Contacts of the helix formed by residues 137 - 159 (chain E) in PDB entry 5JKL
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 TYR 137 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E GLU* 4.2 8.5 - - - -
65E HIS* 2.7 52.7 + + + -
68E LYS* 3.4 19.8 - - + +
69E LEU* 3.4 21.4 + - + +
114E LEU* 3.9 35.4 - - + -
132E PHE* 3.4 36.6 - + - -
133E ILE* 2.9 16.4 + - + +
135E THR 3.6 0.6 - - - -
136E HIS* 1.3 98.2 - - + +
138E LEU* 1.3 65.4 + - - +
139E ASN 3.4 2.0 - - - +
140E GLU* 3.2 6.8 + - + +
141E GLN* 3.0 29.4 + - - +
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Residues in contact with LEU 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D PRO* 3.7 32.8 - - + -
128D HIS* 3.9 26.5 - - + +
131D ASP* 6.0 0.9 - - + +
111E ASN* 4.3 8.2 - - - +
114E LEU* 4.0 22.4 - - + +
115E LEU* 4.0 16.8 - - + -
118E HIS* 4.5 1.6 - - + -
133E ILE* 3.0 36.8 + - + +
134E GLU* 3.8 22.1 + - + +
137E TYR* 1.3 76.2 - - - +
139E ASN* 1.3 62.3 + - - +
141E GLN* 3.3 4.9 + - - +
142E VAL* 3.1 25.8 + - - +
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Residues in contact with ASN 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLN* 4.5 7.5 + - - +
128D HIS* 2.9 32.1 + - + +
131D ASP* 5.0 7.6 - - - +
136D HIS* 6.0 1.6 + - - -
134E GLU 4.1 8.5 + - - +
135E THR 5.8 2.0 + - - +
137E TYR 3.4 0.4 - - - +
138E LEU* 1.3 76.8 - - - +
140E GLU* 1.3 62.2 + - - +
142E VAL* 4.0 7.5 - - - +
143E LYS* 2.9 56.7 + - - +
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Residues in contact with GLU 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E GLU* 4.0 13.9 - - - +
65E HIS* 5.0 15.5 - - + +
135E THR 5.5 1.8 - - - +
136E HIS* 3.4 25.3 - - - +
137E TYR* 3.2 9.3 + - + +
139E ASN* 1.3 79.2 + - - +
141E GLN* 1.3 62.4 + - - +
143E LYS* 3.0 32.7 + - - +
144E ALA* 3.0 28.9 + - - +
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Residues in contact with GLN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E HIS* 4.6 7.3 + - - -
107E GLU* 2.7 52.9 + - - +
110E VAL* 3.9 9.7 - - - +
111E ASN* 3.4 26.7 - - + +
114E LEU* 3.5 32.5 - - + +
137E TYR* 3.0 13.5 + - - +
138E LEU 3.7 3.8 - - - +
140E GLU* 1.3 77.2 - - - +
142E VAL* 1.3 66.6 + - - +
144E ALA* 3.1 3.7 + - - +
145E ILE* 2.9 30.4 + - + +
201E FE 4.0 14.2 - - - -
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Residues in contact with VAL 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D GLN* 3.8 38.3 - - + +
76D ARG* 3.9 18.8 - - - +
128D HIS* 3.7 37.2 - - + +
111E ASN* 5.0 12.1 - - - +
138E LEU 3.1 15.2 + - - +
139E ASN* 3.3 7.2 + - - +
141E GLN* 1.3 76.1 - - - +
143E LYS* 1.3 62.6 + - - +
145E ILE* 3.4 7.5 + - + +
146E LYS* 3.0 22.7 + - - +
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Residues in contact with LYS 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D GLN* 4.0 20.9 - - - +
139E ASN* 2.9 39.4 + - - +
140E GLU* 3.0 37.5 + - - +
142E VAL* 1.3 77.0 - - - +
144E ALA* 1.3 62.3 + - - +
146E LYS* 3.4 6.2 + - - +
147E GLU* 3.0 24.7 + - - +
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Residues in contact with ALA 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 6.0 1.8 - - - +
107E GLU* 4.2 27.4 - - + +
140E GLU 3.0 18.1 + - - +
141E GLN* 3.1 5.8 + - - +
143E LYS* 1.3 77.2 - - - +
145E ILE* 1.3 56.9 + - - +
147E GLU* 3.3 7.0 + - - +
148E LEU* 2.9 38.6 + - + +
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Residues in contact with ILE 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.6 40.0 - - + +
10D GLN* 3.8 22.7 - - + +
75D GLN 5.7 0.9 - - - +
104E LEU* 3.8 18.8 - - + +
107E GLU* 3.8 30.5 - - + +
108E LYS* 3.9 13.0 - - + -
111E ASN* 3.9 16.4 - - + +
141E GLN 2.9 22.0 + - - +
142E VAL* 3.8 7.0 - - + +
144E ALA* 1.3 76.3 - - - +
146E LYS* 1.3 58.9 + - - +
148E LEU* 3.4 1.2 + - - -
149E GLY 2.9 24.1 + - - -
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Residues in contact with LYS 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ASP* 2.8 38.3 + - - -
44C ASP* 3.9 17.0 - - + +
47C ALA* 5.8 0.2 - - - +
8D VAL* 4.1 7.2 - - + -
74D ASN* 3.6 31.0 - - - +
75D GLN* 4.2 22.6 + - + +
142E VAL 3.0 17.7 + - - +
143E LYS* 3.8 7.0 - - - +
145E ILE* 1.3 79.0 - - - +
147E GLU* 1.3 56.2 + - - +
149E GLY* 3.4 1.2 + - - -
150E ASP* 2.9 67.2 + - - +
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Residues in contact with GLU 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TYR* 2.5 33.3 + - - +
58E GLN* 4.3 5.9 + - - -
143E LYS 3.0 17.4 + - - +
144E ALA* 3.6 7.6 - - - +
146E LYS* 1.3 77.9 - - - +
148E LEU* 1.3 57.8 + - + +
150E ASP* 3.2 10.4 + - - +
151E HIS* 2.9 50.4 + - + +
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Residues in contact with LEU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E TYR* 4.0 6.7 - - + +
54E TYR* 3.6 23.1 - - + +
100E MET* 3.6 31.0 - - - +
103E ALA* 3.8 25.4 - - + +
104E LEU* 3.8 18.8 - - + +
107E GLU* 3.5 33.7 - - + -
144E ALA* 2.9 21.6 + - + +
145E ILE* 3.9 3.1 - - - +
147E GLU* 1.3 77.0 - - - +
149E GLY* 1.3 56.9 + - - +
151E HIS* 3.2 5.0 + - + +
152E VAL* 2.8 35.1 + - - +
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Residues in contact with GLY 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP* 4.1 2.9 - - - -
7D GLN* 3.0 35.7 + - - -
8D VAL* 4.2 7.4 - - - -
104E LEU* 4.3 5.0 - - - +
145E ILE 2.9 16.9 + - - -
146E LYS 3.8 1.8 - - - -
148E LEU* 1.3 76.6 - - - +
150E ASP* 1.3 54.9 + - - +
152E VAL* 3.3 2.1 + - - +
153E THR* 2.9 26.7 + - - -
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Residues in contact with ASP 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP* 3.3 16.3 - - - -
47C ALA* 3.8 21.5 - - + +
146E LYS* 2.9 52.0 + - - +
147E GLU* 3.2 11.4 + - - +
149E GLY* 1.3 73.0 - - - +
151E HIS* 1.3 68.1 + - + +
153E THR* 3.3 1.7 + - - -
154E ASN* 3.0 32.9 + - - +
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Residues in contact with HIS 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E TYR* 3.7 21.3 + + - -
100E MET* 3.9 31.9 - - + -
147E GLU* 2.9 41.3 + - + +
148E LEU* 3.6 6.5 - - - +
150E ASP* 1.3 78.6 - - + +
152E VAL* 1.3 64.2 + - - +
154E ASN* 3.3 3.3 + - - +
155E LEU* 3.0 30.9 + - - +
170E PHE* 3.5 21.9 - + + -
174E THR* 3.8 22.5 - - + +
175E LEU* 4.0 11.8 - - + +
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Residues in contact with VAL 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLN* 3.6 9.0 - - - +
97E LEU* 3.9 12.3 - - + +
100E MET* 3.8 34.1 - - + +
101E GLU* 3.9 11.4 - - + +
104E LEU* 4.5 8.1 - - + -
148E LEU 2.8 21.4 + - - +
149E GLY 3.3 4.0 + - - +
151E HIS* 1.3 77.0 - - - +
153E THR* 1.3 61.0 + - - +
155E LEU* 3.4 2.8 + - - +
156E ARG* 2.9 68.6 + - - +
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Residues in contact with THR 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C ASP 2.6 22.6 + - - +
45C ASP* 3.6 32.4 - - - +
46C VAL 3.8 15.5 - - - +
47C ALA* 4.2 1.6 - - + -
7D GLN* 3.2 14.6 + - - -
149E GLY 2.9 8.3 + - - -
150E ASP 3.6 3.6 - - - -
152E VAL* 1.3 78.6 - - - +
154E ASN* 1.3 59.0 + - - +
156E ARG* 3.7 9.0 + - - +
157E LYS* 2.9 40.4 + - + +
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Residues in contact with ASN 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46C VAL 4.6 2.9 - - - +
47C ALA* 2.9 33.9 + - - +
48C LEU* 4.0 10.6 - - - +
168C TYR* 3.5 27.0 - - + +
150E ASP* 3.0 30.2 + - - +
151E HIS* 3.9 4.3 + - - +
152E VAL 3.3 0.2 - - - -
153E THR* 1.3 77.4 - - - +
155E LEU* 1.3 58.7 + - - +
157E LYS* 3.2 6.5 + - - +
158E MET* 2.9 37.5 + - - +
170E PHE* 3.9 19.2 - - + -
174E THR* 5.8 0.2 - - - -
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Residues in contact with LEU 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E PHE* 4.2 11.0 - - + -
97E LEU* 4.0 31.9 - - + +
100E MET* 4.0 21.8 - - + -
151E HIS 3.0 19.8 + - - +
152E VAL 3.8 3.4 - - - +
154E ASN* 1.3 78.8 - - - +
156E ARG* 1.3 60.8 + - - +
158E MET* 3.4 4.8 + - - +
159E GLY 3.3 3.8 + - - -
160E ALA* 3.0 43.3 + - + +
166E ALA 4.5 2.2 - - - +
167E GLU* 4.3 16.8 - - + -
170E PHE* 3.6 39.9 - - + -
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Residues in contact with ARG 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLN* 3.6 17.0 + - - +
97E LEU* 3.9 15.9 - - + -
101E GLU* 2.9 29.9 + - - +
104E LEU* 6.3 0.2 - - - +
152E VAL* 2.9 44.6 + - - +
153E THR* 3.7 8.2 + - - +
155E LEU* 1.3 77.0 - - - +
157E LYS* 1.3 64.1 + - + +
159E GLY* 3.1 14.9 + - - -
160E ALA 4.2 8.3 - - - +
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Residues in contact with LYS 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C TYR* 5.7 1.6 + - - -
45C ASP 3.0 25.8 + - - -
46C VAL* 4.1 18.3 + - - +
48C LEU* 6.5 0.9 - - + -
94C GLU 5.9 1.2 + - - -
164C GLY* 3.5 35.5 + - - +
165C LEU 3.6 0.9 + - - -
153E THR* 2.9 33.1 + - + +
154E ASN* 3.9 6.7 - - - +
156E ARG* 1.3 77.8 - - + +
158E MET* 1.3 62.0 + - + +
159E GLY 3.4 0.9 + - - -
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Residues in contact with MET 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164C GLY 4.8 0.2 - - - +
165C LEU* 3.9 40.8 - - + +
168C TYR* 3.5 62.8 - - + -
154E ASN 2.9 28.5 + - - +
155E LEU* 3.8 5.4 - - - +
156E ARG 3.3 0.2 - - - -
157E LYS* 1.3 76.1 - - + +
159E GLY* 1.3 56.6 + - - +
160E ALA 3.8 0.2 - - - -
163E SER* 4.4 4.0 + - - -
166E ALA* 3.3 44.8 - - + +
169E LEU* 4.1 4.3 - - + -
170E PHE* 3.8 19.3 - - - +
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Residues in contact with GLY 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156E ARG 3.1 11.6 + - - -
157E LYS 3.3 1.6 + - - -
158E MET* 1.3 77.0 - - - +
160E ALA* 1.3 68.4 + - - +
162E ARG* 3.4 6.8 + - - +
163E SER* 3.0 27.0 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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