Contacts of the helix formed by residues 313 - 347 (chain A) in PDB entry 1GM5
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 THR 313 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A GLU* 3.7 14.3 + - - +
53A LEU* 4.7 0.3 - - - +
100A LEU* 2.9 47.0 + - + +
154A ARG* 5.0 1.1 - - - +
254A ILE* 3.8 6.9 - - - +
311A PRO* 3.8 4.2 - - - +
312A LYS* 1.3 78.9 + - - +
314A PHE* 1.3 63.5 + - - +
315A TYR* 2.5 53.8 - - + +
316A HIS* 2.6 24.1 + - - +
317A LEU 3.6 2.6 + - - -
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Residues in contact with PHE 314 (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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23A GLU* 3.1 15.5 + - - +
150A TYR* 4.6 20.6 - + + -
152A ASP* 3.5 36.3 - - + -
154A ARG* 3.4 18.8 - - - -
254A ILE* 3.7 20.6 - - + -
313A THR* 1.3 71.3 - - - +
315A TYR* 1.4 54.1 + - - +
317A LEU* 3.2 30.1 + - + +
318A GLU* 2.8 35.4 + - - +
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Residues in contact with TYR 315 (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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23A GLU* 3.3 9.0 + - + +
93A GLU* 3.7 16.4 + - - -
96A ARG* 3.6 48.7 - - + +
97A SER* 4.7 4.7 + - - -
100A LEU* 4.2 17.5 - - + -
101A ILE* 3.5 28.0 - - + -
297A LYS* 4.8 6.2 - - - +
313A THR* 2.5 35.5 - - + +
314A PHE* 1.4 68.6 - - - +
316A HIS* 1.3 72.7 + - - +
318A GLU* 3.2 17.5 - - + +
319A LYS* 2.7 51.1 + - + +
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Residues in contact with HIS 316 (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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100A LEU 4.1 3.1 + - - +
101A ILE* 3.8 28.6 - - + +
102A ASP* 3.6 34.2 + - + +
299A LEU* 4.3 14.6 - - + +
303A ASP* 4.0 9.1 + - + +
306A TYR* 4.5 7.4 - + - -
307A GLY* 3.6 28.4 + - - -
310A PHE 4.3 2.5 - - - -
311A PRO* 3.4 20.2 - - + +
312A LYS 3.8 5.7 + - - +
313A THR* 2.6 30.5 - - - +
315A TYR* 1.3 81.0 - - - +
317A LEU* 1.3 55.9 + - - +
319A LYS* 2.4 26.0 + - - +
320A ALA* 3.1 3.8 + - + -
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Residues in contact with LEU 317 (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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150A TYR* 2.9 50.3 - - + +
307A GLY 4.5 8.1 - - - +
308A MET* 4.8 5.4 - - - -
311A PRO* 4.0 16.7 - - + +
313A THR 3.6 0.6 + - - +
314A PHE* 3.2 38.9 + - + +
316A HIS* 1.3 77.5 - - - +
318A GLU* 1.3 68.2 + - - +
320A ALA* 2.8 16.8 + - - +
321A ARG* 2.9 50.6 + - - +
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Residues in contact with GLU 318 (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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314A PHE 2.8 15.9 + - - +
315A TYR* 3.2 24.0 - - + +
316A HIS 2.9 0.4 + - - -
317A LEU* 1.3 70.2 - - - +
319A LYS* 1.3 58.0 + - + +
320A ALA 2.3 18.5 + - - -
321A ARG* 4.9 6.7 - - - +
322A GLU* 3.1 33.3 + - + +
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Residues in contact with LYS 319 (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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93A GLU* 4.2 10.9 + - - -
101A ILE* 4.5 4.0 - - + -
296A ARG 5.1 0.8 + - - -
297A LYS* 3.8 23.1 - - - +
298A LEU* 2.9 52.1 - - + +
299A LEU* 3.7 25.7 - - + +
315A TYR* 2.7 48.8 + - + +
316A HIS 2.4 16.1 + - - +
318A GLU* 1.3 74.3 - - + +
320A ALA* 1.3 56.7 + - - -
322A GLU* 3.7 29.7 + - - +
323A ARG* 3.5 4.0 + - - +
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Residues in contact with ALA 320 (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 LEU* 4.8 0.9 - - + -
304A ALA* 3.5 33.7 - - - +
307A GLY* 4.3 4.9 - - - -
308A MET* 4.1 12.8 - - - +
316A HIS* 3.1 6.7 + - + +
317A LEU* 2.8 17.2 + - - +
318A GLU 2.3 16.0 + - - -
319A LYS* 1.3 70.0 - - - +
321A ARG* 1.3 53.8 + - - +
323A ARG* 3.1 1.9 + - - +
324A LEU* 2.6 40.7 + - - +
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Residues in contact with ARG 321 (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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150A TYR* 4.2 18.6 + - - -
308A MET* 3.6 20.6 - - + +
317A LEU* 2.9 48.3 + - + +
318A GLU* 4.1 5.3 - - - +
320A ALA* 1.3 72.5 - - - +
322A GLU* 1.3 56.6 + - - +
324A LEU* 2.3 31.9 + - - -
325A ALA* 2.7 12.7 + - - -
738A LEU* 3.1 30.7 - - + +
742A LYS* 4.8 11.7 - - - +
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Residues in contact with GLU 322 (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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296A ARG* 4.6 2.9 - - - +
298A LEU* 1.9 60.0 - - + +
318A GLU* 3.1 24.8 + - + +
319A LYS* 3.7 22.0 + - - +
321A ARG* 1.3 79.1 - - - +
323A ARG* 1.3 59.6 + - - +
325A ALA* 3.9 5.2 - - - -
326A TYR* 3.2 23.7 + - + +
742A LYS* 5.3 7.0 - - + +
745A ASP* 4.6 13.3 - - - +
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Residues in contact with ARG 323 (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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286A GLU* 3.0 27.5 + - - -
287A THR* 3.3 11.1 + - - -
288A LEU* 4.1 20.0 - - - +
293A LEU* 5.2 1.0 - - - +
298A LEU* 2.2 39.3 + - + +
299A LEU* 2.5 23.1 + - + +
300A GLY* 2.4 17.9 + - - +
301A VAL* 3.6 9.0 - - - +
304A ALA* 4.3 7.8 - - + +
319A LYS 3.6 8.7 - - - +
320A ALA 3.1 3.1 + - - +
321A ARG 2.6 2.0 + - - -
322A GLU* 1.3 72.0 - - - +
324A LEU* 1.3 66.3 + - - +
325A ALA 2.9 6.9 + - - -
326A TYR* 4.0 5.0 - - - +
327A GLU* 1.9 68.6 + - - +
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Residues in contact with LEU 324 (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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146A PHE* 3.6 32.5 - - + -
301A VAL* 5.6 1.1 - - + -
304A ALA* 4.5 10.5 - - + -
305A TYR* 3.1 40.8 - - + +
308A MET* 4.0 10.1 - - + -
320A ALA 2.6 17.1 + - - +
321A ARG 2.3 16.5 + - - +
323A ARG* 1.3 74.8 - - - +
325A ALA* 1.3 55.0 + - - +
327A GLU* 3.9 21.1 - - + +
328A GLU* 3.8 11.6 + - - +
738A LEU* 3.2 31.7 - - + +
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Residues in contact with ALA 325 (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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321A ARG 2.7 16.4 + - - +
322A GLU* 4.2 2.7 - - - +
324A LEU* 1.3 72.6 - - - +
326A TYR* 1.3 71.3 + - - +
327A GLU 3.0 0.7 - - - -
328A GLU* 2.7 18.2 + - - +
329A LEU* 3.0 12.9 + - - +
738A LEU* 3.9 21.1 - - + +
739A SER* 3.7 26.5 - - - +
742A LYS* 4.8 4.3 - - - -
745A ASP* 4.5 7.9 - - - +
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Residues in contact with TYR 326 (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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288A LEU* 3.2 30.7 - - + -
292A ILE* 3.5 21.5 - - + +
296A ARG* 5.0 4.9 - - + -
298A LEU* 6.2 0.9 - - + -
322A GLU* 3.2 17.5 + - + +
323A ARG* 4.0 6.1 - - - +
325A ALA* 1.3 75.8 - - - +
327A GLU* 1.3 69.9 + - - +
329A LEU* 2.7 19.7 + - - +
330A PHE* 2.8 24.5 + + + -
745A ASP* 4.1 18.4 + - - +
748A ARG* 4.3 15.5 - - + -
749A ASP* 4.2 10.3 - - - -
752A LEU* 2.9 30.2 - - + +
753A LEU* 3.0 28.9 - - + +
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Residues in contact with GLU 327 (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 THR* 2.8 27.3 + - - +
288A LEU* 4.7 5.9 + - - +
301A VAL* 5.7 1.2 - - - +
323A ARG* 1.9 61.5 + - - +
324A LEU* 3.9 16.9 - - + +
326A TYR* 1.3 84.8 - - - +
328A GLU* 1.3 65.0 + - + +
330A PHE* 2.8 30.2 + - - +
331A VAL* 3.2 12.1 + - + +
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Residues in contact with GLU 328 (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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324A LEU 3.8 14.5 - - - +
325A ALA* 2.7 20.1 + - - +
327A GLU* 1.3 77.7 - - + +
329A LEU* 1.3 66.2 + - + +
331A VAL* 3.9 20.8 - - + +
332A LEU* 4.0 10.6 - - - +
736A HIS* 2.8 30.9 + - + +
737A GLY* 2.8 35.7 + - - -
738A LEU* 3.6 14.5 + - - +
739A SER* 4.7 1.8 - - - +
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Residues in contact with LEU 329 (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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325A ALA 3.0 10.5 + - - +
326A TYR* 2.7 12.5 + - - +
328A GLU* 1.3 75.4 - - + +
330A PHE* 1.3 69.7 + - - +
331A VAL 3.2 0.2 - - - -
332A LEU* 2.7 19.8 + - + +
333A GLN* 2.9 16.4 + - - +
534A ALA* 5.5 4.5 - - + +
736A HIS* 3.4 37.0 - - + +
739A SER* 4.3 18.4 - - - +
741A PHE* 6.1 3.4 - - + -
742A LYS 6.1 0.9 - - - +
745A ASP* 4.2 23.1 - - + +
746A LEU* 3.7 34.3 - - + -
749A ASP* 4.0 13.5 - - - +
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Residues in contact with PHE 330 (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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288A LEU* 4.0 24.9 - - + -
289A PRO* 5.1 4.3 - - + -
292A ILE* 4.6 14.8 - - + -
326A TYR* 2.8 25.6 + + + +
327A GLU* 2.8 22.2 - - - +
329A LEU* 1.3 75.2 - - - +
331A VAL* 1.3 55.7 + - + -
332A LEU 2.5 13.7 + - - -
333A GLN* 4.6 3.4 - - - +
334A LEU* 2.6 58.8 + - + +
749A ASP* 4.9 0.8 + - - -
752A LEU 4.6 3.4 - - - -
753A LEU* 3.6 39.0 - - + -
755A TRP 5.2 9.2 - - - -
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Residues in contact with VAL 331 (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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327A GLU* 3.2 14.1 + - + +
328A GLU* 4.0 14.4 - - + +
329A LEU 3.2 0.2 - - - -
330A PHE* 1.3 82.4 - - + +
332A LEU* 1.3 81.5 + - + +
334A LEU* 3.8 6.3 - - - +
335A ALA* 3.5 16.5 + - - +
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Residues in contact with LEU 332 (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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328A GLU 4.0 11.0 - - - +
329A LEU* 2.7 15.9 + - + +
330A PHE 2.5 4.4 + - - -
331A VAL* 1.3 85.8 - - + +
333A GLN* 1.3 55.9 + - + +
334A LEU 2.5 16.6 + - - -
335A ALA* 2.7 18.9 + - + +
336A PHE* 3.0 20.2 + - + -
534A ALA 2.7 30.1 - - - +
535A PHE* 3.7 29.6 - - + +
736A HIS* 5.0 6.5 - - + +
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Residues in contact with GLN 333 (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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329A LEU 2.9 14.8 + - - +
330A PHE* 4.0 2.2 - - - +
332A LEU* 1.3 73.1 - - + +
334A LEU* 1.3 66.1 + - - +
336A PHE* 3.7 21.3 - - - +
337A GLN* 3.3 29.3 + - + +
533A LEU 3.4 24.3 + - - +
534A ALA* 5.3 2.7 - - - +
537A GLY* 5.5 2.6 - - - -
746A LEU* 3.8 21.4 + - + +
749A ASP* 3.9 24.5 - - + +
750A LEU* 4.5 16.7 - - - +
753A LEU* 4.1 22.2 - - + +
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Residues in contact with LEU 334 (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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330A PHE* 2.6 58.3 + - + +
331A VAL* 3.8 7.2 - - - +
332A LEU 2.5 4.9 + - - -
333A GLN* 1.3 76.1 - - - +
335A ALA* 1.3 66.0 + - - +
336A PHE 2.8 2.3 + - - -
337A GLN* 3.9 1.4 - - - +
338A LYS* 3.0 42.1 + - + +
753A LEU 4.5 7.2 - - - +
754A GLU 4.5 16.2 - - - +
755A TRP* 5.1 6.7 - - - -
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Residues in contact with ALA 335 (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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331A VAL 3.5 9.9 + - - +
332A LEU* 2.7 13.7 + - + +
334A LEU* 1.3 75.3 - - - +
336A PHE* 1.3 56.3 + - + +
338A LYS* 3.4 12.0 - - - +
339A ILE* 2.2 44.4 + - + +
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Residues in contact with PHE 336 (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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332A LEU* 3.0 31.5 + - + -
333A GLN* 3.7 24.2 - - - +
334A LEU 2.8 1.6 + - - -
335A ALA* 1.3 73.4 - - + +
337A GLN* 1.3 74.4 + - - +
338A LYS 2.9 0.4 - - - -
339A ILE* 2.4 20.6 + - + +
340A ARG* 2.7 13.5 + - + +
534A ALA 4.2 11.4 - - - -
535A PHE 3.1 17.3 - - - -
536A TYR* 1.7 52.3 - - - -
537A GLY* 4.0 0.7 - - - -
538A ASP* 2.6 42.8 - - + +
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Residues in contact with GLN 337 (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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333A GLN* 3.3 12.1 + - + +
334A LEU* 3.2 3.1 + - - +
336A PHE* 1.3 80.9 - - - +
338A LYS* 1.3 53.0 + - - +
339A ILE 2.5 6.6 + - - -
340A ARG* 2.6 43.0 + - - +
341A LYS* 2.5 38.2 + - + +
750A LEU* 4.7 15.3 - - - +
753A LEU 3.4 24.0 - - - +
754A GLU* 4.3 24.1 - - - +
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Residues in contact with LYS 338 (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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334A LEU* 3.0 37.7 + - + +
335A ALA* 3.4 15.0 - - - +
336A PHE 2.8 1.0 + - - -
337A GLN* 1.3 75.3 - - - +
339A ILE* 1.3 58.8 + - + +
341A LYS* 3.8 21.3 - - - +
342A GLU* 4.0 5.0 - - - +
755A TRP* 6.4 2.2 - - - -
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Residues in contact with ILE 339 (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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335A ALA* 2.2 44.5 + - + +
336A PHE* 2.4 19.3 + - - +
338A LYS* 1.3 73.0 - - + +
340A ARG* 1.3 67.3 + - - +
341A LYS 2.7 6.1 + - - -
342A GLU* 2.8 19.9 + - + +
343A ARG* 3.3 34.2 + - + +
538A ASP* 4.8 14.8 - - + +
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Residues in contact with ARG 340 (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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336A PHE* 2.7 6.7 + - - +
337A GLN* 2.6 48.9 + - - +
339A ILE* 1.3 79.1 - - + +
341A LYS* 1.3 55.2 - - - +
343A ARG* 3.3 22.2 - - + +
344A GLU* 2.6 31.7 - - - +
388A LYS* 6.0 1.3 - - - +
537A GLY 2.9 35.4 + - - -
538A ASP* 3.4 22.5 + - + +
540A ASP* 4.0 26.8 + - - +
750A LEU* 5.2 8.1 - - - +
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Residues in contact with LYS 341 (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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337A GLN* 2.5 22.3 + - + +
338A LYS* 3.8 14.4 - - - +
339A ILE 2.7 0.6 + - - -
340A ARG* 1.3 69.9 - - - +
342A GLU* 1.3 96.2 + - + +
343A ARG 2.8 5.8 + - - -
344A GLU* 2.6 36.6 + - + +
345A LYS* 3.0 36.3 + - - +
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Residues in contact with GLU 342 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338A LYS 4.0 7.4 - - - +
339A ILE* 2.8 13.0 + - - +
341A LYS* 1.3 101.1 - - + +
343A ARG* 1.3 59.8 + - + +
345A LYS* 3.6 17.0 - - - +
346A HIS* 3.7 33.0 + - - +
516A MET* 5.0 1.4 - - - +
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Residues in contact with ARG 343 (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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339A ILE* 3.3 28.8 + - + +
340A ARG* 3.3 20.5 - - - +
341A LYS 2.8 0.4 - - - -
342A GLU* 1.3 78.7 - - + +
344A GLU* 1.3 65.3 + - - +
345A LYS 3.2 0.4 - - - -
346A HIS* 3.7 1.1 + - - +
347A GLY* 3.0 28.8 + - - -
388A LYS* 5.5 0.9 - - - +
389A PRO* 4.2 25.4 - - + +
391A ASN* 2.0 52.8 + - - +
516A MET* 4.3 21.8 - - + +
538A ASP* 3.8 25.5 + - - +
539A LEU* 5.6 0.2 - - - +
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Residues in contact with GLU 344 (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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340A ARG* 2.6 33.0 + - - +
341A LYS* 2.6 17.3 + - + +
343A ARG* 1.3 77.3 - - - +
345A LYS* 1.3 70.6 + - + +
347A GLY* 3.5 7.3 + - - -
388A LYS* 1.9 49.4 + - - +
389A PRO* 5.9 0.2 - - - -
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Residues in contact with LYS 345 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341A LYS* 3.0 41.3 + - - +
342A GLU* 3.6 22.7 - - - +
343A ARG 3.2 0.2 - - - -
344A GLU* 1.3 78.3 - - + +
346A HIS* 1.3 61.1 + - + +
347A GLY* 2.3 21.0 + - - -
----------------------------------------------------------
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Residues in contact with HIS 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLU* 3.7 30.9 + - - +
343A ARG 3.7 2.5 + - - +
345A LYS* 1.3 80.4 - - + +
347A GLY* 1.3 66.1 + - - +
511A MET* 2.7 45.1 - - + +
514A GLY* 3.3 10.5 - - - +
515A LYS* 3.2 17.7 + - - +
516A MET* 3.9 22.7 - - + -
----------------------------------------------------------
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Residues in contact with GLY 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG 3.0 13.9 + - - -
344A GLU* 3.9 6.1 - - - -
345A LYS 2.3 19.0 + - - -
346A HIS* 1.3 79.8 - - - +
348A GLY* 1.3 55.8 - - - -
388A LYS* 5.7 1.1 - - - -
389A PRO* 4.2 1.1 - - - -
515A LYS* 3.0 4.7 - - - -
516A MET* 2.6 33.1 + - - +
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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