Contacts of the helix formed by residues 113 - 134 (chain A) in PDB entry 2OG9
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 GLY 113 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A SER* 1.3 78.8 - - - +
114A LEU* 1.3 65.5 + - - -
115A SER 3.3 0.9 - - - -
116A THR* 3.2 2.9 + - - -
117A GLN* 2.8 35.6 + - - +
268A THR* 3.8 10.9 + - - -
109B ALA 3.1 22.2 - - - -
110B GLY* 5.2 0.2 - - - -
112B SER 3.8 7.6 - - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A SER* 4.7 0.4 - - - +
72A GLY* 3.8 25.1 - - - +
75A GLY* 4.2 13.7 - - - -
76A GLN* 3.8 15.4 - - + +
79A HIS* 5.4 0.2 - - - -
112A SER 4.1 0.4 + - - -
113A GLY* 1.3 70.8 - - - -
115A SER* 1.3 62.5 + - - +
117A GLN* 3.4 15.0 + - - +
118A ALA* 3.0 23.6 + - - +
75B GLY 4.9 0.4 - - - +
79B HIS* 3.6 36.8 - - + +
109B ALA* 3.5 28.8 + - + -
112B SER 5.0 0.2 + - - -
114B LEU* 4.0 23.7 - - + +
115B SER* 3.9 17.4 - - - +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 3.4 32.6 - - - -
106A GLY 5.2 0.9 - - - -
109A ALA* 3.6 34.8 + - - +
110A GLY 3.9 10.2 + - - -
112A SER 4.0 4.7 + - - -
113A GLY 3.3 0.2 + - - -
114A LEU* 1.3 78.3 - - - +
116A THR* 1.3 61.3 + - - +
118A ALA* 3.3 5.0 + - - +
119A ILE* 3.0 32.9 + - - +
114B LEU* 3.9 9.1 + - - +
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Residues in contact with THR 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A TRP* 3.8 27.8 - - + -
103A CYS* 4.4 2.2 - - - -
110A GLY 4.2 6.1 - - - +
111A ARG* 3.4 32.5 + - - +
112A SER* 3.0 26.7 - - - +
113A GLY 3.2 4.2 + - - -
115A SER* 1.3 80.3 + - - +
117A GLN* 1.3 60.8 + - - +
118A ALA 3.2 0.2 - - - -
119A ILE* 3.3 15.9 + - + +
120A GLY 2.8 21.8 + - - -
268A THR 4.4 3.8 + - - -
292A VAL 4.8 1.6 + - - -
293A GLY* 3.3 15.0 - - - -
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Residues in contact with GLN 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.2 24.7 - - - -
67A TYR 4.3 3.2 + - - +
68A SER* 4.7 0.5 + - - -
76A GLN* 2.7 37.7 + - - +
113A GLY 2.8 23.5 + - - +
114A LEU* 3.7 16.9 - - - +
116A THR* 1.3 75.1 - - - +
118A ALA* 1.3 66.6 + - - +
120A GLY* 3.1 8.9 + - - +
121A ALA 3.3 1.0 + - - -
268A THR* 3.7 8.5 - - - +
290A PRO 3.9 13.9 - - - +
291A ARG* 3.1 37.7 + - - +
293A GLY* 4.5 1.1 - - - +
108B SER* 2.8 29.5 + - - +
109B ALA* 4.1 2.2 - - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A LEU* 4.0 13.4 - - - +
76A GLN* 3.6 25.3 - - - +
79A HIS* 4.3 8.1 - - + -
80A ALA* 3.9 17.3 - - + +
83A ILE* 5.0 1.1 - - + -
114A LEU 3.0 13.0 + - - +
115A SER 3.4 10.5 - - - +
116A THR 3.2 0.2 - - - -
117A GLN* 1.3 77.4 - - - +
119A ILE* 1.3 63.3 + - - +
121A ALA* 3.1 18.9 + - - +
122A PHE* 3.5 12.8 - - - -
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Residues in contact with ILE 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A HIS* 5.6 1.1 - - - +
83A ILE* 3.8 18.2 - - + -
99A TRP* 3.4 43.1 - - + +
102A LEU* 3.6 12.8 - - + +
103A CYS* 3.4 42.2 - - + +
115A SER* 3.0 19.5 + - - +
116A THR* 3.4 20.2 - - + +
118A ALA* 1.3 76.1 - - - +
120A GLY* 1.3 57.6 + - - +
122A PHE* 3.0 15.1 + - - +
123A ASP* 2.9 23.0 + - + -
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Residues in contact with GLY 120 (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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65A PHE 4.7 2.2 - - - -
66A SER* 5.0 0.9 - - - -
116A THR 2.8 11.1 + - - -
117A GLN 3.1 5.8 + - - -
118A ALA 3.1 0.6 - - - -
119A ILE* 1.3 77.6 - - - +
121A ALA* 1.3 56.0 + - - +
123A ASP* 3.5 1.9 - - - +
124A VAL* 2.9 36.8 + - - +
290A PRO* 5.3 2.7 - - - -
293A GLY* 3.1 31.0 - - - -
294A GLY* 3.8 2.2 - - - -
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Residues in contact with ALA 121 (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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50A LEU* 3.9 27.6 - - + +
52A ALA* 3.6 21.9 - - + +
64A GLY* 3.4 12.6 - - - -
65A PHE* 3.9 14.1 - - - +
66A SER* 4.0 12.2 - - - +
117A GLN 3.3 4.0 + - - -
118A ALA 3.1 11.9 + - - +
120A GLY* 1.3 75.5 - - - +
122A PHE* 1.3 63.4 + - + +
125A ALA 3.3 14.6 + - - -
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Residues in contact with PHE 122 (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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18A VAL* 3.6 26.7 - - + -
20A ILE* 3.6 22.9 - - + -
52A ALA* 3.8 13.0 - - + -
54A ILE* 3.7 7.5 - - + +
80A ALA* 3.6 35.7 - - + -
83A ILE* 4.1 13.7 - - + -
84A ALA* 4.1 8.7 - - + -
87A LEU* 3.6 26.2 - - + -
102A LEU* 3.8 21.1 - - + -
118A ALA 3.5 21.5 - - - -
119A ILE* 3.0 8.1 + - + +
121A ALA* 1.3 75.7 - - + +
123A ASP* 1.3 59.5 + - - +
125A ALA* 3.1 4.0 + - - +
126A LEU* 2.9 35.2 + - + +
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Residues in contact with ASP 123 (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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95A ILE* 3.2 13.3 - - - +
99A TRP* 3.6 18.7 - - + +
119A ILE* 2.9 12.8 + - + +
120A GLY* 3.3 14.1 + - - +
122A PHE* 1.3 78.3 - - - +
124A VAL* 1.3 62.1 + - - +
126A LEU* 3.2 10.9 + - - +
127A TRP* 3.1 32.3 + - - -
293A GLY 4.1 0.9 - - - +
295A ILE 2.9 12.5 + - - -
296A THR* 2.7 51.6 + - - -
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Residues in contact with VAL 124 (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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64A GLY* 3.6 15.7 - - - -
65A PHE* 4.1 16.2 - - + +
120A GLY 2.9 21.0 + - - +
121A ALA 3.9 0.2 - - - +
123A ASP* 1.3 76.7 - - - +
125A ALA* 1.3 57.9 + - - +
127A TRP* 3.1 3.6 + - - +
128A ASP* 2.9 26.9 + - - +
290A PRO* 5.7 1.8 - - + -
294A GLY* 4.3 10.3 - - - -
295A ILE* 4.2 30.0 - - + +
320A LEU* 4.3 17.3 - - + -
363A LEU* 3.4 30.3 - - + -
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Residues in contact with ALA 125 (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 ALA 3.8 10.1 - - - +
54A ILE* 3.8 17.7 - - + -
62A GLY* 3.4 12.5 - - - +
63A LEU 3.5 15.0 - - - -
64A GLY* 3.5 16.1 - - - +
121A ALA 3.3 8.2 + - - +
122A PHE* 3.1 9.8 + - - +
124A VAL* 1.3 80.0 - - - +
126A LEU* 1.3 57.1 + - - +
128A ASP* 3.2 2.4 + - - +
129A LEU* 2.9 29.8 + - - +
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Residues in contact with LEU 126 (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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15A ILE* 4.1 8.5 - - + -
54A ILE* 3.9 21.1 - - + -
87A LEU* 4.8 7.4 - - + -
92A PRO* 3.7 38.1 - - + +
95A ILE* 3.8 27.9 - - + +
98A LEU* 3.9 29.6 - - + -
99A TRP 5.9 0.2 - - - +
122A PHE* 2.9 20.7 + - + +
123A ASP* 3.2 12.3 + - - +
125A ALA* 1.3 75.0 - - - +
127A TRP* 1.3 58.1 + - - +
129A LEU* 3.3 7.7 + - + +
130A LYS* 2.9 28.6 + - - +
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Residues in contact with TRP 127 (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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95A ILE* 3.4 26.5 - - + +
123A ASP* 3.1 28.7 + - - -
124A VAL 3.5 7.0 - - - +
126A LEU* 1.3 74.0 - - - +
128A ASP* 1.3 65.9 + - - +
130A LYS* 3.3 11.8 + - + +
131A ALA* 2.9 25.1 + - - +
138A LEU* 4.1 13.8 - - + +
141A LEU* 3.9 29.1 - - + +
142A LEU* 3.6 19.7 - - + -
295A ILE* 3.5 42.7 - - + +
296A THR* 3.2 23.7 + - - -
299A LEU* 3.8 24.9 - - + -
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Residues in contact with ASP 128 (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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62A GLY* 3.4 1.7 - - - -
63A LEU* 2.8 33.4 + - - +
124A VAL 2.9 13.2 + - - +
125A ALA 3.4 8.1 - - - +
127A TRP* 1.3 76.8 - - - +
129A LEU* 1.3 58.2 + - - +
131A ALA* 3.4 1.7 + - - +
132A LYS* 2.8 70.4 + - - +
138A LEU* 5.7 2.0 - - - +
295A ILE* 5.5 0.2 - - - +
362A GLY* 3.3 6.9 - - - -
363A LEU* 2.8 40.5 + - + +
364A GLY 4.3 0.5 + - - -
365A LEU 5.3 1.2 + - - +
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Residues in contact with LEU 129 (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 ILE* 4.1 17.0 - - + +
56A THR* 3.8 24.5 - - + -
60A HIS* 3.9 14.9 + - + +
61A GLN* 3.5 35.4 - - - +
62A GLY* 3.9 3.3 - - - +
92A PRO* 4.4 15.9 - - + +
125A ALA 2.9 15.3 + - - +
126A LEU* 3.6 7.4 - - + +
128A ASP* 1.3 77.3 - - - +
130A LYS* 1.3 67.5 + - - +
132A LYS* 3.4 3.3 + - - +
133A ARG* 3.0 47.3 + - - +
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Residues in contact with LYS 130 (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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92A PRO 5.8 0.2 - - - +
93A SER* 2.7 49.4 + - - +
95A ILE* 4.0 18.9 - - + +
126A LEU 2.9 15.8 + - - +
127A TRP* 3.8 13.7 - - + +
129A LEU* 1.3 81.7 - - + +
131A ALA* 1.3 63.7 + - - +
133A ARG* 3.2 27.2 + - + +
134A ALA* 3.3 8.0 + - - +
141A LEU* 4.0 22.6 - - + +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A TRP 2.9 18.1 + - - +
130A LYS* 1.3 77.6 - - - +
132A LYS* 1.3 63.0 + - - +
134A ALA* 2.9 13.5 + - - +
136A LEU 3.1 34.9 + - - +
137A SER 4.1 1.1 - - - +
138A LEU* 4.1 12.8 - - - -
141A LEU* 3.5 22.8 - - + +
362A GLY* 3.5 16.8 - - - -
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Residues in contact with LYS 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A HIS* 5.4 2.5 - - - +
61A GLN* 3.5 28.8 + - + +
62A GLY* 4.6 2.0 - - - -
63A LEU* 4.7 3.2 - - - +
128A ASP* 2.8 50.0 + - - +
129A LEU* 3.7 5.2 - - - +
131A ALA* 1.3 75.5 - - - +
133A ARG* 1.3 61.6 - - - +
135A GLY* 2.9 14.2 + - - -
361A PRO* 3.9 28.1 - - + +
362A GLY 3.9 10.8 - - - +
364A GLY* 5.3 2.0 - - - +
365A LEU 4.6 11.8 + - - +
366A THR* 5.8 3.4 - - - +
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Residues in contact with ARG 133 (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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12A SER* 4.2 12.3 + - - -
13A ASP* 3.1 36.3 + - - +
60A HIS* 3.1 49.9 + - + +
92A PRO* 3.8 6.7 - - - +
93A SER* 4.0 15.7 + - - -
129A LEU* 3.0 35.8 + - - +
130A LYS* 3.2 17.3 - - - +
131A ALA 3.1 0.2 - - - -
132A LYS* 1.3 77.3 - - - +
134A ALA* 1.3 58.7 + - - +
135A GLY 3.3 0.6 + - - -
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Residues in contact with ALA 134 (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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130A LYS 3.3 6.6 + - - +
131A ALA 2.9 9.1 + - - +
133A ARG* 1.3 77.7 - - - +
135A GLY* 1.3 64.2 + - - +
136A LEU* 3.3 28.7 + - + +
141A LEU* 4.6 9.0 - - + -
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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
------------------------------------------------------------
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