 3.9 20.2 - - + -
5259a ILE* 5.7 2.0 - - + -
5562a PHO 3.2 76.7 - + + +
5564a PQ9 5.8 1.6 - - + -
5485c UNK 5.0 11.4 - - + -
5037d LEU* 3.3 21.2 - - + +
5121d GLY 2.9 19.3 + - - +
5122d LEU* 4.1 4.3 - - - +
5123d ILE 3.5 0.2 - - - -
5124d GLY* 1.3 70.8 - - - +
5126d MET* 1.3 62.3 + - - +
5128d ARG* 3.4 14.0 - - - +
5129d GLN* 3.2 48.2 + - + +
5146d PHE* 3.9 12.6 - + - -
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Residues in contact with MET5126 (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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5467b ILE* 3.1 33.0 - - + -
5518b CLA 3.4 20.2 - - + -
5122d LEU 3.1 16.7 + - - +
5123d ILE* 3.9 0.9 - - - +
5124d GLY 3.1 1.4 - - - -
5125d PHE* 1.3 73.4 - - - +
5127d LEU* 1.3 67.6 + - - +
5128d ARG 3.0 2.0 - - - -
5129d GLN* 3.0 18.0 + - - +
5130d PHE* 3.0 20.9 + - + +
5143d ALA* 3.0 32.8 - - + +
5146d PHE* 3.1 44.2 - - + +
5147d SER* 3.3 8.7 - - - +
5150d ILE* 3.7 8.3 - - + -
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Residues in contact with LEU5127 (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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5518b CLA 3.5 82.6 - - + +
5481c UNK 4.0 28.4 - - + +
5033d SER* 3.8 13.7 - - - -
5036d LEU* 4.4 8.5 - - + -
5123d ILE* 3.1 19.8 + - + +
5124d GLY* 2.9 10.9 + - - +
5126d MET* 1.3 76.1 - - - +
5128d ARG* 1.3 52.0 + - - +
5130d PHE* 2.9 9.8 + - + +
5131d GLU* 2.7 34.1 + - - +
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Residues in contact with ARG5128 (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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5257a ARG 3.1 18.6 + - - -
5258a LEU* 2.6 50.9 + - + -
5259a ILE 5.0 0.6 + - - -
5485c UNK 3.8 13.3 - - - +
5028d VAL* 4.4 2.4 - - - +
5029d PHE* 3.4 23.7 + - + +
5030d VAL 4.6 1.9 + - - -
5033d SER* 3.4 21.2 - - - +
5034d GLY* 6.3 0.4 - - - -
5037d LEU* 4.4 11.9 - - + +
5038d PHE* 2.9 40.4 - - - -
5124d GLY 3.0 9.5 + - - +
5125d PHE* 3.4 17.7 - - - +
5126d MET 3.0 0.4 - - - -
5127d LEU* 1.3 71.7 - - - +
5129d GLN* 1.3 58.8 + - - +
5130d PHE 2.8 0.7 - - - -
5131d GLU* 2.6 23.5 + - + -
5132d ILE* 2.8 32.8 + - + +
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Residues in contact with GLN5129 (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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5254a TYR* 3.1 22.5 + - - +
5258a LEU* 3.7 12.1 - - + -
5562a PHO 2.8 19.4 + - - -
5125d PHE* 3.2 26.6 + - + +
5126d MET* 3.0 30.5 + - - +
5128d ARG* 1.3 76.5 - - - +
5130d PHE* 1.3 57.3 + - - +
5132d ILE* 5.0 0.4 - - - -
5133d ALA* 3.0 30.0 + - - +
5140d PRO* 5.6 0.3 - - - +
5142d ASN* 2.6 38.2 + - - +
5143d ALA* 3.9 10.9 - - + +
5146d PHE* 3.5 16.5 - - - +
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Residues in contact with PHE5130 (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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5467b ILE* 3.7 18.2 - - + -
5471b ALA* 3.1 38.4 - - + -
5475b PHE* 4.0 16.1 - + - -
5518b CLA 3.4 49.1 - + + -
5481c UNK 3.9 18.3 - - + +
5126d MET* 3.0 10.6 + - + +
5127d LEU* 2.9 13.4 + - + +
5128d ARG 2.7 1.4 + - - -
5129d GLN* 1.3 76.9 - - - +
5131d GLU* 1.3 58.2 + - - -
5133d ALA* 4.1 1.6 - - - -
5134d ARG* 3.5 21.7 + - - +
5140d PRO* 3.3 25.8 - - + -
5143d ALA* 3.6 24.5 - - + -
5144d ILE* 4.8 2.9 - - + -
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Residues in contact with GLU5131 (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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5481c UNK 4.0 20.4 - - + +
5483c UNK 5.4 2.5 - - + -
5023d LYS* 4.3 14.1 - - - -
5029d PHE* 4.2 9.6 - - + -
5031d GLY* 2.9 12.9 - - - -
5032d TRP* 2.6 38.2 + - + -
5033d SER* 2.6 38.2 + - - +
5127d LEU 2.7 8.6 + - - +
5128d ARG* 2.6 15.4 + - - +
5130d PHE* 1.3 69.9 - - - +
5132d ILE* 1.3 66.1 + - + +
5133d ALA 3.2 1.1 - - - -
5134d ARG* 3.5 3.7 + - - +
5135d LEU* 3.2 29.6 + - + +
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Residues in contact with ILE5132 (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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5254a TYR* 3.3 36.1 - - + +
5257a ARG* 3.1 38.1 - - + +
5258a LEU* 3.5 7.4 - - + -
5029d PHE* 4.0 28.7 - - + -
5128d ARG* 2.8 40.9 + - + +
5129d GLN* 5.0 0.2 - - - -
5131d GLU* 1.3 73.3 - - - +
5133d ALA* 1.3 58.4 + - - +
5135d LEU* 3.7 6.0 - - - +
5136d VAL* 3.0 39.5 + - + +
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Residues in contact with ALA5133 (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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5254a TYR* 3.4 19.5 - - + -
5475b PHE* 3.9 16.6 - - + -
5129d GLN 3.0 21.3 + - - +
5130d PHE* 4.3 1.3 - - - +
5131d GLU 3.2 0.2 - - - -
5132d ILE* 1.3 79.0 - - - +
5134d ARG* 1.3 65.5 + - - +
5137d GLY* 2.9 18.9 + - - -
5138d VAL* 3.1 25.3 + - + +
5139d ARG 4.6 4.9 - - - +
5140d PRO* 4.7 5.6 - - + -
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Residues in contact with ARG5134 (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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5230b ARG* 4.1 18.8 - - - +
5474b LEU* 3.3 27.4 + - - -
5475b PHE* 3.5 16.2 - - + +
5477b ASP* 2.8 42.4 + - - -
5478b VAL* 3.6 11.9 - - - +
5481c UNK 5.2 3.6 - - + -
5490c UNK 4.0 25.4 - - + -
5130d PHE 3.5 17.7 + - - +
5131d GLU* 3.5 6.2 + - - +
5132d ILE 3.4 0.4 - - - -
5133d ALA* 1.3 78.9 - - - +
5135d LEU* 1.3 69.8 + - + +
5137d GLY* 3.3 16.1 + - - -
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Residues in contact with LEU5135 (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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5023d LYS* 3.9 39.0 - - + +
5029d PHE* 3.6 37.5 - - + -
5131d GLU* 3.2 19.6 + - + +
5132d ILE* 3.7 5.2 - - - +
5134d ARG* 1.3 79.1 - - + +
5136d VAL* 1.3 64.9 + - + +
5137d GLY* 2.8 10.4 + - - -
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Residues in contact with VAL5136 (chain d).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5250a ALA* 4.3 11.8 - - + +
5253a GLY* 4.1 20.9 - - - +
5254a TYR* 4.2 9.9 - - + +
5257a ARG* 4.0 25.8 - - - -
5489b GLU* 4.7 15.9 - - + -
5132d ILE* 3.0 29.1 + - + +
5133d ALA 4.5 1.1 - - - +
5135d LEU* 1.3 73.8 - - + +
5137d GLY* 1.3 61.7 + - - +
5138d VAL* 3.6 7.0 - - + +
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Residues in contact with GLY5137 (chain d).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5478b VAL* 4.1 17.9 - - - +
5482b ILE* 4.2 10.0 - - - +
5483b ASP 5.2 1.2 + - - -
5133d ALA 2.9 9.1 + - - -
5134d ARG* 3.3 17.0 + - - -
5135d LEU 2.8 8.7 + - - -
5136d VAL* 1.3 78.5 - - - +
5138d VAL* 1.3 59.2 + - - +
----------------------------------------------------------
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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
------------------------------------------------------------
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