Contacts of the helix formed by residues 75 - 97 (chain E) in PDB entry 5DO9
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 75 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E LYS* 4.5 9.4 - - - -
60E ARG* 5.7 1.3 - - - -
67E TYR* 3.8 34.1 - + - -
71E ASP* 3.2 20.4 - - + -
72E LYS 2.8 11.5 + - - +
74E GLY* 1.3 80.7 - - - +
76E THR* 1.3 62.1 + - - +
77E LYS 3.4 2.5 - - - -
78E LEU* 3.2 24.7 + - + +
79E VAL* 3.0 25.2 + - + +
174E PRO* 4.4 6.1 - - + -
179E VAL* 3.7 35.4 - - + -
182E VAL* 4.0 27.8 - - + -
184E VAL* 6.0 1.1 - - + -
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Residues in contact with THR 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E LYS 3.8 0.8 + - - -
73E ARG* 2.8 24.4 + - - +
75E PHE* 1.3 75.3 - - - +
77E LYS* 1.3 64.8 + - - +
79E VAL* 3.1 7.3 + - - +
80E TYR* 3.0 55.9 + - + +
172E TYR* 4.0 18.8 + - + +
174E PRO* 3.5 24.2 - - + +
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Residues in contact with LYS 77 (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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73E ARG 4.7 0.6 + - - -
74E GLY 4.9 4.6 + - - +
75E PHE 3.4 0.6 - - - -
76E THR* 1.3 78.2 - - - +
78E LEU* 1.3 59.3 + - + +
80E TYR* 3.3 12.8 + - - +
81E GLN* 2.8 53.4 + - - +
119E GLU 4.5 8.2 + - - -
120E LYS 5.9 0.2 - - - -
121E VAL 3.5 26.9 - - - +
122E SER* 4.3 16.8 - - - +
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Residues in contact with LEU 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74E GLY 4.9 4.9 - - - +
75E PHE* 3.2 34.6 + - + +
76E THR 3.1 0.6 - - - -
77E LYS* 1.3 76.2 - - + +
79E VAL* 1.3 61.5 + - - +
81E GLN* 3.7 20.0 - - + +
82E ASN* 2.8 40.1 + - - +
182E VAL* 3.8 13.9 - - + -
183E ARG 5.4 0.2 - - - +
184E VAL* 3.8 31.2 - - + -
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Residues in contact with VAL 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E PHE* 3.0 18.6 + - + +
76E THR 3.1 6.7 + - - +
78E LEU* 1.3 74.9 - - - +
80E TYR* 1.3 64.5 + - - +
82E ASN* 3.0 16.8 + - - +
83E ILE* 3.1 29.3 + - + +
160E TYR* 3.8 36.1 - - + +
167E VAL* 4.0 11.2 - - + -
172E TYR* 3.6 28.7 - - + +
174E PRO* 4.6 3.8 - - + -
178E ASP* 4.6 8.1 - - + +
182E VAL* 4.6 6.5 - - + -
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Residues in contact with TYR 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76E THR* 3.0 39.6 + - + +
77E LYS* 3.5 8.7 - - - +
79E VAL* 1.3 76.1 - - + +
81E GLN* 1.3 64.2 + - - +
83E ILE* 3.3 7.0 + - - +
84E PHE* 3.2 29.4 + - + -
121E VAL* 3.9 14.4 - - + -
122E SER 3.4 27.8 - - - -
123E ALA* 3.8 9.0 - - - -
124E PHE* 3.6 37.1 + + + +
167E VAL* 3.7 34.4 + - + -
168E ALA 5.6 0.3 + - - -
169E ASP 4.8 2.9 + - - -
170E PRO 5.6 1.0 + - - -
172E TYR* 3.7 19.1 + + - +
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Residues in contact with GLN 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77E LYS* 2.8 39.5 + - - +
78E LEU* 3.7 26.8 - - + +
79E VAL 3.2 0.2 - - - -
80E TYR* 1.3 75.8 - - - +
82E ASN* 1.3 64.4 + - - +
84E PHE* 4.6 1.3 - - - +
85E THR* 3.0 29.3 + - - +
118E VAL* 2.9 42.2 + - + +
119E GLU* 3.6 26.7 + - - +
121E VAL* 4.0 18.3 + - + +
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Residues in contact with ASN 82 (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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78E LEU* 2.8 26.4 + - - +
79E VAL 3.0 8.3 + - - +
81E GLN* 1.3 74.6 - - - +
83E ILE* 1.3 54.2 + - - +
85E THR* 3.2 6.1 + - - -
86E ALA* 2.8 37.2 + - - +
154E SER* 5.2 4.0 + - - -
156E SER* 5.5 1.2 - - - -
160E TYR* 4.1 20.7 - - + -
181E ARG 4.6 0.2 - - - +
182E VAL* 3.6 11.5 - - - +
183E ARG* 2.8 51.5 + - - +
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Residues in contact with ILE 83 (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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79E VAL* 3.1 20.8 + - + +
80E TYR* 3.5 9.4 - - - +
81E GLN 3.2 0.2 - - - -
82E ASN* 1.3 77.4 - - - +
84E PHE* 1.3 65.4 + - + +
86E ALA* 3.2 5.6 + - - +
87E MET* 3.0 22.2 + - - +
124E PHE* 4.5 10.1 - - + -
132E ILE* 4.3 16.2 - - + -
160E TYR* 3.8 26.5 - - + -
161E LEU* 3.9 23.1 - - + +
164E LEU* 4.1 20.9 - - + -
167E VAL* 3.8 30.3 - - + -
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Residues in contact with PHE 84 (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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80E TYR* 3.2 24.7 + - + +
81E GLN 4.0 3.1 - - - +
83E ILE* 1.3 79.5 - - + +
85E THR* 1.3 57.7 + - - +
87E MET* 3.3 5.5 + - - +
88E GLN* 2.8 36.5 + - - +
113E VAL* 4.4 10.3 - - + +
116E VAL* 3.8 36.3 - - + -
118E VAL* 4.2 16.8 - - + -
121E VAL* 4.2 29.4 - - + -
123E ALA 4.6 5.2 - - - -
124E PHE* 3.8 26.9 - + - -
125E GLU 6.0 0.2 - - - -
128E TYR* 3.7 36.3 - + + -
132E ILE* 4.1 14.4 - - + -
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Residues in contact with THR 85 (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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81E GLN 3.0 20.1 + - - -
82E ASN* 3.6 6.5 - - - +
84E PHE* 1.3 75.9 - - - +
86E ALA* 1.3 64.4 + - - +
88E GLN* 3.3 6.0 + - - +
89E ALA* 3.0 22.6 + - + +
118E VAL* 3.5 22.5 - - - +
154E SER* 6.2 4.3 - - - -
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Residues in contact with ALA 86 (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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82E ASN 2.8 18.4 + - - +
83E ILE* 3.6 6.1 - - - +
85E THR* 1.3 78.1 - - - +
87E MET* 1.3 63.2 + - - +
89E ALA* 3.0 13.6 + - - +
90E MET* 3.1 16.4 + - + +
153E LEU* 3.6 14.2 - - + +
154E SER* 5.6 4.9 - - - +
157E THR* 3.5 39.5 - - + +
161E LEU* 5.1 2.7 - - + -
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Residues in contact with MET 87 (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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83E ILE 3.0 16.3 + - - +
84E PHE 3.9 2.5 - - - +
86E ALA* 1.3 75.7 - - - +
88E GLN* 1.3 62.1 - - - +
90E MET* 3.4 25.8 + - + +
91E ILE* 3.0 39.6 + - + +
113E VAL* 4.1 10.3 - - + -
132E ILE* 3.9 25.6 - - + +
135E LEU* 3.8 34.3 - - + -
136E TRP* 3.8 28.0 - - - +
141E ILE* 4.4 10.8 - - + -
161E LEU* 3.9 15.7 - - + +
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Residues in contact with GLN 88 (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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84E PHE* 2.8 17.2 + - + +
85E THR* 3.8 5.8 - - - +
86E ALA 3.2 0.2 - - - -
87E MET* 1.3 74.8 - - - +
89E ALA* 1.3 65.8 + - - +
91E ILE* 3.8 6.7 - - - +
92E ARG* 3.0 40.2 + - - +
113E VAL* 3.0 32.0 + - + +
114E ARG* 3.5 18.4 + - - +
116E VAL* 3.0 30.8 + - - +
118E VAL* 3.4 24.4 - - - +
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Residues in contact with ALA 89 (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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85E THR* 3.0 14.4 + - + +
86E ALA 3.0 9.9 + - - +
88E GLN* 1.3 77.7 - - - +
90E MET* 1.3 62.9 + - - +
92E ARG* 3.5 20.5 + - - +
93E ALA* 3.0 22.9 + - - +
151E TYR* 4.1 8.3 - - + -
152E GLN 4.0 15.0 - - - +
153E LEU* 3.7 17.5 - - + -
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Residues in contact with MET 90 (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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86E ALA 3.1 18.5 + - - +
87E MET* 3.8 22.9 - - + +
89E ALA* 1.3 74.8 - - - +
91E ILE* 1.3 59.5 + - - +
93E ALA* 3.0 7.3 + - - +
94E MET* 2.9 34.4 + - - +
136E TRP* 4.1 17.9 - - + -
141E ILE* 4.3 20.2 - - + -
144E CYS* 3.6 5.5 - - - -
145E TYR* 4.1 12.8 - - - -
151E TYR* 3.5 17.0 - - - +
153E LEU* 4.0 20.9 - - + -
157E THR* 4.3 4.0 - - + -
161E LEU* 3.6 31.4 - - + -
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Residues in contact with ILE 91 (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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87E MET* 3.0 35.9 + - + +
88E GLN* 3.8 6.1 - - - +
90E MET* 1.3 74.2 - - - +
92E ARG* 1.3 63.6 + - - +
93E ALA 3.2 0.7 + - - -
94E MET* 3.3 17.4 + - - +
95E ASP* 3.7 8.0 + - - +
101E TYR* 4.0 17.6 + - - +
110E ALA* 3.7 38.8 - - + +
113E VAL* 3.8 26.9 - - + -
114E ARG* 3.5 36.1 - - + +
135E LEU* 4.2 3.4 - - + -
141E ILE* 5.0 2.7 - - + -
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Residues in contact with ARG 92 (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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88E GLN* 3.0 36.4 + - - +
89E ALA* 3.7 16.1 + - - +
91E ILE* 1.3 76.6 - - - +
93E ALA* 1.3 58.4 + - - +
95E ASP* 3.2 7.6 + - + +
96E THR* 3.0 34.6 + - - +
114E ARG* 4.0 18.5 - - - +
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Residues in contact with ALA 93 (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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89E ALA 3.0 16.7 + - - +
90E MET 3.0 6.5 + - - +
92E ARG* 1.3 73.3 - - - +
94E MET* 1.3 61.1 + - - +
95E ASP 3.1 1.6 - - - -
96E THR* 4.0 9.0 - - - -
97E LEU* 2.8 37.6 + - + +
144E CYS* 3.6 18.4 - - - -
151E TYR* 3.8 30.1 - - + -
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Residues in contact with MET 94 (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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90E MET 2.9 19.1 + - - +
91E ILE 3.4 7.9 - - - +
93E ALA* 1.3 76.1 - - - +
95E ASP* 1.3 59.6 + - - +
98E LYS* 3.1 5.9 + - - -
99E ILE* 2.9 56.0 + - + +
100E PRO 3.8 5.2 - - - +
101E TYR* 3.7 53.6 - - + +
140E GLY 3.6 36.1 - - - +
141E ILE* 3.8 9.6 - - + +
144E CYS* 3.6 16.8 - - - -
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Residues in contact with ASP 95 (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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91E ILE 3.7 5.4 + - - +
92E ARG 3.2 7.6 + - - +
93E ALA 3.1 0.6 - - - -
94E MET* 1.3 79.8 - - - +
96E THR* 1.3 65.9 + - - +
98E LYS* 3.3 18.6 + - - +
101E TYR* 5.7 3.6 - - - -
114E ARG* 3.4 33.3 + - - -
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Residues in contact with THR 96 (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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92E ARG* 3.0 23.0 + - - +
93E ALA* 3.0 11.9 + - - -
95E ASP* 1.3 79.9 - - - +
97E LEU* 1.3 72.9 + - + +
98E LYS* 3.7 13.7 + - - -
150E GLU 6.0 1.8 - - - +
151E TYR* 6.3 2.9 - - + -
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Residues in contact with LEU 97 (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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93E ALA* 2.8 18.8 + - + +
96E THR* 1.3 89.2 - - + +
98E LYS* 1.3 70.6 + - - +
99E ILE* 3.4 29.5 + - + +
144E CYS* 4.6 0.9 - - - -
147E ARG* 3.8 31.8 + - + +
150E GLU* 3.4 32.5 - - + +
151E TYR* 4.2 29.2 - - + -
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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) + - + + + + + -
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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