Contacts of the strand formed by residues 304 - 328 (chain A) in PDB entry 5U2H
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 VAL 304 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLN* 4.1 26.9 - - - +
300A LYS* 3.3 5.8 - - - +
301A GLU 2.9 33.9 + - - +
302A ASN* 3.2 19.1 - - + +
303A ASN* 1.3 79.8 - - - +
305A GLU* 1.3 76.7 + - - +
306A LYS* 3.4 4.0 + - + +
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Residues in contact with GLU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLN* 3.8 12.8 - - - +
116A GLN 5.1 1.2 + - - -
167A TRP* 5.5 11.1 - - + -
298A TYR* 4.5 16.2 - - + +
299A TYR 4.4 3.6 - - - -
300A LYS* 4.6 10.5 - - - +
304A VAL* 1.3 84.2 - - - +
306A LYS* 1.3 66.2 + - - +
403A 7S1 5.0 15.3 - - + -
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Residues in contact with LYS 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY* 5.2 3.8 - - - +
114A GLN 3.6 10.8 - - - +
115A GLN* 4.6 4.3 - - + +
167A TRP* 5.1 1.1 - - - -
298A TYR* 3.4 7.6 - - - +
299A TYR* 2.8 62.8 + - + +
301A GLU* 5.0 3.8 - - + +
304A VAL* 4.3 5.6 - - + +
305A GLU* 1.3 79.4 - - - +
307A ARG* 1.3 61.9 + - - +
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Residues in contact with ARG 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A GLY 4.0 0.7 - - - -
114A GLN* 2.8 40.5 + - + +
167A TRP* 3.7 28.0 - - + -
296A ALA* 5.1 1.3 - - + -
297A LYS 3.7 5.6 - - - -
298A TYR* 3.3 31.0 - - + -
299A TYR* 4.7 2.5 - - - +
306A LYS* 1.3 73.3 - - - +
308A THR* 1.3 64.5 + - - +
309A LEU* 6.0 2.5 - - + -
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A THR 3.1 21.5 - - - +
112A GLU* 3.9 21.9 - - + +
295A TYR 3.9 0.5 - - - +
296A ALA* 3.0 8.9 - - - -
297A LYS* 2.9 42.9 + - + +
299A TYR* 3.1 25.3 + - - -
307A ARG* 1.3 71.7 + - - +
309A LEU* 1.3 58.6 + - - +
310A ILE* 4.1 22.9 - - + +
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Residues in contact with LEU 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ILE 4.3 0.3 - - - +
111A THR* 3.0 40.6 + - - +
114A GLN* 3.3 33.5 + - - +
167A TRP* 5.5 13.5 - - + +
171A GLU* 3.8 28.9 - - + +
294A ARG* 4.1 31.0 - - + +
295A TYR 4.0 0.4 - - - -
296A ALA* 3.6 25.1 - - + +
307A ARG* 4.1 4.6 + - + -
308A THR* 1.3 71.1 - - - +
310A ILE* 1.3 61.7 + - - +
311A LYS 4.2 0.4 + - - -
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Residues in contact with ILE 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 5.5 2.2 - - + -
108A PHE* 4.5 13.5 - - + -
109A ILE 3.5 10.1 - - - +
110A LYS* 4.4 15.7 - - + -
171A GLU* 5.7 0.2 - - - -
293A PHE 3.5 1.6 - - - +
294A ARG* 3.6 2.3 - - - -
295A TYR* 2.9 47.5 + - + +
297A LYS* 6.3 2.9 - - + -
308A THR* 4.1 19.5 - - + +
309A LEU* 1.3 80.2 - - - +
311A LYS* 1.3 64.2 - - - +
312A VAL* 3.5 21.0 + - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.3 5.2 - - - +
109A ILE* 2.9 50.1 + - + +
171A GLU* 3.5 28.5 + - - +
174A LYS 5.8 0.7 - - - +
288A TYR* 4.7 12.7 + - + -
292A ASN* 4.2 15.5 - - + +
293A PHE* 3.7 7.7 - - - +
294A ARG* 3.4 36.5 - - + +
309A LEU 4.2 0.4 - - - -
310A ILE* 1.3 70.1 - - - +
312A VAL* 1.3 59.9 + - - +
313A PHE* 3.3 39.1 - - + -
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Residues in contact with VAL 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.7 28.9 - - + -
105A MET* 3.5 33.2 - - + -
107A ASN 4.1 2.2 - - - -
108A PHE* 4.6 0.2 - - - +
292A ASN* 2.6 34.8 - - - -
293A PHE* 2.9 35.5 + - + +
295A TYR* 4.3 9.0 - - + -
310A ILE* 3.7 29.4 - - + +
311A LYS* 1.3 72.4 - - - +
313A PHE* 1.3 56.2 - - - +
314A GLY 4.2 0.4 + - - -
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Residues in contact with PHE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A MET* 3.9 2.1 - - - +
106A THR* 3.0 5.2 + - - -
107A ASN* 2.7 58.7 + - + +
108A PHE* 4.0 0.7 - - - -
109A ILE* 3.7 27.8 - - + -
174A LYS 5.4 1.8 - - - -
176A ALA* 5.0 12.8 - - + -
247A ILE 4.0 14.4 - - - +
248A GLN* 3.7 22.9 - - - +
249A GLY 4.5 0.4 - - - +
291A TYR 3.1 6.7 - - - +
292A ASN* 3.3 35.4 - - + -
311A LYS* 3.3 40.2 - - + -
312A VAL* 1.3 74.6 - - - +
314A GLY* 1.3 57.5 + - - +
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Residues in contact with GLY 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.4 17.5 - - - -
104A VAL 3.3 12.6 - - - -
106A THR* 3.7 10.3 - - - -
249A GLY* 3.4 1.6 - - - -
250A GLY 2.9 19.5 + - - -
291A TYR* 2.9 20.0 + - - +
313A PHE* 1.3 75.4 - - - +
315A ILE* 1.3 64.8 + - - -
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Residues in contact with ILE 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.9 1.6 - - - -
104A VAL* 2.8 34.2 + - + +
106A THR* 3.7 20.2 - - + +
231A LEU* 6.3 0.4 - - + -
235A PHE* 3.4 41.7 - - + -
242A PHE* 4.0 11.4 - - + -
245A VAL* 4.2 10.3 - - + -
246A ALA* 4.9 4.0 - - - -
249A GLY* 4.6 1.1 - - - -
250A GLY* 2.6 29.4 - - - +
252A MET* 3.9 12.3 - - + +
314A GLY* 1.3 74.8 - - - -
316A ARG* 1.3 60.7 + - - +
317A PHE* 3.6 29.4 - - + -
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Residues in contact with ARG 316 (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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102A PHE 3.5 8.3 - - - +
103A PHE* 4.0 8.5 - - + +
250A GLY 2.9 7.1 + - - -
251A ILE* 3.4 14.3 - - + +
252A MET 2.8 30.1 + - - +
291A TYR* 3.9 37.5 - - + +
315A ILE* 1.3 73.6 - - - +
317A PHE* 1.3 55.7 + - - +
318A ASP* 4.0 6.2 - - - +
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Residues in contact with PHE 317 (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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101A SER* 3.0 5.5 - - - -
102A PHE* 2.7 76.3 + + + -
104A VAL* 4.5 10.1 - - + -
231A LEU* 3.9 27.6 - - + -
234A ILE* 4.1 23.8 - - + -
235A PHE* 4.8 8.3 - + - -
252A MET* 2.6 29.2 - - + +
253A GLY* 5.1 0.2 - - - -
254A ILE* 4.5 17.9 - - + -
315A ILE* 3.6 37.9 - - + -
316A ARG* 1.3 69.6 - - - +
318A ASP* 1.3 64.8 + - - +
319A ILE* 4.0 0.8 + - + -
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Residues in contact with ASP 318 (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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100A ASN 4.9 0.2 - - - +
101A SER* 3.2 20.5 + - - -
251A ILE* 4.6 13.2 - - - +
252A MET 2.9 8.7 + - - -
253A GLY* 3.1 8.2 - - - -
254A ILE 2.9 23.7 + - - -
316A ARG* 4.0 13.8 - - - +
317A PHE* 1.3 76.9 - - - +
319A ILE* 1.3 63.5 + - - +
320A LEU* 3.5 20.3 + - + +
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Residues in contact with ILE 319 (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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61A VAL* 3.4 35.2 - - + -
63A THR* 3.2 35.2 - - + -
97A LEU* 5.0 1.3 - - + -
100A ASN* 3.0 33.7 + - - +
102A PHE* 4.1 17.0 - - + -
192A ILE* 4.3 12.6 - - + -
254A ILE* 3.6 21.5 - - + +
256A ILE* 4.9 11.2 - - + -
317A PHE* 4.0 1.3 + - + +
318A ASP* 1.3 70.8 - - - +
320A LEU* 1.3 67.9 + - - +
321A VAL* 4.2 10.2 + - + +
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Residues in contact with LEU 320 (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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253A GLY* 5.8 3.6 - - - -
254A ILE 2.9 12.5 + - - +
255A GLU* 4.3 14.4 - - + -
256A ILE* 2.9 31.5 + - - +
318A ASP* 3.9 23.6 - - + +
319A ILE* 1.3 80.8 - - - +
321A VAL* 1.3 62.6 + - - +
322A PHE* 4.1 1.3 - - + -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A LEU* 4.6 16.6 - - + +
59A SER* 3.0 41.2 + - - +
61A VAL* 4.0 20.6 - - + -
100A ASN* 5.8 1.1 - - - +
194A ASN* 5.2 4.7 - - + -
196A ILE* 6.2 0.4 - - + -
256A ILE* 3.8 11.9 - - + -
258A TRP* 3.7 26.0 - - + +
319A ILE* 4.2 8.0 + - + +
320A LEU* 1.3 79.4 - - - +
322A PHE* 1.3 61.5 + - - +
323A GLY 4.4 0.3 + - - -
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Residues in contact with PHE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ILE 2.9 16.8 + - - +
257A TYR* 3.1 5.4 - - + +
258A TRP* 2.9 23.4 + - - -
320A LEU* 4.1 1.7 - - + -
321A VAL* 1.3 74.6 - - - +
323A GLY* 1.3 58.3 + - - +
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Residues in contact with GLY 323 (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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55A GLU 4.1 5.6 - - - +
56A PRO* 4.1 10.2 - - - +
57A LEU* 4.3 22.3 + - - +
258A TRP* 3.4 23.5 - - - -
321A VAL 4.3 0.6 - - - -
322A PHE* 1.3 74.8 - - - +
324A THR* 1.3 66.5 + - - -
325A GLY 4.3 0.2 - - - -
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Residues in contact with THR 324 (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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54A LYS* 4.5 14.6 - - + -
55A GLU 3.7 4.3 - - - +
57A LEU* 5.3 0.8 - - - +
258A TRP* 2.9 13.3 + - - +
259A ASP* 5.2 2.7 - - - -
260A CYS* 2.7 38.2 + - - +
323A GLY* 1.3 76.0 + - - -
325A GLY* 1.3 62.5 + - - +
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Residues in contact with GLY 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS 2.6 17.2 - - - +
54A LYS* 2.7 21.1 - - - +
55A GLU* 2.9 22.1 + - - -
56A PRO 5.8 0.7 - - - -
260A CYS* 3.8 7.2 - - - -
323A GLY 4.3 0.2 - - - -
324A THR* 1.3 76.7 - - - +
326A GLY* 1.3 52.1 + - - -
327A LYS 4.2 0.2 - - - -
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Residues in contact with GLY 326 (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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52A GLN* 3.6 20.1 - - - +
53A LYS 2.3 24.2 - - - -
54A LYS* 4.5 0.4 - - - -
260A CYS 3.7 8.6 + - - -
261A ASN* 3.4 4.8 - - - -
262A LEU* 2.4 37.4 + - - +
263A ASP 3.6 2.3 + - - -
325A GLY* 1.3 64.7 - - - -
327A LYS* 1.3 53.6 + - - +
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Residues in contact with LYS 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A LYS* 2.9 35.2 + - + +
200A GLY 6.6 0.4 - - - -
201A HIS* 6.6 0.2 - - - -
262A LEU* 3.5 19.5 - - + +
325A GLY 4.2 0.4 - - - -
326A GLY* 1.3 71.0 - - - +
328A PHE* 1.3 68.8 + - - +
329A ASN* 3.3 1.2 + - - +
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Residues in contact with PHE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 3.6 31.4 - - + +
52A GLN* 3.7 5.9 - - - +
262A LEU 5.1 0.8 - - - -
263A ASP* 5.1 11.7 - - + +
326A GLY 3.9 2.2 + - - -
327A LYS* 1.3 73.6 - - - +
329A ASN* 1.3 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) + - + + + + + -
------------------------------------------------------------
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