Contacts of the helix formed by residues 246 - 275 (chain A) in PDB entry 3GUC
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 ARG 246 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 1.3 66.9 - - - +
248A GLY* 3.2 42.3 - - - +
249A VAL* 3.3 38.6 - - + +
250A CYS* 3.5 12.1 + - - -
69B GLU* 4.5 14.8 + - - +
70B LYS* 4.0 48.1 - - - +
274B LEU* 5.3 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 1.3 75.6 - - - +
248A GLY* 1.3 52.2 + - - +
250A CYS* 3.3 12.9 + - - +
251A ALA* 2.8 41.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 3.2 28.6 - - - +
247A GLU* 1.3 75.7 - - - +
249A VAL* 1.3 62.5 + - - +
251A ALA* 4.1 6.6 - - - +
252A ALA* 3.2 25.5 + - - +
69B GLU* 5.5 9.1 + - - -
274B LEU* 4.3 5.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A VAL* 5.0 7.2 - - + -
246A ARG* 3.3 36.0 - - + +
248A GLY* 1.3 77.6 - - - +
250A CYS* 1.3 56.5 + - - +
252A ALA* 3.6 1.9 - - - +
253A SER* 2.7 40.0 + - - +
288A MET* 5.5 1.3 - - + -
274B LEU* 4.5 15.5 - - + +
276B PHE* 3.7 53.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A GLU 5.3 1.8 - - - +
210A ASN* 3.4 26.9 - - - -
211A ALA* 4.1 12.8 - - + -
212A VAL* 5.5 1.3 - - - -
246A ARG 3.5 11.9 + - - +
247A GLU* 3.3 16.0 + - - +
249A VAL* 1.3 83.4 - - - +
251A ALA* 1.3 57.7 + - - +
253A SER* 4.3 1.6 - - - +
254A LEU* 2.8 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 2.8 29.1 + - + +
248A GLY* 4.1 7.4 - - - +
249A VAL 3.4 0.2 - - - -
250A CYS* 1.3 72.0 - - - +
252A ALA* 1.3 56.8 + - - +
254A LEU* 4.6 2.4 - - - +
255A PRO* 3.2 23.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A GLY 3.2 19.4 + - - +
249A VAL 3.7 2.7 - - - +
251A ALA* 1.3 77.3 - - - +
253A SER* 1.3 64.6 + - - +
255A PRO* 3.4 6.9 - - - +
256A THR* 3.1 18.7 - - - +
71B ILE* 5.2 7.6 - - + -
95B CYS* 3.8 19.9 - - + +
270B LEU* 3.5 26.8 - - + +
274B LEU* 4.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A ALA 3.6 15.3 - - - -
212A VAL* 4.0 12.2 - - - +
249A VAL 2.7 18.2 + - - -
250A CYS* 3.1 3.3 + - - -
252A ALA* 1.3 73.3 - - - +
254A LEU* 1.3 67.1 + - - +
256A THR* 2.8 5.2 + - - +
257A THR* 2.8 24.3 + - - -
267B GLN* 3.1 22.5 + - - +
270B LEU* 4.2 2.7 - - - +
276B PHE* 3.3 28.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 3.7 21.5 - - + -
208A SER 4.7 2.5 - - - +
209A GLU 5.4 2.2 - - - +
211A ALA* 3.6 23.3 - - + +
250A CYS* 2.8 20.6 + - + +
251A ALA* 4.6 2.2 - - - +
253A SER* 1.3 72.7 - - - +
255A PRO* 1.4 71.1 - - + +
257A THR* 3.3 0.9 + - - -
258A MET* 3.0 57.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 5.9 0.7 - - - +
251A ALA 3.2 22.2 - - - +
252A ALA* 3.4 10.1 - - - +
254A LEU* 1.4 97.4 - - + +
256A THR* 1.3 58.0 + - + +
258A MET* 3.4 12.6 + - + +
259A GLY* 3.0 22.2 + - - -
91B MET* 4.7 3.1 - - + +
94B ARG* 6.1 7.4 - - + +
95B CYS* 5.4 8.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ALA 3.1 22.4 - - - +
253A SER* 2.8 5.1 + - - +
255A PRO* 1.3 76.5 - - + +
257A THR* 1.3 64.5 + - - +
259A GLY* 3.2 2.6 + - - -
260A VAL* 3.0 23.6 + - - +
91B MET* 3.4 25.2 - - + +
95B CYS* 4.3 7.4 - - - -
263B GLY 3.6 15.4 + - - -
266B VAL* 4.1 9.9 - - + -
267B GLN* 3.5 18.0 + - - +
270B LEU* 3.6 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A VAL* 4.3 8.5 - - + -
211A ALA 2.8 28.5 + - - +
213A SER 4.0 24.9 - - - +
253A SER 2.8 14.7 + - - -
254A LEU* 3.8 3.1 - - - -
256A THR* 1.3 73.2 + - - +
258A MET* 1.3 62.0 + - - +
260A VAL* 3.1 2.1 + - - +
261A VAL* 2.9 33.8 + - + +
285A TYR* 3.7 25.1 - - + -
287A ALA* 3.9 3.1 - - - +
267B GLN* 2.9 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLY* 3.5 37.5 - - - +
84A VAL* 4.3 9.3 - - - +
87A VAL* 4.8 8.5 - - + -
207A VAL* 4.0 19.5 - - + -
254A LEU* 3.0 49.8 + - + +
255A PRO* 3.5 13.5 - - + +
257A THR* 1.3 75.1 - - - +
259A GLY* 1.3 56.2 + - - +
261A VAL* 3.4 0.7 + - - +
262A ALA* 2.8 35.0 + - - +
402A ANP 3.9 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.6 15.6 - - - +
91A MET* 5.2 0.9 - - - +
255A PRO 3.0 14.0 + - - -
256A THR* 3.2 5.6 + - - -
258A MET* 1.3 77.6 - - - +
260A VAL* 1.3 56.7 + - - +
262A ALA* 4.0 0.9 - - - +
263A GLY* 3.0 26.9 + - - -
91B MET* 4.9 7.9 - - - -
259B GLY 5.0 8.4 - - - +
263B GLY* 5.6 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A THR* 3.0 18.3 + - - +
257A THR 3.1 6.3 + - - +
259A GLY* 1.3 75.8 - - - +
261A VAL* 1.3 58.9 + - - +
263A GLY* 3.4 1.6 + - - -
264A ILE* 3.0 49.2 + - + +
285A TYR* 3.7 43.3 - - + +
292A PHE* 4.4 4.0 - - + -
260B VAL* 4.6 9.8 - - + +
263B GLY* 3.7 31.4 - - - +
264B ILE* 3.8 11.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 261 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.3 15.3 - - + -
205A SER* 4.8 2.0 - - - -
206A GLY 4.0 16.2 - - - +
207A VAL* 3.9 11.0 - - + -
214A GLY* 3.9 27.4 - - - -
215A HIS* 4.1 13.2 - - - +
216A ILE* 4.2 10.3 - - + +
257A THR* 2.9 20.0 + - + +
258A MET 3.9 2.2 - - - +
260A VAL* 1.3 78.1 - - - +
262A ALA* 1.3 52.0 + - - +
264A ILE* 3.3 6.4 + - - +
265A LEU* 2.8 34.0 + - + +
285A TYR* 4.1 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 262 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.1 8.4 - - + +
87A VAL* 3.5 32.5 - - + -
88A THR* 3.6 22.9 - - - +
91A MET* 4.0 3.4 - - - -
258A MET 2.8 22.8 + - - +
259A GLY 4.0 0.7 - - - +
261A VAL* 1.3 72.5 - - - +
263A GLY* 1.3 52.4 + - - +
265A LEU* 3.3 4.0 - - - +
266A VAL* 2.8 39.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 263 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A MET* 3.8 21.2 - - - -
259A GLY 3.0 18.1 + - - -
260A VAL 3.8 0.9 - - - -
262A ALA* 1.3 77.1 - - - +
264A ILE* 1.3 56.3 + - - +
266A VAL 3.4 0.5 + - - -
267A GLN* 3.0 24.6 + - - +
256B THR* 3.3 11.2 - - - +
259B GLY 5.5 0.7 - - - -
260B VAL* 3.6 18.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A ILE* 3.9 19.3 - - + -
260A VAL* 3.0 40.3 + - + +
261A VAL* 3.9 5.4 - - - +
263A GLY* 1.3 71.5 - - - +
265A LEU* 1.3 65.1 + - - +
267A GLN* 3.4 4.8 + - - +
268A ASN* 3.1 29.7 + - - +
283A LEU* 4.0 27.8 - - + -
285A TYR* 5.3 2.0 - - + -
292A PHE* 3.9 22.0 - - + -
260B VAL* 4.1 17.5 - - + -
285B TYR* 4.8 3.4 - - - +
290B ASP* 4.2 4.9 - - - +
292B PHE* 4.1 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 265 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 4.5 1.8 - - + -
88A THR* 3.5 33.9 - - + +
179A LEU* 4.2 14.6 - - + -
181A CYS* 4.1 9.9 - - - -
203A MET* 3.8 37.0 - - + -
205A SER* 3.9 22.7 - - - +
216A ILE* 4.0 26.8 - - + +
261A VAL 2.8 17.9 + - - +
262A ALA* 3.3 9.2 - - - +
264A ILE* 1.3 72.5 - - - +
266A VAL* 1.3 57.1 + - - +
268A ASN* 3.0 5.5 + - - +
269A VAL* 2.9 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A THR* 4.0 24.5 - - + -
91A MET* 3.8 31.2 - - + -
92A LEU* 3.6 25.8 - - + -
95A CYS* 4.5 4.3 - - - -
262A ALA 2.8 23.3 + - - +
263A GLY 3.4 4.2 + - - +
265A LEU* 1.3 70.4 - - - +
267A GLN* 1.3 65.9 + - - +
269A VAL* 3.1 7.5 + - - +
270A LEU* 2.9 28.4 + - + +
256B THR* 3.9 21.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 267 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A GLY 3.0 16.7 + - - +
264A ILE* 3.8 6.1 - - - +
266A VAL* 1.3 75.8 - - - +
268A ASN* 1.3 59.8 + - - +
270A LEU* 3.3 8.5 + - - +
271A LYS* 2.9 39.6 + - + +
276A PHE* 5.0 3.6 - - + -
253B SER* 2.8 33.8 + - - +
256B THR* 3.7 10.7 + - - +
257B THR* 2.9 34.2 + - - +
285B TYR* 2.9 29.0 + - - +
287B ALA* 3.7 21.2 - - - +
290B ASP* 5.6 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 268 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A MET* 3.6 15.6 - - + +
216A ILE* 3.8 23.1 - - + +
264A ILE* 3.1 20.2 + - - +
265A LEU 3.0 9.0 + - - +
267A GLN* 1.3 76.3 - - - +
269A VAL* 1.3 58.4 + - - +
271A LYS* 3.3 10.2 + - - +
272A PHE* 2.8 32.1 + - - +
279A VAL* 3.3 14.9 - - - +
280A SER* 2.9 29.6 + - - +
290B ASP* 2.8 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 6.6 0.2 - - + -
76A VAL* 4.5 8.1 - - + -
92A LEU* 4.3 20.4 - - + -
177A LEU* 3.8 17.9 - - + -
179A LEU* 3.8 35.7 - - + -
203A MET* 4.0 11.2 - - - +
265A LEU* 2.9 24.6 + - + +
266A VAL* 3.1 11.0 + - - +
268A ASN* 1.3 75.1 - - - +
270A LEU* 1.3 58.3 + - + +
272A PHE* 3.3 1.2 + - - +
273A LEU* 2.8 53.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 270 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ILE* 3.9 33.0 - - + -
92A LEU* 4.9 4.7 - - + -
95A CYS* 4.4 7.2 - - - -
266A VAL* 2.9 25.0 + - + +
267A GLN* 3.7 10.5 - - - +
269A VAL* 1.3 78.1 - - + +
271A LYS* 1.3 58.6 + - - +
273A LEU* 4.5 2.5 - - + +
274A LEU* 2.8 46.9 + - + +
276A PHE* 3.8 9.2 - - + -
252B ALA* 3.8 33.7 - - + +
253B SER* 4.0 8.3 - - - +
256B THR* 3.7 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A GLN* 2.9 27.9 + - + +
268A ASN* 3.7 18.6 - - - +
270A LEU* 1.3 78.3 - - - +
272A PHE* 1.3 58.0 + - - +
275A ASN* 2.8 28.2 + - - -
276A PHE* 3.4 44.6 + - + +
277A GLY* 4.3 2.5 - - - -
278A THR 2.6 29.3 + - - +
279A VAL* 3.7 13.0 - - + +
287B ALA 3.1 26.9 + - - +
288B MET* 3.3 14.2 + - - +
290B ASP* 3.3 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASP* 4.0 20.2 - - + -
177A LEU* 3.9 18.4 - - + -
201A THR* 3.8 28.9 - - + -
203A MET* 3.9 12.6 - - + -
218A LEU* 4.7 12.6 - - + -
220A ILE* 5.0 9.9 - - + -
268A ASN 2.8 17.7 + - - +
269A VAL* 3.7 2.2 - - - +
271A LYS* 1.3 77.7 - - - +
273A LEU* 1.3 81.4 + - + +
275A ASN* 3.7 7.6 + - - +
279A VAL* 3.5 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 5.1 0.9 - - - +
71A ILE* 4.9 6.1 - - + -
74A PHE* 3.4 57.5 - - + -
76A VAL* 4.1 5.2 - - + -
97A ILE* 4.0 15.5 - - + -
176A ASP* 3.9 28.0 - - + +
177A LEU* 4.6 5.6 - - + -
269A VAL* 2.8 43.6 + - + +
270A LEU* 4.1 2.5 - - - +
272A PHE* 1.3 93.6 - - + +
274A LEU* 1.3 64.0 + - + +
275A ASN* 4.7 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 3.2 59.5 + - + +
71A ILE* 4.0 19.5 - - + +
74A PHE* 4.1 8.3 - - + -
270A LEU* 2.8 41.4 + - + +
273A LEU* 1.3 75.1 - - + +
275A ASN* 1.3 73.1 + - - +
276A PHE* 3.5 23.1 - - + +
252B ALA* 4.8 9.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 275 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LYS* 5.4 0.9 - - - +
271A LYS 2.8 15.2 + - - -
272A PHE 4.3 5.6 - - - +
273A LEU 3.4 4.2 - - - +
274A LEU* 1.3 83.4 - - - +
276A PHE* 1.3 57.0 + - - +
----------------------------------------------------------
Back to top of page
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