Contacts of the helix formed by residues 222 - 254 (chain B) in PDB entry 2PDA
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 PRO 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A PHE* 3.6 15.7 - - + -
365A LEU 5.1 0.2 - - - +
366A GLY 3.3 20.2 - - - +
367A SER* 3.2 34.8 - - - +
368A LYS* 2.8 37.0 + - - +
652A ASP* 4.6 2.0 - - - +
221B ASN* 1.3 99.9 - - + +
223B ASP* 1.3 54.7 + - - +
224B ILE 3.2 0.9 + - - -
225B TYR* 3.9 3.9 + - + +
226B PHE 4.4 1.2 + - - -
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Residues in contact with ASP 223 (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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368A LYS* 2.5 20.3 + - - +
646A ILE* 3.6 24.5 - - - +
649A GLN* 5.3 5.2 - - - +
651A GLY* 3.0 15.0 + - - +
652A ASP* 3.2 33.9 + - - +
221B ASN* 3.7 19.3 + - - +
222B PRO* 1.3 76.5 - - - +
224B ILE* 1.3 84.6 + - - +
227B GLN* 2.7 17.0 - - - +
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Residues in contact with ILE 224 (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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646A ILE* 4.1 27.1 - - + -
651A GLY 3.6 9.0 - - - +
659A PHE* 3.5 36.7 - - + -
665A PHE* 4.4 3.8 - - + -
848A ALA* 4.0 17.9 - - + -
220B GLN* 3.8 40.7 + - + +
221B ASN 4.6 0.9 - - - +
223B ASP* 1.3 104.6 + - - +
225B TYR* 1.3 68.5 + - - +
226B PHE 3.5 1.6 - - - -
227B GLN* 3.5 8.3 + - - +
228B GLY* 3.2 16.3 + - - -
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Residues in contact with TYR 225 (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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115A ALA* 4.0 9.2 - - + +
116A ILE 2.5 27.5 + - - -
118A ALA 4.5 0.9 + - - -
119A HIS* 4.0 15.7 - + - -
120A ALA 3.6 20.9 + - - -
121A LEU 4.2 4.7 - - - -
122A SER* 3.7 20.9 - - - +
128A GLN* 4.0 17.7 + - - -
365A LEU* 4.1 3.4 - - + -
366A GLY* 3.6 30.5 - - - +
220B GLN* 3.8 13.2 - - + +
221B ASN 3.2 22.0 + - - +
222B PRO* 3.9 1.7 + - + -
224B ILE* 1.3 80.2 - - - +
226B PHE* 1.3 71.3 + - - +
227B GLN 2.9 0.2 + - - -
228B GLY* 3.1 8.3 + - - -
229B ARG* 3.1 38.8 + - + +
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Residues in contact with PHE 226 (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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362A ARG* 3.7 22.4 - - + -
363A TYR* 4.0 13.9 - - - -
365A LEU* 3.4 46.1 + - + +
368A LYS* 3.6 36.1 - - + -
391A THR* 3.8 15.0 - - + -
392A VAL 3.7 21.1 - - - -
394A ILE* 3.5 16.4 - - + -
222B PRO 4.4 1.8 + - - -
224B ILE 3.5 0.4 - - - -
225B TYR* 1.3 80.4 - - - +
227B GLN* 1.3 64.6 + - - +
229B ARG* 3.4 11.1 - - - +
230B GLU* 3.4 27.4 + - + +
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Residues in contact with GLN 227 (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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368A LYS* 2.7 37.6 - - - +
394A ILE* 3.9 21.9 - - + +
651A GLY 3.2 8.0 - - - +
652A ASP 3.9 4.3 - - - +
654A LEU 3.1 26.2 - - - +
655A PRO* 4.4 5.2 - - + -
656A VAL* 4.0 16.8 - - - +
659A PHE* 3.5 19.3 - - + -
223B ASP 2.7 18.5 + - - +
224B ILE* 3.5 11.1 - - - +
225B TYR 2.9 1.2 + - - -
226B PHE* 1.3 68.1 - - - +
228B GLY* 1.3 54.9 + - - +
229B ARG 2.9 4.0 - - - -
230B GLU* 2.7 27.7 + - - +
231B ALA* 3.0 9.2 + - - +
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Residues in contact with GLY 228 (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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119A HIS* 3.5 25.9 + - - -
659A PHE* 4.1 17.2 - - - -
660A GLU 4.8 2.3 - - - +
661A ALA 4.3 7.1 - - - +
663A GLY* 6.2 0.4 - - - -
220B GLN* 4.9 2.2 - - - -
224B ILE 3.2 7.9 + - - -
225B TYR 3.1 6.9 + - - -
227B GLN* 1.3 78.2 - - - +
229B ARG* 1.3 58.5 + - - +
231B ALA* 3.5 21.4 + - - +
232B ALA* 4.7 0.5 + - - +
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Residues in contact with ARG 229 (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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118A ALA* 3.4 26.3 - - - +
119A HIS* 3.3 16.7 + - + -
128A GLN* 3.3 35.4 + - - +
331A LYS* 2.6 52.9 + - + +
333A PRO* 4.4 17.8 - - - +
365A LEU* 3.7 22.0 - - + -
98B TYR* 4.6 14.5 - - - -
102B GLY* 5.4 3.0 - - - -
225B TYR* 3.1 28.4 + - + +
226B PHE* 3.4 12.3 - - - +
227B GLN 2.8 0.8 + - - -
228B GLY* 1.3 76.2 - - - +
230B GLU* 1.3 57.3 + - - +
231B ALA 3.2 1.7 + - - -
232B ALA* 4.1 9.7 + - - +
233B ASN* 4.6 0.2 + - - -
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Residues in contact with GLU 230 (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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331A LYS* 3.0 24.2 + - - +
362A ARG* 2.9 33.1 + - - -
365A LEU* 4.6 0.3 - - - +
391A THR* 3.9 14.1 - - - +
394A ILE* 3.7 26.9 - - + -
396A ASP* 5.3 2.9 - - - +
398A VAL* 4.8 1.6 - - - +
399A THR* 4.3 2.3 + - - -
401A THR* 4.3 5.7 + - - +
656A VAL* 4.5 8.9 - - + +
226B PHE* 3.4 14.7 + - + +
227B GLN 2.7 11.8 + - - +
229B ARG* 1.3 71.4 - - + +
231B ALA* 1.3 57.9 + - - +
232B ALA 3.0 7.4 + - - -
233B ASN* 2.9 47.5 + - - +
234B PRO* 4.7 0.3 - - - +
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Residues in contact with ALA 231 (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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398A VAL* 4.8 3.1 - - + +
656A VAL* 4.2 19.0 - - - +
659A PHE 3.8 22.4 - - - +
660A GLU 4.2 1.8 - - - +
661A ALA* 3.6 22.9 - - - +
227B GLN 3.0 6.1 + - - +
228B GLY* 3.5 22.0 - - - +
229B ARG 3.2 1.4 - - - -
230B GLU* 1.3 76.5 - - - +
232B ALA* 1.3 57.6 + - - +
233B ASN 3.4 0.4 - - - -
234B PRO* 3.7 11.9 - - - +
235B TYR* 4.9 0.3 - - - -
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Residues in contact with ALA 232 (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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661A ALA* 4.1 16.7 + - - +
101B SER 5.7 0.7 - - - +
102B GLY 5.5 2.2 - - - +
104B LEU* 4.3 16.4 - - + -
228B GLY 4.7 0.4 + - - +
229B ARG 4.1 7.2 + - - +
230B GLU 3.0 2.2 + - - -
231B ALA* 1.3 74.6 - - - +
233B ASN* 1.3 67.4 + - - +
234B PRO* 3.2 4.9 - - - -
235B TYR* 3.0 25.2 + - - +
236B TYR* 3.5 23.6 + - + -
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Residues in contact with ASN 233 (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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331A LYS* 3.8 14.1 - - - +
396A ASP* 4.3 1.6 - - - +
399A THR* 2.6 40.6 + - + +
401A THR* 4.8 2.1 + - - +
229B ARG 4.6 0.2 + - - -
230B GLU* 2.9 50.4 + - - +
232B ALA* 1.3 75.7 - - - +
234B PRO* 1.3 71.2 - - + +
235B TYR 2.8 2.4 + - - -
236B TYR* 2.9 18.7 + - - +
237B LEU* 3.0 15.4 + - + +
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Residues in contact with PRO 234 (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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398A VAL* 3.9 23.8 - - + -
399A THR* 5.2 1.3 - - + +
231B ALA 3.7 12.6 - - - +
232B ALA 3.2 6.3 - - - -
233B ASN* 1.3 93.9 - - + +
235B TYR* 1.3 69.6 + - + +
237B LEU* 3.3 16.1 + - + +
238B LYS* 3.1 51.5 + - - +
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Residues in contact with TYR 235 (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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661A ALA* 3.6 22.4 - - + +
104B LEU* 4.1 26.0 - - + +
163B SER* 3.3 23.7 - - - +
164B ASN* 4.4 11.7 - - + -
165B VAL* 4.1 15.1 - - + +
231B ALA 4.9 1.3 - - - -
232B ALA* 3.2 19.5 - - - +
233B ASN 2.8 4.0 + - - -
234B PRO* 1.3 80.6 - - + +
236B TYR* 1.3 59.6 + - + +
237B LEU 3.0 4.3 - - - -
238B LYS* 2.9 13.2 + - + +
239B VAL* 2.9 28.2 + - - +
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Residues in contact with TYR 236 (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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333A PRO* 3.8 29.0 - - + +
334A GLY* 4.2 13.7 - - - +
101B SER* 3.6 23.3 + - - -
104B LEU* 4.4 5.6 - - + -
137B GLY* 2.9 33.0 + - - -
138B PHE 5.5 0.4 - - - -
139B ALA* 6.1 0.4 - - - -
165B VAL* 3.9 28.2 - - + +
232B ALA* 3.5 29.6 - - + -
233B ASN* 2.9 12.8 + - - +
235B TYR* 1.3 78.0 - - + +
237B LEU* 1.3 61.3 + - + +
239B VAL* 3.4 20.4 - - + +
240B PRO* 3.4 7.8 - - - +
307B PRO* 3.9 16.3 - - + +
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Residues in contact with LEU 237 (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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399A THR* 3.5 29.4 - - + -
233B ASN* 3.0 20.3 + - + +
234B PRO* 3.3 20.4 - - + +
235B TYR 3.0 0.2 - - - -
236B TYR* 1.3 81.2 - - + +
238B LYS* 1.3 60.4 + - + +
240B PRO* 3.1 16.3 - - - +
241B GLY 5.0 0.9 + - - -
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Residues in contact with LYS 238 (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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163B SER* 5.4 0.4 - - - -
234B PRO* 3.1 40.5 + - - +
235B TYR* 2.9 12.4 + - + +
237B LEU* 1.3 79.0 - - + +
239B VAL* 1.3 63.4 + - - +
240B PRO* 3.2 3.1 - - - -
241B GLY* 3.6 2.9 + - - +
242B ILE* 3.1 36.5 + - + +
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Residues in contact with VAL 239 (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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139B ALA* 4.4 4.0 - - + -
159B ALA 5.3 0.2 - - - +
163B SER* 4.0 19.3 - - - +
165B VAL* 4.1 19.1 - - + -
167B PHE* 3.6 34.3 - - + -
235B TYR 2.9 7.7 + - - +
236B TYR* 3.4 31.4 - - + +
238B LYS* 1.3 77.4 - - - +
240B PRO* 1.4 60.1 - - - +
242B ILE* 3.5 5.8 + - + +
243B VAL* 3.0 26.4 + - + +
304B LEU* 5.2 0.7 - - - -
307B PRO* 3.7 21.8 - - + -
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Residues in contact with PRO 240 (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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236B TYR 3.4 11.2 - - - +
237B LEU 3.1 20.4 - - - +
238B LYS 3.3 1.1 - - - -
239B VAL* 1.4 90.0 - - + +
241B GLY* 1.3 60.3 + - - +
243B VAL* 3.0 4.3 + - - +
244B ALA* 2.8 27.8 + - - +
260B LEU* 3.9 11.5 - - + +
304B LEU* 4.2 12.6 - - + -
307B PRO* 4.3 13.5 - - + -
309B VAL* 3.7 31.2 - - + -
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Residues in contact with GLY 241 (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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237B LEU 5.0 1.4 + - - -
238B LYS* 3.6 5.6 + - - +
240B PRO* 1.3 79.3 - - - +
242B ILE* 1.3 51.1 + - - +
244B ALA* 3.1 8.4 + - - +
245B GLU* 2.6 37.9 + - - +
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Residues in contact with ILE 242 (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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159B ALA* 3.7 30.7 - - + +
162B GLU* 3.7 26.7 - - + +
163B SER* 3.6 31.0 - - - +
238B LYS* 3.1 27.5 + - + +
239B VAL* 3.7 5.8 - - - +
240B PRO 3.1 0.6 - - - -
241B GLY* 1.3 77.2 - - - +
243B VAL* 1.3 59.8 + - - +
245B GLU* 3.4 8.9 + - - +
246B TYR* 3.1 35.6 + - + -
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Residues in contact with VAL 243 (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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141B LEU* 4.6 2.2 - - + -
155B VAL* 4.2 9.9 - - + +
159B ALA* 4.2 9.9 - - + -
167B PHE* 3.3 35.0 - - + -
239B VAL* 3.0 20.2 + - + +
240B PRO* 3.0 9.9 + - + +
242B ILE* 1.3 72.8 - - - +
244B ALA* 1.3 61.4 + - - +
246B TYR* 3.2 2.9 + - - +
247B MET* 2.9 48.6 + - + +
260B LEU* 3.8 18.2 - - + -
304B LEU* 4.0 17.9 - - + -
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Residues in contact with ALA 244 (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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240B PRO 2.8 12.1 + - - +
241B GLY* 3.4 12.1 - - - +
243B VAL* 1.3 75.7 - - - +
245B GLU* 1.3 63.8 + - - +
247B MET* 3.3 5.6 + - - +
248B GLN* 2.9 44.6 + - - +
259B LYS* 6.4 0.7 - - - +
260B LEU* 4.1 17.5 - - + +
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Residues in contact with GLU 245 (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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162B GLU* 3.3 33.9 - - - +
196B ASN* 5.2 1.4 + - - -
241B GLY 2.6 19.8 + - - +
242B ILE* 3.5 13.1 - - - +
243B VAL 3.2 0.2 - - - -
244B ALA* 1.3 73.0 - - - +
246B TYR* 1.3 61.7 + - + +
248B GLN* 3.3 11.8 - - - +
249B LYS* 2.8 59.4 + - + +
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Residues in contact with TYR 246 (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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155B VAL* 4.3 19.1 - - + +
158B LEU* 3.6 47.3 + - + +
159B ALA* 3.7 12.3 - - - -
162B GLU* 2.9 28.6 + - - -
194B LEU* 3.3 27.8 + - + -
196B ASN* 3.8 18.5 + - - +
242B ILE* 3.1 29.6 + - + +
243B VAL 3.9 2.9 - - - +
245B GLU* 1.3 82.5 + - + +
247B MET* 1.3 63.5 + - - +
248B GLN 2.9 1.8 - - - -
249B LYS* 3.9 25.3 + - + +
250B VAL* 3.0 28.6 + - - +
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Residues in contact with MET 247 (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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141B LEU* 3.8 13.5 - - + -
152B MET* 4.2 4.5 - - + -
155B VAL* 4.1 18.6 - - + -
243B VAL* 2.9 41.5 + - + +
244B ALA* 3.8 5.8 - - - +
246B TYR* 1.3 75.8 - - - +
248B GLN* 1.3 56.1 + - - +
250B VAL* 4.1 1.6 - - - +
251B ALA* 3.1 28.2 + - - +
256B ARG 4.6 1.2 - - - +
258B TYR* 3.5 52.8 + - + +
259B LYS* 3.6 22.7 - - - +
260B LEU* 4.0 7.0 - - - +
303B ARG* 3.7 23.3 - - + -
304B LEU 5.0 0.4 - - - +
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Residues in contact with GLN 248 (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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244B ALA* 2.9 36.8 + - - +
245B GLU* 3.3 12.9 - - - +
246B TYR 2.9 0.2 - - - -
247B MET* 1.3 77.8 - - - +
249B LYS* 1.3 63.9 + - + +
251B ALA* 3.4 6.5 + - - +
252B SER* 3.0 20.6 + - - -
257B SER* 6.0 1.1 - - - +
258B TYR 4.4 12.9 + - - +
259B LYS* 5.8 3.4 - - - +
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Residues in contact with LYS 249 (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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194B LEU* 4.1 30.9 + - + +
196B ASN* 5.8 1.8 - - - +
245B GLU* 2.8 47.5 + - - +
246B TYR* 3.3 32.5 + - + +
248B GLN* 1.3 71.0 - - + +
250B VAL* 1.3 62.6 + - - +
252B SER* 2.8 30.0 + - - -
253B LEU* 3.3 8.1 + - - +
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Residues in contact with VAL 250 (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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150B HIS* 5.8 0.2 - - + -
151B ASP* 4.7 20.2 - - + +
154B LEU* 3.4 33.7 - - + -
155B VAL* 4.5 13.9 - - + -
158B LEU* 4.3 15.9 - - + -
186B LEU* 4.8 0.7 - - + -
194B LEU* 4.3 4.7 - - + -
246B TYR 3.0 16.3 + - - +
247B MET 4.2 2.7 - - - +
249B LYS* 1.3 75.4 - - + +
251B ALA* 1.3 58.4 + - - +
253B LEU* 3.0 9.9 + - - +
254B THR* 2.7 51.1 + - + +
256B ARG 5.2 1.3 - - - +
258B TYR* 5.9 2.9 - - + -
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Residues in contact with ALA 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B MET 3.1 20.0 + - - +
248B GLN* 3.6 7.0 - - - +
249B LYS 3.1 0.2 - - - -
250B VAL* 1.3 76.9 - - - +
252B SER* 1.3 60.3 - - - +
254B THR* 3.6 1.8 - - - -
255B GLY* 2.7 27.8 + - - -
256B ARG 3.2 26.9 - - - +
257B SER* 3.3 25.1 - - - +
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Residues in contact with SER 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B GLN 3.0 12.6 + - - -
249B LYS* 2.8 18.5 + - - -
251B ALA* 1.3 78.8 - - - +
253B LEU* 1.3 60.1 + - - +
255B GLY 4.8 0.7 + - - -
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Residues in contact with LEU 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 3.3 22.6 + - - +
186B LEU* 4.0 24.5 - - + +
190B ASP* 4.0 27.6 - - + +
193B SER* 5.0 6.3 - - - +
194B LEU* 3.4 38.1 - - + -
249B LYS 3.3 6.7 + - - +
250B VAL* 3.0 6.9 + - - +
252B SER* 1.3 82.4 - - - +
254B THR* 1.3 64.2 + - + +
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B LYS* 3.6 11.8 + - - -
151B ASP* 4.6 0.4 + - - +
184B GLU* 3.4 17.7 - - - +
186B LEU* 3.8 24.5 - - + -
250B VAL* 2.7 41.0 + - + +
251B ALA* 3.6 0.2 - - - -
253B LEU* 1.3 78.6 - - - +
255B GLY* 1.3 59.7 + - - +
256B ARG* 3.0 58.2 + - - +
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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) + - + + + + + -
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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