Contacts of the helix formed by residues 92 - 115 (chain D) in PDB entry 1ORR
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 ASN 92 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63C ASN* 2.9 22.8 + - - +
64C ASP* 5.4 1.4 + - - -
67C ARG* 3.2 39.4 + - - +
88D THR* 2.8 19.8 + - + +
89D SER 3.5 2.5 - - - -
91D ASP* 1.4 76.2 - - - +
93D PRO* 1.3 67.3 - - - +
94D CYS* 3.7 3.8 + - - +
95D MET* 3.1 39.9 + - + +
96D ASP* 3.1 19.6 + - - +
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Residues in contact with PRO 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 5.4 2.9 - - + +
109B GLU* 3.5 20.6 - - - +
112B ARG* 3.9 15.3 - - - +
175B TYR* 5.1 2.5 + - + -
179B TYR* 3.4 17.0 - - + +
183B PHE* 3.8 15.9 - - + -
67C ARG* 5.5 0.4 - - - +
89D SER 3.1 17.0 - - - +
90D ILE 3.8 4.7 - - - +
91D ASP 3.6 7.0 - - - +
92D ASN* 1.3 89.9 - - - +
94D CYS* 1.3 57.6 + - + +
96D ASP* 3.6 6.1 - - + +
97D PHE* 2.9 30.3 + - - +
164D PRO* 4.1 16.0 - - + +
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Residues in contact with CYS 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B LYS* 4.6 21.1 - - - +
105B LEU* 6.1 1.3 - - - -
109B GLU* 4.2 18.5 + - + +
63C ASN* 3.6 32.1 - - - +
92D ASN* 3.1 2.6 - - - +
93D PRO* 1.3 81.7 - - - +
95D MET* 1.3 63.1 + - - +
97D PHE* 3.3 8.4 + - - +
98D GLU* 3.0 50.1 + - - +
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Residues in contact with MET 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ASN* 3.6 8.2 - - - +
64C ASP* 4.4 6.3 - - - +
60D ARG* 3.7 19.5 - - - +
83D GLN* 3.8 24.9 - - + +
88D THR* 4.1 20.2 - - + -
92D ASN* 3.1 35.4 + - + +
94D CYS* 1.3 78.8 - - - +
96D ASP* 1.3 64.2 + - - +
98D GLU* 3.3 7.5 + - - +
99D ILE* 3.0 43.1 + - + +
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Residues in contact with ASP 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B TYR* 4.3 0.7 + - - -
83D GLN* 2.8 35.1 + - + +
89D SER* 3.6 22.2 - - - -
92D ASN 3.1 12.2 + - - +
93D PRO* 3.6 7.6 - - + +
95D MET* 1.3 76.8 - - - +
97D PHE* 1.3 64.5 + - - +
100D ASN* 2.9 44.2 + - - +
164D PRO* 2.9 19.9 - - - +
165D TYR* 3.8 3.6 - - - -
168D SER* 2.5 23.8 + - - -
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Residues in contact with PHE 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.7 24.9 - + - -
101B VAL* 3.4 30.1 - - + -
102B GLY* 4.4 15.5 - - - -
105B LEU* 4.1 21.3 - - + -
175B TYR* 3.5 31.6 - + + +
93D PRO 2.9 17.5 + - - +
94D CYS* 3.5 6.7 - - - +
96D ASP* 1.3 78.6 + - - +
98D GLU* 1.3 71.3 + - + +
101D VAL* 2.9 43.5 + - + +
102D GLY* 3.1 7.7 + - - -
168D SER* 4.1 2.7 - - - -
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Residues in contact with GLU 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C ASN* 2.9 34.6 + - - +
63C ASN* 4.5 4.7 + - - +
60D ARG* 3.6 29.1 + - + +
94D CYS* 3.0 42.7 + - - +
95D MET* 3.3 5.6 + - - +
97D PHE* 1.3 89.2 - - + +
99D ILE* 1.3 58.0 + - - +
102D GLY* 3.3 8.5 - - - +
103D GLY 2.9 23.4 + - - -
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Residues in contact with ILE 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE* 3.9 17.1 - - + +
60D ARG* 3.5 28.0 - - + +
79D HIS* 5.4 0.3 + - - -
81D ALA 4.4 3.0 - - - +
82D GLY* 3.6 13.9 - - - +
83D GLN* 3.5 33.7 - - + +
95D MET* 3.0 43.7 + - + +
96D ASP 4.2 1.3 - - - +
98D GLU* 1.3 76.6 - - - +
100D ASN* 1.3 64.8 + - - +
103D GLY* 3.2 20.3 + - - -
104D THR* 4.0 1.2 + - - -
1500D NAD 3.7 24.0 - - - +
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Residues in contact with ASN 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81D ALA 5.5 0.9 - - - -
82D GLY* 3.2 10.6 - - - -
83D GLN* 2.8 38.2 + - - +
96D ASP* 2.9 38.8 + - - +
99D ILE* 1.3 74.8 - - - +
101D VAL* 1.3 59.3 + - - +
104D THR* 2.7 29.7 + - - -
122D TYR* 4.4 2.3 + - - +
165D TYR* 4.1 0.8 - - - -
168D SER* 3.1 25.4 + - - +
169D LYS* 3.7 24.0 + - + +
172D ALA* 3.6 5.2 - - - +
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Residues in contact with VAL 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 3.4 28.3 - - + -
101B VAL* 5.1 1.3 - - + -
175B TYR* 4.2 1.1 - - + +
97D PHE* 2.9 32.2 + - + +
100D ASN* 1.3 70.3 - - - +
102D GLY* 1.3 69.1 + - - +
104D THR* 3.3 1.4 + - - -
105D LEU* 2.9 32.3 + - + +
168D SER* 3.4 40.8 - - - +
171D ALA* 4.1 20.2 - - + -
172D ALA* 4.7 5.4 - - - +
175D TYR* 5.0 2.5 - - + -
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Residues in contact with GLY 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B PHE* 4.5 15.6 - - - -
60D ARG 5.3 0.7 - - - -
97D PHE* 3.1 10.9 + - - -
98D GLU* 3.3 11.7 - - - -
101D VAL* 1.3 79.8 - - - +
103D GLY* 1.3 56.9 + - - +
105D LEU* 3.3 2.9 + - - +
106D ASN* 2.8 39.9 + - - +
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Residues in contact with GLY 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE* 3.2 39.6 - - - +
79D HIS* 4.3 1.1 - - - -
98D GLU 2.9 12.6 + - - -
99D ILE 3.2 14.0 + - - -
102D GLY* 1.3 72.3 - - - +
104D THR* 1.3 60.6 + - - +
106D ASN* 3.1 3.8 + - - +
107D LEU* 3.0 22.5 + - - +
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Residues in contact with THR 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79D HIS* 3.0 24.4 + - + -
99D ILE 4.0 0.4 + - - -
100D ASN* 2.7 26.8 + - - -
101D VAL 3.3 3.2 + - - -
103D GLY* 1.3 72.8 - - - +
105D LEU* 1.3 63.2 + - + +
107D LEU* 3.2 2.8 + - - +
108D LEU* 2.8 37.1 + - + +
122D TYR* 3.8 5.9 - - + -
172D ALA* 3.8 26.7 - - + +
176D MET* 3.5 29.8 - - + -
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO 5.5 2.9 - - - +
94B CYS* 5.9 1.3 - - - -
97B PHE* 4.2 30.1 - - + -
101D VAL* 2.9 26.7 + - + +
102D GLY* 3.8 5.6 - - - +
104D THR* 1.3 79.6 - - - +
106D ASN* 1.3 66.2 + - - +
108D LEU* 4.3 4.0 - - + -
109D GLU* 2.9 34.8 + - + +
172D ALA* 5.5 0.9 - - - -
175D TYR* 3.6 47.3 - - + -
179D TYR* 3.7 28.9 - - + +
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Residues in contact with ASN 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D ILE 2.9 17.8 + - - +
60D ARG* 2.9 30.3 + - - +
61D ASN 3.6 0.2 - - - -
62D LYS* 3.4 39.1 - - + +
65D VAL* 3.8 17.0 - - + +
66D THR* 5.1 2.3 + - - -
102D GLY* 2.8 21.9 + - - +
103D GLY 3.1 7.8 + - - +
105D LEU* 1.3 79.3 - - - +
107D LEU* 1.3 62.8 + - - +
109D GLU* 4.0 4.0 - - - +
110D ALA* 3.1 24.8 + - - +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D LEU* 4.8 4.3 - - + -
7D THR* 5.1 4.9 - - + -
59D ILE* 5.1 2.0 - - + -
65D VAL* 3.7 13.9 - - + -
68D LEU* 5.6 0.9 - - + -
69D ILE* 3.9 29.2 - - + -
77D CYS* 4.1 19.5 - - + -
79D HIS* 3.6 43.1 - - + +
103D GLY 3.0 12.8 + - - +
104D THR* 3.6 7.0 - - - +
106D ASN* 1.3 78.1 - - - +
108D LEU* 1.3 63.3 + - - +
110D ALA* 3.2 2.6 + - - +
111D VAL* 2.9 31.9 + - + +
120D ILE* 4.4 13.2 - - + -
176D MET* 4.6 5.2 - - + -
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Residues in contact with LEU 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104D THR* 2.8 35.9 + - + +
105D LEU* 3.9 7.2 - - + +
107D LEU* 1.3 74.5 - - - +
109D GLU* 1.3 56.0 + - - +
111D VAL* 3.8 3.7 - - - +
112D ARG* 2.8 32.1 + - - +
120D ILE* 4.3 6.1 - - + -
175D TYR* 4.0 39.0 - - + +
176D MET* 3.9 28.7 - - + +
179D TYR* 3.8 27.5 - - + -
185D LEU* 4.1 22.1 - - + +
187D THR* 4.3 7.0 - - + -
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Residues in contact with GLU 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B PRO* 3.6 4.8 - - - +
94B CYS* 3.8 28.5 + - + +
62D LYS* 5.2 13.7 + - - +
105D LEU* 2.9 26.9 + - + +
106D ASN* 4.0 4.3 - - - +
108D LEU* 1.3 75.8 - - - +
110D ALA* 1.4 57.0 + - - +
112D ARG* 2.9 40.7 + - - +
113D GLN* 2.9 48.7 + - - +
179D TYR* 2.7 27.2 + - - +
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65D VAL* 4.3 1.6 - - + +
66D THR* 4.0 24.0 - - - +
69D ILE* 3.8 28.8 - - + +
106D ASN 3.1 19.0 + - - +
107D LEU 3.7 3.4 - - - +
109D GLU* 1.4 75.2 - - - +
111D VAL* 1.3 59.5 + - - +
113D GLN* 5.4 0.4 - - - +
114D TYR* 2.8 48.1 + - + +
115D ASN 3.7 0.2 + - - -
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Residues in contact with VAL 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ILE* 4.3 23.1 - - + -
77D CYS* 6.1 0.4 - - + -
107D LEU* 2.9 23.7 + - + +
108D LEU 3.9 2.7 - - - +
110D ALA* 1.3 78.0 - - - +
112D ARG* 1.3 63.0 + - - +
115D ASN* 3.0 24.7 + - - +
116D SER* 3.0 29.3 + - - -
118D CYS* 4.1 22.7 - - + +
120D ILE* 4.0 25.6 - - + -
185D LEU* 3.8 19.7 - - + -
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ARG* 6.0 1.4 - - - +
90B ILE 5.2 1.2 + - - -
91B ASP 5.2 4.2 + - - -
93B PRO* 3.9 20.6 - - - +
108D LEU 2.8 23.4 + - - +
109D GLU* 2.9 39.8 + - - +
111D VAL* 1.3 74.6 - - - +
113D GLN* 1.3 84.8 + - - +
116D SER* 3.8 12.5 - - - -
179D TYR* 3.8 7.4 - - + -
183D PHE* 3.5 53.1 - - + -
185D LEU* 4.2 15.9 - - + -
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Residues in contact with GLN 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62D LYS* 6.0 3.6 - - - +
109D GLU* 2.9 34.3 + - - +
110D ALA* 5.4 0.2 - - - +
112D ARG* 1.3 109.3 + - - +
114D TYR* 1.3 93.1 + - + +
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Residues in contact with TYR 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 3.5 23.1 + + - -
66D THR* 3.8 24.3 - - + +
69D ILE* 4.6 2.7 - - + -
70D THR* 3.7 29.8 - - + -
73D MET* 3.2 22.8 - - - +
110D ALA* 2.8 34.9 + - + +
113D GLN* 1.3 109.4 + - + +
115D ASN* 1.3 60.3 + - + +
116D SER 3.9 0.7 - - - -
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Residues in contact with ASN 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69D ILE* 3.7 20.5 - - + +
73D MET* 3.6 23.7 - - - +
74D PRO* 2.8 49.5 + - - +
110D ALA 3.7 0.2 + - - -
111D VAL* 3.0 13.4 + - - +
114D TYR* 1.3 82.3 - - - +
116D SER* 1.3 59.8 + - - +
117D ASN* 3.1 10.3 + - - +
118D CYS* 3.2 26.2 + - - +
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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