Contacts of the helix formed by residues 277 - 309 (chain A) in PDB entry 3ZG2
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 SER 277 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A ARG 3.6 4.2 + - - -
276A MET* 1.3 71.7 - - - +
278A LEU* 1.3 58.3 + - - +
279A HIS* 3.0 10.2 + - - +
280A GLU* 2.9 37.3 + - - +
281A VAL* 2.7 29.7 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 3.0 47.4 - - + +
238A LYS* 5.2 1.1 - - - -
240A LEU* 4.3 9.0 - - + -
241A GLY* 3.7 25.6 - - - +
244A ILE* 4.2 17.9 - - + -
262A LEU* 6.2 1.3 - - + -
276A MET 3.9 0.2 + - - -
277A SER* 1.3 73.0 - - - +
279A HIS* 1.3 56.8 + - - +
281A VAL* 3.7 9.1 - - + +
282A CYS* 2.8 29.8 + - + +
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Residues in contact with HIS 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE 4.3 1.2 - - - +
111A GLY* 3.6 29.9 - - - -
112A GLU* 4.3 9.7 + - + -
114A VAL* 4.7 2.1 - - + +
233A ARG* 2.9 35.2 + - - -
237A GLN* 2.4 32.3 + - - +
277A SER* 3.0 10.3 + - - +
278A LEU* 1.3 70.9 - - - +
280A GLU* 1.3 66.4 + - + +
282A CYS* 3.5 0.5 + - - +
283A GLY* 3.1 19.2 + - - -
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A GLY 4.7 3.8 - - - -
114A VAL* 3.6 19.1 - - + +
122A ARG* 3.5 23.0 + - - -
126A GLN* 3.5 13.0 + - - +
270A TYR* 2.6 28.6 + - - -
275A ARG 4.6 3.5 - - - +
276A MET* 3.5 17.7 - - + -
277A SER* 2.9 33.6 + - - +
279A HIS* 1.3 76.1 - - + +
281A VAL* 1.3 64.1 + - - +
283A GLY* 3.2 2.8 + - - -
284A MET* 2.9 26.5 + - - +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244A ILE* 6.3 0.9 - - + -
262A LEU* 4.4 12.1 - - + -
265A LEU* 3.9 26.2 - - + +
266A LEU* 4.8 17.5 - - + -
276A MET* 3.6 28.5 - - + +
277A SER 2.7 29.1 + - - +
278A LEU* 3.7 10.5 - - + +
280A GLU* 1.3 75.5 - - - +
282A CYS* 1.3 64.2 + - - +
284A MET* 3.3 4.6 + - - +
285A ILE* 2.9 42.6 + - + +
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Residues in contact with CYS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ARG* 3.5 20.6 - - - +
236A LEU* 4.0 16.3 - - - +
237A GLN* 3.6 34.8 - - + -
240A LEU* 3.8 26.7 - - + -
278A LEU* 2.8 22.6 + - - +
279A HIS 3.7 4.3 - - - +
281A VAL* 1.3 72.9 - - - +
283A GLY* 1.3 57.8 + - - +
285A ILE* 3.2 6.7 + - - +
286A VAL* 2.9 31.7 + - - +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.4 19.4 - - - -
114A VAL* 4.3 5.8 - - - -
233A ARG* 3.1 18.1 - - - +
279A HIS 3.1 8.9 + - - -
280A GLU 3.6 3.1 - - - -
282A CYS* 1.3 78.9 - - - +
284A MET* 1.3 50.8 + - - +
286A VAL* 3.2 6.4 + - - +
287A ALA* 2.6 38.3 + - - +
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Residues in contact with MET 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A VAL* 4.2 8.0 - - + +
115A ALA* 5.1 2.0 - - - -
126A GLN* 3.7 40.6 - - + +
127A LEU* 4.7 2.7 - - - +
130A LEU* 3.6 45.2 - - + +
261A LEU* 5.5 0.2 - - - -
265A LEU* 3.7 18.8 - - + -
276A MET* 3.5 21.3 - - + -
280A GLU 2.9 16.5 + - - +
281A VAL 3.6 7.9 - - - +
283A GLY* 1.3 75.2 - - - +
285A ILE* 1.3 57.2 - - - +
287A ALA* 3.7 6.5 - - - +
288A ALA* 2.8 30.7 + - - +
1490A UDO 5.0 9.2 - - + -
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A PHE* 4.1 30.3 - - + -
188A LEU* 6.1 0.4 - - + -
197A PHE* 4.7 6.5 - - + -
236A LEU* 5.9 2.0 - - + -
240A LEU* 4.8 16.4 - - + -
261A LEU* 3.9 25.6 - - + -
262A LEU* 3.9 24.5 - - + -
265A LEU* 4.0 7.6 - - + -
281A VAL* 2.9 45.0 + - + +
282A CYS* 3.6 8.7 - - - +
284A MET* 1.3 72.7 - - - +
286A VAL* 1.3 64.8 + - + +
288A ALA* 3.6 1.2 + - - +
289A MET* 3.0 33.8 + - + +
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A VAL* 3.5 34.8 - - + +
110A PHE* 4.3 1.8 - - + -
197A PHE* 5.0 4.3 - - + -
201A LEU* 4.7 4.3 - - + -
204A MET* 3.7 30.7 - - + -
233A ARG* 4.7 1.6 - - - +
236A LEU* 3.7 29.2 - - + -
282A CYS* 2.9 22.6 + - - +
283A GLY* 3.3 8.7 - - - +
285A ILE* 1.3 76.1 - - - +
287A ALA* 1.3 55.8 + - - +
289A MET* 2.9 5.9 + - - +
290A PHE* 2.7 34.4 + - + +
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Residues in contact with ALA 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PHE* 3.7 35.2 - - + -
114A VAL* 5.6 0.9 - - + -
115A ALA* 5.6 0.2 - - + -
283A GLY 2.6 20.7 + - - +
284A MET* 3.7 11.7 - - + +
286A VAL* 1.3 72.8 - - - +
288A ALA* 1.3 62.2 + - - +
290A PHE* 4.3 0.8 - - - +
291A ALA* 2.9 27.3 + - - +
1490A UDO 3.9 24.4 - - + -
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Residues in contact with ALA 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LEU* 3.5 35.1 - - + +
183A LEU* 5.6 3.6 - - + -
261A LEU* 4.3 13.0 - - + -
284A MET 2.8 21.8 + - - +
285A ILE 3.8 3.8 - - - +
286A VAL 3.3 0.2 - - - -
287A ALA* 1.3 72.4 - - - +
289A MET* 1.3 67.2 + - + +
291A ALA* 3.4 6.2 - - - +
292A GLY* 3.3 16.6 + - - -
1480A HEM 3.7 15.6 - - + +
1490A UDO 5.6 0.2 - - - -
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Residues in contact with MET 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A ILE* 5.2 6.5 - - - +
179A ALA* 4.7 19.1 - - - +
180A CYS* 5.1 3.8 - - - -
183A LEU* 3.4 38.1 - - + -
184A PHE* 3.5 24.5 - - + -
197A PHE* 3.5 36.3 - - + -
201A LEU* 3.9 6.9 - - + +
261A LEU* 4.3 9.2 - - + -
285A ILE* 3.0 24.7 + - + +
286A VAL 2.9 3.8 + - - +
288A ALA* 1.3 78.1 - - + +
290A PHE* 1.3 66.1 + - - +
292A GLY* 3.5 1.3 + - - -
293A GLN* 3.1 24.9 + - - +
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Residues in contact with PHE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A MET* 3.1 35.2 - - + -
109A VAL* 5.4 4.5 - - + -
110A PHE* 4.2 13.5 - + + -
201A LEU* 4.1 16.0 - - + +
205A GLU* 4.0 22.0 - - + -
208A LEU* 4.6 9.9 - - + -
286A VAL* 2.7 24.3 + - + +
287A ALA* 4.3 0.9 - - - +
289A MET* 1.3 70.4 - - - +
291A ALA* 1.3 69.4 + - - +
293A GLN* 3.1 18.0 + - + +
294A HIS* 4.1 24.4 + + - -
460A MET* 4.5 14.4 - - - -
461A VAL* 4.9 9.2 - - + -
1490A UDO 3.5 30.6 - + - -
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A ALA 2.9 21.1 + - - +
288A ALA* 3.4 8.1 - - - +
289A MET 3.2 0.2 - - - -
290A PHE* 1.3 80.9 - - - +
292A GLY* 1.3 57.9 + - - +
295A THR* 3.0 16.5 + - - +
1480A HEM 3.5 32.7 - - + -
1490A UDO 3.1 42.4 - - + -
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Residues in contact with GLY 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.3 2.8 - - - +
288A ALA 3.3 8.5 + - - -
289A MET 4.0 1.3 - - - -
290A PHE 3.2 0.4 - - - -
291A ALA* 1.3 80.0 - - - +
293A GLN* 1.3 65.3 + - - +
295A THR* 3.6 4.5 - - - -
296A SER* 2.5 29.5 + - - -
427A PHE* 6.3 0.2 - - - -
431A GLN* 5.9 1.3 - - - -
1480A HEM 3.5 26.9 - - - -
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Residues in contact with GLN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A GLY* 3.7 19.3 + - - -
175A ILE* 3.1 22.8 - - - +
176A ILE* 3.6 30.8 - - - +
198A ALA* 4.5 9.9 + - - +
201A LEU* 3.9 17.0 - - + +
205A GLU* 5.6 0.9 - - - +
289A MET 3.1 18.0 + - - +
290A PHE* 3.1 11.4 + - + +
292A GLY* 1.3 80.6 - - - +
294A HIS* 1.3 70.0 + - + +
297A THR* 2.3 34.8 + - + +
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Residues in contact with HIS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A SER* 6.1 1.6 - - - -
205A GLU* 2.7 35.8 + - - -
290A PHE* 4.1 26.2 + + - -
293A GLN* 1.3 84.8 - - + +
295A THR* 1.3 69.1 + - + +
297A THR* 3.2 7.8 + - - +
298A ILE* 2.8 34.8 + - + +
461A VAL* 3.7 28.9 - - + +
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Residues in contact with THR 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ALA 3.0 16.6 + - - +
292A GLY 3.3 4.9 + - - -
294A HIS* 1.3 76.0 - - + +
296A SER* 1.3 64.0 + - - +
298A ILE* 3.7 2.9 - - - +
299A THR* 2.9 30.8 + - - -
355A PRO* 4.3 17.1 - - + +
356A LEU* 4.7 5.8 - - + -
461A VAL* 4.4 13.9 - - + -
1480A HEM 3.3 34.4 - - + +
1490A UDO 3.5 31.9 - - + -
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A ILE* 4.1 10.3 - - - +
292A GLY* 2.5 28.1 + - - -
295A THR* 1.3 78.2 + - - +
297A THR* 1.3 56.5 + - - +
299A THR* 3.5 7.0 - - - -
300A THR* 2.7 39.4 + - - -
428A ALA* 4.5 7.6 - - - +
431A GLN* 3.9 18.2 + - - -
432A VAL* 4.3 15.7 - - - -
1480A HEM 4.2 12.8 - - - +
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 3.8 9.7 + - - +
171A CYS* 3.5 8.9 - - - +
172A GLY* 3.1 39.0 + - - -
175A ILE* 3.8 16.2 - - + +
293A GLN* 2.3 39.8 + - - +
294A HIS* 3.2 17.3 - - - +
296A SER* 1.3 70.5 - - - +
298A ILE* 1.3 61.6 + - + +
301A SER* 2.8 29.7 + - - -
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Residues in contact with ILE 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.5 9.6 - - + -
294A HIS* 2.8 28.8 + - + +
295A THR 3.7 3.8 - - - +
297A THR* 1.3 72.2 + - + +
299A THR* 1.3 64.9 + - - +
301A SER* 3.1 8.3 + - - -
302A TRP* 2.9 50.9 + - + +
353A ASP 5.1 0.4 - - - +
355A PRO* 4.5 12.1 - - + -
461A VAL* 3.7 24.0 - - + +
462A VAL 3.2 33.7 - - - +
463A GLY* 3.5 17.5 - - - +
464A PRO* 4.0 3.6 - - + -
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Residues in contact with THR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A THR 2.9 22.8 + - - -
296A SER* 3.2 8.9 + - - -
298A ILE* 1.3 78.4 - - - +
300A THR* 1.3 56.8 + - - +
302A TRP* 3.6 5.7 + - - +
303A SER* 2.6 34.6 + - - +
346A VAL* 3.5 33.4 - - + +
349A SER* 4.3 2.5 - - - -
350A ILE* 3.7 22.4 - - + +
355A PRO* 4.2 8.1 - - - +
432A VAL* 4.2 9.6 - - + -
1480A HEM 3.4 14.4 - - + +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A CYS* 4.1 14.8 - - - -
174A MET* 5.9 0.2 - - + -
175A ILE* 3.4 17.3 - - + +
296A SER 2.7 26.8 + - - -
297A THR 3.9 3.8 - - - -
299A THR* 1.3 69.8 - - - +
301A SER* 1.3 59.8 + - - +
303A SER* 3.4 2.6 + - - -
304A MET* 2.8 42.5 + - + +
432A VAL* 3.2 27.0 - - + +
435A ILE* 4.0 29.8 - - + -
436A LEU* 4.2 7.6 - - + -
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Residues in contact with SER 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 4.7 3.5 - - - +
168A LEU* 3.7 30.2 - - - +
171A CYS* 3.4 24.0 - - - +
297A THR 2.8 17.8 + - - -
298A ILE 3.1 8.5 + - - -
300A THR* 1.3 73.5 - - - +
302A TRP* 1.3 54.8 + - - +
304A MET* 3.0 6.3 + - - +
305A LEU* 2.7 41.6 + - - +
464A PRO* 4.3 9.6 - - - -
469A CYS* 5.6 0.7 - - - -
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Residues in contact with TRP 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298A ILE* 2.9 47.4 + - + +
299A THR* 4.1 5.4 - - - +
301A SER* 1.3 72.5 - - - +
303A SER* 1.3 58.5 + - - +
305A LEU* 3.0 5.5 + - + +
306A HIS* 2.8 53.4 + - + +
349A SER* 4.1 11.7 - - - -
352A ARG* 4.1 3.4 - - - -
353A ASP* 3.5 51.1 + - + +
452A VAL* 3.7 18.6 - - + -
453A PRO 3.4 27.8 - - - -
455A PRO* 3.8 19.7 - - + -
462A VAL* 4.9 1.0 + - + +
463A GLY* 4.0 5.3 - - - -
464A PRO* 3.4 42.9 - - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A THR 2.6 22.5 + - - -
300A THR* 3.6 5.9 - - - -
301A SER 3.2 0.6 - - - -
302A TRP* 1.3 77.7 - - - +
304A MET* 1.3 64.8 + - - +
306A HIS* 3.3 3.4 + - - +
307A LEU* 2.9 33.5 + - - +
345A CYS* 4.9 3.8 - - - -
346A VAL* 4.0 15.7 - - - +
349A SER* 3.2 22.0 + - - -
400A TRP* 5.0 1.6 - - - -
436A LEU* 4.0 23.8 - - - -
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A TRP* 5.4 1.3 - - + -
167A LEU* 3.7 24.2 - - + -
171A CYS* 4.1 21.3 - - - -
174A MET* 5.2 7.0 - - - -
300A THR* 2.8 30.1 + - - +
301A SER* 3.4 5.8 - - - +
303A SER* 1.3 74.5 - - - +
305A LEU* 1.3 62.9 + - - +
307A LEU* 3.9 1.0 - - - +
308A MET* 3.0 31.8 + - + +
435A ILE* 5.4 2.0 - - - -
436A LEU* 3.7 13.7 - - + +
439A ALA* 4.2 22.4 - - + -
440A PHE* 3.7 34.6 - - + -
445A PHE* 4.2 20.2 - - + -
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A LEU* 4.5 8.5 - - + -
301A SER* 2.7 23.9 + - - +
302A TRP* 3.4 14.1 - - + +
304A MET* 1.3 74.6 - - - +
306A HIS* 1.3 65.6 + - - +
308A MET* 3.4 12.8 + - - +
309A HIS* 3.4 12.3 + - - +
447A LEU* 4.4 14.0 - - + +
452A VAL* 4.0 15.9 - - + +
453A PRO* 3.6 37.2 - - + -
464A PRO* 3.8 26.0 - - + -
469A CYS* 4.3 11.9 - - - +
471A VAL* 4.3 23.8 - - + -
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Residues in contact with HIS 306 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A TRP* 2.8 52.7 + + + +
303A SER 3.7 2.0 - - - +
305A LEU* 1.3 75.6 - - - +
307A LEU* 1.3 63.5 + - - +
309A HIS* 3.2 5.9 + - - +
312A ASN* 2.6 30.1 + - - +
349A SER* 3.7 6.6 + - - -
352A ARG* 3.4 43.9 + - - -
353A ASP* 4.1 2.4 + - - -
400A TRP* 3.4 53.1 - + + +
452A VAL* 4.4 21.1 - - + +
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Residues in contact with LEU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A SER* 2.9 25.8 + - - +
304A MET 3.9 2.9 - - - +
306A HIS* 1.3 77.6 - - - +
308A MET* 1.3 60.8 + - - +
309A HIS 3.2 8.1 + - - +
312A ASN* 3.9 6.2 - - - +
315A TRP* 4.3 5.2 - - + +
316A LEU* 3.9 49.4 - - + +
319A LEU* 4.0 22.7 - - + -
345A CYS* 4.3 16.8 - - + -
400A TRP* 3.9 25.4 - - + -
436A LEU* 4.4 16.6 - - + -
440A PHE* 4.1 22.4 - - + -
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167A LEU* 3.9 15.3 - - + -
304A MET* 3.0 23.6 + - + +
305A LEU* 4.0 7.9 - - - +
306A HIS 3.3 0.4 - - - -
307A LEU* 1.3 74.3 - - - +
309A HIS* 1.3 64.3 + - - +
310A PRO* 3.7 4.7 - - - +
316A LEU* 5.2 6.5 - - - +
440A PHE* 4.8 8.5 - - + -
445A PHE* 3.0 53.5 - - + +
446A GLN* 3.9 0.9 - - - -
447A LEU* 3.6 32.1 + - + +
471A VAL* 3.3 37.9 - - + -
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Residues in contact with HIS 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A LEU 3.4 8.9 + - - +
306A HIS 3.2 14.3 + - - +
307A LEU 3.2 2.3 - - - +
308A MET* 1.3 81.2 - - - +
310A PRO* 1.3 76.2 - - + +
311A LYS* 3.0 63.0 - - + -
312A ASN* 2.9 33.8 + - - +
313A LYS* 3.7 2.5 + - - +
447A LEU* 4.4 12.3 - - + +
449A ARG 5.7 0.4 - - - -
450A ASP 3.1 29.1 + - - -
451A GLU* 4.1 9.4 - - - -
452A VAL* 3.5 22.3 + - + +
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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