Contacts of the helix formed by residues 97 - 120 (chain C) in PDB entry 5CYP
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 ASN 97 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C PHE* 5.4 1.1 - - + -
92C GLY* 3.1 38.2 + - - +
94C HIS* 3.7 23.2 + - - +
96C ASN* 1.3 74.9 - - - +
98C GLU* 1.3 64.6 + - - +
99C ASN 3.2 2.0 - - - -
100C CYS* 3.2 14.5 + - + +
101C TRP* 3.1 22.0 + - - +
150C LEU* 3.9 21.1 - - + +
154C PHE* 5.2 1.2 - - - -
92D GLY 5.8 0.4 + - - -
94D HIS 3.4 24.5 + - - -
95D ILE* 3.3 20.9 + - + +
97D ASN* 3.8 3.2 - - - +
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Residues in contact with GLU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96C ASN* 3.6 4.3 - - + +
97C ASN* 1.3 77.0 - - - +
99C ASN* 1.3 56.8 + - - +
100C CYS 3.0 5.4 + - - -
101C TRP* 3.3 8.1 + - - +
102C GLN* 3.2 24.1 + - - +
157C ARG* 4.7 10.1 + - - +
95D ILE* 4.1 20.6 - - + +
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Residues in contact with ASN 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ASN* 4.5 11.1 + - + +
97C ASN 3.2 0.8 - - - -
98C GLU* 1.3 77.5 - - - +
100C CYS* 1.3 61.2 + - - +
102C GLN* 4.7 4.4 - - - +
103C PRO* 3.5 19.9 - - - +
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Residues in contact with CYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLY 5.1 2.5 - - - +
91C PHE* 3.6 28.2 - - + +
93C ASP* 4.0 7.6 - - - -
94C HIS* 3.7 29.2 - - - -
96C ASN 4.6 2.7 - - - -
97C ASN* 3.2 22.1 + - - +
98C GLU 3.0 0.6 - - - -
99C ASN* 1.3 82.9 - - - +
101C TRP* 1.3 62.5 + - - +
102C GLN 3.2 1.6 - - - -
103C PRO* 3.4 12.4 - - - +
104C ILE* 4.4 10.9 - - - +
154C PHE* 4.4 7.2 - - - -
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Residues in contact with TRP 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97C ASN 3.1 13.8 + - - +
98C GLU 3.3 3.3 + - - +
100C CYS* 1.3 75.6 - - - +
102C GLN* 1.3 58.9 + - - +
103C PRO 3.7 0.2 - - - -
104C ILE* 4.2 3.0 + - - +
105C MET* 3.1 29.3 + - + +
154C PHE* 3.5 35.1 - - + -
157C ARG* 3.1 31.9 - - - +
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Residues in contact with GLN 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98C GLU 3.2 14.5 + - - +
99C ASN* 4.7 4.7 - - - -
101C TRP* 1.3 75.5 - - - +
103C PRO* 1.4 72.6 - - + +
104C ILE 3.2 1.8 - - - -
105C MET* 3.3 6.1 + - - +
106C LYS* 3.0 23.6 + - - +
157C ARG* 5.5 1.1 - - - +
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Residues in contact with PRO 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C ILE* 3.6 21.0 - - + +
89C PRO* 6.1 4.7 - - + -
99C ASN 3.5 16.6 - - - +
100C CYS* 3.4 16.6 - - - +
102C GLN* 1.4 93.5 - - + +
104C ILE* 1.3 60.1 + - + +
106C LYS* 3.6 7.6 + - + +
107C PHE* 3.2 16.3 + - - +
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Residues in contact with ILE 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 3.9 24.5 - - + -
29C VAL* 3.8 20.4 - - + -
67C ILE* 4.4 10.1 - - + -
88C THR* 3.8 32.3 - - + +
89C PRO* 4.8 7.6 - - + +
91C PHE* 4.7 7.6 - - + -
100C CYS 4.4 9.4 - - - +
101C TRP 4.2 5.1 + - - +
102C GLN 3.2 0.6 - - - -
103C PRO* 1.3 77.1 - - + +
105C MET* 1.3 64.8 + - - +
106C LYS 3.2 0.2 - - - -
107C PHE* 3.3 3.6 + - - +
108C ILE* 3.1 31.0 + - + +
154C PHE* 4.2 20.6 - - + -
158C LEU* 4.5 9.2 - - + -
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Residues in contact with MET 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C TRP 3.1 20.4 + - - +
102C GLN* 3.3 7.7 + - - +
104C ILE* 1.3 77.6 - - + +
106C LYS* 1.3 59.6 + - - +
108C ILE* 3.6 5.1 + - + +
109C ASN* 2.9 45.9 + - - +
154C PHE* 5.8 2.5 - - + -
157C ARG* 4.5 31.2 - - + +
158C LEU* 4.1 25.1 - - - -
161C VAL* 3.7 34.8 - - + -
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Residues in contact with LYS 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C GLN 3.0 16.8 + - - +
103C PRO* 3.8 7.4 - - + +
105C MET* 1.3 75.1 - - - +
107C PHE* 1.3 58.7 + - - +
109C ASN* 3.4 5.4 + - - +
110C ASP* 2.8 57.3 + - - +
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Residues in contact with PHE 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 3.5 23.1 - - + -
67C ILE* 3.8 30.5 - - + -
69C SER* 3.8 21.5 - - - -
86C ILE* 3.7 29.8 - - + -
103C PRO 3.2 12.1 + - - +
104C ILE* 3.3 7.8 + - - +
106C LYS* 1.3 78.7 - - - +
108C ILE* 1.3 61.9 + - - +
110C ASP* 3.3 6.5 + - - -
111C GLN* 3.1 61.4 + - + +
114C LYS* 6.1 0.2 - - - -
131C THR* 5.4 1.6 - - - -
133C VAL* 4.4 2.2 - - + -
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Residues in contact with ILE 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C MET* 4.4 11.7 - - + -
104C ILE* 3.1 23.8 + - + +
105C MET* 3.8 7.4 - - + +
107C PHE* 1.3 78.0 - - - +
109C ASN* 1.3 65.6 + - - +
111C GLN* 3.2 10.6 + - - +
112C TYR* 3.1 44.2 + - + -
133C VAL* 4.4 22.3 + - + +
158C LEU* 3.8 29.4 - - + -
161C VAL* 4.2 24.0 - - + +
162C VAL* 4.5 13.7 - - + -
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Residues in contact with ASN 109 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C MET* 2.9 36.3 + - - +
106C LYS* 4.0 5.0 - - - +
108C ILE* 1.3 77.7 - - - +
110C ASP* 1.3 56.9 + - - +
112C TYR* 3.2 14.0 + - - +
113C GLU* 2.7 33.8 + - - +
161C VAL* 4.8 9.9 - - - +
285C TYR* 3.4 30.2 + - + +
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Residues in contact with ASP 110 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C LYS* 2.8 53.1 + - - +
107C PHE* 3.6 8.2 - - - +
108C ILE 3.2 0.2 - - - -
109C ASN* 1.3 75.2 - - - +
111C GLN* 1.3 68.9 + - - +
113C GLU* 3.2 11.5 + - - +
114C LYS* 2.8 39.1 + - + +
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Residues in contact with GLN 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PHE* 3.1 60.9 + - + +
108C ILE* 3.2 7.8 + - - +
110C ASP* 1.3 80.2 - - - +
112C TYR* 1.3 64.2 + - - +
114C LYS* 3.4 22.6 + - - +
115C TYR* 3.2 18.0 + - - +
131C THR* 2.3 60.0 + - - +
132C ARG* 3.6 22.6 - - - +
133C VAL* 4.5 4.0 - - + +
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Residues in contact with TYR 112 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ILE* 3.1 26.6 + - + -
109C ASN* 3.4 15.9 - - - +
111C GLN* 1.3 76.2 - - - +
113C GLU* 1.3 60.3 + - - +
115C TYR 4.0 0.2 - - - -
116C LEU* 3.3 15.2 + - - +
132C ARG* 3.6 29.6 - - + -
133C VAL 4.1 8.6 + - - -
161C VAL* 2.8 33.1 + - + -
162C VAL* 4.4 1.0 - - - +
277C THR* 3.8 13.9 - - + +
281C HIS* 3.5 25.8 - - + +
282C PHE* 3.3 35.8 - + + -
285C TYR* 3.3 43.2 - + + -
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Residues in contact with GLU 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109C ASN 2.7 11.3 + - - +
110C ASP* 3.3 14.8 - - - +
111C GLN 3.1 0.2 - - - -
112C TYR* 1.3 76.8 - - - +
114C LYS* 1.3 59.8 + - + +
115C TYR 3.2 0.2 - - - -
116C LEU* 3.2 6.1 + - - +
117C GLN* 3.0 35.5 + - + +
285C TYR* 2.3 36.2 + - - +
289C ARG* 2.6 33.6 + - - -
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Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C PHE* 6.1 0.4 - - - -
110C ASP* 2.8 22.5 + - - +
111C GLN* 3.6 35.7 + - - +
113C GLU* 1.3 77.4 - - + +
115C TYR* 1.3 60.6 + - - +
117C GLN* 3.8 4.8 + - - +
118C GLU* 3.2 33.9 + - - +
129C PRO 6.1 0.2 - - - -
131C THR* 4.0 15.1 + - + -
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Residues in contact with TYR 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLN 3.2 15.3 + - - +
113C GLU 3.2 0.2 - - - -
114C LYS* 1.3 77.4 - - - +
116C LEU* 1.3 63.1 + - - +
118C GLU* 3.5 2.9 + - - +
119C GLU* 3.2 44.5 + - + +
128C ILE* 3.9 37.9 + - + +
129C PRO 4.1 7.9 - - - -
130C ASP* 3.8 21.6 + - + -
131C THR* 4.9 1.3 - - + +
132C ARG* 3.5 57.2 + - + -
282C PHE* 3.8 14.8 - + + -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C TYR 3.3 16.0 + - - +
113C GLU* 3.2 9.5 + - - +
115C TYR* 1.3 76.9 - - - +
117C GLN* 1.3 63.2 + - - +
118C GLU 3.1 1.8 - - - -
119C GLU* 3.9 1.7 - - - +
120C VAL* 3.3 33.4 + - + +
282C PHE* 4.1 6.0 - - + -
285C TYR* 4.1 20.6 - - + -
286C ARG* 3.6 50.3 - - + +
289C ARG* 4.2 23.1 - - + +
290C LEU* 4.6 17.3 - - + -
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Residues in contact with GLN 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C GLU* 3.0 24.5 + - + +
114C LYS* 4.2 6.1 - - - +
115C TYR 3.4 0.2 - - - -
116C LEU* 1.3 76.2 - - - +
118C GLU* 1.3 60.1 + - + +
120C VAL* 3.6 15.8 - - - +
121C ASN* 3.5 16.1 + - - +
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Residues in contact with GLU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C LYS* 3.2 22.3 - - - +
115C TYR 3.5 1.5 + - - +
116C LEU 3.1 0.4 - - - -
117C GLN* 1.3 81.0 - - + +
119C GLU* 1.3 56.3 + - - +
120C VAL 3.5 0.4 - - - -
121C ASN* 3.4 16.7 + - - +
124C ARG* 2.4 42.5 + - - -
127C ARG 5.0 0.3 - - - +
128C ILE* 3.7 26.3 - - + +
129C PRO* 3.4 32.8 - - - +
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Residues in contact with GLU 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115C TYR* 3.2 34.8 + - + +
116C LEU 3.4 4.9 + - - +
118C GLU* 1.3 75.7 - - - +
120C VAL* 1.3 60.2 + - + +
121C ASN 3.1 6.7 + - - -
124C ARG* 3.7 15.7 + - - +
128C ILE* 3.5 19.4 - - + +
282C PHE* 4.0 10.7 - - - -
286C ARG* 2.3 41.3 + - - +
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Residues in contact with VAL 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116C LEU* 3.3 31.6 + - + +
117C GLN* 3.6 15.5 - - - +
119C GLU* 1.3 76.1 - - + +
121C ASN* 1.3 60.3 + - - +
122C ILE* 2.9 14.9 + - - +
286C ARG* 5.7 5.6 - - - +
290C LEU* 5.7 8.1 - - + -
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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