Contacts of the helix formed by residues 307 - 341 (chain A) in PDB entry 2A7P
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 GLY 307 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 6.0 0.2 - - - +
78A GLY* 5.6 0.2 - - - -
80A THR* 4.4 10.6 - - - +
305A LEU 3.9 0.8 + - - -
306A LEU* 1.3 72.7 - - - +
308A ARG* 1.3 65.8 + - - +
309A ALA* 3.3 2.4 + - - +
310A THR* 3.6 6.6 + - - -
311A LEU* 3.2 27.6 + - - +
390A FMN 3.2 36.0 + - - -
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Residues in contact with ARG 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 2.8 23.8 + - + +
28A GLU* 3.5 30.2 + - - -
29A GLY 2.9 27.5 + - - -
37A VAL* 4.1 9.4 - - - +
256A GLY* 3.2 28.9 + - - -
258A ARG* 3.4 10.1 - - - +
288A ARG* 3.7 15.1 - - - +
307A GLY* 1.3 70.0 - - - +
309A ALA* 1.3 66.4 + - - +
311A LEU* 2.9 10.8 + - - +
312A TYR* 2.9 43.6 + - + +
390A FMN 3.0 69.4 + - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.9 24.9 - - + +
287A PHE 4.1 18.6 - - - +
288A ARG* 4.7 4.5 - - - +
306A LEU* 4.4 20.4 - - + -
307A GLY 3.3 1.7 - - - +
308A ARG* 1.3 80.8 - - - +
310A THR* 1.3 61.8 + - - +
312A TYR* 3.2 26.0 + - - +
313A GLY 3.6 3.1 + - - -
325A VAL* 4.0 10.9 - - - +
329A LEU* 4.8 5.6 - - + -
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.9 23.2 - - + +
94A LEU* 4.5 4.9 - - - +
306A LEU* 3.6 27.7 + - + +
307A GLY 3.6 8.7 + - - -
309A ALA* 1.3 78.4 - - - +
311A LEU* 1.3 63.3 + - - +
313A GLY* 3.1 4.3 + - - -
314A LEU* 3.0 16.6 + - - +
322A VAL* 3.8 26.4 - - + +
325A VAL* 4.1 13.5 - - + -
326A LEU* 3.8 29.4 - - + -
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Residues in contact with LEU 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A LEU* 3.5 26.5 - - + -
77A ILE* 5.9 1.8 - - + -
80A THR* 3.6 39.7 - - + +
83A ASN* 3.9 10.3 - - - +
86A LEU* 3.8 22.2 - - + +
94A LEU* 3.9 21.8 - - + -
307A GLY 3.2 15.9 + - - +
308A ARG* 2.9 8.8 + - - +
310A THR* 1.3 78.2 - - - +
312A TYR* 1.3 58.3 + - - +
314A LEU* 3.1 6.0 + - + +
315A ALA* 2.8 31.7 + - - +
390A FMN 4.1 11.9 - - + -
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 3.5 30.7 - - + -
9A GLU* 5.9 0.4 - - - -
11A TYR* 3.8 22.9 - - + +
12A ARG* 3.5 35.3 - - + -
15A ALA* 3.8 8.7 - - + +
24A TYR* 5.2 1.3 - + - -
27A LEU* 4.1 19.7 - - + -
28A GLU* 2.5 38.7 + - - -
288A ARG* 4.1 16.4 + - - -
308A ARG* 2.9 44.1 + - + +
309A ALA 3.5 3.8 - - - +
310A THR 3.2 0.4 - - - -
311A LEU* 1.3 76.9 - - - +
313A GLY* 1.3 58.9 + - - +
315A ALA* 4.7 0.2 - - - -
316A ALA* 2.9 32.6 + - - +
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Residues in contact with GLY 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.7 11.2 - - - -
309A ALA 3.6 3.8 + - - -
310A THR 3.1 7.6 + - - -
312A TYR* 1.3 81.6 - - - +
314A LEU* 1.3 55.7 + - - +
317A ARG 2.9 24.1 + - - -
318A GLY 3.4 0.5 - - - +
321A GLY* 3.2 23.8 - - - -
325A VAL* 3.7 22.5 - - - +
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Residues in contact with LEU 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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83A ASN* 3.9 15.7 - - + +
86A LEU* 4.1 9.4 - - + -
87A TRP* 3.3 22.4 - - + -
90A GLY* 3.9 18.2 - - - +
93A ALA* 3.7 31.0 - - + -
94A LEU* 3.8 25.4 - - + -
310A THR 3.0 11.0 + - - +
311A LEU* 3.1 15.0 + - + +
313A GLY* 1.3 75.9 - - - +
315A ALA* 1.3 60.0 + - - +
318A GLY* 2.6 40.4 + - - -
322A VAL* 3.9 11.8 - - + +
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Residues in contact with ALA 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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15A ALA* 3.9 13.2 - - + -
18A ARG* 4.5 10.9 - - - +
19A LEU* 3.7 37.0 - - + +
27A LEU* 4.8 1.3 - - + -
86A LEU* 3.7 23.7 - - + +
87A TRP* 3.5 13.0 - - - -
311A LEU 2.8 19.8 + - - +
312A TYR* 4.7 0.2 - - - -
314A LEU* 1.3 74.2 - - - +
316A ALA* 1.3 62.0 + - - +
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Residues in contact with ALA 316 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 3.9 20.2 - - + +
14A LEU* 3.6 31.4 - - + -
15A ALA* 3.9 7.6 - - - +
18A ARG* 2.6 35.9 + - - +
87A TRP* 3.7 3.5 - - - -
312A TYR 2.9 20.1 + - - +
313A GLY 4.1 1.3 - - - +
315A ALA* 1.3 80.6 - - - +
317A ARG* 1.3 56.5 + - + +
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Residues in contact with ARG 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU* 3.8 22.4 - - - +
11A TYR* 4.3 4.5 - - - -
14A LEU* 4.0 10.8 - - + -
18A ARG* 3.8 14.8 - - - +
87A TRP* 3.8 11.8 - - - -
313A GLY 2.9 8.3 + - - -
316A ALA* 1.3 80.8 - - - +
318A GLY* 1.3 67.7 + - - +
320A THR* 3.5 20.1 + - - +
321A GLY* 3.0 18.1 + - - +
324A GLU* 2.8 41.2 + - - -
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Residues in contact with GLY 318 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A TRP* 3.3 33.4 - - - -
313A GLY 3.4 3.1 - - - +
314A LEU* 2.6 34.1 + - - -
317A ARG* 1.3 71.1 - - - +
319A GLU* 1.3 54.5 + - - -
321A GLY* 2.8 21.8 + - - -
322A VAL* 3.1 9.5 + - - +
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Residues in contact with GLU 319 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A TRP* 4.6 2.6 - - - +
92A LEU* 5.7 0.3 - - - +
93A ALA* 3.3 43.5 - - + +
96A ARG* 3.9 32.0 + - + +
97A ALA 4.6 2.5 - - - +
100A LYS* 2.6 33.4 + - - +
317A ARG 3.6 0.2 + - - -
318A GLY* 1.3 69.7 - - - -
320A THR* 1.3 64.1 + - - +
322A VAL* 3.1 6.5 + - - +
323A ASP* 3.0 23.4 + - - +
890A MES 6.2 5.3 - - - -
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Residues in contact with THR 320 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A ARG* 3.5 20.5 + - - +
318A GLY 3.3 0.6 - - - -
319A GLU* 1.3 78.0 - - - +
321A GLY* 1.3 62.3 + - - +
323A ASP* 3.4 14.4 + - + +
324A GLU* 3.0 44.9 + - + +
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Residues in contact with GLY 321 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A TYR* 4.0 2.8 - - - -
313A GLY* 3.2 25.7 - - - -
317A ARG* 3.0 20.0 + - - +
318A GLY 2.8 5.6 + - - -
320A THR* 1.3 74.9 - - - +
322A VAL* 1.3 63.2 + - - -
324A GLU* 3.2 11.2 + - - +
325A VAL* 3.0 26.2 + - - +
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Residues in contact with VAL 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.8 24.2 - - + -
94A LEU* 3.6 26.9 - - + -
97A ALA* 3.3 26.5 - - + -
310A THR* 3.8 22.2 - - + +
313A GLY* 4.5 2.0 - - - -
314A LEU* 3.9 13.5 - - + +
318A GLY 3.1 13.1 + - - +
319A GLU* 3.1 4.2 + - - +
321A GLY* 1.3 71.6 - - - +
323A ASP* 1.3 68.1 + - - +
325A VAL* 3.1 6.9 + - - +
326A LEU* 2.9 24.8 + - + +
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Residues in contact with ASP 323 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 3.2 24.7 - - - +
100A LYS* 3.0 36.4 + - - +
319A GLU 3.0 19.3 + - - +
320A THR* 3.5 18.0 + - + +
322A VAL* 1.3 74.9 - - - +
324A GLU* 1.3 53.8 + - + +
326A LEU* 3.2 6.6 + - - +
327A THR* 2.8 41.1 + - - +
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Residues in contact with GLU 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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5A LEU* 4.2 1.6 - - - +
11A TYR* 2.5 34.9 + - - +
317A ARG* 2.8 45.2 + - - -
320A THR* 3.0 25.3 + - + +
321A GLY* 3.3 7.1 - - - +
322A VAL 3.1 0.2 - - - -
323A ASP* 1.3 80.8 - - + +
325A VAL* 1.3 56.6 + - - +
327A THR* 3.1 7.4 + - - -
328A LEU* 2.8 36.4 + - + +
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Residues in contact with VAL 325 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A VAL* 4.2 13.7 - - + -
11A TYR* 3.9 21.8 - - + -
309A ALA 4.0 16.8 - - - +
310A THR* 4.1 14.8 - - + -
313A GLY* 3.7 24.7 - - - +
321A GLY 3.0 18.0 + - - +
322A VAL* 3.6 8.3 - - - +
324A GLU* 1.3 75.3 - - - +
326A LEU* 1.3 58.2 + - - +
328A LEU* 3.4 7.9 + - - +
329A LEU* 2.9 48.1 + - + +
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Residues in contact with LEU 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A MET* 4.2 11.6 - - + +
75A LEU* 4.9 2.9 - - + -
77A ILE* 4.3 4.0 - - + -
97A ALA* 3.5 32.8 - - + +
98A ALA* 4.1 6.1 - - - +
101A ALA* 3.7 19.7 - - + -
103A ILE* 4.1 18.8 - - + -
306A LEU* 4.1 15.0 - - + -
310A THR* 3.8 21.8 - - + -
322A VAL* 2.9 25.1 + - + +
323A ASP* 3.5 9.2 - - - +
325A VAL* 1.3 76.0 - - - +
327A THR* 1.3 57.5 + - - +
329A LEU* 3.9 2.8 - - - +
330A LYS* 3.0 30.3 + - - +
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Residues in contact with THR 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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323A ASP* 2.8 18.1 + - - +
324A GLU* 3.1 12.0 + - - +
326A LEU* 1.3 74.7 - - - +
328A LEU* 1.3 70.2 + - + +
330A LYS* 3.2 6.9 + - - +
331A ALA* 2.9 25.6 + - + +
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Residues in contact with LEU 328 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A LEU 4.0 6.5 - - - +
6A PHE* 3.9 39.3 - - + +
7A ASN* 4.0 7.6 - - - +
8A VAL* 5.9 2.0 - - + +
11A TYR* 3.7 32.8 - - + +
324A GLU* 2.8 22.3 + - + +
325A VAL* 3.8 5.6 - - - +
327A THR* 1.3 75.9 - - + +
329A LEU* 1.3 55.1 + - + +
331A ALA* 3.2 8.2 + - + +
332A ASP* 2.6 35.9 + - - +
335A ARG* 5.2 0.9 + - - -
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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
----------------------------------------------------------
8A VAL* 4.2 13.7 - - + -
75A LEU* 4.5 10.8 - - + -
288A ARG 3.7 23.1 - - - +
289A ARG 4.4 2.0 - - - -
290A GLY 4.2 17.7 - - - +
293A ILE* 4.5 9.2 - - + -
306A LEU* 3.7 38.8 - - + -
309A ALA* 4.8 2.7 - - + -
325A VAL* 2.9 32.5 + - + +
326A LEU* 4.0 4.3 - - - +
328A LEU* 1.3 76.3 - - + +
330A LYS* 1.3 60.3 + - - +
332A ASP* 3.3 7.2 - - - +
333A ILE* 2.7 37.0 + - - +
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Residues in contact with LYS 330 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A LEU* 3.7 24.6 - - + +
72A SER* 4.3 25.9 + - - -
73A MET* 3.8 29.3 - - + -
101A ALA 4.9 3.0 + - - +
326A LEU 3.0 19.5 + - - +
327A THR* 3.6 6.5 - - - +
329A LEU* 1.3 75.7 - - - +
331A ALA* 1.3 59.5 + - - +
333A ILE* 4.5 3.4 - - - -
334A ASP* 2.9 31.6 + - + +
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Residues in contact with ALA 331 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327A THR* 2.9 16.2 + - + +
328A LEU* 3.5 11.9 - - + +
330A LYS* 1.3 77.0 - - - +
332A ASP* 1.3 58.6 + - - +
334A ASP* 3.7 7.4 - - - +
335A ARG* 2.9 53.0 + - - +
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Residues in contact with ASP 332 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A ARG* 4.0 20.7 + - - -
290A GLY* 3.0 30.0 + - - -
291A SER* 4.2 1.9 + - - -
328A LEU 2.6 22.3 + - - +
329A LEU* 3.3 14.4 - - + +
331A ALA* 1.3 73.6 - - - +
333A ILE* 1.3 61.7 + - - +
335A ARG* 3.3 18.7 + - - +
336A THR* 2.8 37.6 + - - -
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Residues in contact with ILE 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LEU* 4.1 13.7 - - + -
73A MET* 4.7 7.4 - - + -
74A PRO* 5.5 3.8 - - + -
75A LEU* 3.9 27.4 - - + -
290A GLY* 4.2 17.7 - - - +
293A ILE* 3.9 26.5 - - + -
294A VAL* 4.3 12.3 - - + -
329A LEU 2.7 24.4 + - - +
330A LYS* 3.7 6.3 - - - +
332A ASP* 1.3 73.1 - - - +
334A ASP* 1.3 63.5 + - - +
336A THR* 2.9 9.0 + - - -
337A LEU* 2.8 27.7 + - + +
345A ILE* 4.1 21.1 - - + -
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Residues in contact with ASP 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 2.7 56.9 + - - +
62A LEU* 3.8 22.7 - - + +
330A LYS* 2.9 22.1 + - + +
331A ALA* 3.7 8.0 - - - +
333A ILE* 1.3 72.3 - - - +
335A ARG* 1.3 66.6 + - - +
337A LEU* 3.2 5.4 + - - +
338A ALA 3.0 19.1 + - - -
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Residues in contact with ARG 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 5.7 1.1 - - - +
328A LEU 5.2 0.6 + - - -
331A ALA* 2.9 41.5 + - - +
332A ASP* 3.5 32.0 + - - +
334A ASP* 1.3 80.0 - - - +
336A THR* 1.3 57.8 + - - +
338A ALA* 3.5 5.0 + - - +
339A GLN* 3.0 46.6 + - - +
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Residues in contact with THR 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A PHE* 4.2 22.7 - - + -
291A SER* 4.3 11.3 + - - -
294A VAL* 3.8 30.3 - - + -
332A ASP* 2.8 29.2 + - - -
333A ILE* 2.9 7.6 + - - -
335A ARG* 1.3 75.5 - - - +
337A LEU* 1.3 67.5 + - - +
339A GLN* 3.2 7.8 + - + +
340A ILE* 3.0 26.9 + - + +
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Residues in contact with LEU 337 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ARG* 4.8 5.8 - - + -
61A SER 4.2 1.3 - - - +
62A LEU* 4.2 25.1 - - + -
294A VAL* 4.5 10.8 - - + -
333A ILE* 2.8 18.9 + - + +
334A ASP* 3.6 7.2 - - - +
336A THR* 1.3 76.7 - - - +
338A ALA* 1.3 63.2 + - - +
340A ILE* 3.3 5.2 - - + +
341A GLY 3.1 4.2 + - - -
342A CYS 3.0 44.0 + - - +
343A PRO 4.4 4.0 - - - +
345A ILE* 3.7 35.7 - - + +
348A LEU* 3.9 38.4 - - + -
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Residues in contact with ALA 338 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ARG* 5.2 0.7 + - - -
57A VAL* 4.0 22.5 - - + +
60A ARG* 3.5 39.1 - - - +
334A ASP 3.0 6.7 + - - +
335A ARG* 3.6 11.4 - - - +
337A LEU* 1.3 77.1 - - - +
339A GLN* 1.3 67.6 + - - +
341A GLY* 3.1 14.0 + - - -
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Residues in contact with GLN 339 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 3.3 6.2 - - + +
53A ARG* 2.7 37.5 + - - +
335A ARG* 3.0 40.6 + - - +
336A THR* 3.2 9.2 + - + +
338A ALA* 1.3 81.3 - - - +
340A ILE* 1.3 59.8 + - + +
341A GLY 3.3 0.4 + - - -
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Residues in contact with ILE 340 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.8 40.6 - - + -
51A PRO* 3.7 12.1 - - + -
52A LYS 2.8 23.3 + - - -
294A VAL* 4.0 16.6 - - + -
336A THR* 3.0 14.1 + - + +
337A LEU* 3.3 16.2 - - - +
339A GLN* 1.3 80.0 - - + +
341A GLY* 1.3 60.2 + - - +
342A CYS* 4.0 6.1 - - + +
348A LEU* 3.7 30.1 - - + -
352A TYR* 3.4 32.1 - - + -
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Residues in contact with GLY 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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52A LYS* 3.4 17.4 + - - +
53A ARG* 5.9 0.2 - - - -
55A VAL* 3.4 17.7 - - - +
57A VAL* 3.9 10.8 - - - -
337A LEU 3.8 0.2 - - - -
338A ALA 3.1 15.1 + - - -
339A GLN 3.3 1.2 + - - -
340A ILE* 1.3 79.8 - - - +
342A CYS* 1.3 59.9 + - - +
343A PRO* 3.3 12.1 - - - +
352A TYR* 4.0 9.0 + - - -
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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