Contacts of the helix formed by residues 81 - 104 (chain G) in PDB entry 5LN3
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 LEU 81 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ILE* 5.2 14.4 - - + -
22F ILE* 5.6 7.0 - - + -
117F GLN* 5.7 2.5 - - - +
152F ASN* 5.1 9.4 - - - +
80G GLY* 1.4 71.3 - - - -
82G LEU* 1.4 70.3 + - + +
83G ALA* 3.9 13.0 - - + +
84G ASP* 3.1 33.1 + - + +
85G ALA* 3.3 8.2 + - - +
130G ARG* 6.2 1.6 - - - +
133G GLY* 3.9 4.8 + - - +
134G CYS* 3.2 25.1 - - - -
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Residues in contact with LEU 82 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153F TYR* 3.8 23.6 - - + +
154F PHE* 4.7 14.1 - - + -
64G ASN* 3.6 29.2 - - + -
65G LYS 3.5 24.0 - - - +
66G ARG* 5.2 0.7 - - - -
68G PHE* 3.6 27.1 - - + -
78G VAL* 5.8 3.1 - - + -
80G GLY 3.7 3.4 + - - -
81G LEU* 1.4 75.5 - - + +
83G ALA* 1.4 66.2 + - - +
85G ALA* 3.2 6.5 + - + +
86G ARG* 3.2 19.2 + - + +
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Residues in contact with ALA 83 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F GLN* 4.1 21.4 - - + +
150F SER 4.9 2.7 - - - +
151F ALA* 4.1 17.9 - - + +
152F ASN* 5.0 3.4 - - - +
153F TYR* 4.7 11.0 - - + -
81G LEU* 3.5 10.8 - - + +
82G LEU* 1.4 64.3 - - - +
84G ASP* 1.3 69.7 + - - +
86G ARG* 3.4 7.2 + - - +
87G SER* 3.2 24.5 + - - -
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Residues in contact with ASP 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117F GLN* 4.1 10.9 - - - +
121F GLN* 3.6 27.6 - - - +
81G LEU* 3.1 30.5 + - + +
83G ALA* 1.3 78.4 - - - +
85G ALA* 1.4 63.4 + - - +
87G SER* 3.1 10.3 + - - -
88G LEU* 3.0 18.5 + - - +
130G ARG* 4.6 8.0 + - - -
131G PRO 5.0 2.4 - - - +
132G PHE* 3.8 26.8 - - + -
133G GLY 5.1 1.9 + - - +
134G CYS* 3.9 17.3 - - - -
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 5.4 4.3 - - + -
78G VAL* 3.7 39.3 - - + -
81G LEU 3.3 11.6 + - - +
82G LEU* 3.2 12.9 + - + +
84G ASP* 1.4 76.1 - - - +
86G ARG* 1.4 62.9 + - - +
88G LEU* 3.3 4.2 + - - +
89G ALA* 3.1 25.4 + - - +
134G CYS* 3.8 2.6 - - - -
136G PHE* 3.7 16.2 - - + -
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Residues in contact with ARG 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1197 GLU* 5.3 1.4 - - - +
1207 GLU* 2.8 41.6 + - - +
107F ARG* 4.9 4.0 - - - +
110F SER* 6.0 7.1 - - - -
114F SER* 5.7 2.0 - - - +
153F TYR* 4.2 20.9 - - + +
63G SER 5.0 1.1 + - - -
68G PHE* 3.5 35.1 - - + -
82G LEU* 3.2 11.2 + - + +
83G ALA* 3.6 10.8 - - - +
84G ASP 3.3 0.2 - - - -
85G ALA* 1.4 79.3 - - - +
87G SER* 1.4 55.5 + - - +
89G ALA* 3.3 9.2 + - - +
90G ASP* 2.9 57.2 + - - +
93G ARG* 3.4 32.0 - - - +
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Residues in contact with SER 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F SER* 4.6 10.4 + - - -
117F GLN* 4.0 20.6 - - - +
118F ILE* 4.3 15.7 - - - +
121F GLN* 4.1 18.0 + - - -
83G ALA 3.2 13.7 + - - -
84G ASP* 3.1 10.9 + - - -
86G ARG* 1.4 73.4 - - - +
88G LEU* 1.3 64.8 + - - +
89G ALA 3.4 0.2 + - - -
90G ASP* 3.9 8.5 + - - +
91G ILE* 3.2 24.1 + - - +
132G PHE* 4.8 2.2 - - - -
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Residues in contact with LEU 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G MET* 4.9 8.1 - - + -
84G ASP 3.0 7.4 + - - +
85G ALA 3.3 7.6 + - - +
87G SER* 1.3 77.5 - - - +
89G ALA* 1.3 64.9 + - - +
91G ILE* 3.4 11.6 + - - +
92G ALA* 3.1 19.6 + - + +
116G VAL* 3.9 37.9 - - + -
119G TYR* 4.1 15.9 - - + -
120G VAL* 5.1 4.0 - - + -
132G PHE* 3.7 37.3 - - + -
136G PHE* 3.4 43.7 - - + -
152G ILE* 6.0 0.2 - - + -
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Residues in contact with ALA 89 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G PHE* 5.4 8.7 - - + -
69G ASN 5.5 0.9 - - - +
70G VAL* 5.1 1.4 - - + +
76G MET* 4.5 18.2 - - - -
85G ALA 3.1 15.8 + - - +
86G ARG* 3.3 11.2 + - - +
88G LEU* 1.3 81.8 - - - +
90G ASP* 1.4 65.2 + - - +
92G ALA* 3.2 8.1 + - - +
93G ARG* 3.1 42.8 + - - +
136G PHE* 5.0 1.3 - - + -
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Residues in contact with ASP 90 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114F SER* 4.3 13.5 + - - -
86G ARG* 2.9 59.9 + - - +
87G SER* 4.3 5.5 + - - +
88G LEU 3.5 0.4 - - - -
89G ALA* 1.4 74.6 - - - +
91G ILE* 1.4 62.4 + - + +
93G ARG* 3.6 17.3 + - - +
94G GLU* 3.3 22.3 + - - +
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Residues in contact with ILE 91 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118F ILE* 5.4 11.9 - - + -
87G SER 3.2 24.5 - - - +
88G LEU* 3.5 10.8 - - - +
90G ASP* 1.4 73.3 - - + +
92G ALA* 1.4 60.4 + - - +
94G GLU* 3.1 8.5 + - + +
95G GLU* 2.9 49.1 + - + +
119G TYR* 3.6 36.6 - - + +
132G PHE* 5.4 2.7 - - + -
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Residues in contact with ALA 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G VAL* 5.0 5.2 - - + -
76G MET* 5.1 11.4 - - + -
88G LEU* 3.1 13.2 + - + +
89G ALA* 3.2 12.3 + - - +
91G ILE* 1.4 79.7 - - - +
93G ARG* 1.4 57.6 - - - +
95G GLU* 3.3 14.1 + - - +
96G ALA* 2.9 29.7 + - - +
112G LEU* 4.2 16.9 - - + +
116G VAL* 4.9 15.3 - - + -
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Residues in contact with ARG 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1177 ILE 5.5 0.9 - - - +
1187 ASP* 4.4 12.6 - - - +
1197 GLU* 4.0 25.5 - - - +
1207 GLU 4.0 0.4 - - - +
68G PHE* 4.2 6.7 - - - +
69G ASN* 2.9 58.8 + - - +
70G VAL* 3.9 10.5 - - + +
71G ASP* 3.2 34.7 - - - +
86G ARG* 3.4 41.9 - - - +
89G ALA* 3.1 23.4 + - - +
90G ASP* 3.8 16.9 + - - +
92G ALA* 1.4 78.6 - - - +
94G GLU* 1.4 54.4 + - - +
96G ALA* 3.3 0.9 - - - +
97G SER* 2.9 36.5 + - - -
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Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147 GLN* 5.1 9.8 + - - +
1187 ASP* 4.7 10.5 + - - +
90G ASP 3.3 12.1 + - - +
91G ILE* 3.1 12.2 + - - +
93G ARG* 1.4 76.5 - - - +
95G GLU* 1.3 62.6 + - + +
97G SER* 3.3 7.9 + - - -
98G ASN* 3.0 41.1 + - - +
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Residues in contact with GLU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91G ILE* 2.9 36.8 + - + +
92G ALA* 3.6 13.4 - - - +
94G GLU* 1.3 76.2 - - + +
96G ALA* 1.3 61.2 + - - +
98G ASN* 3.6 11.4 + - - +
99G PHE* 3.4 19.6 + - - +
112G LEU* 6.2 0.4 - - + -
115G ARG* 5.3 20.5 - - + +
116G VAL* 5.8 2.6 - - - +
119G TYR* 5.5 8.4 - - - -
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Residues in contact with ALA 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G VAL* 5.0 0.2 - - + -
71G ASP* 3.4 24.7 - - - +
92G ALA 2.9 13.5 + - - +
93G ARG* 3.3 10.5 - - - +
95G GLU* 1.3 74.7 - - - +
97G SER* 1.3 57.6 + - - +
99G PHE* 3.2 7.5 - - - +
100G ARG* 2.9 28.9 + - - +
107G ILE* 4.2 18.8 - - + +
112G LEU* 4.1 17.2 - - + +
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Residues in contact with SER 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1147 GLN* 4.2 15.3 - - - -
1177 ILE* 3.6 30.9 + - - +
1187 ASP* 3.7 12.7 + - - -
71G ASP* 4.0 5.5 + - - -
93G ARG 2.9 19.1 + - - -
94G GLU* 3.4 12.3 - - - -
96G ALA* 1.3 72.9 - - - +
98G ASN* 1.4 64.9 + - - +
100G ARG* 3.2 8.6 + - - +
101G SER* 3.1 28.2 + - - -
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Residues in contact with ASN 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1147 GLN* 3.5 18.9 + - - +
94G GLU* 3.0 32.7 + - - +
95G GLU* 3.6 10.3 + - - +
96G ALA 3.4 0.2 - - - -
97G SER* 1.4 74.0 - - - +
99G PHE* 1.3 56.1 + - - +
101G SER* 4.0 4.0 - - - -
102G ASN* 3.0 31.6 + - - +
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Residues in contact with PHE 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1001 HIS* 3.8 22.4 - + - -
1041 LEU* 4.1 14.6 - - + -
95G GLU 3.4 9.6 + - - +
96G ALA* 3.2 11.6 + - - +
97G SER 3.2 0.2 - - - -
98G ASN* 1.3 78.4 - - - +
100G ARG* 1.4 60.0 + - - +
102G ASN* 3.1 4.2 + - - +
103G PHE* 2.8 67.4 + + + +
105G TYR* 4.6 12.1 - + + -
107G ILE* 3.8 41.7 - - + -
108G PRO* 4.5 3.8 - - + -
111G HIS* 3.9 23.6 - + - -
115G ARG* 5.3 5.6 - - - -
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Residues in contact with ARG 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177 ILE* 4.0 40.5 - - + +
71G ASP* 3.8 31.9 - - - +
72G ARG* 4.0 16.6 + - - +
73G HIS* 3.8 5.0 + - - +
96G ALA 2.9 16.4 + - - +
97G SER* 3.2 7.2 + - - +
99G PHE* 1.4 76.2 - - - +
101G SER* 1.4 57.0 + - - +
104G GLY* 2.9 27.2 + - - -
105G TYR 3.1 25.5 - - - +
106G ASN* 3.5 30.2 + - - +
107G ILE* 4.9 5.6 - - + +
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Residues in contact with SER 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 SER* 4.6 4.3 + - - -
1107 GLN* 4.1 38.2 + - - +
1137 GLY 5.9 0.2 - - - -
1147 GLN* 5.3 8.9 + - - +
1177 ILE* 5.0 8.0 - - - +
97G SER 3.1 14.8 + - - -
98G ASN* 4.0 4.3 - - - -
100G ARG* 1.4 76.7 - - - +
102G ASN* 1.3 63.1 + - - +
104G GLY* 3.6 9.9 + - - -
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Residues in contact with ASN 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1151 SER* 3.2 27.0 - - - -
1161 LEU* 4.7 10.6 - - - +
1191 GLU* 4.6 20.9 - - - +
1107 GLN* 5.5 1.8 - - - -
98G ASN 3.0 20.9 + - - +
99G PHE* 3.1 5.5 + - - +
101G SER* 1.3 75.3 - - - +
103G PHE* 1.3 93.6 + - - +
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Residues in contact with PHE 103 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
961 GLN* 5.3 9.2 - - + -
1001 HIS* 3.1 48.2 - + + +
1111 HIS* 3.3 20.8 - - - +
1121 THR* 3.4 25.0 + - + +
1151 SER* 4.6 1.6 - - - -
1161 LEU* 4.0 31.0 - - + -
99G PHE* 2.8 50.9 + + + +
102G ASN* 1.3 103.9 - - - +
104G GLY* 1.4 56.9 + - - +
105G TYR* 3.3 8.4 + - + +
115G ARG* 6.3 0.7 - - - -
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Residues in contact with GLY 104 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1111 HIS* 3.1 32.5 + - - -
1151 SER* 4.8 4.7 - - - -
100G ARG 2.9 19.2 + - - -
101G SER* 3.8 9.0 - - - -
102G ASN 3.3 1.6 - - - -
103G PHE* 1.4 76.4 - - - +
105G TYR* 1.4 56.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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