Contacts of the helix formed by residues 251 - 281 (chain C) in PDB entry 1T9G
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 251 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 5.1 2.5 - - + +
106C MET* 3.6 31.6 - - + +
107C PRO* 4.2 18.4 - - + -
110C ILE* 3.7 5.3 - - + +
133C TYR* 4.9 7.0 - - + -
247C VAL 3.7 3.1 + - - +
248C ALA 3.2 12.7 + - - +
250C GLY* 1.3 78.1 - - - +
252C PHE* 1.3 68.6 + - + +
254C LYS 3.1 10.6 + - - -
255C THR* 3.1 19.8 + - - +
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Residues in contact with PHE 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C LEU* 4.2 5.6 - - + -
133C TYR* 3.1 40.4 - + - -
144C VAL* 5.6 10.3 - - + -
248C ALA* 3.9 14.1 - - + -
249C MET* 4.1 28.7 - - + +
250C GLY 3.3 0.6 - - - -
251C ALA* 1.3 78.7 - - + +
253C ASP* 1.3 62.2 + - - +
255C THR* 3.0 5.6 + - - -
256C ARG* 2.7 70.6 + - + +
376C GLU* 3.2 27.8 - - - -
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Residues in contact with ASP 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249C MET 4.9 4.0 + - - +
250C GLY* 4.0 14.9 + - - +
252C PHE* 1.3 76.3 - - - +
254C LYS* 1.3 63.7 + - + +
257C PRO* 3.4 9.4 - - - +
319C VAL* 4.1 13.3 - - + +
323C ARG 4.8 0.5 - - - +
324C ARG* 3.6 15.9 - - - +
325C ASN* 3.2 57.4 + - - +
326C THR* 3.4 22.1 + - - +
329C ALA* 5.3 2.0 - - - +
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Residues in contact with LYS 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65C HIS* 3.9 17.2 + - - +
77C THR* 3.5 32.3 + - - +
106C MET* 3.8 31.4 - - + -
109C ILE* 4.8 10.0 - - + +
110C ILE* 3.5 27.5 - - + +
250C GLY 5.3 2.0 - - - +
251C ALA 3.1 6.8 + - - +
253C ASP* 1.3 84.3 - - + +
255C THR* 1.3 62.3 + - - +
257C PRO* 4.1 2.0 - - - -
258C VAL* 4.0 3.1 - - - +
319C VAL* 4.2 20.2 - - + -
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Residues in contact with THR 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 5.2 0.9 - - - +
102C SER* 4.5 12.1 - - - +
103C LEU* 4.3 17.0 - - + +
106C MET* 3.9 28.0 - - + -
251C ALA 3.1 19.1 + - - +
252C PHE* 3.0 12.0 + - - -
254C LYS* 1.3 84.8 - - - +
256C ARG* 1.3 67.9 + - - +
257C PRO* 3.2 2.7 - - - -
258C VAL* 2.9 21.1 + - + +
259C VAL* 3.3 11.3 + - - +
376C GLU* 3.6 11.8 + - - -
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Residues in contact with ARG 256 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252C PHE* 2.7 57.1 + - + +
255C THR* 1.3 71.7 + - - +
257C PRO* 1.3 67.2 - - + +
259C VAL* 3.0 18.8 - - - +
260C ALA* 3.1 11.2 + - - +
326C THR* 6.3 0.8 - - - +
329C ALA* 3.8 23.9 - - + +
330C SER* 4.2 6.5 + - - -
333C LYS* 4.1 15.2 - - + +
376C GLU* 2.8 52.2 + - - +
377C GLY* 4.1 13.1 - - - +
381C ILE* 5.0 2.4 - - - +
382C GLN* 3.9 18.3 + - - +
385C ILE* 4.3 16.2 - - - +
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Residues in contact with PRO 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C THR* 4.1 11.2 - - + -
81C CYS* 3.4 22.3 - - - -
253C ASP 3.4 14.8 - - - +
254C LYS 4.1 1.3 - - - -
255C THR 3.2 6.1 - - - +
256C ARG* 1.3 95.4 - - + +
258C VAL* 1.3 55.6 + - - +
260C ALA* 3.6 6.1 + - + -
261C ALA* 3.0 20.8 + - - +
312C TYR* 3.6 14.4 - - + +
315C ALA* 3.8 20.6 - - + -
316C ALA 4.3 0.2 - - - +
325C ASN* 3.6 24.9 - - - +
329C ALA* 4.1 4.3 - - + -
332C ALA* 5.2 2.5 - - + -
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Residues in contact with VAL 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C HIS* 4.7 3.1 - - - +
77C THR* 4.6 2.5 - - + +
80C ALA* 3.9 23.1 - - + +
81C CYS* 3.7 18.6 - - - -
84C SER* 3.1 29.4 - - - +
95C GLN* 4.1 1.6 + - - -
99C GLU* 3.8 25.4 - - + +
102C SER* 6.5 0.4 - - - -
254C LYS 4.0 15.7 - - - +
255C THR* 2.9 14.2 + - - +
257C PRO* 1.3 74.4 - - - +
259C VAL* 1.3 60.5 + - - +
260C ALA 3.2 0.2 - - - -
261C ALA* 3.2 4.3 + - - +
262C GLY* 2.9 21.5 + - - -
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Residues in contact with VAL 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C GLN* 5.2 3.4 - - - +
99C GLU* 5.8 2.5 - - + -
255C THR 3.3 2.8 + - - +
256C ARG* 3.0 20.0 - - - +
258C VAL* 1.3 75.6 - - - +
260C ALA* 1.3 65.1 + - - +
262C GLY* 2.9 12.5 + - - +
263C ALA 3.1 11.3 + - - -
333C LYS* 4.0 20.9 - - + -
372C TYR* 3.4 28.3 - - + -
375C TYR* 4.1 15.0 - - + +
376C GLU* 3.4 38.6 - - + +
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Residues in contact with ALA 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C ARG 3.1 12.5 + - - +
257C PRO 3.7 9.0 - - - +
259C VAL* 1.3 80.5 - - - +
261C ALA* 1.4 56.3 + - - +
263C ALA* 3.2 7.7 + - - +
264C VAL* 3.0 25.5 + - - +
312C TYR* 3.9 13.0 - - + -
332C ALA* 3.8 22.0 - - + -
333C LYS* 3.9 7.4 - - - +
336C ALA* 3.6 25.7 - - + +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C CYS* 3.7 38.1 - - + +
84C SER* 4.1 2.7 - - - -
85C GLU* 3.6 12.4 - - - +
257C PRO 3.0 15.0 + - - +
258C VAL 3.4 9.4 - - - +
259C VAL 3.1 0.2 - - - -
260C ALA* 1.4 74.7 - - - +
262C GLY* 1.3 58.7 + - - +
264C VAL* 3.3 3.1 + - - +
265C GLY 3.0 23.7 + - - -
312C TYR* 3.7 22.0 - - + -
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Residues in contact with GLY 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84C SER* 4.6 1.3 - - - -
88C ALA* 3.5 20.8 - - - +
92C THR* 4.3 1.4 - - - +
95C GLN* 4.2 9.9 - - - -
258C VAL 2.9 10.4 + - - -
259C VAL 2.9 10.0 + - - -
261C ALA* 1.3 72.5 - - - +
263C ALA* 1.3 65.6 + - - -
265C GLY* 2.9 13.7 + - - -
266C LEU* 3.0 10.9 + - - -
372C TYR* 3.8 14.6 - - - -
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Residues in contact with ALA 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C VAL 3.1 7.1 + - - +
260C ALA* 3.4 10.3 - - - +
262C GLY* 1.3 71.0 - - - +
264C VAL* 1.3 58.2 + - - +
266C LEU* 3.1 3.4 + - - +
267C ALA* 2.8 29.0 + - - +
336C ALA* 3.8 29.4 - - + +
337C GLY 4.0 1.8 - - - +
340C ALA* 3.8 11.7 - - + +
372C TYR* 3.5 35.8 - - + -
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLU* 3.7 25.6 - - - +
260C ALA 3.0 17.1 + - - +
261C ALA 3.6 7.9 - - - +
262C GLY 3.2 0.2 - - - -
263C ALA* 1.3 75.1 - - - +
265C GLY* 1.3 53.1 + - - +
267C ALA* 3.1 9.1 + - - +
268C GLN* 2.8 33.3 + - - +
305C VAL* 4.2 9.1 - - + +
308C ALA* 3.5 39.5 - - + +
309C ARG* 4.1 18.4 - - + +
312C TYR* 3.7 14.6 - - + -
336C ALA* 4.1 5.8 - - + -
339C ILE* 5.3 0.9 - - + -
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Residues in contact with GLY 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85C GLU* 3.6 31.7 - - - +
88C ALA* 4.2 0.9 - - - -
89C TYR* 3.3 27.7 - - - +
261C ALA 3.0 8.6 + - - -
262C GLY 2.9 8.5 + - - -
264C VAL* 1.3 74.0 - - - +
266C LEU* 1.3 59.2 + - - -
268C GLN* 3.5 2.7 + - - -
269C ARG 3.3 12.6 + - - -
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Residues in contact with LEU 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88C ALA 4.0 7.0 + - - +
92C THR* 4.0 20.2 - - + +
262C GLY 3.0 8.6 + - - +
263C ALA 3.1 5.8 + - - +
265C GLY* 1.3 72.2 - - - +
267C ALA* 1.3 68.7 + - - +
269C ARG* 3.3 6.4 + - - +
270C ALA* 3.0 19.0 + - + +
340C ALA* 4.1 14.8 - - + +
344C ALA* 4.3 4.5 - - + -
365C LEU* 3.7 37.3 - - + +
368C ASP* 3.7 17.5 - - + -
369C ALA* 3.6 41.1 - - + +
372C TYR* 4.2 9.9 - - + -
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Residues in contact with ALA 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263C ALA 2.8 12.9 + - - +
264C VAL* 3.1 11.9 - - - +
266C LEU* 1.3 84.5 - - - +
268C GLN* 1.3 62.0 + - - +
270C ALA* 3.2 5.7 + - - +
271C LEU* 3.1 17.3 + - - +
305C VAL* 3.9 9.2 - - + -
339C ILE* 3.8 28.7 - - + -
340C ALA* 4.3 7.2 - - - +
343C LEU* 3.5 18.8 - - + +
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B TYR* 3.7 6.9 + - - -
32C ARG* 5.3 2.0 - - - +
85C GLU* 4.6 5.8 - - + +
89C TYR* 3.8 17.7 - - + -
264C VAL 2.8 18.3 + - - +
265C GLY* 3.9 5.8 - - - +
266C LEU 3.3 0.2 - - - -
267C ALA* 1.3 69.3 - - - +
269C ARG* 1.3 56.9 + - - +
271C LEU* 3.2 15.2 + - - +
272C ASP* 2.6 70.4 + - - +
305C VAL* 3.6 14.5 - - + +
306C GLU* 5.7 0.9 - - - +
309C ARG* 3.0 32.0 + - - +
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Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C ILE* 4.2 27.2 + - - +
39C ALA* 5.9 0.4 - - - +
89C TYR* 2.9 58.0 + - + +
90C GLY* 3.1 21.4 + - - -
265C GLY 3.3 10.6 + - - +
266C LEU* 3.3 11.6 + - - +
268C GLN* 1.3 76.7 - - - +
270C ALA* 1.3 53.1 + - - +
272C ASP* 2.9 3.8 + - - +
273C GLU* 2.8 56.1 + - + +
361C PRO* 4.0 23.4 - - - +
365C LEU* 3.9 26.4 - - + +
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C LEU* 3.0 10.8 + - + +
267C ALA* 3.3 10.3 - - - +
269C ARG* 1.3 78.1 - - - +
271C LEU* 1.3 57.7 + - - +
273C GLU* 3.4 2.6 + - - +
274C ALA* 2.9 32.1 + - - +
301C MET* 4.6 0.7 - - - -
343C LEU* 3.8 29.8 - - + +
344C ALA* 4.3 4.3 - - - +
347C ALA* 3.8 13.4 - - + +
365C LEU* 3.6 18.7 - - + +
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Residues in contact with LEU 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327B TYR* 6.0 0.7 - - - +
390B HIS* 3.5 31.0 - - + +
394B TYR* 4.2 4.9 - - - +
267C ALA 3.1 10.3 + - - +
268C GLN* 3.4 17.7 - - - +
270C ALA* 1.3 78.3 - - - +
272C ASP* 1.3 56.4 + - - +
274C ALA 3.3 0.7 + - - -
275C THR* 2.6 47.0 + - - +
298C LEU* 3.9 10.8 - - + +
301C MET* 3.6 40.5 - - + +
302C ALA* 3.8 20.0 - - - -
305C VAL* 4.3 11.0 - - + -
343C LEU* 4.4 4.5 - - + -
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Residues in contact with ASP 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B TYR* 2.4 42.0 + - + -
32C ARG* 4.3 5.4 + - - -
89C TYR* 3.0 35.5 + - - +
268C GLN* 2.6 37.2 + - - +
269C ARG 3.4 7.0 - - - +
271C LEU* 1.3 71.0 - - - +
273C GLU* 1.3 68.6 + - + +
275C THR* 3.3 1.4 + - - -
276C LYS* 2.9 33.0 + - + +
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Residues in contact with GLU 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 5.3 2.4 + - - -
269C ARG* 2.8 51.4 + - + +
270C ALA 3.8 4.3 - - - +
272C ASP* 1.3 74.4 - - - +
274C ALA* 1.3 57.3 + - - +
276C LYS* 3.7 10.3 + - - +
277C TYR* 3.1 28.2 + - - +
351C LEU* 4.3 4.1 - - + +
361C PRO* 3.7 30.5 - - + +
362C VAL* 4.0 19.1 - - + -
365C LEU* 5.0 1.6 - - + -
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Residues in contact with ALA 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ALA 2.9 19.8 + - - +
271C LEU 3.8 2.9 - - - +
273C GLU* 1.3 74.2 - - - +
275C THR* 1.3 61.1 + - - +
277C TYR* 3.9 0.2 - - - +
278C ALA* 3.0 29.3 + - - +
298C LEU* 4.3 6.2 - - + +
301C MET* 4.4 4.0 - - + -
347C ALA* 4.0 16.4 - - - -
350C ILE* 3.6 32.3 - - + +
351C LEU* 4.0 11.0 - - + -
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Residues in contact with THR 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390B HIS* 3.1 34.3 + - + +
391B ILE* 4.8 9.9 - - + -
394B TYR* 3.8 32.5 - - + -
271C LEU* 2.6 21.9 + - - +
272C ASP 3.7 2.7 - - - -
274C ALA* 1.3 73.3 - - - +
276C LYS* 1.4 66.8 + - - +
277C TYR 3.1 0.3 + - - -
278C ALA* 3.2 4.2 + - - +
279C LEU* 3.0 28.6 + - + +
289C VAL* 5.8 0.4 - - + -
298C LEU* 3.6 18.0 - - + +
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Residues in contact with LYS 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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394B TYR* 4.6 13.8 - - + -
272C ASP* 2.9 28.2 + - + +
273C GLU* 3.9 11.4 - - - +
275C THR* 1.4 71.1 - - - +
277C TYR* 1.3 62.0 + - - +
279C LEU* 3.2 18.3 + - - +
280C GLU* 3.4 18.9 + - - +
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Residues in contact with TYR 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C GLU 3.1 19.7 + - - +
274C ALA 3.9 1.1 - - - +
275C THR 3.1 0.4 - - - -
276C LYS* 1.3 71.8 - - - +
278C ALA* 1.3 60.7 + - - +
279C LEU 3.0 4.0 - - - -
280C GLU* 3.0 24.2 + - - +
281C ARG* 2.9 68.3 + - + +
288C LEU* 4.5 3.8 - - + -
350C ILE* 3.9 9.2 - - + -
351C LEU* 3.4 62.6 + - + -
354C ASN* 3.2 27.8 + - - -
360C TYR* 4.7 13.9 - + - -
399D FAD 5.2 0.7 - - - -
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274C ALA 3.0 19.0 + - - +
275C THR 3.9 1.6 - - - +
277C TYR* 1.3 77.0 - - - +
279C LEU* 1.3 60.4 + - - +
280C GLU 3.3 0.6 + - - -
281C ARG 3.9 1.4 - - - +
287C LEU* 4.0 1.7 - - - +
288C LEU* 3.3 46.2 + - + -
289C VAL* 3.4 27.6 + - + +
294C ILE* 4.2 1.1 - - + -
298C LEU* 4.2 11.2 - - + -
350C ILE* 4.1 10.8 - - + -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391B ILE* 3.9 22.0 - - + +
394B TYR* 3.8 40.8 - - + +
395B LYS* 4.7 7.9 - - + +
275C THR* 3.0 21.9 + - + +
276C LYS* 3.5 11.9 - - - +
277C TYR 3.0 0.4 - - - -
278C ALA* 1.3 80.2 - - - +
280C GLU* 1.3 57.8 + - + +
287C LEU* 3.2 26.9 - - + +
289C VAL* 3.9 24.9 - - + -
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Residues in contact with GLU 280 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LYS* 3.4 13.5 + - - +
277C TYR* 3.0 28.8 + - + +
279C LEU* 1.3 80.4 - - - +
281C ARG* 1.3 66.3 + - + +
282C LYS* 3.7 6.8 + - - +
287C LEU* 3.4 8.9 - - - +
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Residues in contact with ARG 281 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277C TYR* 2.9 54.1 + - + +
278C ALA 3.9 0.2 - - - +
280C GLU* 1.3 78.9 - - + +
282C LYS* 1.3 74.0 + - - +
283C THR* 5.1 0.7 - - - -
287C LEU* 3.3 3.7 - - - +
288C LEU* 2.8 39.8 + - + +
351C LEU 5.5 0.4 + - - -
354C ASN* 4.8 5.9 - - - +
137D GLU 4.6 0.4 + - - -
138D PRO 3.5 10.1 + - - -
139D GLY* 2.9 45.7 + - - +
140D ALA* 3.6 2.0 - - - +
399D FAD 2.2 58.8 + - - +
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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) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il