Contacts of the helix formed by residues 94 - 117 (chain A) in PDB entry 4JYY
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 PRO 94 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.5 35.4 - - + +
78A LEU* 4.9 4.0 - - + -
92A SER 3.8 1.5 - - - +
93A LEU* 1.3 93.9 - - + +
95A LYS* 1.3 66.3 + - - +
96A ASP* 3.1 18.3 + - - +
97A ILE* 3.1 18.5 + - + +
98A ALA 3.1 10.2 + - - -
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Residues in contact with LYS 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU 3.2 5.4 + - - -
94A PRO* 1.3 71.1 - - - +
96A ASP* 1.3 63.9 + - - +
97A ILE 3.3 0.9 + - - -
98A ALA* 3.6 14.2 + - - +
99A THR* 4.8 3.1 + - - -
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Residues in contact with ASP 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A LYS* 2.7 36.5 + - - +
75A TYR* 2.6 29.0 + - - -
94A PRO* 3.4 11.1 - - - +
95A LYS* 1.3 79.4 + - - +
97A ILE* 1.3 65.5 + - - +
99A THR 5.5 0.2 - - - -
100A THR* 4.8 4.9 + - - -
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Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.8 28.3 - - + +
72A LEU* 4.1 5.4 - - + -
74A LYS* 5.2 2.5 - - + -
75A TYR* 3.6 23.3 - - + -
78A LEU* 3.5 32.8 - - + -
93A LEU* 4.8 3.1 - - + -
94A PRO* 3.5 19.1 - - + +
96A ASP* 1.3 94.3 - - - +
98A ALA* 1.3 62.4 + - - +
99A THR 3.3 2.9 - - - -
100A THR* 3.2 9.1 + - - -
101A VAL* 2.8 46.9 + - + +
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Residues in contact with ALA 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 3.6 27.3 - - - +
93A LEU* 4.4 14.1 - - + +
94A PRO 3.1 15.7 + - - +
95A LYS* 3.6 10.5 + - - +
97A ILE* 1.3 77.3 - - - +
99A THR* 1.3 58.2 + - - +
101A VAL* 3.4 4.4 + - - +
102A ARG* 2.9 28.9 + - - +
302A AZI 4.4 12.9 + - - +
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Residues in contact with THR 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LYS 4.8 2.8 + - - -
96A ASP 5.5 0.4 - - - -
97A ILE 3.3 0.2 - - - -
98A ALA* 1.3 75.3 - - - +
100A THR* 1.3 67.6 + - - +
102A ARG* 3.3 5.4 + - - +
103A ASN* 3.0 39.0 + - - +
302A AZI 2.9 27.3 + - - +
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Residues in contact with THR 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LYS* 4.7 5.2 - - + +
68A LEU* 5.7 0.7 - - - -
71A ALA* 3.8 27.6 - - + -
96A ASP 4.8 4.0 + - - -
97A ILE* 3.2 14.4 + - - -
99A THR* 1.3 79.8 - - - +
101A VAL* 1.3 56.4 + - - +
103A ASN* 4.7 2.9 - - - -
104A ASN* 2.9 51.0 + - + +
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Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A LEU* 4.3 7.9 - - + -
71A ALA* 5.3 2.9 - - + -
72A LEU* 4.1 16.6 - - + -
86A LEU* 4.0 15.7 - - + -
90A LEU* 3.9 8.7 - - + -
93A LEU* 3.6 25.4 - - + -
97A ILE* 2.8 44.1 + - + +
98A ALA 3.7 3.8 - - - +
100A THR* 1.3 75.6 - - - +
102A ARG* 1.3 61.9 + - - +
105A ALA* 2.7 50.9 + - + +
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Residues in contact with ARG 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 4.2 3.3 - - - +
90A LEU* 3.6 32.2 - - + +
98A ALA 2.9 14.3 + - - +
99A THR* 3.3 10.9 - - - +
101A VAL* 1.3 76.7 - - - +
103A ASN* 1.3 66.9 + - - +
106A GLY* 3.1 25.3 + - - -
176A PRO* 5.6 0.6 - - - +
178A GLN 4.0 5.4 - - - +
179A ASP* 2.9 43.4 + - - +
302A AZI 3.1 32.4 + - - +
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Residues in contact with ASN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A TYR* 4.0 5.9 - - + -
99A THR* 3.0 33.0 + - - +
100A THR* 3.9 4.7 - - - +
102A ARG* 1.3 93.5 - - - +
104A ASN* 1.3 67.0 + - - +
107A GLY* 3.0 20.3 + - - -
177A ASN* 5.4 6.3 - - - +
178A GLN* 3.4 22.5 - - + +
179A ASP* 4.7 3.8 + - - -
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.4 42.5 - - - +
67A LYS* 3.3 37.6 - - - +
68A LEU* 3.8 14.5 - - + +
100A THR* 2.9 38.2 + - - +
103A ASN* 1.3 80.8 - - - +
105A ALA* 1.3 62.8 + - - +
106A GLY 3.1 1.3 - - - -
107A GLY 4.2 0.2 - - - +
108A ALA* 2.9 28.9 + - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A LEU* 3.9 24.6 - - + +
83A LEU* 4.2 8.9 - - + +
86A LEU* 4.1 12.6 - - + -
87A LEU* 4.1 13.8 - - + +
101A VAL* 2.7 36.5 + - + +
104A ASN* 1.3 73.9 - - - +
106A GLY* 1.3 56.1 + - - +
108A ALA* 3.8 0.7 - - - +
109A TYR* 2.9 32.9 + - - +
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Residues in contact with GLY 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A LEU* 3.8 15.6 - - - +
102A ARG 3.1 23.3 + - - -
104A ASN 3.1 0.6 - - - -
105A ALA* 1.3 79.5 - - - +
107A GLY* 1.3 56.2 + - - +
109A TYR* 3.9 0.2 - - - +
110A ASN* 2.9 36.5 + - - +
178A GLN* 3.4 18.2 - - - -
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Residues in contact with GLY 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A TYR* 3.6 27.3 - - - -
103A ASN 3.0 11.5 + - - -
104A ASN 3.3 0.6 + - - -
106A GLY* 1.3 76.1 - - - +
108A ALA* 1.3 62.2 + - - +
111A HIS* 2.7 32.0 + - - +
178A GLN* 3.5 19.9 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A PHE* 6.1 1.1 - - + -
61A TYR* 3.4 18.7 - - + -
64A TYR* 3.7 3.2 - - + +
65A VAL* 3.9 25.8 - - + +
68A LEU* 4.8 2.9 - - + -
83A LEU* 4.1 22.6 - - + +
104A ASN 2.9 18.4 + - - +
105A ALA* 3.8 4.0 - - - +
107A GLY* 1.3 76.5 - - - +
109A TYR* 1.3 63.0 + - - +
112A LYS* 3.1 23.0 + - - +
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Residues in contact with TYR 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.8 30.2 - - + +
84A CYS* 3.8 25.0 - - - -
87A LEU* 3.7 21.3 - - + -
105A ALA 2.9 18.8 + - - +
106A GLY 3.9 0.7 - - - +
108A ALA* 1.3 78.2 - - - +
110A ASN* 1.3 75.7 + - - +
112A LYS* 3.8 8.4 - - + +
113A PHE* 3.0 43.7 + + + +
161A TRP* 5.7 1.6 - + - -
180A SER* 4.2 4.3 - - - -
182A VAL* 3.6 28.1 - - + +
188A PRO* 4.1 18.8 - - + +
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Residues in contact with ASN 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A GLY 2.9 20.1 + - - +
107A GLY 4.1 0.7 - - - +
109A TYR* 1.3 81.8 - - - +
111A HIS* 1.3 57.7 + - - +
113A PHE* 3.5 5.4 + - - +
114A PHE* 2.8 29.1 + - - +
159A TRP* 3.4 30.0 - - + +
161A TRP* 3.5 21.1 - - + -
178A GLN* 3.0 48.3 + - - +
179A ASP 3.7 6.5 + - - -
180A SER* 3.7 17.3 - - - -
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Residues in contact with HIS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A HIS* 3.2 24.4 + + - -
60A HIS* 4.7 1.4 - - - +
61A TYR* 3.7 31.0 - - + -
64A TYR* 3.4 26.8 - + - -
107A GLY* 2.7 28.9 + - - +
110A ASN* 1.3 73.3 - - - +
112A LYS* 1.3 65.9 + - - +
113A PHE 3.1 0.7 - - - -
114A PHE* 3.7 4.9 - + - +
115A PHE* 2.9 41.1 + + + -
159A TRP* 3.8 12.9 - + - -
178A GLN* 3.5 14.4 - - - -
193A ASP* 3.5 1.3 + - - -
197A HIS* 4.0 1.2 + - - -
301A FE 2.2 29.8 - - - -
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Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LYS 5.2 6.1 - - - -
35A LYS* 4.0 29.6 - - + +
61A TYR* 3.5 29.8 - - - +
83A LEU* 4.2 23.4 - - + +
108A ALA 3.1 14.7 + - - +
109A TYR* 3.8 8.7 - - + +
111A HIS* 1.3 75.5 - - - +
113A PHE* 1.3 63.6 + - - +
115A PHE* 4.0 2.5 - - - +
116A ASP* 3.1 34.9 + - - +
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Residues in contact with PHE 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A TYR* 3.0 39.3 + + + +
110A ASN* 3.5 7.0 - - - +
112A LYS* 1.3 79.9 - - - +
114A PHE* 1.3 61.0 + - - +
116A ASP* 3.3 7.7 + - - +
117A ILE* 3.0 31.4 + - + +
159A TRP* 5.8 0.2 - + - -
161A TRP* 4.0 18.6 - + + -
188A PRO* 3.5 31.6 - - + -
189A ILE 3.6 11.9 - - - -
190A ILE* 3.9 2.5 - - - -
191A GLY* 3.7 25.4 - - - -
226A ASN* 3.4 33.2 - - - -
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Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ILE* 5.1 3.6 - - + -
53A MET* 6.3 0.4 - - - -
56A HIS* 3.7 32.5 - + - -
110A ASN 2.8 21.4 + - - +
111A HIS* 3.2 4.9 + + - +
113A PHE* 1.3 74.2 - - - +
115A PHE* 1.3 72.8 + + - +
117A ILE* 3.1 22.7 + - + +
118A MET* 3.6 30.8 + - + +
159A TRP* 3.7 18.6 - + + -
191A GLY 3.3 19.7 - - - -
192A LEU* 3.8 1.3 - - - -
193A ASP* 3.5 19.3 - - + -
210A TYR* 3.7 22.0 - - - -
214A TRP* 3.5 28.3 - + - -
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Residues in contact with PHE 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.8 25.8 - - + -
38A PRO* 4.3 7.2 - - + -
39A TYR* 2.7 32.0 + - - -
53A MET* 4.7 11.7 - - - -
56A HIS* 3.8 33.0 - + + -
57A HIS* 3.7 42.8 - + + -
61A TYR* 3.8 24.9 - + + -
111A HIS* 2.9 35.0 + + + +
112A LYS* 4.3 2.5 - - - +
114A PHE* 1.3 84.9 - + - +
116A ASP* 1.3 63.1 + - - +
117A ILE 3.4 0.3 + - - -
118A MET* 3.5 15.0 - - + +
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Residues in contact with ASP 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LYS* 2.8 42.0 + - - +
38A PRO* 3.5 15.8 - - - +
112A LYS* 3.1 28.2 + - - +
113A PHE* 3.6 7.2 - - + +
115A PHE* 1.3 77.4 - - - +
117A ILE* 1.3 59.8 + - - +
118A MET 3.2 3.9 + - - +
219A ASN* 3.7 18.0 + - - -
222A GLY* 5.2 2.1 - - - -
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Residues in contact with ILE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A PHE* 3.0 21.1 + - + +
114A PHE* 3.1 18.7 + - + +
116A ASP* 1.3 78.2 - - - +
118A MET* 1.3 57.7 + - + +
189A ILE 3.5 21.3 - - - +
190A ILE* 3.9 22.7 - - + -
191A GLY 3.8 21.5 - - - +
214A TRP* 4.2 10.3 - - + -
218A VAL* 3.6 5.6 - - + -
219A ASN* 2.8 30.9 + - - +
222A GLY* 4.0 3.8 - - - -
223A ALA* 3.6 25.6 - - - +
226A ASN* 3.7 11.2 - - - +
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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
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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