Contacts of the helix formed by residues 70 - 91 (chain F) in PDB entry 3J9X
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 70 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227 T 3.5 25.4 + - - +
3237 A 4.4 2.2 + - - -
111C PHE* 3.5 19.4 - - - -
90D ILE* 5.6 0.8 - - - +
69F THR* 1.3 75.1 - - - +
71F PRO* 1.3 67.3 - - - +
73F ARG* 2.9 36.0 + - - +
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Residues in contact with PRO 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227 T 3.6 22.9 - - + +
3237 A 3.9 32.1 - - - +
71C PRO* 3.6 19.6 - - + +
74C ALA* 4.8 2.7 - - + -
75C ILE* 3.5 36.6 - - + +
107C TYR* 6.5 0.9 - - + -
111C PHE* 4.6 6.5 - - + -
69F THR 4.4 0.2 - - - +
70F GLY* 1.3 84.6 - - - +
72F ASN* 1.3 64.2 + - - +
73F ARG 3.1 0.4 - - - -
74F ALA* 3.1 4.7 + - - +
75F ILE* 3.0 24.9 + - - +
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Residues in contact with ASN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 3.1 24.4 - - - +
75C ILE* 3.5 11.5 - - - +
111C PHE 3.3 25.3 + - - -
112C ASN* 4.8 8.3 + - - +
68F ILE* 3.5 15.7 - - + -
69F THR 3.3 15.2 + - - +
70F GLY 3.0 0.6 - - - -
71F PRO* 1.3 75.6 - - - +
73F ARG* 1.3 65.9 + - - +
75F ILE* 3.3 19.2 + - + +
76F TYR* 3.0 26.4 - - + -
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Residues in contact with ARG 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3227 T 3.0 35.6 + - - +
89D ARG 4.6 0.8 + - - -
90D ILE* 3.7 27.2 + - - +
60F SER* 2.7 47.1 + - - +
63F LEU* 3.5 16.6 - - + +
64F THR* 2.9 31.9 + - - +
68F ILE* 2.8 56.5 + - + +
69F THR* 3.9 7.9 - - - +
70F GLY 2.9 15.2 + - - +
72F ASN* 1.3 76.2 - - - +
74F ALA* 1.3 58.4 + - - +
76F TYR* 3.0 5.0 + - - -
77F GLN* 2.8 30.5 + - - +
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3217 A 4.1 16.7 - - + +
3227 T 3.0 41.6 + - + +
278 A 4.7 5.2 - - + -
288 T 4.4 5.5 - - - +
71C PRO* 4.8 3.6 - - + -
70F GLY 3.6 0.8 + - - -
71F PRO 3.1 8.6 + - - +
73F ARG* 1.3 77.2 - - - +
75F ILE* 1.3 64.8 + - - +
77F GLN* 3.6 10.3 - - - +
78F GLY* 2.9 21.7 + - - -
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Residues in contact with ILE 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288 T 5.8 0.2 - - - -
71C PRO* 3.6 27.3 - - + +
72C ASN* 3.5 35.9 - - - +
71F PRO 3.0 14.4 + - - +
72F ASN* 3.4 22.7 - - - +
74F ALA* 1.3 78.4 - - - +
76F TYR* 1.3 67.3 + - + +
78F GLY* 3.4 0.7 + - - -
79F PHE* 3.1 21.7 + - - +
107F TYR* 3.5 30.4 - - + -
111F PHE* 4.6 11.0 - - + +
112F ASN 5.9 0.7 - - - +
113F ALA* 4.1 19.5 - - + -
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Residues in contact with TYR 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F VAL* 4.4 2.9 - - - +
63F LEU* 3.6 28.9 - - + -
68F ILE* 4.0 18.4 - - + +
72F ASN* 3.0 27.4 - - + -
73F ARG 3.0 5.2 + - - +
75F ILE* 1.3 80.1 - - + +
77F GLN* 1.3 61.2 + - - +
79F PHE* 3.3 5.9 + - - +
80F GLY* 2.8 27.4 + - - -
112F ASN 5.0 0.3 + - - -
113F ALA* 3.9 9.2 - - + -
114F ASN* 2.9 39.2 + - - +
117F VAL* 3.7 31.2 - - + +
118F LEU* 3.7 30.3 - - + -
121F VAL* 4.2 11.4 - - + +
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Residues in contact with GLN 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3217 A 3.4 34.4 + - + +
3227 T 3.1 21.1 + - - +
55F VAL* 5.4 0.7 - - - +
56F ASN* 3.4 23.5 + - - +
59F VAL* 3.3 21.6 - - - +
60F SER* 3.5 26.7 - - - +
63F LEU* 4.0 1.9 - - + +
73F ARG 2.8 21.3 + - - +
74F ALA* 3.6 9.2 - - - +
76F TYR* 1.3 77.4 - - - +
78F GLY* 1.3 57.4 + - - +
80F GLY* 3.3 0.3 + - - -
81F LEU* 2.9 41.3 + - + +
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Residues in contact with GLY 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3217 A 5.4 0.8 + - - -
288 T 5.1 3.6 - - - -
298 A 4.1 24.8 - - - +
74F ALA 2.9 16.0 + - - -
75F ILE 3.8 1.8 - - - -
77F GLN* 1.3 77.0 - - - +
79F PHE* 1.3 61.1 + - - +
81F LEU* 3.8 4.9 - - - +
82F LYS* 3.0 24.9 + - - +
107F TYR* 3.5 13.1 + - - -
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Residues in contact with PHE 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ILE 3.1 14.3 + - - +
76F TYR 3.5 8.3 - - - +
78F GLY* 1.3 75.5 - - - +
80F GLY* 1.3 64.3 + - - +
82F LYS* 3.1 5.5 + - - +
83F VAL* 2.9 32.7 + - + +
100F ILE* 5.1 1.8 - - + -
103F LEU* 3.7 23.8 - - + -
104F LYS* 3.8 23.3 - - + -
107F TYR* 3.5 33.5 + + + -
118F LEU* 3.3 52.7 - - + -
121F VAL* 3.8 16.6 - - + -
122F VAL* 3.7 24.5 - - + -
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Residues in contact with GLY 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F VAL* 4.5 5.8 - - - -
59F VAL* 5.0 2.0 - - - -
76F TYR 2.8 16.7 + - - -
77F GLN* 3.8 0.9 - - - -
79F PHE* 1.3 73.0 - - - +
81F LEU* 1.3 63.1 + - - +
83F VAL* 3.1 2.9 + - - -
84F ALA* 3.0 20.1 + - - +
121F VAL* 3.5 26.9 - - - -
125F ILE* 3.1 17.1 - - - +
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Residues in contact with LEU 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3207 T 5.5 1.8 - - - +
3217 A 5.6 3.4 - - - +
298 A 4.1 19.3 - - + +
308 T 3.4 37.0 - - - +
52F PHE* 3.5 42.5 - - + +
55F VAL* 4.5 6.3 - - + +
56F ASN* 3.4 31.0 - - - +
77F GLN* 2.9 29.4 + - + +
78F GLY* 3.8 4.3 - - - +
80F GLY* 1.3 75.3 - - - +
82F LYS* 1.3 57.9 + - - +
84F ALA* 3.2 3.9 + - - -
85F ARG 2.9 23.7 + - - -
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Residues in contact with LYS 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3127 T 3.2 13.7 + - - -
298 A 3.7 25.8 + - - +
308 T 3.3 27.4 + - - +
106E TYR* 2.8 34.7 + - - -
78F GLY 3.0 17.7 + - - +
79F PHE* 3.5 5.2 - - - +
81F LEU* 1.3 73.8 - - - +
83F VAL* 1.3 65.7 + - - +
85F ARG* 3.3 11.6 + - - +
86F ALA* 3.1 22.2 + - - +
99F MET* 5.9 3.0 - - - -
103F LEU* 3.5 35.5 - - + +
106F TYR* 5.0 6.3 - - + -
107F TYR* 4.6 3.8 - - + -
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Residues in contact with VAL 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79F PHE* 2.9 42.5 + - + +
80F GLY* 3.3 8.7 - - - +
82F LYS* 1.3 75.7 - - - +
84F ALA* 1.3 61.5 + - - +
86F ALA* 3.3 8.6 + - - +
87F LEU* 3.0 19.9 + - + +
96F LEU* 4.5 2.6 - - + +
100F ILE* 4.3 28.0 - - + -
103F LEU* 3.7 18.6 - - + -
122F VAL* 4.6 8.7 - - + -
125F ILE* 3.9 26.0 - - + -
126F THR* 4.5 5.4 - - + -
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51F LYS 5.7 0.2 - - - +
52F PHE* 3.6 20.6 - - + -
55F VAL* 4.2 19.7 - - + -
80F GLY 3.0 11.6 + - - +
81F LEU* 3.5 8.3 - - - +
83F VAL* 1.3 73.6 - - - +
85F ARG* 1.3 67.7 + - - +
87F LEU* 3.1 12.8 + - + +
88F ASN* 3.0 25.2 + - - +
125F ILE* 4.4 10.5 - - + -
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Residues in contact with ARG 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3117 A 3.8 36.4 + - - -
3127 T 2.9 33.7 + - - +
308 T 3.0 36.5 + - - +
318 A 3.4 30.3 + - - +
52F PHE* 3.5 11.3 - - - -
81F LEU 2.9 14.4 + - - +
82F LYS* 3.3 20.8 - - - +
83F VAL 3.2 0.4 - - - -
84F ALA* 1.3 75.0 - - - +
86F ALA* 1.3 63.3 + - - +
88F ASN* 3.0 6.3 + - - +
89F ARG* 3.0 44.5 + - - +
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Residues in contact with ALA 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3117 A 5.6 2.9 - - - +
82F LYS* 3.1 8.9 + - + +
83F VAL* 3.6 9.9 - - - +
85F ARG* 1.3 78.8 - - - +
87F LEU* 1.3 57.8 + - - +
89F ARG* 4.5 2.9 - - - +
90F ILE* 2.7 47.2 + - + +
96F LEU* 3.8 17.0 - - + -
99F MET* 3.8 26.5 - - + -
100F ILE* 6.0 0.4 - - + -
103F LEU* 6.2 0.4 - - + -
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Residues in contact with LEU 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F VAL* 3.0 14.4 + - + +
84F ALA* 3.1 12.8 + - + +
86F ALA* 1.3 75.2 - - - +
88F ASN* 1.3 65.6 + - - +
91F GLY* 2.7 30.7 + - - +
92F SER* 3.6 30.3 - - - +
96F LEU* 3.6 23.7 - - + +
125F ILE* 4.5 25.8 - - + +
126F THR* 6.0 2.9 - - + -
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Residues in contact with ASN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318 A 5.4 1.7 + - - +
48F ASN* 4.9 5.4 + - - +
51F LYS* 3.8 31.3 + - - +
52F PHE* 3.4 33.9 - - - -
84F ALA* 3.0 12.9 + - - +
85F ARG* 3.0 7.6 + - - +
87F LEU* 1.3 86.1 - - - +
89F ARG* 1.3 64.8 + - + +
90F ILE 4.8 0.3 - - - -
91F GLY 4.5 1.0 + - - -
7G SER* 4.6 13.1 - - - +
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Residues in contact with ARG 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3097 A 4.6 10.3 + - - -
3107 T 3.6 28.7 + - - +
3117 A 3.3 31.3 + - - +
318 A 4.1 17.2 + - - +
328 T 4.3 15.6 + - - -
85F ARG* 3.0 45.5 + - - +
86F ALA* 4.3 2.5 - - - +
88F ASN* 1.3 80.4 - - + +
90F ILE* 1.3 61.3 + - + +
7G SER* 4.1 31.9 - - - +
60H SER* 4.5 5.9 + - - -
73H ARG* 4.6 1.7 + - - -
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Residues in contact with ILE 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3107 T 5.6 0.7 - - - +
3117 A 4.5 10.8 - - - +
86F ALA* 2.7 29.7 + - + +
88F ASN 4.8 1.1 - - - -
89F ARG* 1.3 78.0 - - - +
91F GLY* 1.3 67.7 + - - +
95F ALA* 3.6 25.8 - - + +
96F LEU* 4.0 5.2 - - + +
99F MET* 3.8 38.4 - - + -
60H SER* 4.9 1.7 + - - -
61H ALA* 5.8 0.5 - - - -
64H THR* 2.6 35.9 + - - +
69H THR* 4.4 10.5 - - + -
70H GLY 5.6 0.4 - - - +
73H ARG* 3.7 18.9 + - - +
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Residues in contact with GLY 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F ALA 3.6 0.4 + - - -
87F LEU* 2.7 30.8 + - - -
88F ASN 4.5 1.1 - - - -
90F ILE* 1.3 90.1 - - - +
92F SER* 1.3 67.1 + - - +
96F LEU* 3.4 9.6 - - - +
64H THR* 3.6 1.4 - - - +
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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