Contacts of the helix formed by residues 57 - 80 (chain f) in PDB entry 5GJQ
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 PHE 57 (chain f).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4f PRO 3.7 11.0 - - - -
5f TYR* 4.1 4.7 - + - -
6f VAL* 3.2 47.6 - - + +
8f ASN* 3.5 4.3 - - - -
55f SER 4.2 0.4 - - - -
56f GLY* 1.3 70.5 - - - -
58f HIS* 1.3 66.2 + - - +
59f GLY* 3.3 12.4 + - - -
60f ASP* 3.2 40.4 + - - +
61f CYS* 2.9 21.1 + - - -
105f TYR* 2.8 33.7 + - + +
100g ARG* 3.2 28.3 - - - -
128g LEU* 3.5 26.5 - - + -
130g VAL* 3.8 9.0 - - + -
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Residues in contact with HIS 58 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8f ASN* 2.6 27.8 + - + +
29f LEU* 3.6 35.2 - - + +
40f SER* 4.0 18.1 + - - -
41f PRO 5.8 0.4 - - - -
42f LYS* 5.4 9.1 - - + +
44f TYR* 4.2 13.0 - - - -
54f CYS 5.8 0.4 + - - -
56f GLY 3.4 2.5 + - - -
57f PHE* 1.3 71.8 - - - +
59f GLY* 1.3 58.0 + - - +
61f CYS* 3.1 14.0 + - + +
62f LEU* 2.9 64.6 + - + +
130g VAL* 4.3 13.0 - - + -
131g ALA 4.0 10.2 + - - -
132g TYR* 5.5 0.6 - - - +
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Residues in contact with GLY 59 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57f PHE* 3.2 21.3 - - - -
58f HIS* 1.3 79.4 - - - +
60f ASP* 1.3 57.4 + - - +
62f LEU* 3.4 3.0 + - - +
63f THR* 2.9 31.9 + - - -
94g ARG* 4.0 1.2 + - - -
97g TYR* 3.8 8.5 - - - -
128g LEU 4.3 1.6 - - - -
129g GLY 3.7 25.1 - - - +
130g VAL* 4.0 2.4 - - - +
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Residues in contact with ASP 60 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5f TYR* 3.7 1.2 - - - -
57f PHE* 3.2 29.3 + - + +
59f GLY* 1.3 74.0 - - - +
61f CYS* 1.3 59.5 + - - +
63f THR* 3.8 2.6 - - - -
64f LEU* 2.9 32.2 + - - +
99f ARG* 4.5 0.9 + - - -
103f PRO 3.6 3.4 - - - +
104f TYR* 3.4 18.0 - - + -
105f TYR 3.0 21.1 + - - +
106f VAL* 3.8 15.7 - - + -
97g TYR* 3.0 14.7 + - - -
100g ARG* 3.0 32.1 + - - -
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Residues in contact with CYS 61 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44f TYR* 5.1 4.5 - - - +
54f CYS* 3.8 42.5 - - + -
55f SER 4.1 10.1 - - - -
56f GLY 4.2 1.3 - - - -
57f PHE 2.9 24.0 + - - -
58f HIS* 3.1 24.2 + - + +
60f ASP* 1.3 75.3 - - - +
62f LEU* 1.3 59.8 + - - +
64f LEU* 3.6 3.5 - - - +
65f THR* 2.8 33.1 + - - -
106f VAL* 3.9 15.9 - - - -
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Residues in contact with LEU 62 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44f TYR* 4.1 18.6 - - + +
58f HIS* 2.9 43.2 + - + +
59f GLY 3.8 4.0 - - - +
61f CYS* 1.3 73.5 - - - +
63f THR* 1.3 67.7 + - - +
65f THR* 3.1 8.7 + - + +
66f LYS* 3.0 27.8 + - + +
93g THR* 5.0 0.9 - - + -
94g ARG* 4.0 15.9 - - - +
129g GLY 4.4 6.1 - - - +
131g ALA* 3.6 37.0 - - + +
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Residues in contact with THR 63 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PHE* 4.6 9.1 - - + -
59f GLY 2.9 14.0 + - - -
60f ASP 3.8 3.1 - - - -
62f LEU* 1.3 78.3 - - - +
64f LEU* 1.3 64.3 + - - +
66f LYS* 3.2 5.3 + - - +
67f ILE* 3.0 40.5 + - + +
99f ARG* 5.2 0.4 - - - +
104f TYR* 4.2 5.4 - - + +
94g ARG* 2.3 35.4 + - - +
97g TYR* 2.9 41.1 - - + +
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Residues in contact with LEU 64 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54f CYS* 4.8 4.0 - - - -
60f ASP 2.9 19.1 + - - +
61f CYS 3.6 3.8 - - - +
63f THR* 1.3 77.0 - - - +
65f THR* 1.3 63.3 + - - +
67f ILE* 3.2 5.2 + - + +
68f ILE* 3.0 38.0 + - + +
92f LEU* 4.2 9.2 - - + -
95f ILE* 4.0 26.5 - - + -
96f LEU* 4.1 18.6 - - + -
104f TYR* 4.1 18.2 - - + +
106f VAL* 3.8 15.7 - - + -
108f ASN* 3.6 36.8 - - - +
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Residues in contact with THR 65 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44f TYR* 3.8 49.0 - - + +
46f LEU* 5.6 3.6 - - + +
52f ILE* 5.1 3.1 - - - +
54f CYS* 4.2 9.3 - - - -
61f CYS 2.8 19.3 + - - -
62f LEU* 3.1 9.8 + - + +
64f LEU* 1.3 76.2 - - - +
66f LYS* 1.3 61.6 + - + +
68f ILE* 3.2 9.7 + - - +
69f GLU* 3.0 45.1 + - + +
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Residues in contact with LYS 66 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96G ARG 3.6 8.3 - - - -
97G PHE* 2.7 51.8 + - + +
100G ASP* 4.0 21.6 - - - +
62f LEU* 3.0 16.9 + - + +
63f THR* 3.8 4.7 - - - +
65f THR* 1.3 79.0 - - + +
67f ILE* 1.3 64.0 + - - +
69f GLU* 3.3 19.5 + - - +
70f ALA* 3.0 23.7 + - - +
90g SER* 3.6 18.4 + - - +
94g ARG* 4.2 26.7 - - - +
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Residues in contact with ILE 67 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97G PHE* 3.9 16.8 - - + -
63f THR* 3.0 26.9 + - + +
64f LEU* 3.5 9.2 - - - +
66f LYS* 1.3 75.1 - - - +
68f ILE* 1.3 64.5 + - - +
70f ALA* 3.4 6.6 + - - +
71f ARG* 3.0 31.0 + - + +
95f ILE* 4.1 31.0 - - + -
104f TYR* 3.2 28.5 - - + +
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Residues in contact with ILE 68 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46f LEU* 3.9 32.5 - - + -
52f ILE* 3.8 21.3 - - + -
54f CYS* 5.9 0.2 - - - -
64f LEU* 3.0 27.1 + - + +
65f THR* 3.6 7.9 - - - +
67f ILE* 1.3 75.0 - - + +
69f GLU* 1.3 66.6 + - - +
71f ARG* 3.2 5.0 + - - +
72f LEU* 3.1 29.6 + - + +
88f ILE* 4.9 4.3 - - + -
91f MET* 4.8 8.5 - - + +
92f LEU* 3.6 30.1 - - + -
95f ILE* 4.2 19.5 - - + -
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Residues in contact with GLU 69 (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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96G ARG* 5.4 6.8 - - - +
100G ASP* 4.8 10.1 - - - +
46f LEU* 5.4 7.9 - - + -
65f THR* 3.0 33.2 + - + +
66f LYS* 3.5 20.9 - - - +
68f ILE* 1.3 76.0 - - - +
70f ALA* 1.3 63.3 + - - +
72f LEU* 3.1 21.6 + - - +
73f LYS* 3.2 26.7 + - - +
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Residues in contact with ALA 70 (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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93G LEU* 3.9 28.8 - - + +
97G PHE* 5.3 8.5 - - + -
66f LYS 3.0 9.4 + - - +
67f ILE* 3.6 11.0 - - - +
69f GLU* 1.3 80.3 - - - +
71f ARG* 1.3 60.4 + - + +
73f LYS* 3.3 5.4 + - - +
74f MET* 3.0 38.9 + - - +
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Residues in contact with ARG 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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102F THR* 3.8 8.7 + - - +
103F TYR* 2.3 39.4 + - - -
67f ILE* 3.0 23.6 + - + +
68f ILE 4.0 2.5 - - - +
70f ALA* 1.3 77.9 - - + +
72f LEU* 1.3 64.8 + - - +
74f MET* 3.5 32.0 + - + +
75f TYR* 3.2 21.0 + - - +
91f MET* 3.5 39.4 - - + +
94f THR* 4.2 6.5 + - - -
95f ILE* 3.9 21.9 - - + +
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Residues in contact with LEU 72 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46f LEU* 3.8 47.8 - - + +
47f THR* 4.4 6.7 - - + -
68f ILE* 3.1 24.1 + - + +
69f GLU* 3.4 10.5 - - - +
71f ARG* 1.3 78.2 - - - +
73f LYS* 1.3 63.4 + - + +
75f TYR* 3.3 5.4 + - - +
76f LYS* 3.1 25.1 + - - +
83f MET* 3.4 36.2 - - + +
88f ILE* 3.5 20.2 - - + -
91f MET* 5.0 2.0 - - + -
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Residues in contact with LYS 73 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67G ASP* 3.9 8.8 + - - +
68G ASN* 3.9 22.1 - - - +
93G LEU* 4.2 21.7 - - + +
96G ARG* 3.1 40.6 - - - +
69f GLU* 3.2 20.2 + - - +
70f ALA 3.7 6.5 - - - +
72f LEU* 1.3 78.7 - - + +
74f MET* 1.3 59.0 + - - +
76f LYS* 3.6 9.0 - - + +
77f HIS* 3.0 39.9 + - + +
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Residues in contact with MET 74 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103F TYR* 6.0 0.4 - - - +
90G GLN* 4.9 13.0 - - - +
93G LEU* 3.9 17.3 - - + -
70f ALA* 3.0 24.6 + - - +
71f ARG* 3.6 38.6 - - + +
72f LEU 3.2 0.2 - - - -
73f LYS* 1.3 74.7 - - - +
75f TYR* 1.3 62.6 + - - +
77f HIS* 3.5 10.7 + - + +
78f SER* 3.1 24.9 + - - -
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Residues in contact with TYR 75 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F HIS* 3.8 17.7 - + - -
103F TYR* 4.1 29.8 + + - +
105F GLU* 2.7 35.5 + - - -
71f ARG 3.2 10.8 + - - +
72f LEU 3.6 8.1 - - - +
73f LYS 3.3 0.2 - - - -
74f MET* 1.3 76.9 - - - +
76f LYS* 1.3 61.8 + - - +
78f SER* 4.6 1.1 - - - -
79f ASN* 2.7 58.4 + - + +
81f LYS* 3.7 30.9 + - + -
82f ALA* 4.0 4.9 + - - -
83f MET* 3.3 46.4 - - + -
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Residues in contact with LYS 76 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65G HIS* 3.7 31.1 + - + +
72f LEU 3.1 13.9 + - - +
73f LYS* 3.6 13.5 - - + +
74f MET 3.2 0.2 - - - -
75f TYR* 1.3 75.3 - - - +
77f HIS* 1.3 63.4 + - - +
80f ASN* 2.7 52.8 + - - +
81f LYS* 3.3 24.2 - - - +
82f ALA* 4.6 7.2 - - + -
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Residues in contact with HIS 77 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F GLN* 4.8 6.4 + - - +
65G HIS* 3.5 27.1 + + - +
66G VAL 3.0 29.6 + - - -
67G ASP* 5.2 0.4 - - - -
89G ARG* 3.1 68.3 + - + +
93G LEU* 5.0 9.7 - - + +
73f LYS* 3.0 24.2 + - + +
74f MET* 3.7 12.1 - - + +
76f LYS* 1.3 81.2 + - + +
78f SER* 1.3 62.3 + - - +
80f ASN* 4.1 13.0 + - - +
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Residues in contact with SER 78 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F HIS* 6.2 0.3 - - - -
111F SER* 2.5 35.0 + - - -
114F GLN* 3.9 21.2 + - - +
89G ARG* 5.8 0.7 - - - +
74f MET 3.1 16.0 + - - -
75f TYR* 4.6 0.7 - - - -
76f LYS 3.2 0.4 - - - -
77f HIS* 1.3 80.5 - - - +
79f ASN* 1.3 64.8 + - - +
80f ASN* 4.6 3.8 + - - -
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Residues in contact with ASN 79 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F HIS* 3.8 19.9 + - - -
108F THR* 3.8 17.7 + - - +
110F GLU* 5.5 1.2 - - - +
111F SER* 3.0 20.2 + - - -
75f TYR* 2.7 59.5 + - + +
78f SER* 1.3 89.7 + - - +
80f ASN* 1.3 74.9 + - - +
81f LYS* 3.1 26.0 - - + +
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Residues in contact with ASN 80 (chain f).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110F GLU* 4.3 23.5 + - - +
114F GLN* 5.9 3.2 - - - +
149F LYS* 6.0 3.8 - - - +
61G LYS* 4.2 18.1 + - - +
76f LYS* 2.7 36.8 + - - +
77f HIS* 4.1 12.0 + - - +
78f SER 4.6 2.6 + - - -
79f ASN* 1.3 77.5 + - - +
81f LYS* 1.3 57.4 + - - +
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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
------------------------------------------------------------
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