Contacts of the helix formed by residues 96 - 132 (chain C) in PDB entry 3MIW
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 GLU 96 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B ILE* 5.1 0.2 - - - -
98B GLN* 2.7 42.3 + - - +
94C MET* 3.0 36.7 + - + -
95C ILE* 1.3 74.7 - - - +
97C GLN* 1.3 62.2 + - - +
98C GLN 3.2 1.6 - - - -
99C MET* 3.4 4.0 - - - -
100C ASP* 2.9 31.7 + - - +
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Residues in contact with GLN 97 (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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28A EDO 4.8 4.9 + - - -
131A HIS* 5.5 0.6 - - - -
132A ASP* 3.2 50.7 + - - +
135A ILE* 4.0 8.3 - - - +
136A THR* 3.5 29.3 + - - +
94C MET* 4.5 6.8 - - + +
95C ILE* 3.9 16.1 + - - +
96C GLU* 1.3 83.7 - - - +
98C GLN* 1.3 64.5 + - + +
100C ASP* 4.5 3.4 - - - +
101C ARG* 3.9 23.7 + - - +
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Residues in contact with GLN 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A EDO 3.6 24.5 + - - +
129A ARG* 5.7 0.4 - - - +
132A ASP* 5.0 1.4 + - - +
95C ILE* 3.6 13.7 + - - +
97C GLN* 1.3 84.7 - - + +
99C MET* 1.3 62.0 + - - +
100C ASP 3.4 0.4 - - - -
101C ARG* 3.6 27.0 - - - +
102C ILE* 3.2 32.4 + - - +
96E GLU* 2.6 32.4 - - - +
99E MET* 3.4 19.9 - - + +
100E ASP* 2.7 33.7 + - - -
103E VAL* 4.4 3.5 - - + +
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Residues in contact with MET 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ILE* 3.3 40.2 - - + +
98B GLN* 3.0 46.3 - - + +
99B MET* 3.5 21.8 - - + +
102B ILE* 4.7 17.5 - - + +
95C ILE 3.2 18.8 - - - +
96C GLU* 3.4 2.2 - - - +
98C GLN* 1.3 80.7 - - - +
100C ASP* 1.3 63.2 + - - +
102C ILE* 3.6 6.4 + - - +
103C VAL* 3.2 22.6 + - - +
99E MET* 4.0 21.3 - - - -
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Residues in contact with ASP 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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98B GLN* 4.2 6.0 - - - +
101B ARG* 5.1 4.3 - - - +
96C GLU 2.9 16.8 + - - +
97C GLN* 4.5 4.0 - - - +
98C GLN 3.4 0.2 - - - -
99C MET* 1.3 77.0 - - - +
101C ARG* 1.3 63.2 + - - +
103C VAL* 2.8 26.9 - - + +
104C LYS* 3.3 11.1 + - - +
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Residues in contact with ARG 101 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A LYS* 4.3 12.9 + - - +
129A ARG* 5.8 2.0 - - - +
132A ASP* 2.4 39.3 + - - -
97C GLN* 3.9 16.8 + - - +
98C GLN* 3.6 39.4 + - - +
99C MET 3.4 0.4 - - - -
100C ASP* 1.3 79.5 - - + +
102C ILE* 1.3 59.0 + - + +
104C LYS* 3.6 6.8 + - - +
105C GLU* 3.1 21.7 + - - +
100E ASP* 4.1 6.1 + - - -
103E VAL* 4.6 22.5 - - + +
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Residues in contact with ILE 102 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 5.1 11.4 - - + -
98C GLN 3.2 20.6 - - - +
99C MET* 3.6 6.7 + - - +
100C ASP 3.3 0.6 - - - -
101C ARG* 1.3 73.3 - - - +
103C VAL* 1.4 58.5 + - - +
104C LYS 3.0 1.6 - - - -
105C GLU* 2.7 31.7 + - - +
106C MET* 2.8 17.8 + - + +
99E MET* 4.5 17.5 - - + +
102E ILE* 4.0 19.5 - - + -
103E VAL* 3.2 36.6 - - + -
106E MET* 3.3 24.0 - - - -
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Residues in contact with VAL 103 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLN* 5.3 2.7 - - + +
101B ARG* 3.4 58.8 - - + +
102B ILE* 5.1 9.7 - - + +
105B GLU* 4.8 7.2 - - + -
99C MET 3.2 17.5 + - - +
100C ASP* 2.8 27.6 - - + +
102C ILE* 1.4 73.0 - - - +
104C LYS* 1.3 64.9 - - + +
106C MET* 3.3 15.4 + - - +
107C ARG* 3.4 27.8 + - - +
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Residues in contact with LYS 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100C ASP 3.3 9.1 + - - +
101C ARG* 3.6 11.7 - - - +
102C ILE 3.0 0.6 - - - -
103C VAL* 1.3 85.4 - - + +
105C GLU* 1.3 64.9 + - - +
107C ARG* 3.5 11.1 + - - +
108C ARG* 3.4 15.6 + - - +
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Residues in contact with GLU 105 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ARG 3.1 11.3 + - - +
102C ILE* 2.7 20.8 + - - +
104C LYS* 1.3 77.2 - - - +
106C MET* 1.3 51.5 + - - +
108C ARG* 2.6 33.3 + - - +
109C GLN* 3.0 10.4 + - - +
103E VAL* 6.0 3.1 - - + -
106E MET* 3.5 24.2 - - + -
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Residues in contact with MET 106 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ILE* 4.1 30.3 - - - +
105B GLU* 4.0 21.7 - - + +
106B MET* 3.4 40.6 - - + +
109B GLN* 3.6 25.0 + - - +
102C ILE* 2.8 21.5 + - - +
103C VAL* 3.3 7.6 + - - +
105C GLU* 1.3 70.4 - - - +
107C ARG* 1.3 55.8 + - - +
108C ARG 3.3 0.2 - - - -
109C GLN* 3.6 8.6 - - - +
110C LEU* 2.9 27.2 + - - +
106E MET* 3.4 26.0 - - + +
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Residues in contact with ARG 107 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B EDO 3.6 19.2 + - - -
101B ARG* 3.0 40.8 - - - +
104B LYS* 5.5 3.4 - - - +
105B GLU* 3.1 38.8 + - - +
33C EDO 5.9 1.2 + - - -
103C VAL* 3.4 20.3 + - - +
104C LYS* 3.7 10.1 - - - +
105C GLU 2.9 1.2 + - - -
106C MET* 1.3 75.1 - - - +
108C ARG* 1.3 61.4 + - - +
110C LEU* 3.7 6.3 - - + +
111C GLU* 2.9 28.1 + - - +
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Residues in contact with ARG 108 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C LYS 3.4 8.5 + - - +
105C GLU* 2.6 12.9 + - - +
107C ARG* 1.3 77.4 - - - +
109C GLN* 1.3 66.5 + - - +
111C GLU* 3.0 6.4 + - - +
112C MET* 2.9 26.1 + - - +
110E LEU* 6.0 4.9 - - + -
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Residues in contact with GLN 109 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 2.8 33.0 + - - +
105C GLU 3.0 9.0 + - - +
106C MET* 3.6 10.4 - - - +
108C ARG* 1.3 76.3 - - - +
110C LEU* 1.3 57.1 + - - +
112C MET* 3.4 5.9 + - - +
113C ILE* 3.0 34.7 + - + +
106E MET* 3.1 29.1 - - - +
109E GLN* 3.3 34.8 + - + +
110E LEU* 4.9 12.2 + - + +
113E ILE* 3.5 27.3 - - + +
106G MET* 5.9 2.4 - - - +
109G GLN* 4.8 3.0 - - - +
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Residues in contact with LEU 110 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B GLU* 3.8 20.9 - - - +
108B ARG* 3.2 42.4 - - + +
109B GLN* 3.6 17.9 - - + +
112B MET* 3.7 23.3 - - + -
106C MET 2.9 18.0 + - - +
107C ARG* 3.7 8.1 - - + +
108C ARG 3.1 0.2 - - - -
109C GLN* 1.3 77.3 - - - +
111C GLU* 1.3 60.9 + - - +
113C ILE* 3.5 6.9 + - + +
114C ASP* 2.8 25.6 + - - +
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Residues in contact with GLU 111 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C EDO 3.4 35.3 + - - +
107C ARG 2.9 21.2 + - - +
108C ARG* 3.0 5.8 + - - +
110C LEU* 1.3 75.8 - - - +
112C MET* 1.3 61.3 + - - +
114C ASP* 3.4 20.0 - - - +
115C LYS* 3.1 23.9 + - - +
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Residues in contact with MET 112 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ARG 2.9 15.3 + - - +
109C GLN* 3.6 6.1 - - - +
111C GLU* 1.3 74.2 - - - +
113C ILE* 1.3 56.8 + - - +
115C LYS* 2.9 7.3 + - - +
116C LEU* 2.6 36.9 + - - +
113E ILE* 4.7 17.3 - - + +
114E ASP* 6.0 1.1 - - - +
117E THR* 4.7 7.6 + - - +
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Residues in contact with ILE 113 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109B GLN* 3.6 39.7 - - + +
112B MET* 3.2 23.6 - - + -
113B ILE* 4.6 19.7 - - + -
116B LEU* 4.9 12.3 - - + -
109C GLN* 3.0 26.0 - - + +
110C LEU* 3.5 8.7 - - + +
112C MET* 1.3 75.6 - - - +
114C ASP* 1.3 67.4 + - - +
116C LEU* 2.9 23.4 + - + +
117C THR* 2.9 14.6 + - - +
113E ILE* 4.8 16.3 - - + +
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Residues in contact with ASP 114 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B MET* 3.2 31.1 - - + +
24C EDO 6.1 0.2 - - - -
37C EDO 4.5 12.8 + - - -
110C LEU 2.8 18.8 + - - +
111C GLU* 3.4 29.0 - - - +
113C ILE* 1.3 78.5 - - - +
115C LYS* 1.3 60.3 + - - +
117C THR* 2.9 22.0 + - - +
118C THR* 3.4 4.9 + - - -
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Residues in contact with LYS 115 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C EDO 4.5 4.9 + - - +
24C EDO 4.5 16.4 - - - +
37C EDO 5.2 3.1 - - - +
111C GLU 3.1 10.6 + - - +
112C MET* 2.9 9.4 + - - +
114C ASP* 1.3 84.0 - - - +
116C LEU* 1.3 61.4 + - - +
118C THR* 3.1 19.8 + - - +
119C ARG* 3.3 20.7 + - - +
117E THR* 5.8 2.7 - - + -
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Residues in contact with LEU 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 4.0 27.6 - - + -
112C MET 2.6 16.3 + - - +
113C ILE* 2.9 16.4 + - + +
115C LYS* 1.3 72.9 - - - +
117C THR* 1.3 61.9 + - - +
119C ARG* 3.1 17.3 + - + +
120C GLU* 3.2 15.0 + - + +
113E ILE* 5.4 5.4 - - + -
116E LEU* 4.2 21.1 - - + -
117E THR* 3.2 38.5 - - + +
120E GLU* 3.3 36.1 - - + +
116I LEU* 6.0 0.2 - - + -
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Residues in contact with THR 117 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B MET* 4.1 12.6 - - - -
115B LYS* 4.2 25.8 - - + -
116B LEU* 3.3 31.3 + - + +
119B ARG* 4.4 17.7 - - + +
113C ILE* 2.9 12.7 + - - +
114C ASP* 3.1 15.0 - - - +
116C LEU* 1.3 77.5 - - - +
118C THR* 1.3 58.6 + - - +
120C GLU* 2.9 17.0 + - - +
121C ILE* 3.1 14.1 + - + +
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Residues in contact with THR 118 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C EDO 4.2 28.2 - - - -
114C ASP 3.4 4.0 + - - -
115C LYS* 3.1 14.6 + - - -
117C THR* 1.3 79.7 - - - +
119C ARG* 1.3 61.2 + - - +
121C ILE* 3.0 26.0 - - - +
122C GLU* 3.3 11.4 + - - +
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Residues in contact with ARG 119 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C EDO 3.6 38.8 + - - -
24C EDO 5.4 0.4 + - - -
115C LYS* 3.5 18.3 + - - +
116C LEU* 3.5 11.7 - - - +
117C THR 3.0 0.8 - - - -
118C THR* 1.3 78.8 + - - +
120C GLU* 1.3 59.9 + - - +
122C GLU* 4.0 1.1 - - - -
123C GLN* 3.0 30.4 + - - +
117E THR* 4.9 8.1 - - + +
120E GLU* 4.5 15.0 - - + -
121E ILE* 4.6 30.3 - - + +
124E ILE* 3.3 29.2 - - + +
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Residues in contact with GLU 120 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LEU* 3.3 22.3 - - + +
119B ARG* 3.7 19.6 - - + +
120B GLU* 2.6 25.7 - - - +
123B GLN* 2.8 36.1 + - - +
116C LEU* 3.5 10.7 - - + +
117C THR 2.9 8.6 + - - +
119C ARG* 1.3 79.9 - - - +
121C ILE* 1.3 59.8 - - - +
123C GLN* 3.0 24.1 + - - +
124C ILE* 3.6 8.0 + - - +
120E GLU* 2.5 37.8 - - - +
120I GLU* 4.3 0.2 - - - +
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Residues in contact with ILE 121 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 4.3 30.5 - - - +
122B GLU* 5.6 1.8 - - - +
117C THR* 3.1 8.1 + - + +
118C THR* 3.0 33.0 - - - +
120C GLU* 1.3 74.6 - - - +
122C GLU* 1.3 63.7 + - - +
123C GLN 3.2 1.8 - - - -
124C ILE* 3.1 26.2 + - + +
125C GLU* 3.4 6.9 + - - +
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Residues in contact with GLU 122 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C THR 3.3 14.3 + - - +
119C ARG* 4.0 6.1 - - - +
120C GLU 3.3 0.2 - - - -
121C ILE* 1.3 80.6 - - + +
123C GLN* 1.3 64.2 + - - +
124C ILE 3.0 2.5 + - - -
125C GLU* 3.1 9.4 + - - +
126C LEU* 3.1 27.2 + - + +
124E ILE* 4.1 18.4 - - + -
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Residues in contact with GLN 123 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN* 2.6 38.1 + - - +
119C ARG 3.0 19.9 + - - +
120C GLU* 3.0 17.5 - - - +
122C GLU* 1.3 78.1 - - - +
124C ILE* 1.3 56.2 + - - +
126C LEU* 3.8 10.0 - - - +
127C LEU* 2.9 31.9 + - - +
120E GLU* 3.1 33.5 + - - +
123E GLN* 3.1 30.3 + - - +
124E ILE* 3.4 16.2 - - + +
127E LEU* 4.3 13.0 - - + +
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Residues in contact with ILE 124 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 4.9 2.2 - - + +
122B GLU* 3.6 28.9 - - + +
123B GLN* 3.4 46.2 - - + +
126B LEU* 3.9 13.9 - - + -
120C GLU 3.7 13.0 - - - +
121C ILE* 3.2 15.9 - - + +
122C GLU 3.0 0.6 - - - -
123C GLN* 1.3 75.3 - - - +
125C GLU* 1.3 60.4 + - - +
126C LEU 2.9 1.1 - - - -
127C LEU* 2.8 3.1 + - + +
128C LYS* 2.6 56.5 + - + +
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Residues in contact with GLU 125 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121C ILE 3.4 5.8 + - - +
122C GLU* 3.1 11.8 + - - +
124C ILE* 1.3 77.8 - - - +
126C LEU* 1.3 57.2 + - + +
128C LYS* 3.7 13.3 + - - +
129C ARG* 2.8 46.1 + - - +
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Residues in contact with LEU 126 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLU* 3.1 19.1 + - + +
123C GLN* 3.8 7.6 - - - +
124C ILE 2.9 0.8 + - - -
125C GLU* 1.3 77.3 - - + +
127C LEU* 1.3 62.8 + - - +
128C LYS 3.2 0.2 - - - -
129C ARG* 3.4 30.8 + - - +
130C ILE* 3.2 33.4 + - + +
124E ILE* 3.5 39.3 - - + +
127E LEU* 3.8 14.4 - - + -
128E LYS* 3.6 26.0 - - + +
131E HIS* 5.2 8.2 - - + +
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Residues in contact with LEU 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLN* 3.8 31.2 - - + +
126B LEU* 3.4 33.8 - - + +
127B LEU* 3.9 19.5 - - + -
130B ILE* 3.9 21.1 - - + +
123C GLN 2.9 23.7 + - - +
124C ILE 2.8 3.8 + - - -
126C LEU* 1.3 74.0 - - - +
128C LYS* 1.3 58.9 + - - +
130C ILE* 3.4 7.2 + - + +
131C HIS* 2.9 30.1 + - - +
127E LEU* 4.3 27.1 - - + -
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Residues in contact with LYS 128 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B LEU* 3.4 28.5 - - + -
1C EDO 4.0 34.5 + - - +
124C ILE* 2.6 35.4 + - + +
125C GLU* 3.9 11.0 - - - +
127C LEU* 1.3 70.5 - - - +
129C ARG* 1.3 56.8 + - + +
130C ILE 3.1 4.5 - - - -
131C HIS* 3.3 5.1 + - - +
132C ASP* 2.5 41.9 + - - +
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Residues in contact with ARG 129 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLU* 2.8 34.2 + - - +
126C LEU* 3.4 25.9 + - - +
128C LYS* 1.3 75.9 - - + +
130C ILE* 1.3 57.9 + - - +
132C ASP* 4.0 9.6 - - - +
133C ASN* 3.7 19.9 + - - +
131E HIS* 3.7 42.2 + - + +
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Residues in contact with ILE 130 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 4.2 19.3 - - + -
126C LEU 3.2 20.8 + - - +
127C LEU* 3.7 7.4 - - + +
128C LYS 3.1 0.4 - - - -
129C ARG* 1.3 77.9 - - - +
131C HIS* 1.3 62.6 + - - +
132C ASP 3.1 1.7 + - - -
133C ASN* 3.7 8.4 + - - +
134C LEU* 3.1 23.4 + - + +
127E LEU* 3.9 30.1 - - + +
130E ILE* 4.7 6.5 - - + -
131E HIS* 3.7 39.9 - - + +
134E LEU* 4.1 16.3 - - + +
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Residues in contact with HIS 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU* 4.9 8.6 - - + +
129B ARG* 3.2 53.2 + - + +
130B ILE* 3.5 18.8 - - + -
133B ASN* 4.4 6.5 + - + +
127C LEU 2.9 17.7 + - - +
128C LYS* 3.3 6.9 + - - +
130C ILE* 1.3 77.4 - - - +
132C ASP* 1.3 69.7 + - - +
133C ASN 3.6 0.2 - - - -
134C LEU* 3.9 10.1 + - - +
135C ILE* 3.3 33.8 - - + +
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Residues in contact with ASP 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C LYS* 2.5 31.0 + - - +
129C ARG* 4.1 8.3 + - - +
130C ILE 3.1 0.4 - - - -
131C HIS* 1.3 91.3 + - - +
133C ASN* 1.3 61.2 + - - +
134C LEU 3.2 2.2 - - - -
135C ILE* 3.3 23.1 + - + +
136C THR* 3.4 14.6 + - - -
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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