Contacts of the helix formed by residues 245 - 279 (chain A) in PDB entry 2FQ6
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 ASP 245 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A HIS* 3.6 0.4 - - - -
219A MET 5.3 0.2 - - - +
243A MET* 4.8 6.1 - - - -
244A VAL* 1.3 80.1 - - - +
246A ALA* 1.3 64.4 + - - +
247A ASP* 3.2 15.5 + - - +
248A THR* 2.6 41.4 + - - -
249A ALA* 3.1 20.6 + - - +
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Residues in contact with ALA 246 (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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28A ILE* 4.6 6.1 - - + -
29A GLN 3.3 29.8 - - - +
30A ARG* 4.4 8.3 - - + -
31A ALA 5.5 0.4 - - - +
61A THR* 4.2 3.6 - - + +
63A THR* 3.4 14.3 - - - +
64A HIS* 3.5 23.8 + - - +
245A ASP* 1.3 72.7 - - - +
247A ASP* 1.3 60.1 + - - +
249A ALA* 3.3 5.4 + - - +
250A TYR* 2.9 23.9 + - - +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A ILE* 3.8 8.4 - - - +
30A ARG* 2.7 54.1 + - - +
245A ASP* 3.2 11.2 + - - +
246A ALA* 1.3 75.5 + - - +
248A THR* 1.3 58.5 + - - +
250A TYR* 3.3 10.7 + - - +
251A ILE* 2.9 28.5 + - - +
30B ARG* 3.1 19.2 + - - +
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Residues in contact with THR 248 (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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218A ALA* 4.0 15.7 - - + +
219A MET 3.3 26.6 + - - +
220A ILE* 3.7 22.0 - - + -
244A VAL* 3.7 6.7 - - + -
245A ASP* 2.6 34.5 + - - -
247A ASP* 1.3 71.2 - - - +
249A ALA* 1.3 64.9 + - - +
251A ILE* 3.3 8.3 + - - +
252A THR* 2.8 29.9 + - - -
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Residues in contact with ALA 249 (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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63A THR* 4.2 16.6 - - + +
64A HIS* 4.2 19.3 - - - +
67A LEU* 4.0 26.1 - - + +
82A LEU* 5.0 0.2 - - + -
220A ILE* 4.6 2.0 - - - -
244A VAL* 4.5 5.3 - - + +
245A ASP 3.1 13.1 + - - +
246A ALA 3.4 9.6 - - - +
248A THR* 1.3 75.6 - - - +
250A TYR* 1.3 62.5 + - - +
252A THR* 3.2 3.6 + - - -
253A SER* 3.0 25.2 + - - -
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Residues in contact with TYR 250 (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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25A ASN* 3.5 34.4 + - + +
26A SER* 3.1 37.9 - - - -
28A ILE* 3.4 30.1 - - + -
63A THR* 3.7 8.6 - - + +
246A ALA 2.9 16.3 + - - +
247A ASP 3.3 9.2 + - - +
249A ALA* 1.3 72.4 - - - +
251A ILE* 1.3 69.1 + - + +
252A THR 3.2 0.2 + - - -
253A SER* 3.3 7.2 + - - -
254A ARG* 2.9 47.6 + - + +
30B ARG* 3.6 44.9 - - + +
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Residues in contact with ILE 251 (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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213A VAL* 4.4 14.7 - - + +
215A HIS* 6.1 2.5 - - - +
217A ASP* 5.2 9.4 - - - +
218A ALA* 3.5 32.5 - - + -
247A ASP 2.9 16.6 + - - +
248A THR* 3.3 9.6 + - - +
250A TYR* 1.3 80.3 - - + +
252A THR* 1.3 61.6 + - - +
254A ARG* 3.5 33.4 - - + +
255A GLY* 3.0 24.1 + - - +
30B ARG* 6.2 0.9 - - - +
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Residues in contact with THR 252 (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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67A LEU* 3.9 17.5 - - + -
71A MET* 5.5 0.7 - - - -
208A ALA* 4.0 14.8 - - + -
212A LEU* 3.9 28.7 - - + +
213A VAL* 3.8 12.3 - - + +
220A ILE* 3.4 29.4 - - + +
222A THR* 5.6 0.7 - - + -
248A THR 2.8 21.9 + - - -
249A ALA 3.7 4.3 - - - -
251A ILE* 1.3 74.4 - - - +
253A SER* 1.3 67.9 + - - +
255A GLY* 3.0 11.3 + - - -
256A LEU* 3.3 12.8 + - + +
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Residues in contact with SER 253 (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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14A GLY* 6.1 0.2 - - - -
26A SER* 4.9 7.5 + - - -
63A THR 4.9 0.9 + - - -
66A SER* 4.3 6.4 + - - -
67A LEU* 3.5 37.4 + - - +
70A ALA* 4.9 0.9 - - - +
249A ALA 3.0 9.1 + - - -
250A TYR* 3.5 10.8 - - - -
252A THR* 1.3 75.0 - - - +
254A ARG* 1.3 62.0 + - - +
256A LEU* 3.1 31.2 + - - +
257A ARG* 3.4 29.0 + - - -
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Residues in contact with ARG 254 (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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25A ASN* 4.5 17.4 + - - +
215A HIS* 5.7 7.9 + - - -
250A TYR* 2.9 38.3 + - + +
251A ILE* 3.5 31.9 - - + +
253A SER* 1.3 76.3 - - - +
255A GLY* 1.3 61.4 + - - +
257A ARG* 3.2 27.7 + - + +
258A THR* 4.2 4.3 + - - +
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Residues in contact with GLY 255 (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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212A LEU 3.1 24.0 - - - -
213A VAL 4.0 10.5 - - - -
215A HIS* 5.5 3.6 - - - -
251A ILE* 3.0 16.0 + - - +
252A THR 3.0 2.3 + - - -
254A ARG* 1.3 68.8 - - - +
256A LEU* 1.3 65.0 + - - +
257A ARG 3.0 3.7 + - - -
258A THR* 3.1 12.1 + - - -
262A ARG* 2.7 22.2 + - - -
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Residues in contact with LEU 256 (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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10A LEU* 3.5 27.6 - - + +
13A ALA* 4.5 0.4 - - + -
67A LEU* 4.6 5.2 - - + -
70A ALA* 3.7 29.4 - - + -
71A MET* 4.4 10.3 - - - -
74A LEU* 3.8 24.0 - - + -
212A LEU* 3.7 31.9 - - + -
252A THR* 3.3 11.8 + - + +
253A SER* 3.1 22.6 + - - +
255A GLY* 1.3 75.7 - - - +
257A ARG* 1.3 70.8 + - - +
259A LEU* 3.0 24.7 + - + +
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Residues in contact with ARG 257 (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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10A LEU* 2.8 37.5 + - - +
11A VAL* 3.3 37.3 + - + +
13A ALA* 2.7 33.9 + - - +
14A GLY 5.0 1.2 - - - -
15A ARG* 3.2 29.4 - - - +
25A ASN* 4.8 10.8 + - - +
26A SER* 5.7 2.8 - - - +
66A SER* 5.4 1.8 + - - -
253A SER* 3.4 33.3 + - - +
254A ARG* 3.2 23.0 - - + +
255A GLY 3.0 0.8 + - - -
256A LEU* 1.3 81.5 - - - +
258A THR* 1.3 64.7 + - + +
259A LEU 3.9 0.2 + - - -
260A GLY 5.1 0.7 + - - -
261A VAL* 5.5 0.2 - - - +
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Residues in contact with THR 258 (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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215A HIS* 4.7 7.7 - - + -
254A ARG 4.7 2.8 + - - +
255A GLY* 3.1 9.7 + - - -
257A ARG* 1.3 82.7 - - + +
259A LEU* 1.3 60.1 + - - +
260A GLY 3.2 3.4 - - - -
261A VAL* 3.2 19.9 - - + +
262A ARG* 2.9 56.7 + - - +
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Residues in contact with LEU 259 (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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10A LEU* 4.0 21.3 - - + -
74A LEU* 5.9 0.2 - - + -
190A ALA* 4.1 3.4 - - + +
192A VAL* 4.1 22.2 - - + -
211A TYR* 3.5 37.2 - - + +
212A LEU* 3.7 25.1 - - + -
255A GLY 3.2 4.4 + - - +
256A LEU* 3.0 17.8 + - + +
258A THR* 1.3 76.6 - - - +
260A GLY* 1.3 56.0 + - - +
262A ARG* 3.4 14.4 - - - +
263A LEU* 2.8 56.1 + - + +
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Residues in contact with GLY 260 (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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6A LEU* 5.6 3.8 - - - -
7A ASP* 3.6 19.1 - - - -
10A LEU* 3.5 15.8 - - - +
257A ARG 5.1 1.0 + - - -
258A THR 3.2 0.6 - - - -
259A LEU* 1.3 75.6 - - - +
261A VAL* 1.3 65.2 + - - +
263A LEU* 4.1 4.2 - - - +
264A ARG* 3.1 38.4 + - - +
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Residues in contact with VAL 261 (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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7A ASP* 4.7 0.2 + - - -
257A ARG 5.5 0.2 - - - +
258A THR* 3.2 29.6 - - + +
260A GLY* 1.3 75.0 - - - +
262A ARG* 1.3 70.6 + - + +
264A ARG* 3.7 23.1 + - - +
265A GLN* 3.4 18.4 + - - +
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Residues in contact with ARG 262 (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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211A TYR* 2.8 40.8 + - - +
212A LEU 3.5 6.7 + - - -
213A VAL 4.8 0.4 - - - -
214A GLY* 3.5 26.8 + - - -
215A HIS* 4.7 8.9 - - - -
255A GLY* 2.7 29.3 + - - -
258A THR* 2.9 35.1 + - - +
259A LEU* 3.4 19.5 - - - +
261A VAL* 1.3 76.1 - - + +
263A LEU* 1.3 66.7 + - + +
265A GLN* 2.9 6.4 + - - +
266A HIS* 2.9 36.8 + - + -
341A GLY 4.4 0.6 + - - -
343A TYR* 6.0 1.3 - - - +
377A LEU* 4.1 26.7 - - + -
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Residues in contact with LEU 263 (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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6A LEU* 5.9 1.6 - - + -
190A ALA* 4.1 5.8 - - + -
192A VAL* 4.0 21.3 - - + -
193A LEU* 4.0 23.3 - - + -
211A TYR* 3.9 33.9 - - + -
259A LEU* 2.8 45.4 + - + +
260A GLY* 4.1 4.7 - - - +
262A ARG* 1.3 73.2 - - - +
264A ARG* 1.3 57.1 + - + +
266A HIS* 3.2 4.2 + - - +
267A HIS* 2.8 31.6 + - - +
307A SER 3.7 7.2 - - - +
308A SER* 3.9 24.5 - - - -
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Residues in contact with ARG 264 (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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6A LEU* 6.1 1.8 - - - +
7A ASP* 2.9 43.1 + - - -
260A GLY* 3.1 22.0 + - - +
261A VAL* 3.7 32.5 - - - +
262A ARG 3.1 0.4 + - - -
263A LEU* 1.3 76.5 - - + +
265A GLN* 1.3 58.2 + - - +
267A HIS* 3.5 7.6 + - + +
268A GLU* 3.0 30.6 + - - +
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Residues in contact with GLN 265 (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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261A VAL 3.4 10.5 + - - +
262A ARG 2.9 9.0 + - - +
264A ARG* 1.3 77.2 - - - +
266A HIS* 1.3 59.9 + - - +
268A GLU* 4.0 16.8 - - - +
269A SER* 3.0 48.9 + - - +
376A GLY 4.8 0.7 - - - +
377A LEU* 3.5 45.8 + - + +
378A GLU 4.4 4.4 + - - -
379A ASP* 5.7 1.6 - - - +
380A VAL 5.9 0.4 - - - +
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Residues in contact with HIS 266 (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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211A TYR* 3.3 28.7 - + - -
262A ARG* 2.9 41.6 + - + +
263A LEU* 3.7 8.1 - - - +
265A GLN* 1.3 75.8 - - - +
267A HIS* 1.3 52.3 + - - +
269A SER* 4.3 1.7 - - - -
270A SER* 2.8 41.1 + - - -
308A SER* 3.7 3.5 - - - +
309A GLY* 3.6 17.9 - - - +
341A GLY 4.9 0.6 + - - -
342A GLY 3.3 26.7 + - - -
374A HIS* 3.8 6.1 + + - -
375A ILE* 2.8 27.6 + - - +
376A GLY* 3.8 8.2 + - - -
377A LEU* 3.7 21.0 - - + +
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Residues in contact with HIS 267 (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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263A LEU 2.8 18.1 + - - +
264A ARG* 3.5 8.3 - - + +
266A HIS* 1.3 73.0 - - - +
268A GLU* 1.3 68.8 + - - +
270A SER* 3.4 4.8 + - - -
271A LEU* 3.1 43.4 + - + +
290A ALA* 4.5 7.0 - - + -
300A TRP* 4.2 12.5 - + - -
306A GLY* 4.1 7.2 - - - -
307A SER* 3.2 47.8 + - - +
308A SER 4.0 3.1 + - - -
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Residues in contact with GLU 268 (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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264A ARG 3.0 18.1 + - - +
265A GLN* 4.0 21.2 + - - +
267A HIS* 1.3 82.4 - - - +
269A SER* 1.3 65.6 + - - +
271A LEU* 4.1 3.1 - - - +
272A LYS* 3.3 20.4 + - - +
380A VAL* 6.1 1.5 - - + +
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Residues in contact with SER 269 (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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265A GLN* 3.0 33.9 + - - +
266A HIS 4.3 0.2 - - - -
268A GLU* 1.3 80.0 + - - +
270A SER* 1.3 65.4 + - - +
272A LYS* 3.3 2.2 + - - -
273A VAL* 3.0 26.7 + - - +
375A ILE* 3.6 21.1 - - - -
376A GLY 4.7 4.0 + - - -
378A GLU 4.7 4.1 + - - -
380A VAL* 3.4 31.5 + - - +
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Residues in contact with SER 270 (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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266A HIS 2.8 24.9 + - - -
267A HIS 3.4 3.8 + - - -
269A SER* 1.3 75.0 - - - +
271A LEU* 1.3 59.1 + - - +
273A VAL* 3.4 2.8 + - - +
274A ALA* 2.8 29.5 + - - +
288A HIS* 2.9 29.5 + - - -
308A SER 3.0 9.4 + - - -
309A GLY* 3.7 22.4 - - - -
311A PHE* 3.7 5.2 - - - -
375A ILE* 3.8 16.7 - - - +
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Residues in contact with LEU 271 (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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267A HIS* 3.1 38.6 + - + +
268A GLU* 4.1 3.6 - - - +
270A SER* 1.3 79.5 + - - +
272A LYS* 1.3 56.9 + - - +
274A ALA* 3.3 5.3 + - + -
275A GLU* 2.9 59.7 + - + +
288A HIS* 4.2 7.0 - - + +
290A ALA* 4.0 32.3 - - + +
291A LEU* 4.3 13.2 - - + +
292A PRO* 5.5 1.1 - - + -
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Residues in contact with LYS 272 (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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268A GLU 3.3 12.2 + - - +
269A SER* 3.3 9.2 + - - +
271A LEU* 1.3 77.9 - - - +
273A VAL* 1.3 61.9 + - - +
275A GLU* 3.3 15.0 + - - +
276A TRP* 3.1 22.6 + - + +
380A VAL* 3.6 25.1 - - + -
381A ASP* 3.3 27.6 + - - -
384A ILE* 4.1 14.6 - - + -
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Residues in contact with VAL 273 (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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269A SER 3.0 17.7 + - - +
270A SER 3.6 6.3 - - - +
272A LYS* 1.3 75.0 - - - +
274A ALA* 1.3 56.3 + - - +
276A TRP* 3.3 8.1 + - + +
277A LEU* 2.8 47.5 + - + +
311A PHE* 3.9 8.7 - - + -
373A LEU* 4.3 3.6 - - + -
375A ILE* 4.0 19.1 - - + -
380A VAL* 3.6 18.8 - - + +
383A LEU* 5.2 4.3 - - + -
384A ILE* 4.2 14.1 - - + -
387A LEU* 3.7 23.3 - - + -
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Residues in contact with ALA 274 (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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270A SER 2.8 21.2 + - - +
271A LEU* 3.3 6.9 + - + +
273A VAL* 1.3 72.9 - - - +
275A GLU* 1.3 58.7 + - - +
277A LEU* 3.3 3.5 + - - +
278A ALA* 3.0 29.8 + - - +
286A VAL* 3.9 14.8 - - + +
288A HIS* 3.7 24.2 - - + +
291A LEU* 4.5 9.6 - - + -
311A PHE* 3.9 19.0 - - + -
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Residues in contact with GLU 275 (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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271A LEU* 2.9 42.7 + - + +
272A LYS* 3.6 15.4 - - - +
273A VAL 3.2 0.2 - - - -
274A ALA* 1.3 75.0 - - - +
276A TRP* 1.3 62.8 + - - +
278A ALA* 3.5 12.2 + - - +
279A GLU* 3.6 14.7 + - - +
291A LEU* 3.8 23.7 - - + +
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Residues in contact with TRP 276 (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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272A LYS* 3.1 11.0 + - + +
273A VAL* 3.5 9.0 - - + +
275A GLU* 1.3 76.2 - - - +
277A LEU* 1.3 98.7 + - + +
279A GLU* 3.2 16.6 + - + +
280A HIS* 3.3 31.1 + + - +
384A ILE* 3.7 45.0 - - + +
387A LEU* 3.7 18.2 - - + -
388A ASP* 3.7 36.8 - - + -
391A PHE* 3.6 18.4 - + - -
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Residues in contact with LEU 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A VAL* 2.8 27.3 + - + +
274A ALA 3.7 4.0 - - - +
276A TRP* 1.3 92.4 - - + +
278A ALA* 1.3 61.7 + - - +
280A HIS* 3.0 14.1 + - - +
283A VAL* 3.2 24.8 - - + +
286A VAL* 3.8 10.8 - - + -
311A PHE* 3.7 28.9 - - + -
313A PHE* 3.5 35.7 - - + -
373A LEU* 4.0 2.0 - - + -
387A LEU* 5.0 3.1 - - + -
391A PHE* 3.6 31.9 - - + -
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Residues in contact with ALA 278 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A ALA 3.0 17.3 + - - +
275A GLU* 3.7 8.3 - - - +
276A TRP 3.3 0.6 - - - -
277A LEU* 1.3 76.1 - - - +
279A GLU* 1.3 64.3 + - - +
280A HIS 3.4 1.7 - - - +
283A VAL* 4.9 4.4 - - - +
285A ARG* 6.3 0.4 - - - +
286A VAL* 3.6 17.2 - - + +
291A LEU* 4.2 16.8 - - + -
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Residues in contact with GLU 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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275A GLU 3.7 10.7 - - - +
276A TRP* 3.6 11.4 - - + +
277A LEU 3.1 0.4 - - - -
278A ALA* 1.3 84.4 - - - +
280A HIS* 1.3 63.8 + - - +
281A PRO* 3.6 6.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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