Contacts of the helix formed by residues 240 - 278 (chain A) in PDB entry 4ZWJ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 240 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 3.7 19.6 + - - +
238A GLN 3.2 3.0 - - - +
239A GLU* 1.3 81.2 - - - +
241A ALA* 1.3 62.5 + - - +
242A THR* 3.5 10.2 + - - -
243A THR* 3.2 30.4 + - - -
244A GLN* 3.5 18.2 + - - +
2083A ASP* 5.3 10.8 + - - +
2086A PHE* 5.6 10.9 - - - +
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Residues in contact with ALA 241 (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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238A GLN 5.0 0.9 - - - -
239A GLU 3.3 7.9 + - - +
240A SER* 1.3 70.8 - - - +
242A THR* 1.3 65.1 + - - +
243A THR 3.3 0.2 - - - -
244A GLN* 3.2 13.1 + - + +
245A LYS* 3.2 30.0 + - - +
2163A ASP* 4.4 11.9 - - - +
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Residues in contact with THR 242 (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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240A SER* 3.3 9.6 + - - -
241A ALA* 1.3 79.0 + - - +
243A THR* 1.3 60.5 + - - +
245A LYS* 3.5 4.3 + - + +
246A ALA* 3.2 21.7 + - - +
2083A ASP* 5.7 5.3 + - - +
2086A PHE* 5.8 2.6 - - - -
2162A GLU* 4.2 10.3 + - - +
2163A ASP* 3.8 35.3 + - + +
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Residues in contact with THR 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A VAL* 5.7 4.0 - - + +
234A ALA* 4.4 19.7 - - + -
237A GLN* 3.5 16.4 + - - +
240A SER* 3.2 23.5 + - - -
241A ALA 3.3 0.6 - - - -
242A THR* 1.3 76.3 - - - +
244A GLN* 1.3 62.5 + - - +
246A ALA* 3.4 7.4 + - + +
247A GLU* 2.9 29.3 + - + +
2082A ARG* 4.0 26.0 + - + +
2083A ASP* 5.4 3.3 + - - +
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Residues in contact with GLN 244 (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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234A ALA* 3.0 41.6 + - - +
237A GLN 3.7 4.6 + - - -
238A GLN* 3.7 29.9 + - - +
240A SER 3.5 14.2 + - - +
241A ALA* 3.2 12.5 + - + +
243A THR* 1.3 76.3 - - - +
245A LYS* 1.3 60.5 + - + +
247A GLU* 3.5 14.4 + - - +
248A LYS* 3.0 29.5 + - - +
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Residues in contact with LYS 245 (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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241A ALA* 3.2 14.8 + - - +
242A THR* 3.9 6.7 - - + +
243A THR 3.4 0.2 - - - -
244A GLN* 1.3 75.0 - - + +
246A ALA* 1.3 65.5 + - - +
248A LYS* 3.5 6.4 + - - +
249A GLU* 3.0 24.3 + - - +
2163A ASP* 3.1 38.9 + - + +
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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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230A VAL* 6.3 0.4 - - + -
242A THR 3.2 12.3 + - - +
243A THR* 3.5 12.6 - - + +
245A LYS* 1.3 76.2 - - - +
247A GLU* 1.3 55.0 + - - +
249A GLU* 3.0 7.9 + - - +
250A VAL* 2.8 39.9 + - - +
2078A LEU 5.7 0.7 - - - -
2079A THR* 3.5 27.4 - - - +
2080A PHE 5.1 1.8 - - - +
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Residues in contact with GLU 247 (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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230A VAL* 3.7 34.2 - - + +
231A LYS* 2.9 40.3 + - + +
234A ALA* 3.9 19.5 - - + +
243A THR 2.9 20.4 + - - +
244A GLN* 3.8 17.0 - - - +
246A ALA* 1.3 71.5 - - - +
248A LYS* 1.3 58.3 + - - +
250A VAL* 3.6 2.9 - - - +
251A THR* 2.7 49.8 + - - +
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Residues in contact with LYS 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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244A GLN 3.0 17.7 + - - +
245A LYS* 3.7 7.0 - - - +
246A ALA 3.1 0.2 - - - -
247A GLU* 1.3 80.9 - - - +
249A GLU* 1.3 67.0 + - - +
250A VAL 3.3 0.2 + - - -
251A THR* 3.4 4.8 + - - -
252A ARG* 3.0 50.0 + - - +
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Residues in contact with GLU 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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245A LYS 3.0 12.9 + - - +
246A ALA* 3.0 11.2 + - - +
248A LYS* 1.3 78.8 - - - +
250A VAL* 1.3 62.4 + - - +
252A ARG* 2.8 41.4 + - - +
253A MET* 3.2 40.2 + - + +
2078A LEU 5.0 8.7 - - - +
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Residues in contact with VAL 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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226A LEU* 4.3 10.8 - - + -
227A VAL* 4.4 6.5 - - + -
230A VAL* 4.9 10.5 - - + -
246A ALA 2.8 20.9 + - - +
247A GLU* 3.6 8.3 - - - +
249A GLU* 1.3 75.3 - - - +
251A THR* 1.3 63.7 + - - +
253A MET* 3.0 5.0 + - - +
254A VAL* 2.9 34.8 + - + +
2078A LEU* 3.5 51.8 - - + +
2079A THR* 3.5 22.9 - - + -
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Residues in contact with THR 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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227A VAL* 4.2 14.2 - - + +
230A VAL* 6.0 0.2 - - - +
231A LYS* 3.7 24.6 + - - +
247A GLU* 2.7 36.6 + - - +
248A LYS* 3.9 5.4 - - - -
250A VAL* 1.3 80.5 - - - +
252A ARG* 1.3 62.3 + - - +
254A VAL* 3.9 5.6 - - + +
255A ILE* 3.1 47.1 + - + +
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Residues in contact with ARG 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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248A LYS* 3.0 42.5 + - - +
249A GLU* 2.8 40.2 + - - +
250A VAL 3.2 0.2 - - - -
251A THR* 1.3 78.7 - - - +
253A MET* 1.3 83.9 + - - +
255A ILE* 3.6 9.0 + - - +
256A ILE* 3.2 41.2 + - + +
309A MET* 5.9 1.4 - - - +
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Residues in contact with MET 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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249A GLU* 3.2 23.8 + - + +
250A VAL 3.0 7.9 + - - +
252A ARG* 1.3 109.0 - - - +
254A VAL* 1.3 54.6 + - - +
256A ILE* 3.1 19.9 + - + +
257A TYR* 2.8 64.5 + - + +
305A ILE* 5.1 3.1 - - - +
309A MET* 4.1 37.7 - - + +
2078A LEU* 3.9 10.8 - - + +
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Residues in contact with VAL 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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223A TYR* 3.8 31.0 - - + +
224A GLY* 5.9 0.2 - - - -
226A LEU* 5.4 0.4 - - + -
227A VAL* 3.6 32.1 - - + -
250A VAL* 2.9 25.8 + - + +
251A THR* 3.9 4.3 - - + +
253A MET* 1.3 72.1 - - - +
255A ILE* 1.3 67.4 + - + +
257A TYR* 3.3 15.0 + - + +
258A VAL* 3.1 30.1 + - + +
2078A LEU* 4.3 13.2 - - + -
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Residues in contact with ILE 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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251A THR* 3.1 35.3 + - + +
252A ARG* 3.8 8.1 - - - +
253A MET 3.3 0.2 - - - -
254A VAL* 1.3 77.2 - - + +
256A ILE* 1.3 60.5 + - + +
258A VAL* 3.4 7.5 + - - +
259A ILE* 3.1 45.7 + - + +
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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
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252A ARG* 3.2 31.4 + - + +
253A MET* 3.1 28.1 + - + +
255A ILE* 1.3 78.5 - - + +
257A TYR* 1.3 60.2 + - - +
259A ILE* 3.8 12.5 - - + +
260A ALA* 2.9 28.6 + - - +
305A ILE* 3.7 36.1 - - + -
309A MET* 5.1 11.0 - - + -
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Residues in contact with TYR 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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135A ARG* 3.1 30.0 + - - -
219A ILE* 6.5 1.6 - - - -
223A TYR* 4.5 25.4 - + + -
253A MET* 2.8 51.6 + - + +
254A VAL* 3.3 15.7 + - + +
256A ILE* 1.3 72.2 - - - +
258A VAL* 1.3 61.8 + - - +
260A ALA* 3.6 4.3 + - - +
261A PHE* 3.1 24.1 + - - +
305A ILE* 3.6 31.0 + - + -
306A TYR* 3.4 48.8 + + - +
2077A GLY 4.1 7.6 + - - -
2078A LEU* 4.2 10.5 - - + +
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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
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219A ILE* 5.9 3.1 - - + -
220A PHE* 3.5 45.3 - - + -
223A TYR* 5.7 8.3 - - + -
254A VAL* 3.1 22.8 + - + +
255A ILE* 3.7 8.5 - - - +
256A ILE 3.3 0.2 - - - -
257A TYR* 1.3 75.7 - - + +
259A ILE* 1.3 62.8 + - + +
261A PHE* 3.2 6.1 + - - +
262A LEU* 2.9 42.6 + - + +
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Residues in contact with ILE 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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255A ILE* 3.1 40.5 + - + +
256A ILE* 3.4 12.3 + - + +
258A VAL* 1.3 78.1 - - + +
260A ALA* 1.3 59.0 + - - +
262A LEU* 4.0 7.2 - - + +
263A ILE* 3.0 52.0 + - + +
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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
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256A ILE 2.9 18.5 + - - +
257A TYR* 3.8 6.1 - - - +
259A ILE* 1.3 77.0 - - - +
261A PHE* 1.3 63.3 + - - +
263A ILE* 4.7 2.2 - - - -
264A CYS* 3.1 24.3 + - - +
301A TYR* 3.4 22.1 + - + -
302A ASN* 4.6 6.4 - - - +
305A ILE* 3.5 25.8 - - + -
306A TYR* 5.2 8.1 - - + -
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Residues in contact with PHE 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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125A LEU* 3.7 26.7 - - + -
128A LEU* 5.3 12.6 - - + -
211A HIS 5.7 0.9 - - - -
212A PHE* 4.9 9.0 - + - -
215A PRO* 4.1 17.7 - - + -
216A MET* 3.8 30.3 - - + -
219A ILE* 4.1 24.5 - - + -
220A PHE* 4.3 17.5 - + + -
257A TYR 3.1 18.1 + - - +
258A VAL* 3.2 5.6 + - - +
260A ALA* 1.3 74.7 - - - +
262A LEU* 1.3 73.9 + - + +
264A CYS* 3.3 5.4 + - - +
265A TRP* 3.1 42.3 + + + +
302A ASN* 6.4 0.4 - - - +
306A TYR* 5.4 3.4 - - - +
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Residues in contact with LEU 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A MET* 5.4 8.7 - - - -
220A PHE* 4.4 17.0 - - + -
258A VAL* 2.9 38.4 + - + +
259A ILE* 4.0 6.7 - - + +
261A PHE* 1.3 86.2 - - + +
263A ILE* 1.3 66.8 + - + +
266A VAL* 2.9 54.8 + - + +
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Residues in contact with ILE 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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259A ILE* 3.0 42.8 + - + +
260A ALA* 4.2 2.7 - - - +
262A LEU* 1.3 76.5 - - + +
264A CYS* 1.3 62.8 + - - +
267A PRO* 3.3 19.1 - - - +
294A PHE* 3.4 32.9 - - + +
301A TYR* 3.5 19.5 - - + +
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Residues in contact with CYS 264 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A ALA 3.1 16.6 + - - +
261A PHE* 3.5 5.8 - - - +
262A LEU 3.1 0.6 - - - -
263A ILE* 1.3 79.7 - - - +
265A TRP* 1.3 98.7 + - + +
267A PRO* 3.6 7.4 - - - +
268A TYR* 4.9 1.7 + - - -
291A PRO 4.9 0.2 - - - +
294A PHE 4.2 4.0 - - - -
295A ALA* 3.9 25.8 + - - +
298A ALA* 3.4 24.2 - - + -
301A TYR* 3.1 15.8 + - - +
302A ASN* 5.2 6.3 - - - +
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Residues in contact with TRP 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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121A GLY* 3.6 35.4 - - - -
122A GLU* 5.4 6.3 - - - -
124A ALA* 6.1 0.2 - - + -
125A LEU* 3.7 34.4 - - + +
128A LEU* 6.1 2.4 - - - +
212A PHE* 3.4 26.0 - + + -
261A PHE* 3.1 38.5 + + + +
264A CYS* 1.3 106.5 - - + +
266A VAL* 1.3 65.6 + - - +
267A PRO* 3.4 2.5 - - - -
268A TYR* 3.5 29.8 + + + +
269A ALA* 3.1 17.2 + - - +
295A ALA* 4.9 7.4 - - + -
302A ASN* 6.0 0.8 - - - +
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Residues in contact with VAL 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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212A PHE* 3.9 20.4 - - + -
261A PHE* 6.2 0.2 - - + -
262A LEU* 2.9 50.8 + - + +
265A TRP* 1.3 77.4 - - + +
267A PRO* 1.4 62.1 - - + +
270A SER* 2.7 44.1 + - - +
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Residues in contact with PRO 267 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262A LEU 3.6 0.7 - - - +
263A ILE* 3.3 27.1 - - - +
264A CYS 3.6 2.7 - - - +
265A TRP 3.5 2.9 - - - -
266A VAL* 1.4 94.4 - - + +
268A TYR* 1.3 59.2 + - - +
270A SER* 3.0 17.7 + - - +
271A VAL* 3.1 21.5 + - + +
290A ILE* 5.0 3.6 - - + -
291A PRO* 3.6 26.9 - - + +
294A PHE* 3.9 22.7 - - + -
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Residues in contact with TYR 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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181A GLU* 3.3 27.0 + - - -
191A TYR* 3.6 42.9 - + - -
264A CYS 4.9 1.3 + - - -
265A TRP* 3.5 27.2 + + + +
266A VAL 3.3 0.4 - - - -
267A PRO* 1.3 80.3 - - - +
269A ALA* 1.3 58.2 + - - +
271A VAL* 4.0 0.9 - - - +
272A ALA* 2.9 32.8 + - - +
288A MET 5.3 1.5 + - - -
291A PRO* 3.7 20.9 - - + -
292A ALA* 3.8 17.6 - - - +
295A ALA* 3.5 33.9 - - + -
296A LYS* 5.1 3.0 - - + -
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Residues in contact with ALA 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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208A PHE* 3.5 29.4 - - + -
212A PHE* 3.4 44.2 - - + -
265A TRP 3.1 4.4 + - - +
266A VAL 3.9 0.9 - - - +
268A TYR* 1.3 81.0 - - - +
270A SER* 1.3 55.9 + - - +
272A ALA* 3.9 1.7 - - - +
273A PHE* 2.9 31.4 + - - +
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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 VAL* 2.7 36.1 + - - +
267A PRO* 3.0 11.1 + - - +
269A ALA* 1.3 70.8 - - - +
271A VAL* 1.3 69.7 + - - +
273A PHE* 3.4 8.1 + - - +
274A TYR* 2.9 30.8 + - - +
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Residues in contact with VAL 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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191A TYR* 4.3 12.8 - - - +
267A PRO* 3.1 19.6 + - + +
268A TYR* 4.1 1.8 - - - +
270A SER* 1.3 83.3 + - - +
272A ALA* 1.3 59.4 + - - +
274A TYR* 3.3 5.9 + - - +
275A ILE* 2.8 50.2 + - + +
287A PHE* 3.9 33.9 - - + +
288A MET* 5.4 2.5 - - - -
290A ILE* 6.1 1.3 - - + -
291A PRO* 3.6 21.3 - - + -
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Residues in contact with ALA 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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191A TYR* 3.4 39.6 - - + +
204A VAL* 5.1 11.5 - - + +
208A PHE* 5.2 6.7 - - + -
268A TYR* 2.9 20.3 + - + +
269A ALA* 3.9 5.6 - - - +
271A VAL* 1.3 76.4 - - - +
273A PHE* 1.3 57.5 - - - +
275A ILE* 3.6 3.0 + - - +
276A PHE* 3.1 28.1 + - - +
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Residues in contact with PHE 273 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A PHE* 4.3 24.8 - + + -
269A ALA 2.9 20.6 + - - +
270A SER* 3.6 7.2 - - - +
272A ALA* 1.3 75.6 - - - +
274A TYR* 1.3 67.0 + + + +
276A PHE* 3.3 8.4 + + + +
277A THR* 3.0 55.5 + - + +
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Residues in contact with TYR 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A SER 2.9 18.6 + - - +
271A VAL* 3.3 6.7 + - - +
273A PHE* 1.3 78.7 - + + +
275A ILE* 1.3 60.6 + - - +
277A THR* 3.0 6.3 + - - -
278A HIS* 2.9 61.0 + + + +
281A SER* 5.9 0.7 - - - -
283A PHE* 3.9 22.2 - + - -
287A PHE* 5.3 10.5 - + + -
1060A LYS* 4.2 22.2 + - - +
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Residues in contact with ILE 275 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.9 20.6 - - + +
192A TYR* 3.9 35.7 - - + +
271A VAL* 2.8 39.2 + - + +
272A ALA* 3.8 4.3 - - - +
274A TYR* 1.3 75.0 - - - +
276A PHE* 1.3 62.3 + - - +
278A HIS 3.0 19.6 - - - +
279A GLN* 3.4 18.2 + - - +
283A PHE* 3.8 44.6 - - + -
287A PHE* 5.1 0.9 - - + -
288A MET* 4.9 9.2 - - + -
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Residues in contact with PHE 276 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR 5.9 2.9 - - - +
194A LEU* 4.5 15.7 - - + -
201A GLU* 4.0 42.0 - - + -
204A VAL* 4.9 16.4 - - + -
205A ILE* 4.3 17.9 - - + -
272A ALA 3.1 18.6 + - - +
273A PHE* 3.3 9.8 + + + +
275A ILE* 1.3 77.6 - - - +
277A THR* 1.3 67.8 + - + +
279A GLN* 3.5 29.4 - - + +
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Residues in contact with THR 277 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A PHE* 3.0 48.8 + - + +
274A TYR* 3.0 18.5 + - - -
276A PHE* 1.3 82.1 - - + +
278A HIS* 1.3 77.5 + - - +
279A GLN* 3.7 2.4 + - - +
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Residues in contact with HIS 278 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274A TYR* 2.9 51.7 + + + +
275A ILE 3.0 11.1 - - - +
277A THR* 1.3 93.4 + - - +
279A GLN* 1.3 62.1 + - - +
280A GLY 3.5 2.9 - - - +
281A SER* 3.8 22.1 + - - +
283A PHE* 3.4 18.8 - - + -
1004A PHE* 6.5 1.3 - + - -
1005A GLU* 6.1 1.6 - - - -
1060A LYS* 4.9 7.1 + - - -
1061A ASP* 5.2 7.5 + - - -
1064A GLU* 6.0 0.2 + - - -
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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