Contacts of the helix formed by residues 110 - 143 (chain A) in PDB entry 2VT4
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 GLY 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A TRP* 2.8 25.5 + - - +
108A LEU 3.7 1.6 - - - -
109A TRP* 1.3 79.8 - - - +
111A SER* 1.3 65.1 + - - -
112A PHE 3.4 2.8 + - - -
113A LEU 3.4 0.8 + - - -
114A CYS 3.1 7.8 + - - -
196A PRO* 4.4 11.6 + - - -
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Residues in contact with SER 111 (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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110A GLY* 1.3 72.3 - - - -
112A PHE* 1.3 59.3 + - - +
114A CYS* 3.2 10.5 - - - +
115A GLU* 3.0 40.5 + - - +
193A TYR 5.3 6.1 - - - -
194A GLN 6.0 0.4 - - - -
196A PRO* 4.1 24.8 - - - +
198A CYS 6.1 0.4 - - - -
401A NA 4.6 8.3 - - - -
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Residues in contact with PHE 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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110A GLY 3.4 0.6 - - - -
111A SER* 1.3 77.7 + - - +
113A LEU* 1.3 74.0 + - + +
115A GLU* 3.1 6.9 + - - +
116A LEU* 2.8 50.4 + - + +
403A SOG 3.7 64.2 - - + +
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Residues in contact with LEU 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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97A PHE* 5.5 6.5 - - + -
107A TRP* 3.8 4.2 - - + -
109A TRP* 3.6 47.3 - - + +
110A GLY 3.4 2.8 + - - +
112A PHE* 1.3 89.2 - - + +
114A CYS* 1.3 53.5 - - - +
116A LEU* 3.8 23.6 - - + +
117A TRP* 2.8 35.9 + - - +
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Residues in contact with CYS 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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107A TRP* 3.6 15.8 - - + +
110A GLY 3.1 13.9 + - - +
111A SER* 3.2 16.2 - - - +
112A PHE 3.1 0.2 - - - -
113A LEU* 1.3 77.4 - - - +
115A GLU* 1.3 63.0 + - - +
117A TRP* 3.6 2.2 - - - +
118A THR* 2.9 33.5 + - - -
198A CYS 4.3 4.9 - - - +
199A CYS* 2.0 56.4 - - - -
200A ASP 5.8 0.4 - - - -
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Residues in contact with GLU 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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111A SER* 3.0 26.7 + - - +
112A PHE* 3.1 4.7 + - - +
114A CYS* 1.3 80.7 - - - +
116A LEU* 1.3 62.8 + - - +
118A THR* 3.9 6.2 - - - -
119A SER* 3.0 27.0 + - - -
177A ILE* 4.0 10.2 - - + +
180A HIS* 4.7 0.3 - - - -
182A TRP* 4.5 15.1 - - + -
183A ARG* 3.2 33.7 + - - -
403A SOG 3.0 39.2 - - + +
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Residues in contact with LEU 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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112A PHE* 2.8 33.8 + - + +
113A LEU* 3.8 23.6 - - + +
115A GLU* 1.3 77.0 - - - +
117A TRP* 1.3 57.6 + - - +
119A SER* 2.9 7.9 - - - -
120A LEU* 2.9 50.0 + - + +
174A PHE* 5.0 2.5 - - + -
403A SOG 3.7 33.3 - - + +
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Residues in contact with TRP 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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93A LEU* 4.0 8.1 - - + -
94A VAL* 2.9 40.5 + - + +
97A PHE* 4.1 8.5 - + + -
98A GLY* 3.5 27.1 - - - +
101A LEU* 4.0 20.6 - - + -
107A TRP* 3.7 19.5 - + + -
113A LEU 2.8 21.9 + - - +
114A CYS 3.6 1.3 - - - +
116A LEU* 1.3 71.2 - - - +
118A THR* 1.3 72.4 + - - +
120A LEU* 3.3 9.8 + - + +
121A ASP* 2.9 30.0 + - - +
199A CYS* 3.6 34.1 - - - -
333A TYR* 4.3 13.7 - + - -
400A P32 3.7 27.4 - - + -
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Residues in contact with THR 118 (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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114A CYS* 2.9 18.2 + - - -
115A GLU* 3.9 6.5 - - - -
116A LEU 3.4 0.2 - - - -
117A TRP* 1.3 86.2 - - - +
119A SER* 1.3 59.0 + - - +
121A ASP* 3.3 7.1 + - - +
122A VAL* 2.9 36.4 + - + +
177A ILE* 3.8 8.5 - - + -
199A CYS* 4.3 5.9 + - - -
201A PHE* 3.5 51.2 - - + +
400A P32 4.1 14.3 - - + +
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Residues in contact with SER 119 (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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115A GLU 3.0 7.5 + - - -
116A LEU* 2.9 16.4 + - - -
118A THR* 1.3 76.5 - - - +
120A LEU* 1.3 56.6 + - - -
122A VAL* 3.2 5.4 + - - +
123A LEU* 2.8 29.1 + - - +
173A SER* 4.5 3.7 + - - -
174A PHE* 3.5 29.4 - - - -
177A ILE* 3.6 19.3 - - - +
403A SOG 3.0 27.5 - - - +
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Residues in contact with LEU 120 (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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89A VAL* 4.8 11.9 - - + -
93A LEU* 4.3 29.8 - - + -
94A VAL* 4.1 12.8 - - + -
116A LEU* 2.9 40.1 + - + +
117A TRP* 3.3 10.3 + - + +
119A SER* 1.3 75.6 - - - +
121A ASP* 1.3 63.0 + - - +
123A LEU* 3.3 13.8 + - + +
124A CYS* 3.1 28.4 + - - -
174A PHE* 3.9 23.8 - - + -
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Residues in contact with ASP 121 (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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90A VAL* 6.4 0.2 - - - -
94A VAL* 3.8 22.2 - - + +
117A TRP* 2.9 20.7 + - + +
118A THR* 3.6 8.1 - - - +
120A LEU* 1.3 78.8 - - - +
122A VAL* 1.3 60.2 + - - +
124A CYS* 3.6 3.0 + - - +
125A VAL* 3.5 21.8 + - - +
333A TYR* 2.5 33.7 + - - -
400A P32 2.6 44.3 + - + +
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Residues in contact with VAL 122 (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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118A THR* 2.9 33.4 + - + +
119A SER* 3.6 6.1 - - - +
121A ASP* 1.3 75.8 - - + +
123A LEU* 1.3 60.6 + - - +
124A CYS 3.4 0.2 + - - -
125A VAL* 3.6 1.9 + - - +
126A THR* 2.8 34.2 + - - +
172A VAL 4.9 0.9 - - - +
173A SER* 3.5 26.5 - - - +
177A ILE* 5.2 2.9 - - + -
201A PHE* 4.5 11.0 - - + -
207A TYR* 4.8 8.3 - - - +
211A SER* 6.2 0.4 - - - -
215A SER* 4.6 2.0 - - - +
400A P32 3.7 45.7 - - + -
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Residues in contact with LEU 123 (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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89A VAL* 5.8 2.0 - - + -
119A SER 2.8 16.8 + - - +
120A LEU* 3.4 20.0 - - + +
122A VAL* 1.3 73.5 - - - +
124A CYS* 1.3 55.9 + - - +
126A THR* 3.2 4.7 + - - -
127A ALA* 2.7 36.4 + - - +
166A TRP* 3.9 29.4 - - + -
169A SER* 3.7 8.7 - - - -
170A ALA* 3.5 28.5 - - + +
173A SER* 3.5 22.1 - - - +
174A PHE* 3.6 24.5 - - + -
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Residues in contact with CYS 124 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A ALA* 3.5 27.6 - - - +
89A VAL* 3.6 27.1 - - - -
90A VAL* 3.6 24.9 - - + -
94A VAL* 4.9 1.6 - - - -
120A LEU 3.1 17.5 + - - +
121A ASP* 4.2 4.0 - - - +
123A LEU* 1.3 83.6 - - - +
125A VAL* 1.3 66.4 + - + +
127A ALA* 3.9 5.0 - - - +
128A SER* 2.8 31.3 + - - -
166A TRP* 5.1 2.9 - - - -
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Residues in contact with VAL 125 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A VAL* 6.5 0.2 - - + -
121A ASP* 3.5 17.6 + - - +
122A VAL 4.1 0.4 - - - +
123A LEU 3.5 0.2 - - - -
124A CYS* 1.3 76.7 - - + +
126A THR* 1.3 64.9 + - - +
128A SER* 3.6 5.1 - - - -
129A ILE* 3.2 26.8 + - + +
215A SER 5.6 1.6 - - - +
216A PHE* 4.7 4.7 - - + -
299A PHE* 4.3 10.7 - - + -
303A TRP* 3.6 42.4 - - + +
307A PHE* 4.1 29.2 - - + -
400A P32 3.9 20.9 - - + -
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Residues in contact with THR 126 (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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122A VAL* 2.8 17.3 + - - +
123A LEU* 3.3 9.2 - - - -
125A VAL* 1.3 78.3 - - - +
127A ALA* 1.3 62.8 + - - +
129A ILE* 3.2 9.9 - - - +
130A GLU* 3.1 44.1 + - - +
169A SER* 3.7 13.0 - - - +
172A VAL* 3.9 21.1 - - + -
173A SER* 4.6 1.1 - - - -
215A SER* 3.1 33.3 + - - +
400A P32 4.0 1.2 - - - -
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Residues in contact with ALA 127 (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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86A ALA* 4.9 2.5 - - + -
123A LEU 2.7 19.6 + - - +
124A CYS* 4.1 3.1 - - - +
126A THR* 1.3 73.5 - - - +
128A SER* 1.3 57.0 + - - +
130A GLU* 3.5 2.4 + - - +
131A THR* 2.9 35.9 + - - +
165A VAL* 4.2 3.1 - - + +
166A TRP* 4.0 44.2 - - + +
169A SER* 3.4 16.9 + - - +
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Residues in contact with SER 128 (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 20.4 - - - +
86A ALA* 3.5 17.2 - - - +
87A ASP* 4.4 6.9 + - - -
90A VAL* 6.1 0.3 - - - +
124A CYS* 2.8 22.0 + - - +
125A VAL* 3.6 6.2 - - - -
126A THR 3.2 0.2 - - - -
127A ALA* 1.3 76.9 - - - +
129A ILE* 1.3 58.0 + - - +
131A THR* 3.2 4.0 + - - -
132A LEU* 2.9 33.9 + - - +
299A PHE* 3.8 19.5 - - - -
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Residues in contact with ILE 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL 3.2 15.7 + - - +
126A THR 3.2 7.6 - - - +
128A SER* 1.3 76.8 - - - +
130A GLU* 1.3 64.3 + - - +
132A LEU* 4.3 2.5 - - + -
133A CYS* 3.1 18.4 + - - +
215A SER 3.2 24.0 - - - +
216A PHE* 4.2 10.3 - - + +
219A PRO* 3.6 21.1 - - + +
220A LEU* 4.0 22.4 - - + +
223A MET* 3.9 24.9 - - - -
299A PHE* 3.6 32.5 - - + -
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Residues in contact with GLU 130 (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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126A THR* 3.1 33.7 + - + +
127A ALA 3.9 2.5 - - - +
129A ILE* 1.3 75.9 - - - +
131A THR* 1.3 64.4 + - - +
133A CYS* 3.0 11.3 + - + +
134A VAL* 3.0 26.1 + - - +
165A VAL* 3.4 26.2 - - + +
168A ILE* 3.8 25.7 - - - +
169A SER* 3.3 19.0 + - - -
172A VAL* 4.9 2.6 - - - +
214A ILE 4.7 8.3 - - - +
219A PRO* 4.5 17.6 - - + +
406A D10 5.3 6.8 - - + +
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Residues in contact with THR 131 (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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79A PHE* 3.6 31.0 - - + +
82A SER* 3.8 21.2 + - - -
83A LEU* 4.3 13.0 + - + -
127A ALA* 2.9 25.1 + - - +
128A SER 3.5 4.9 - - - -
130A GLU* 1.3 75.1 - - - +
132A LEU* 1.3 57.4 + - - +
134A VAL* 3.4 7.3 + - + +
135A ILE* 2.9 36.7 + - + +
162A ILE* 6.2 0.2 - - + -
165A VAL* 3.8 14.5 - - - +
166A TRP* 5.0 0.9 + - - -
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Residues in contact with LEU 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 3.5 28.5 - - + -
128A SER* 2.9 19.5 + - - +
129A ILE* 3.7 5.4 - - - +
130A GLU 3.2 0.4 - - - -
131A THR* 1.3 72.8 - - - +
133A CYS* 1.3 66.0 + - - +
135A ILE* 3.3 10.8 + - + +
136A ALA* 3.1 19.2 + - - +
223A MET* 3.6 23.1 - - - +
295A ILE* 3.8 20.2 - - + +
296A MET* 3.7 22.3 - - + +
299A PHE* 3.6 47.3 - - + -
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Residues in contact with CYS 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ILE 3.1 11.3 + - - +
130A GLU* 3.0 14.1 + - + +
132A LEU* 1.3 77.6 - - - +
134A VAL* 1.3 64.0 + - + +
136A ALA* 3.2 5.2 + - - +
137A ILE* 3.0 30.5 + - + +
219A PRO* 2.9 39.9 - - - -
222A ILE* 3.7 17.5 - - + +
223A MET* 3.7 21.7 - - - +
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Residues in contact with VAL 134 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A PHE* 3.8 36.8 - - + -
130A GLU 3.0 15.6 + - - +
131A THR* 3.7 9.2 - - + +
133A CYS* 1.3 76.9 - - + +
135A ILE* 1.3 58.3 + - - +
137A ILE* 3.3 9.2 + - + +
138A ASP* 2.9 30.6 + - + +
161A ILE* 4.0 17.9 - - + -
165A VAL* 3.8 25.1 - - + -
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Residues in contact with ILE 135 (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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76A THR* 4.8 8.1 - - + +
79A PHE* 3.4 38.8 - - + -
80A ILE* 4.3 12.1 - - + -
83A LEU* 4.1 19.1 - - + -
131A THR* 2.9 31.4 + - + +
132A LEU* 3.6 10.5 - - + +
133A CYS 3.3 0.2 - - - -
134A VAL* 1.3 75.7 - - - +
136A ALA* 1.3 60.6 + - - +
138A ASP* 3.7 6.1 - - - +
139A ARG* 3.2 23.7 + - - +
292A LEU* 4.2 27.6 - - + -
296A MET* 4.0 14.8 - - + -
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Residues in contact with ALA 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU 3.1 13.5 + - - +
133A CYS* 3.2 8.7 + - - +
135A ILE* 1.3 74.4 - - - +
137A ILE* 1.3 60.5 + - - +
139A ARG* 3.3 2.8 + - - +
140A TYR* 2.9 30.3 + - - +
223A MET* 4.3 12.3 - - + +
226A VAL* 3.5 24.4 - - + +
230A VAL* 3.9 1.9 - - - +
296A MET* 3.9 4.0 - - + +
405A SOG 3.9 26.2 - - + -
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Residues in contact with ILE 137 (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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133A CYS* 3.0 25.7 + - + +
134A VAL* 3.9 7.9 - - + +
136A ALA* 1.3 75.5 - - - +
138A ASP* 1.3 58.3 + - - +
140A TYR* 3.8 4.6 - - + +
141A LEU* 2.9 50.0 + - + +
222A ILE* 4.5 16.4 - - + -
226A VAL* 4.0 23.3 - - + -
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Residues in contact with ASP 138 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.9 0.5 - - - +
76A THR* 3.4 11.9 + - - +
79A PHE* 3.6 30.6 - - + -
134A VAL* 2.9 19.2 + - + +
135A ILE* 3.7 4.8 - - - +
137A ILE* 1.3 77.7 - - - +
139A ARG* 1.3 79.3 + - - +
141A LEU* 3.3 5.2 + - - +
142A ALA* 2.9 27.9 + - - +
149A TYR* 2.8 34.4 + - - -
153A MET* 4.3 14.2 - - + +
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Residues in contact with ARG 139 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 5.4 0.8 - - - +
76A THR* 3.2 25.4 + - - +
135A ILE* 3.2 19.2 + - + +
136A ALA* 3.8 4.3 - - - +
138A ASP* 1.3 86.7 + - - +
140A TYR* 1.3 66.6 + - - +
142A ALA* 3.0 37.2 + - - +
143A ILE* 3.2 16.7 + - + +
149A TYR* 3.0 28.5 + - - -
230A VAL* 4.5 9.9 - - + -
285A GLU* 5.6 4.0 + - - -
289A LEU* 4.0 24.4 - - + +
292A LEU* 3.7 24.0 - - + -
405A SOG 5.0 3.8 - - + -
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Residues in contact with TYR 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A ALA 2.9 16.8 + - - +
137A ILE* 3.8 5.2 - - + +
139A ARG* 1.3 72.6 - - - +
141A LEU* 1.3 83.4 + - + +
143A ILE* 3.2 17.6 - - + +
144A THR* 3.1 41.3 + - + +
226A VAL* 4.2 9.6 - - + -
229A ARG* 4.1 31.4 + - + -
230A VAL* 3.2 32.1 - - + +
233A GLU* 4.6 8.2 + - + -
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Residues in contact with LEU 141 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137A ILE* 2.9 37.2 + - + +
138A ASP* 3.8 5.6 - - - +
140A TYR* 1.3 94.5 - - + +
142A ALA* 1.3 59.7 + - - +
143A ILE 2.9 9.5 + - - -
144A THR* 4.2 5.4 - - - +
145A SER* 3.4 33.7 + - - +
149A TYR* 3.9 13.6 - - + +
153A MET* 6.3 3.1 - - + -
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Residues in contact with ALA 142 (chain A).
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----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A ASP 2.9 11.2 + - - +
139A ARG* 3.0 42.9 + - - +
141A LEU* 1.3 75.5 - - - +
143A ILE* 1.3 59.5 + - - +
144A THR 3.7 0.4 - - - -
146A PRO* 3.9 19.9 - - - +
149A TYR* 3.4 26.7 - - + -
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Residues in contact with ILE 143 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139A ARG 3.4 11.4 - - - +
140A TYR* 3.2 20.4 - - + +
141A LEU 2.9 1.2 - - - -
142A ALA* 1.3 81.9 - - - +
144A THR* 1.3 70.4 + - + +
145A SER 3.8 0.2 - - - -
146A PRO* 4.5 4.7 - - - -
230A VAL* 4.8 6.1 - - + +
233A GLU* 4.0 17.6 - - + +
234A ALA* 4.5 14.8 - - - +
237A GLN* 3.9 34.7 + - - +
289A LEU* 4.3 23.3 - - + -
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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