Contacts of the helix formed by residues 126 - 160 (chain A) in PDB entry 4DJH
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 PHE 126 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A PHE* 3.4 33.2 - + + -
117A THR* 3.3 34.8 - - + -
118A VAL* 4.0 7.9 - - + -
124A TRP* 3.3 28.2 - + - +
125A PRO* 1.3 91.8 - - + +
127A GLY* 1.3 62.1 + - - +
129A VAL* 4.4 4.5 - - - +
130A LEU* 3.4 48.1 + - + +
56B PRO* 3.3 35.8 - - + +
57B ALA* 5.4 0.4 - - - -
59B PRO* 5.6 1.8 - - + -
60B VAL* 3.7 19.3 - - + -
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Residues in contact with GLY 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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124A TRP* 2.9 24.4 + - - +
125A PRO 3.2 6.0 + - - -
126A PHE* 1.3 80.8 - - - +
128A ASP* 1.3 66.1 + - - -
129A VAL* 3.6 1.6 - - - -
131A CYS* 3.2 6.6 + - - +
199A THR* 3.7 9.9 - - - -
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Residues in contact with ASP 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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127A GLY* 1.3 68.4 - - - -
129A VAL* 1.3 71.3 + - + +
131A CYS* 3.0 5.9 + - - +
132A LYS* 2.8 45.7 + - + +
198A GLY* 3.7 6.7 - - - -
199A THR* 2.8 42.3 + - - +
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Residues in contact with VAL 129 (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 PHE 4.4 6.3 - - - +
127A GLY* 4.9 0.7 - - - -
128A ASP* 1.3 78.6 - - + +
130A LEU* 1.3 83.6 + - + +
132A LYS* 3.2 10.5 + - + +
133A ILE* 3.0 32.8 + - + +
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Residues in contact with LEU 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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114A PHE* 4.1 17.5 - - + -
124A TRP* 3.7 4.7 - - + -
126A PHE* 3.4 54.1 - - + +
127A GLY 3.8 1.2 + - - -
128A ASP 3.3 0.4 - - - -
129A VAL* 1.3 87.8 - - + +
131A CYS* 1.3 59.1 + - - +
133A ILE* 3.0 17.6 + - + -
134A VAL* 2.8 36.9 + - + +
56B PRO* 5.6 4.9 - - + -
57B ALA* 6.5 0.7 - - - -
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Residues in contact with CYS 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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124A TRP* 3.3 10.4 - - + +
127A GLY 3.2 13.7 + - - +
128A ASP* 3.0 12.3 + - - +
130A LEU* 1.3 76.7 - - - +
132A LYS* 1.3 62.0 + - - +
134A VAL* 3.7 0.7 - - - +
135A LEU* 3.1 34.8 + - - +
198A GLY 3.4 34.8 - - - -
199A THR* 4.3 1.1 - - - +
210A CYS* 2.0 47.3 - - + -
211A SER 3.7 3.6 - - - -
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Residues in contact with LYS 132 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A ASP* 2.8 37.3 + - + +
129A VAL* 3.6 11.4 - - + +
131A CYS* 1.3 72.6 - - - +
133A ILE* 1.3 61.4 + - + +
135A LEU* 4.6 0.2 - - - -
136A SER* 3.2 21.8 + - - -
193A ALA 3.9 8.1 - - - +
194A ILE* 2.9 45.4 + - + +
195A VAL* 3.9 12.0 + - - +
197A GLY* 3.0 31.6 - - - +
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Residues in contact with ILE 133 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 3.0 25.2 + - + +
130A LEU* 3.0 21.5 + - + +
132A LYS* 1.3 75.2 - - + +
134A VAL* 1.3 63.9 + - + +
135A LEU 3.1 1.8 - - - -
136A SER* 2.6 23.4 + - - +
137A ILE* 2.9 31.1 + - + +
194A ILE* 5.4 3.8 - - + -
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Residues in contact with VAL 134 (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 THR* 4.5 15.4 - - + +
114A PHE* 4.2 25.8 - - + -
124A TRP* 3.5 25.4 - - + -
130A LEU* 2.8 23.0 + - + +
131A CYS 3.7 5.4 - - - +
133A ILE* 1.3 76.6 - - + +
135A LEU* 1.3 56.7 + - - +
137A ILE* 3.3 12.4 + - + +
138A ASP* 2.7 34.7 + - - +
1300A JDC 3.4 34.7 - - + +
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Residues in contact with LEU 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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131A CYS* 3.1 33.1 + - - +
132A LYS 3.9 3.4 - - - +
133A ILE 3.1 0.6 - - - -
134A VAL* 1.3 79.2 - - - +
136A SER* 1.3 59.9 + - - +
138A ASP* 3.1 10.0 + - - +
139A TYR* 2.9 44.0 + - + -
193A ALA* 3.8 13.0 - - + +
197A GLY* 3.7 26.9 - - - -
211A SER* 3.8 20.6 - - - -
212A LEU* 3.9 13.0 - - + -
1300A JDC 3.8 27.1 - - + -
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Residues in contact with SER 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LYS 3.2 7.1 + - - -
133A ILE* 2.6 24.2 + - - +
135A LEU* 1.3 77.6 - - - +
137A ILE* 1.3 57.4 + - - +
139A TYR* 4.0 0.9 - - - +
140A TYR* 2.8 43.1 + - - -
190A GLY* 3.0 25.2 - - - -
193A ALA* 3.6 10.2 - - - +
194A ILE* 3.4 24.2 - - - +
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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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107A LEU* 3.7 53.4 - - + +
108A VAL* 4.0 6.7 - - + +
110A THR* 4.8 4.3 - - - +
111A THR* 3.8 18.4 - - + -
133A ILE* 2.9 35.5 + - + +
134A VAL* 3.4 14.1 - - + +
136A SER* 1.3 76.5 - - - +
138A ASP* 1.3 68.7 + - - +
140A TYR* 3.0 7.3 + - + -
141A ASN* 2.7 26.0 + - + +
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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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108A VAL* 5.4 0.7 - - - -
134A VAL 2.7 20.6 + - - +
135A LEU* 3.2 13.7 - - + +
137A ILE* 1.3 77.3 - - - +
139A TYR* 1.3 66.6 + - - +
141A ASN* 3.8 6.0 + - - +
142A MET* 3.3 20.1 + - - +
1300A JDC 2.6 96.0 + - + +
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Residues in contact with TYR 139 (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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135A LEU* 2.9 34.0 + - + +
136A SER 4.2 2.0 - - - +
138A ASP* 1.3 88.2 - - - +
140A TYR* 1.3 64.8 + - - +
142A MET* 3.3 31.3 + - + +
143A PHE* 3.1 32.0 + + - +
189A VAL* 3.2 38.1 - - + +
193A ALA* 4.2 10.5 - - + -
212A LEU* 3.6 33.8 - - + +
226A MET* 4.5 12.2 - - - +
227A LYS* 5.6 4.5 - - - +
230A VAL* 4.1 12.8 - - + -
1300A JDC 3.7 24.0 + + - -
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Residues in contact with TYR 140 (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 LEU* 5.9 3.4 - - + -
136A SER* 2.8 36.2 + - - +
137A ILE* 3.6 7.0 - - + +
139A TYR* 1.3 70.7 - - - +
141A ASN* 1.3 57.9 + - - +
144A THR* 2.7 40.8 + - - -
183A TRP* 3.6 38.6 - + + -
186A SER* 3.4 22.2 - - - -
187A SER* 3.0 50.0 + - - -
190A GLY* 3.7 15.2 - - - -
191A ILE* 3.9 10.4 - - - +
194A ILE* 5.4 4.7 - - + -
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Residues in contact with ASN 141 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ALA* 3.4 24.6 + - - +
105A ASP* 3.7 14.8 + - - -
107A LEU* 5.9 0.7 - - + -
108A VAL* 3.4 45.8 - - + +
137A ILE* 2.7 20.5 + - + +
138A ASP 3.9 4.0 - - - +
140A TYR* 1.3 71.4 - - - +
142A MET* 1.3 62.8 + - - +
145A SER* 2.8 36.0 + - - -
183A TRP* 5.6 0.4 - - - -
287A TRP* 3.1 29.3 - - - -
323A SER* 4.7 0.8 + - - -
1300A JDC 4.8 0.3 - - - +
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Residues in contact with MET 142 (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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138A ASP* 3.3 11.2 + - - +
139A TYR* 3.3 44.4 - - + +
140A TYR 3.2 0.6 - - - -
141A ASN* 1.3 87.1 + - - +
143A PHE* 1.3 63.2 + - + +
145A SER* 3.7 3.1 + - - -
146A ILE* 3.2 23.9 + - - +
230A VAL* 3.9 10.1 - - + -
234A ALA* 4.3 8.4 - - + +
283A PHE* 4.9 2.8 - - - -
287A TRP* 3.7 24.2 - - + -
291A HIS* 3.6 30.5 - - + +
1300A JDC 3.7 33.0 - - + -
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Residues in contact with PHE 143 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TYR 3.1 19.6 + - - +
142A MET* 1.3 84.3 - - + +
144A THR* 1.3 67.7 + - - +
146A ILE* 3.0 20.0 - - - +
147A PHE* 3.1 37.9 + + + -
185A LEU 5.8 0.7 - - - -
186A SER* 3.7 21.1 - - - +
189A VAL* 3.7 37.7 - - + -
229A CYS 5.1 0.4 - - - -
230A VAL* 4.2 28.5 - - + -
233A PHE* 4.0 20.2 - + + -
234A ALA* 3.8 27.8 - - + -
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Residues in contact with THR 144 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A ASN* 4.1 13.7 - - - +
104A ALA* 3.6 21.3 - - + -
140A TYR 2.7 25.8 + - - -
141A ASN 4.1 0.7 - - - -
143A PHE* 1.3 73.4 - - - +
145A SER* 1.3 55.4 + - - +
147A PHE 3.5 0.2 + - - -
148A THR* 2.7 45.2 + - - +
182A ILE* 3.8 8.0 - - + +
183A TRP* 3.7 37.2 - - + -
186A SER* 3.4 17.0 + - - -
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Residues in contact with SER 145 (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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101A LEU* 3.6 23.5 - - - +
104A ALA* 4.4 10.3 - - - -
105A ASP* 4.4 9.2 - - - -
141A ASN* 2.8 26.3 + - - -
142A MET* 3.7 4.0 + - - -
144A THR* 1.3 80.8 - - - +
146A ILE* 1.3 63.1 + - - +
148A THR* 3.7 2.6 - - - -
149A LEU* 3.1 31.6 + - - +
283A PHE* 3.5 21.4 - - - -
287A TRP* 5.1 0.7 - - - -
322A ASN* 6.1 0.2 - - - -
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Residues in contact with ILE 146 (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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142A MET 3.2 15.3 - - - +
143A PHE* 3.0 23.3 - - - +
145A SER* 1.3 82.9 + - - +
147A PHE* 1.3 68.4 + - + +
149A LEU* 3.4 5.0 + - + +
150A THR* 2.8 29.5 + - - +
234A ALA* 3.7 23.8 - - - +
235A PHE* 5.5 0.4 - - + -
238A PRO* 3.5 30.3 - - + -
239A VAL* 4.5 12.3 - - + -
242A ILE* 4.5 11.9 - - + -
283A PHE* 3.6 33.0 - - + -
284A VAL* 5.8 0.7 - - + -
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Residues in contact with PHE 147 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A PHE* 3.1 46.4 + + - +
146A ILE* 1.3 84.6 - - + +
148A THR* 1.3 66.6 + - - +
150A THR* 3.3 6.4 + - - -
151A MET* 3.0 28.5 + - + +
182A ILE* 3.5 33.4 - - + -
185A LEU* 4.4 26.9 - - + -
186A SER* 4.1 9.6 - - - -
233A PHE* 3.6 26.0 - + + -
238A PRO* 4.9 9.0 - - + -
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Residues in contact with THR 148 (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 TYR* 3.4 42.8 - - + +
100A ASN* 2.7 30.4 + - + +
101A LEU* 4.2 12.3 - - + +
144A THR* 2.7 23.4 + - - +
145A SER* 3.7 7.2 - - - -
147A PHE* 1.3 77.3 - - - +
149A LEU* 1.3 57.5 + - - +
151A MET* 3.1 4.2 + - - +
152A MET* 2.8 31.0 + - - +
182A ILE* 3.8 10.0 - - - +
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Residues in contact with LEU 149 (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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101A LEU* 3.5 33.0 - - + -
145A SER 3.1 19.8 + - - +
146A ILE* 3.7 6.3 - - + +
147A PHE 3.3 0.2 - - - -
148A THR* 1.3 79.4 - - - +
150A THR* 1.3 57.2 + - - +
152A MET* 3.5 17.3 + - + +
153A SER* 3.0 31.1 + - - -
242A ILE* 4.2 7.2 - - + -
279A VAL* 3.8 15.5 - - + +
280A VAL* 4.1 23.7 - - + +
283A PHE* 3.6 46.9 - - + -
326A ASN* 6.3 0.2 - - - +
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Residues in contact with THR 150 (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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146A ILE 2.8 15.9 + - - -
147A PHE* 3.6 9.8 - - - -
148A THR 3.2 0.2 - - - -
149A LEU* 1.3 77.8 - - - +
151A MET* 1.3 63.2 + - - +
153A SER* 3.2 4.5 + - - -
154A VAL* 2.9 34.6 + - + +
238A PRO* 3.3 24.5 - - + +
241A ILE* 3.6 34.8 - - + -
242A ILE* 3.5 19.9 - - + +
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Residues in contact with MET 151 (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 TYR* 4.0 14.4 + - + +
147A PHE* 3.0 19.1 + - + +
148A THR 3.6 7.4 - - - +
150A THR* 1.3 79.1 - - - +
152A MET* 1.3 60.6 + - - +
154A VAL* 3.4 24.9 + - + +
155A ASP* 2.8 28.9 + - - +
178A ILE* 3.8 44.0 - - + -
182A ILE* 3.9 9.9 - - + -
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Residues in contact with MET 152 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A THR* 4.2 6.7 - - + +
97A TYR* 3.2 44.9 - - + -
98A ILE* 4.2 26.5 - - + -
101A LEU* 4.7 4.7 - - + -
148A THR* 2.8 15.2 + - - +
149A LEU* 3.5 31.4 - - + +
151A MET* 1.3 74.9 - - - +
153A SER* 1.3 65.8 + - - +
155A ASP* 3.2 4.3 + - - +
156A ARG* 2.9 26.0 + - - +
275A LEU* 5.7 0.9 - - + -
276A VAL* 3.4 42.8 - - + +
279A VAL* 5.4 5.4 - - + -
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Residues in contact with SER 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU 3.0 15.0 + - - -
150A THR 3.4 9.0 - - - -
152A MET* 1.3 75.4 - - - +
154A VAL* 1.3 58.2 + - - +
156A ARG* 3.1 5.6 + - - +
157A TYR* 2.8 24.8 + - - +
242A ILE* 4.0 10.1 - - - +
245A CYS* 3.4 21.4 - - - -
246A TYR* 3.2 32.3 + - - -
249A MET* 3.8 2.1 - - - +
276A VAL* 4.2 6.6 - - - +
280A VAL* 3.9 9.9 - - - +
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Residues in contact with VAL 154 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR* 2.9 26.3 + - + +
151A MET* 3.6 29.8 - - + +
152A MET 3.2 0.2 - - - -
153A SER* 1.3 75.4 - - - +
155A ASP* 1.3 63.6 + - - +
157A TYR* 3.2 17.4 + - + +
158A ILE* 3.2 21.7 + - + +
241A ILE* 5.0 7.2 - - + -
245A CYS* 3.7 17.9 - - - -
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Residues in contact with ASP 155 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA* 3.3 30.0 - - - +
94A THR* 3.7 5.7 + - - -
97A TYR* 3.7 20.5 + - + +
151A MET 2.8 14.6 + - - +
152A MET* 3.3 9.6 - - - +
154A VAL* 1.3 77.1 - - - +
156A ARG* 1.3 85.3 + - - +
157A TYR 3.2 0.5 + - - -
158A ILE* 3.2 22.7 + - - +
159A ALA* 3.0 22.1 + - - +
171A THR* 4.7 6.1 - - - +
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Residues in contact with ARG 156 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A ALA* 5.3 2.8 - - - +
94A THR* 3.4 19.6 + - - +
152A MET 2.9 15.9 + - - +
153A SER* 3.1 6.5 + - - +
155A ASP* 1.3 89.2 + - - +
157A TYR* 1.3 61.7 + - - +
159A ALA* 3.3 31.2 + - - +
160A VAL* 3.4 12.1 - - - +
166A ALA* 5.4 7.1 - - - +
246A TYR* 4.6 1.8 - - - +
249A MET* 3.2 23.1 - - + +
269A LEU* 3.7 20.8 + - - +
272A ILE* 3.1 32.0 - - - +
273A THR* 3.4 36.2 + - - +
276A VAL* 3.6 30.3 - - + -
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A SER 2.8 12.0 + - - +
154A VAL* 3.2 13.0 - - + +
155A ASP 3.1 0.2 - - - -
156A ARG* 1.3 78.6 - - - +
158A ILE* 1.3 68.5 + - + +
159A ALA 3.1 0.2 - - - -
160A VAL* 3.3 11.1 - - - +
245A CYS* 3.3 34.1 - - - -
248A LEU* 3.5 43.3 - - + +
249A MET* 3.2 14.1 - - + +
252A ARG* 3.3 64.8 + - - +
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Residues in contact with ILE 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 3.2 25.5 + - + +
155A ASP* 3.3 24.5 - - - +
157A TYR* 1.3 85.0 - - + +
159A ALA* 1.3 62.2 + - - +
160A VAL 3.4 1.1 - - - -
161A CYS 3.8 1.3 + - - -
162A HIS* 3.1 35.0 + - + +
165A LYS* 6.5 1.3 - - - -
252A ARG* 4.1 8.1 - - - +
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Residues in contact with ALA 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A ASP* 3.0 16.1 + - - +
156A ARG* 3.3 37.2 - - - +
157A TYR 3.1 0.4 - - - -
158A ILE* 1.3 79.2 - - - +
160A VAL* 1.3 65.3 + - - +
161A CYS 3.1 0.4 - - - -
162A HIS 3.1 25.5 + - - +
163A PRO 3.7 1.4 - - - -
166A ALA* 5.4 5.4 - - + -
269A LEU* 3.9 20.2 - - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A ARG 3.4 14.6 - - - +
157A TYR 3.3 5.4 - - - +
159A ALA* 1.3 77.1 - - + +
161A CYS* 1.3 61.5 + - - +
163A PRO* 4.6 7.4 - - - +
249A MET* 4.0 18.2 - - + +
252A ARG* 3.2 47.1 - - + +
253A LEU* 3.5 30.7 - - + +
256A VAL* 4.0 19.9 - - + +
269A LEU* 4.0 16.5 - - + +
273A THR* 5.1 6.1 - - + +
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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
------------------------------------------------------------
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