Contacts of the helix formed by residues 244 - 276 (chain P) in PDB entry 3FKS
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 ALA 244 (chain P).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390O ILE* 3.7 22.0 - - + -
13P ILE* 3.9 4.8 - - + +
16P ILE* 4.2 18.4 - - + -
17P GLU* 4.3 16.2 - - + +
240P ALA 2.6 16.8 + - - +
243P ASN* 1.3 77.9 - - - +
245P GLY* 1.3 59.9 + - - +
246P ASP 3.2 1.8 - - - -
247P MET* 2.8 19.6 + - - +
248P ILE* 2.8 17.4 + - - +
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Residues in contact with GLY 245 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P GLU* 3.7 23.9 - - - +
241P SER 3.6 11.2 + - - -
242P LYS* 4.1 2.8 - - - -
243P ASN 3.7 0.2 - - - -
244P ALA* 1.3 78.9 - - - +
246P ASP* 1.3 56.8 + - - +
247P MET 3.0 5.2 + - - -
248P ILE* 3.0 16.6 + - - +
249P ASN* 3.2 19.1 + - - +
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Residues in contact with ASP 246 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K GLU* 3.2 23.0 - - - +
242P LYS* 3.4 20.6 + - - +
243P ASN* 4.7 7.9 - - - +
244P ALA 3.2 1.2 - - - -
245P GLY* 1.3 75.1 - - - +
247P MET* 1.3 57.5 + - - +
249P ASN* 4.5 11.2 + - - +
250P ARG* 3.8 18.2 + - - +
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Residues in contact with MET 247 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386O ASP* 4.6 20.9 - - - +
389O ALA* 4.6 16.8 - - + -
390O ILE* 4.1 20.9 - - - -
9P ARG* 5.3 4.3 - - - -
13P ILE* 3.5 25.2 - - + +
243P ASN 4.3 3.8 - - - +
244P ALA* 2.8 19.6 + - - +
246P ASP* 1.3 78.4 - - - +
248P ILE* 1.3 65.5 + - - +
249P ASN 3.2 0.9 - - - -
250P ARG* 3.9 17.5 - - - +
251P TYR* 3.0 45.5 + - + +
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Residues in contact with ILE 248 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LEU* 4.1 5.8 - - + +
13P ILE* 3.3 43.5 - - + +
14P LYS* 3.4 46.7 - - + +
17P GLU* 4.5 14.4 - - + +
244P ALA 2.8 17.3 + - - +
245P GLY* 3.4 14.1 - - - +
247P MET* 1.3 78.5 - - - +
249P ASN* 1.3 64.9 + - - +
251P TYR* 3.8 1.2 - - - -
252P SER* 2.8 32.6 + - - -
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Residues in contact with ASN 249 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357K GLU* 5.5 4.6 + - - -
245P GLY 3.2 14.5 + - - +
246P ASP* 5.0 9.5 + - - +
248P ILE* 1.3 86.2 - - - +
250P ARG* 1.3 64.9 + - - +
252P SER* 3.2 14.3 + - - -
253P ILE* 3.2 21.7 + - - +
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Residues in contact with ARG 250 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338O GLY* 5.8 5.5 - - - -
341O GLU* 5.0 12.1 + - - -
246P ASP 3.8 19.1 + - - +
247P MET* 3.7 19.9 + - - +
248P ILE 3.6 0.2 - - - -
249P ASN* 1.3 78.7 - - - +
251P TYR* 1.3 67.9 + - + +
253P ILE* 3.4 14.1 + - - +
254P LEU* 3.6 9.5 + - - +
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Residues in contact with TYR 251 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
386O ASP* 4.7 12.8 + - - -
6P VAL* 4.4 10.5 - - + +
9P ARG* 3.6 45.1 + - + +
10P LEU* 4.4 10.6 - - + +
13P ILE* 3.4 27.1 - - + -
247P MET* 3.0 42.8 + - + +
248P ILE 4.1 1.8 - - - +
250P ARG* 1.3 80.3 - - + +
252P SER* 1.3 65.1 + - - +
253P ILE 3.1 2.7 - - - -
254P LEU* 3.1 28.5 + - + +
255P TYR* 3.1 21.1 + - - +
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Residues in contact with SER 252 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10P LEU* 4.2 17.1 - - - +
14P LYS* 5.3 4.2 + - - -
248P ILE* 2.8 25.3 + - - -
249P ASN* 3.2 11.6 + - - -
251P TYR* 1.3 75.8 - - - +
253P ILE* 1.3 61.2 + - - +
255P TYR* 3.7 6.7 + - - +
256P ASN* 3.0 34.4 + - - -
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Residues in contact with ILE 253 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332K GLN 4.6 3.4 - - - +
333K GLY* 3.7 33.9 - - - +
335K ASP* 4.1 30.5 - - + +
318N THR* 5.0 6.1 - - + -
249P ASN 3.3 15.5 - - - +
250P ARG* 3.6 9.0 - - - +
251P TYR 3.1 0.4 - - - -
252P SER* 1.3 78.0 - - - +
254P LEU* 1.3 67.6 + - - +
255P TYR 3.1 1.3 - - - -
256P ASN* 3.0 15.4 + - + +
257P ARG* 2.9 26.7 + - + +
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Residues in contact with LEU 254 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P ALA* 4.1 23.8 - - + -
6P VAL* 4.0 19.1 - - + -
250P ARG 3.6 6.2 + - - +
251P TYR* 3.1 33.1 + - + +
253P ILE* 1.3 79.3 - - - +
255P TYR* 1.3 54.8 + - - +
257P ARG* 3.7 6.0 + - + +
258P THR* 2.6 34.9 + - - +
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Residues in contact with TYR 255 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335J ASP* 5.0 6.9 + - - -
337J SER* 5.4 2.9 + - - -
314N ALA* 5.7 5.9 - - + +
3P LEU 4.8 9.0 - - - -
6P VAL* 3.6 19.9 - - + +
7P GLU* 3.7 54.4 + - + -
10P LEU* 4.5 17.0 - - + -
251P TYR 3.1 8.8 + - - +
252P SER* 3.7 11.2 - - - +
253P ILE 3.1 0.6 - - - -
254P LEU* 1.3 76.9 - - - +
256P ASN* 1.3 65.7 + - - +
258P THR* 3.1 6.9 + - - -
259P ARG* 2.7 62.1 + - + +
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Residues in contact with ASN 256 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314N ALA 5.4 0.7 - - - +
315N ASP 5.8 0.2 + - - -
316N ASP* 3.2 37.0 + - - +
317N LEU 5.6 0.2 - - - +
318N THR* 3.8 19.7 + - + +
252P SER* 3.0 23.7 + - - -
253P ILE* 3.0 17.3 + - + +
255P TYR* 1.3 88.4 - - - +
257P ARG* 1.3 63.8 + - - +
258P THR 2.9 5.6 + - - -
259P ARG* 2.9 14.7 + - - +
260P GLN* 3.0 20.3 + - - +
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Residues in contact with ARG 257 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335K ASP* 4.7 14.1 - - - +
253P ILE* 2.9 21.3 + - + +
254P LEU* 4.1 7.0 - - + +
256P ASN* 1.3 73.5 - - - +
258P THR* 1.3 57.0 + - - +
260P GLN* 4.7 4.1 - - - +
261P ALA* 3.2 24.9 + - - +
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Residues in contact with THR 258 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1P ALA* 4.8 8.5 - - + +
2P THR* 4.8 22.0 - - - +
3P LEU* 4.8 6.1 - - - +
6P VAL* 4.6 10.9 - - + +
254P LEU* 2.6 24.1 + - - +
255P TYR* 3.1 9.4 + - - -
256P ASN 2.9 0.8 - - - -
257P ARG* 1.3 78.8 - - - +
259P ARG* 1.3 65.4 - - - +
260P GLN 3.3 0.2 - - - -
261P ALA* 3.4 3.7 + - - +
262P VAL* 3.0 40.4 + - + +
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Residues in contact with ARG 259 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ARG* 5.0 3.4 - - - +
337J SER* 5.1 9.4 + - - -
279N VAL* 4.7 2.6 - - - +
313N PRO* 4.7 2.8 + - - +
314N ALA* 4.1 28.0 - - - +
316N ASP* 2.9 30.7 + - - +
319N ASP* 2.8 29.5 + - - +
255P TYR* 2.7 49.8 + - + +
256P ASN* 2.9 4.9 + - - +
258P THR* 1.3 75.7 - - - +
260P GLN* 1.3 74.0 + - - +
262P VAL* 3.3 9.4 + - - +
263P ILE* 3.2 43.0 + - + +
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Residues in contact with GLN 260 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279N VAL* 3.4 29.2 - - + +
316N ASP* 3.0 22.3 + - - +
318N THR* 3.1 31.3 + - - +
319N ASP* 3.7 1.0 - - - +
320N PRO* 4.0 8.3 - - - +
256P ASN* 3.0 16.2 + - - +
257P ARG* 4.7 3.6 - - - +
259P ARG* 1.3 92.5 - - - +
261P ALA* 1.3 58.1 + - - +
262P VAL 3.1 0.6 + - - -
263P ILE* 3.2 9.6 + - - +
264P THR* 2.9 33.6 + - - -
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Residues in contact with ALA 261 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257P ARG 3.2 20.3 + - - +
258P THR* 3.4 6.2 + - + +
259P ARG 3.4 0.6 - - - -
260P GLN* 1.3 77.9 - - - +
262P VAL* 1.3 58.7 + - + +
264P THR* 4.4 7.0 - - - -
265P ASN* 3.0 42.5 + - - +
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Residues in contact with VAL 262 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3P LEU* 4.6 34.3 - - + -
258P THR* 3.0 33.8 + - + +
259P ARG* 3.6 6.7 - - - +
260P GLN 3.1 1.0 - - - -
261P ALA* 1.3 79.6 - - + +
263P ILE* 1.3 66.7 + - + +
265P ASN* 4.3 2.5 - - - +
266P GLU* 3.1 26.0 + - + +
----------------------------------------------------------
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Residues in contact with ILE 263 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J ARG* 3.3 57.9 - - + +
294J GLU* 5.8 0.7 - - + -
279N VAL* 3.8 31.9 - - + -
259P ARG* 3.2 42.2 - - + +
260P GLN* 3.2 4.2 + - - +
262P VAL* 1.3 76.9 - - + +
264P THR* 1.3 68.9 + - - +
266P GLU* 3.1 12.3 + - - +
267P LEU* 3.1 23.4 + - + +
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Residues in contact with THR 264 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292K GLY 5.2 1.8 - - - +
294K GLU* 4.8 10.5 - - - +
295K ALA* 4.7 17.9 - - + +
277N SER 4.7 10.8 - - - +
278N ALA* 3.9 2.8 - - - +
279N VAL* 2.8 30.9 + - - +
280N GLY 5.4 1.6 - - - +
260P GLN* 2.9 17.9 + - - +
261P ALA* 4.4 5.8 - - - -
263P ILE* 1.3 77.6 - - - +
265P ASN* 1.3 71.1 + - - +
267P LEU* 2.9 19.0 + - - +
268P VAL* 3.0 28.5 + - + +
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Residues in contact with ASN 265 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294K GLU 5.9 1.0 + - - -
279O VAL* 5.3 11.3 - - - +
261P ALA* 3.0 28.6 + - - +
262P VAL* 4.3 2.5 - - - +
264P THR* 1.3 86.1 - - - +
266P GLU* 1.3 62.7 + - - +
268P VAL* 3.5 8.4 + - - +
269P ASP* 3.2 27.6 + - - +
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Residues in contact with GLU 266 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294J GLU* 3.5 43.2 + - - +
278M ALA* 4.8 3.3 - - - +
279M VAL* 4.1 33.7 + - + +
262P VAL* 3.1 22.9 + - + +
263P ILE* 3.1 8.6 + - - +
264P THR 3.0 0.8 + - - -
265P ASN* 1.3 79.4 - - - +
267P LEU* 1.3 66.3 + - - +
269P ASP* 3.5 8.6 + - - +
270P ILE* 3.4 22.2 + - + +
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Residues in contact with LEU 267 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292J GLY 3.4 21.3 - - - +
293J ARG* 3.5 13.9 - - + -
294J GLU 3.4 27.8 - - - +
276N PRO* 3.7 22.2 - - + +
277N SER 5.6 2.7 - - - +
280N GLY* 3.7 30.3 - - - +
263P ILE* 3.1 17.2 + - + +
264P THR* 2.9 9.8 + - - +
266P GLU* 1.3 80.5 - - - +
268P VAL* 1.3 56.3 + - + +
270P ILE* 2.8 11.8 + - + +
271P ILE* 2.7 44.4 + - + +
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Residues in contact with VAL 268 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K PRO* 4.0 45.5 - - + +
292K GLY 5.2 3.8 - - - +
295K ALA* 6.2 0.2 - - + -
276N PRO 6.2 0.2 - - - +
277N SER 6.0 0.9 - - - +
276O PRO* 6.4 1.6 - - + -
279O VAL* 6.2 2.5 - - - +
280O GLY 5.8 3.1 - - - +
264P THR* 3.0 29.6 + - + +
265P ASN* 3.9 9.6 - - - +
267P LEU* 1.3 77.1 - - + +
269P ASP* 1.3 62.0 + - - +
271P ILE* 4.0 8.0 - - + +
272P THR* 2.7 43.1 + - - +
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Residues in contact with ASP 269 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291L PRO* 4.8 2.9 - - - +
292L GLY 4.0 15.5 - - - +
293L ARG* 3.6 10.9 - - - +
294L GLU* 2.8 38.7 + - - +
295L ALA* 4.1 3.8 + - - +
276M PRO* 4.7 3.3 - - - +
279M VAL* 6.4 1.6 - - - -
280M GLY* 6.0 4.5 - - - +
265P ASN 3.2 12.3 + - - +
266P GLU* 3.5 12.7 - - - +
267P LEU 3.2 0.4 - - - -
268P VAL* 1.3 81.1 - - - +
270P ILE* 1.3 62.4 + - + +
272P THR* 4.1 4.8 - - - -
273P GLY* 3.5 15.9 + - - -
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Residues in contact with ILE 270 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J PRO* 3.9 29.8 - - + -
292J GLY 4.8 3.8 - - - +
294J GLU* 4.2 6.1 - - - -
295J ALA* 3.5 36.1 - - + +
275M ILE* 5.2 0.7 - - + -
276M PRO* 3.5 24.9 - - + +
277M SER 3.5 17.5 - - - +
278M ALA* 4.3 6.1 - - - -
279M VAL 5.1 2.5 - - - +
280M GLY 5.7 1.1 - - - +
266P GLU* 3.4 18.4 + - + +
267P LEU* 2.8 15.6 + - + +
269P ASP* 1.3 78.7 - - + +
271P ILE* 1.3 67.0 + - + +
273P GLY 3.2 1.4 + - - -
274P ALA* 3.0 19.4 + - - +
----------------------------------------------------------
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Residues in contact with ILE 271 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J PRO* 4.6 22.0 - - + +
292J GLY 5.6 0.4 - - - +
288K ARG* 5.9 2.0 - - - +
291K PRO* 5.4 11.2 - - + -
275N ILE* 4.4 27.6 - - + -
276N PRO* 3.6 34.8 - - + +
267P LEU* 2.7 31.0 + - + +
268P VAL* 4.0 6.5 - - + +
270P ILE* 1.3 76.7 - - + +
272P THR* 1.3 64.0 + - - +
274P ALA* 3.0 20.6 + - + +
275P SER* 3.5 7.6 + - - -
----------------------------------------------------------
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Residues in contact with THR 272 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291K PRO* 5.7 1.7 - - - +
291L PRO* 3.7 19.1 - - + +
295L ALA* 6.1 1.1 - - + -
275O ILE* 3.6 28.9 - - + +
276O PRO* 3.8 30.1 + - + +
277O SER 5.6 1.6 + - - +
268P VAL* 2.7 32.6 + - - +
269P ASP* 4.1 5.7 - - - -
271P ILE* 1.3 78.0 - - - +
273P GLY* 1.3 58.7 + - - +
275P SER* 2.7 25.2 + - - +
276P SER 4.3 1.4 + - - -
----------------------------------------------------------
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Residues in contact with GLY 273 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290L PRO* 4.7 8.0 - - - +
291L PRO* 4.2 21.0 - - - +
274M ARG 4.9 0.9 - - - +
275M ILE* 5.0 0.9 - - - +
276M PRO* 3.2 31.7 - - - +
269P ASP 3.5 6.8 + - - -
270P ILE 3.2 3.4 + - - -
271P ILE 3.2 0.6 - - - -
272P THR* 1.3 76.9 - - - +
274P ALA* 1.3 62.2 + - - +
275P SER 3.3 4.2 + - - -
276P SER* 4.5 7.7 - - - -
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Residues in contact with ALA 274 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291J PRO* 4.8 13.5 - - + -
275M ILE* 4.0 33.7 - - + +
276M PRO* 4.3 1.6 - - - -
270P ILE 3.0 12.4 + - - +
271P ILE* 3.0 19.4 + - + +
273P GLY* 1.3 77.3 - - - +
275P SER* 1.3 65.3 + - - +
----------------------------------------------------------
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Residues in contact with SER 275 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288L ARG* 5.7 1.8 - - - -
275O ILE* 4.0 16.7 - - - +
276O PRO* 6.1 0.2 - - - +
271P ILE 3.5 6.0 + - - -
272P THR* 2.7 22.2 + - - +
274P ALA* 1.3 82.6 - - - +
276P SER* 1.3 83.6 + - - +
----------------------------------------------------------
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Residues in contact with SER 276 (chain P).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288L ARG* 4.2 34.4 + - - -
290L PRO* 3.3 36.3 - - - +
275O ILE* 4.8 7.4 - - - +
272P THR 4.3 2.2 + - - -
273P GLY 4.5 7.6 - - - -
274P ALA 5.0 0.2 - - - -
275P SER* 1.3 96.9 + - - +
----------------------------------------------------------
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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