Contacts of the helix formed by residues 250 - 286 (chain A) in PDB entry 4O8M
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 250 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ASN 3.9 1.1 + - - +
249A LEU* 1.3 75.3 - - - +
251A PRO* 1.3 70.6 - - - +
252A GLU* 3.3 17.6 + - - +
253A GLN* 3.0 41.0 + - + +
254A GLN* 3.1 20.1 + - - +
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Residues in contact with PRO 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A LEU 3.8 2.9 - - - +
250A THR* 1.3 87.8 - - - +
252A GLU* 1.3 75.9 + - - +
254A GLN* 3.4 15.5 + - - +
255A LYS* 3.1 24.3 + - - +
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Residues in contact with GLU 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A THR* 3.1 18.1 + - - +
251A PRO* 1.3 89.4 - - - +
253A GLN* 1.3 64.4 + - + +
255A LYS* 3.5 7.0 + - - +
256A ILE* 3.2 32.7 + - + +
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Residues in contact with GLN 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A THR* 3.1 32.4 + - - -
59A ASP* 3.0 28.1 + - - +
60A ILE* 3.7 21.4 - - + +
249A LEU* 3.7 21.6 - - + +
250A THR* 3.0 45.1 + - + +
252A GLU* 1.3 72.8 - - + +
254A GLN* 1.3 65.9 + - - +
256A ILE* 3.2 5.0 + - + +
257A ILE* 3.1 32.7 + - + +
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Residues in contact with GLN 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A TRP* 2.8 66.4 + - + +
247A ASN* 3.9 8.5 + - - +
249A LEU* 3.7 19.8 + - + +
250A THR 3.1 17.3 + - - +
251A PRO* 3.5 15.9 - - - +
253A GLN* 1.3 77.1 - - - +
255A LYS* 1.3 56.3 + - - +
257A ILE* 3.3 5.2 + - - +
258A VAL* 2.9 35.5 + - + +
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Residues in contact with LYS 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A PRO 3.1 14.5 + - - +
252A GLU* 3.8 7.6 - - - +
253A GLN 3.3 0.2 - - - -
254A GLN* 1.3 77.9 - - - +
256A ILE* 1.3 60.5 + - + +
258A VAL* 4.5 4.7 - - - +
259A ASP* 2.7 62.0 + - - +
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Residues in contact with ILE 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 4.1 19.5 - - + +
55A LYS* 3.9 32.0 - - + +
56A SER* 3.9 25.4 - - - -
60A ILE* 4.0 16.8 - - + -
252A GLU* 3.2 23.0 + - + +
253A GLN* 3.2 8.0 + - + +
255A LYS* 1.3 77.0 - - + +
257A ILE* 1.3 58.8 + - - +
259A ASP* 3.9 4.8 - - - +
260A ALA* 2.9 32.2 + - - +
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Residues in contact with ILE 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ILE* 4.1 18.8 - - + -
48A TRP* 3.1 33.7 + - + +
52A VAL* 4.1 10.1 - - + -
60A ILE* 4.3 15.0 - - + -
62A PHE* 4.2 16.2 - - + -
87A ILE* 4.4 3.1 - - + -
141A ILE* 4.0 5.2 - - + -
246A TRP* 3.9 23.3 - - + -
249A LEU* 3.9 26.9 - - + -
253A GLN* 3.1 16.9 + - + +
254A GLN 3.6 5.6 - - - +
256A ILE* 1.3 76.3 - - - +
258A VAL* 1.3 57.8 + - - +
260A ALA 3.3 0.5 + - - -
261A SER* 2.9 25.1 + - - -
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Residues in contact with VAL 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A HIS* 5.9 1.3 - - - +
141A ILE* 4.1 21.1 - - + +
246A TRP* 3.9 21.8 - - + -
254A GLN 2.9 22.3 + - - +
255A LYS* 4.2 4.0 - - - +
257A ILE* 1.3 74.0 - - - +
259A ASP* 1.3 69.5 + - - +
261A SER* 2.7 26.8 + - - +
262A ARG* 3.2 17.8 + - + +
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Residues in contact with ASP 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A LYS* 6.4 2.0 - - - -
255A LYS* 2.7 62.1 + - - +
256A ILE* 3.9 4.8 - - - +
258A VAL* 1.3 76.0 - - - +
260A ALA* 1.3 62.1 + - - +
262A ARG* 3.2 21.8 + - - +
263A GLU* 3.6 12.3 + - - +
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Residues in contact with ALA 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 4.5 2.9 - - - -
48A TRP* 3.7 7.2 - - + -
51A LYS* 4.0 19.1 - - + -
52A VAL* 3.6 23.3 - - + +
55A LYS* 5.7 2.5 - - + +
256A ILE* 2.9 19.5 + - + +
257A ILE 3.6 4.0 - - - +
259A ASP* 1.3 77.3 - - - +
261A SER* 1.3 57.1 + - - +
263A GLU* 3.2 15.1 + - - +
264A MET* 2.9 26.7 + - - +
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Residues in contact with SER 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A TRP* 3.5 25.5 - - - +
141A ILE* 4.3 4.7 + - - -
142A VAL* 3.6 26.2 - - - +
257A ILE 2.9 15.7 + - - -
258A VAL* 2.7 21.2 + - - +
260A ALA* 1.3 76.8 - - - +
262A ARG* 1.3 61.1 + - - +
264A MET* 3.2 8.7 + - - +
265A VAL* 2.9 34.0 + - - +
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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
----------------------------------------------------------
118A SER* 4.9 1.6 + - - -
122A HIS* 3.5 23.6 + - - -
142A VAL* 3.8 15.2 - - - +
143A PRO* 4.2 4.6 - - - +
144A ASP* 2.8 42.0 + - - -
258A VAL* 3.2 24.4 + - + +
259A ASP* 3.6 10.5 - - - +
260A ALA 3.2 0.4 - - - -
261A SER* 1.3 85.7 + - - +
263A GLU* 1.3 62.6 - - + +
265A VAL* 3.3 18.6 + - - +
266A THR* 3.3 23.8 + - - -
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A PHE* 3.8 18.0 - - + -
51A LYS* 2.5 40.7 + - + +
55A LYS* 4.4 6.4 + - - -
259A ASP 3.6 12.3 + - - +
260A ALA* 3.2 9.4 + - - +
262A ARG* 1.3 75.8 - - + +
264A MET* 1.3 60.1 + - - +
266A THR* 3.2 7.5 + - - -
267A TYR* 2.8 31.2 + - - +
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Residues in contact with MET 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ALA* 3.3 36.6 - - + +
45A MET* 4.0 11.7 - - + -
47A PHE* 3.8 13.4 - - + -
48A TRP* 3.9 37.9 - - + -
142A VAL* 4.0 14.4 - - + -
145A VAL* 3.7 33.9 - - + -
260A ALA 2.9 14.0 + - - +
261A SER* 3.2 17.4 + - - +
263A GLU* 1.3 75.7 - - - +
265A VAL* 1.3 60.6 + - + +
267A TYR* 3.7 0.9 - - - +
268A GLY* 2.8 27.3 + - - -
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A SER* 5.7 0.7 - - - +
142A VAL* 3.5 24.9 - - + -
144A ASP* 3.6 37.2 - - - +
145A VAL* 3.9 20.9 - - + +
146A ILE* 5.5 7.3 + - + +
261A SER 2.9 17.1 + - - +
262A ARG* 3.6 18.2 - - - +
263A GLU 3.2 0.4 - - - -
264A MET* 1.3 80.9 - - + +
266A THR* 1.3 59.2 + - - +
268A GLY* 3.4 1.1 + - - -
269A GLY* 3.0 25.3 + - - -
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Residues in contact with THR 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ARG 3.3 11.5 + - - -
263A GLU* 3.2 10.3 + - - -
265A VAL* 1.3 75.9 - - - +
267A TYR* 1.3 66.1 + - - +
269A GLY* 3.2 3.6 + - - -
270A GLY* 3.2 16.5 + - - -
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Residues in contact with TYR 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LYS* 3.8 16.0 + - - +
44A ALA* 4.2 5.4 - - - -
47A PHE* 3.4 53.4 - + + -
263A GLU 2.8 17.5 + - - +
264A MET 3.7 2.5 - - - +
266A THR* 1.3 74.5 - - - +
268A GLY* 1.3 66.7 + - - +
270A GLY* 3.0 5.1 + - - -
271A LEU* 3.0 59.0 + - + +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 5.5 1.1 - - - +
44A ALA* 4.6 8.7 - - - -
145A VAL* 6.3 2.7 - - - -
146A ILE* 5.4 4.6 - - - +
264A MET* 2.8 19.9 + - - -
265A VAL* 3.8 1.8 - - - -
267A TYR* 1.3 75.6 - - - +
269A GLY* 1.3 57.3 + - - +
271A LEU* 3.2 18.1 + - - +
272A ILE* 2.9 34.0 + - - +
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Residues in contact with GLY 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ILE* 4.3 15.5 - - - +
265A VAL 3.0 14.6 + - - -
266A THR* 3.2 5.6 + - - -
267A TYR 3.2 0.4 - - - -
268A GLY* 1.3 76.2 - - - +
270A GLY* 1.3 61.1 + - - +
272A ILE* 3.3 11.3 - - - +
273A GLU* 3.2 24.4 + - - +
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Residues in contact with GLY 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A THR 3.2 8.8 + - - -
267A TYR* 3.0 8.0 + - - -
269A GLY* 1.3 76.5 - - - +
271A LEU* 1.3 64.9 + - - +
272A ILE 3.4 0.2 + - - -
273A GLU* 3.6 14.9 + - - +
274A GLN 4.6 1.4 + - - -
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 3.5 36.3 - - + +
43A LYS* 3.7 25.6 - - + +
44A ALA 3.8 2.5 - - - +
267A TYR* 3.0 60.2 + - + +
268A GLY* 3.5 13.7 - - - +
270A GLY* 1.3 77.4 - - - +
272A ILE* 1.3 61.2 + - - +
273A GLU 3.5 0.2 + - - -
274A GLN* 4.1 0.7 + - - +
275A ALA* 3.0 25.8 + - - +
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Residues in contact with ILE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 4.3 24.5 - - + -
146A ILE* 3.9 38.1 - - + +
147A TYR 4.0 16.6 - - - +
213A VAL* 4.4 8.1 - - + -
268A GLY 2.9 19.0 + - - +
269A GLY* 3.3 15.0 - - - +
271A LEU* 1.3 76.6 - - + +
273A GLU* 1.3 71.0 + - - +
274A GLN 3.2 1.4 + - - -
275A ALA* 3.2 9.3 + - - -
276A GLU* 3.5 47.7 + - + +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A GLY 3.2 18.0 + - - +
270A GLY* 3.6 11.9 - - - +
271A LEU 3.3 0.6 - - - -
272A ILE* 1.3 80.1 - - - +
274A GLN* 1.3 90.9 + - + +
276A GLU* 4.9 2.3 + - - +
277A ASN* 4.8 5.2 + - - -
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Residues in contact with GLN 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A GLY 4.6 1.0 + - - -
271A LEU 4.1 1.8 + - - -
273A GLU* 1.3 111.6 + - + +
275A ALA* 1.3 66.1 + - - +
276A GLU 3.2 2.9 + - - -
277A ASN* 3.4 31.6 + - - +
278A GLU* 2.9 24.2 + - + +
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Residues in contact with ALA 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40A PRO* 4.0 20.4 - - + -
213A VAL* 3.4 13.6 - - + +
271A LEU* 3.0 25.2 + - + +
272A ILE* 3.2 6.8 + - - -
274A GLN* 1.3 79.2 - - - +
276A GLU* 1.3 57.1 + - - +
278A GLU* 3.6 17.6 - - - +
279A ALA* 2.9 24.9 + - - +
----------------------------------------------------------
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Residues in contact with GLU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A PHE* 4.4 10.2 - - - -
148A GLY* 3.3 17.2 - - - -
149A THR* 2.8 37.6 + - - +
151A HIS* 5.8 0.2 + - - -
211A PRO* 4.0 8.1 - - - +
212A THR* 2.8 30.9 + - + +
213A VAL* 4.0 5.2 - - + -
272A ILE* 3.5 33.9 + - + +
273A GLU 5.4 2.0 - - - +
274A GLN 3.2 1.0 - - - -
275A ALA* 1.3 78.3 - - - +
277A ASN* 1.3 62.0 + - - +
279A ALA 3.4 0.2 + - - -
280A LEU* 3.0 19.6 + - - +
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Residues in contact with ASN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A GLU 4.8 4.7 + - - -
274A GLN* 3.4 35.2 + - - +
275A ALA 3.3 0.2 - - - -
276A GLU* 1.3 78.2 - - - +
278A GLU* 1.3 65.1 + - - +
280A LEU* 3.1 19.4 + - + +
281A GLU* 3.0 27.5 + - + +
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Residues in contact with GLU 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A GLN* 2.9 17.4 + - + +
275A ALA* 3.6 17.1 - - - +
277A ASN* 1.3 76.1 - - - +
279A ALA* 1.3 57.8 + - - +
281A GLU* 3.2 9.4 + - - +
282A ASN* 2.8 43.1 + - - +
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Residues in contact with ALA 279 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 3.5 33.2 - - - +
213A VAL* 3.7 11.4 - - + +
216A PHE* 4.4 7.9 - - + -
275A ALA 2.9 17.4 + - - +
278A GLU* 1.3 74.8 - - - +
280A LEU* 1.3 56.0 + - - +
282A ASN* 3.1 12.3 + - - +
283A LEU* 2.7 40.8 + - - +
----------------------------------------------------------
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 4.0 8.4 - - + -
227A LEU* 3.3 31.4 - - + -
229A LEU* 4.6 8.7 - - + -
276A GLU 3.0 13.8 + - - +
277A ASN* 3.2 22.0 - - + +
279A ALA* 1.3 75.6 - - - +
281A GLU* 1.3 71.6 + - - +
283A LEU* 3.2 11.4 + - - +
284A LYS* 3.1 32.2 + - - +
290A VAL* 4.0 22.0 - - + -
----------------------------------------------------------
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Residues in contact with GLU 281 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ASN* 3.0 17.6 + - + +
278A GLU* 3.5 9.2 - - - +
280A LEU* 1.3 83.5 - - - +
282A ASN* 1.3 65.7 + - - +
284A LYS* 3.0 40.2 + - - +
285A LYS* 3.0 38.6 + - - +
----------------------------------------------------------
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Residues in contact with ASN 282 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 3.5 41.3 - - + -
278A GLU* 2.8 34.9 + - - +
279A ALA* 3.1 10.1 + - - +
281A GLU* 1.3 73.8 - - - +
283A LEU* 1.3 66.3 + - - +
285A LYS* 3.4 21.7 + - - +
286A ALA* 3.2 22.5 + - - +
----------------------------------------------------------
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Residues in contact with LEU 283 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A LEU* 5.6 2.9 - - + -
212A THR* 4.0 34.5 - - + +
215A LEU* 4.4 12.8 - - + -
216A PHE* 3.9 19.1 - - + +
221A PHE* 3.7 37.5 - - + +
227A LEU* 4.3 17.5 - - + -
279A ALA 2.7 23.9 + - - +
280A LEU* 3.2 5.6 + - - +
282A ASN* 1.3 72.8 - - - +
284A LYS* 1.3 62.5 + - + +
286A ALA* 3.1 13.2 + - - +
287A GLY 3.3 0.7 + - - -
288A VAL* 3.1 34.2 + - + +
290A VAL* 6.0 0.2 - - + -
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Residues in contact with LYS 284 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A LEU* 3.1 18.2 + - + +
281A GLU* 3.0 48.0 + - - +
283A LEU* 1.3 74.6 - - - +
285A LYS* 1.3 58.9 + - + +
287A GLY* 2.9 19.9 + - - -
288A VAL 3.5 14.7 + - - +
290A VAL* 3.5 33.0 - - + -
----------------------------------------------------------
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Residues in contact with LYS 285 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A GLU* 3.0 28.9 + - - +
282A ASN* 3.7 21.0 + - - +
283A LEU 3.3 0.4 - - - -
284A LYS* 1.3 77.3 - - + +
286A ALA* 1.3 58.8 + - - +
287A GLY* 3.2 1.1 + - - -
----------------------------------------------------------
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 4.7 3.6 - - + -
221A PHE* 3.7 39.8 - - + +
225A LYS* 4.4 12.6 - - - -
282A ASN 3.2 13.6 + - - +
283A LEU* 3.1 8.3 + - - +
285A LYS* 1.3 76.6 - - - +
287A GLY* 1.3 57.9 + - - +
288A VAL* 3.6 1.0 - - - +
----------------------------------------------------------
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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) + - + + + + + -
------------------------------------------------------------
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