Contacts of the helix formed by residues 133 - 159 (chain F) in PDB entry 3V5I
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 ALA 133 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131F GLY 3.9 1.0 + - - -
132F GLN* 1.3 71.9 - - - +
134F THR* 1.3 57.7 + - - +
136F ILE* 3.3 11.2 + - - +
137F GLU* 3.0 29.2 + - - +
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Residues in contact with THR 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F GLN* 4.3 4.7 - - - +
133F ALA* 1.3 76.4 - - - +
135F GLU* 1.3 57.4 + - - +
137F GLU* 3.3 16.3 + - - +
138F ILE* 3.1 34.9 + - + +
171G ARG* 3.7 43.0 + - + +
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Residues in contact with GLU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ALA* 5.0 0.8 - - - +
130F GLN 4.0 9.6 - - - +
131F GLY* 3.5 8.0 - - - -
132F GLN* 2.8 40.6 + - + +
134F THR* 1.3 72.5 - - - +
136F ILE* 1.3 64.9 + - - +
138F ILE* 3.4 10.9 + - + +
139F ALA* 3.1 22.0 + - - +
171G ARG* 3.7 32.9 + - - +
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Residues in contact with ILE 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ALA* 4.1 33.9 - - + +
130F GLN* 4.5 1.1 - - - -
131F GLY 3.5 28.9 - - - +
132F GLN 2.9 15.9 + - - +
133F ALA* 3.7 10.8 - - - +
135F GLU* 1.3 69.7 - - - +
137F GLU* 1.3 61.1 + - - +
139F ALA* 3.1 3.1 + - - +
140F ALA* 2.8 33.5 + - + +
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Residues in contact with GLU 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F ALA 3.0 13.4 + - - +
134F THR* 3.4 18.0 + - - +
136F ILE* 1.3 75.7 - - - +
138F ILE* 1.3 65.5 + - + +
140F ALA* 3.3 7.2 + - + +
141F ASN* 2.9 45.1 + - - +
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Residues in contact with ILE 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134F THR* 3.1 30.9 + - + +
135F GLU* 3.7 10.8 - - + +
136F ILE 3.3 0.2 - - - -
137F GLU* 1.3 79.0 - - + +
139F ALA* 1.3 60.2 + - - +
141F ASN* 3.5 8.3 + - - +
142F HIS* 3.1 21.8 + - - +
171G ARG* 3.8 29.8 - - + -
172G ASP* 3.8 32.5 - - + +
174G PHE* 4.4 13.2 - - + -
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Residues in contact with ALA 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F GLY 4.4 6.7 - - - +
129F ALA* 3.5 31.2 - - + -
135F GLU 3.1 10.7 + - - +
136F ILE 3.1 3.6 + - - +
138F ILE* 1.3 74.7 - - - +
140F ALA* 1.3 66.2 + - - +
142F HIS* 3.3 7.3 + - - +
143F ILE* 3.0 25.0 + - - +
174G PHE* 5.6 2.5 - - - -
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Residues in contact with ALA 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F ALA* 5.3 0.6 - - - +
136F ILE* 2.8 24.2 + - + +
137F GLU* 3.7 7.9 - - - +
139F ALA* 1.3 73.5 - - - +
141F ASN* 1.3 64.8 + - - +
143F ILE* 3.3 9.3 + - - +
144F LEU* 3.0 35.8 + - + +
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Residues in contact with ASN 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F GLU* 2.9 39.6 + - - +
138F ILE* 3.8 7.9 - - - +
140F ALA* 1.3 76.6 - - - +
142F HIS* 1.3 62.6 + - - +
144F LEU* 3.3 12.6 + - - +
145F LYS* 2.9 24.9 + - - +
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Residues in contact with HIS 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F THR* 6.0 1.3 - - + -
138F ILE 3.1 17.9 + - - +
139F ALA* 3.6 6.0 + - - +
140F ALA 3.1 0.2 - - - -
141F ASN* 1.3 79.8 - - - +
143F ILE* 1.3 60.6 + - - +
145F LYS* 3.2 8.0 + - + +
146F THR* 3.0 40.5 + - - -
95G MET* 4.7 2.5 - - + -
119G GLU* 3.1 33.3 + - - -
174G PHE* 3.5 58.7 - + + -
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Residues in contact with ILE 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F PRO* 4.0 24.9 - - + +
126F LEU 3.6 10.8 - - - +
127F GLY* 3.6 32.8 - - - +
139F ALA 3.0 14.9 + - - +
140F ALA* 3.4 15.0 - - - +
142F HIS* 1.3 77.5 - - - +
144F LEU* 1.3 70.2 + - + +
146F THR* 3.3 8.1 + - + -
147F ARG* 2.9 27.0 + - - +
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Residues in contact with LEU 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F GLN* 6.3 0.9 - - - +
140F ALA* 3.0 29.8 + - + +
141F ASN* 3.8 11.2 - - - +
143F ILE* 1.3 80.8 - - + +
145F LYS* 1.3 64.7 + - - +
147F ARG* 3.1 16.0 + - + +
148F GLU* 3.1 27.7 + - - +
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Residues in contact with LYS 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141F ASN 2.9 17.7 + - - +
142F HIS* 3.6 10.5 - - + +
143F ILE 3.2 0.2 - - - -
144F LEU* 1.3 78.5 - - - +
146F THR* 1.3 55.5 + - - +
148F GLU* 3.2 20.5 + - - +
149F LYS* 3.0 27.8 + - - +
176G THR* 3.8 22.7 - - + +
179G GLU* 3.8 22.0 + - - -
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Residues in contact with THR 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 3.7 32.5 - - + -
75F PHE* 5.2 3.4 - - + -
125F PRO* 4.9 4.9 - - + -
142F HIS* 3.0 26.4 + - - -
143F ILE* 3.5 13.9 - - + -
145F LYS* 1.3 74.6 - - - +
147F ARG* 1.3 59.5 + - - +
149F LYS* 3.3 8.9 + - + +
150F LEU* 2.9 35.7 + - + +
119G GLU* 3.7 20.3 + - - +
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Residues in contact with ARG 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F GLN* 3.5 36.3 + - - +
125F PRO* 3.8 24.1 - - + +
143F ILE 2.9 12.4 + - - +
144F LEU* 3.1 20.2 + - + +
146F THR* 1.3 77.9 - - - +
148F GLU* 1.3 55.4 + - - +
150F LEU* 3.2 3.2 + - + +
151F ASN* 2.9 47.3 + - - +
166F GLN* 3.0 53.6 + - - +
169F THR* 2.9 39.0 + - - -
170F ASP* 3.7 8.7 + - - +
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Residues in contact with GLU 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144F LEU* 3.1 18.5 + - - +
145F LYS* 3.2 22.1 + - + +
147F ARG* 1.3 75.0 - - - +
149F LYS* 1.3 58.4 + - - +
151F ASN* 3.8 6.4 - - - +
152F ARG* 2.9 35.8 + - - +
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Residues in contact with LYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F PHE* 3.5 35.1 - - + -
145F LYS 3.0 12.8 + - - +
146F THR* 3.5 13.5 - - - +
147F ARG 3.2 0.2 - - - -
148F GLU* 1.3 75.9 - - - +
150F LEU* 1.3 63.8 + - - +
152F ARG* 3.3 28.9 + - - +
153F ILE* 3.2 24.7 + - + +
117G ASN* 2.8 44.1 + - - +
118G ALA 4.6 0.8 + - - -
119G GLU* 3.5 30.5 + - - +
176G THR* 6.2 4.2 - - + +
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Residues in contact with LEU 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71F VAL* 4.3 2.7 - - + -
75F PHE* 3.6 28.9 - - + -
99F MET* 3.6 34.3 - - + -
102F PHE* 3.7 24.5 - - + -
125F PRO* 4.0 30.7 - - + -
146F THR* 2.9 29.2 + - + +
147F ARG* 3.2 4.5 + - + +
149F LYS* 1.3 78.3 - - - +
151F ASN* 1.3 68.5 + - - +
153F ILE* 3.2 1.0 + - - -
154F LEU* 2.9 26.3 + - + +
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Residues in contact with ASN 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147F ARG* 2.9 32.4 + - - +
148F GLU* 3.9 6.1 - - - +
150F LEU* 1.3 79.5 - - - +
152F ARG* 1.3 58.0 + - - +
154F LEU* 3.3 3.7 + - - +
155F SER* 2.8 31.4 + - - -
162F ILE* 4.3 14.2 + - + +
165F ILE* 3.6 29.3 - - + +
166F GLN* 3.0 43.8 + - - +
169F THR* 4.3 6.4 + - - +
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Residues in contact with ARG 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148F GLU* 2.9 20.7 + - - +
149F LYS* 3.7 36.1 - - - +
151F ASN* 1.3 78.2 - - - +
153F ILE* 1.3 71.1 + - - +
155F SER* 3.2 3.6 + - - -
156F GLU* 3.2 39.2 + - + +
162F ILE* 4.3 23.0 - - + +
117G ASN* 4.0 21.4 - - - +
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Residues in contact with ILE 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F PHE* 3.8 17.5 - - + -
78F TYR* 3.3 33.2 - - + +
102F PHE* 3.7 14.6 - - + -
149F LYS* 3.2 18.1 + - + +
150F LEU 3.9 3.1 - - - +
152F ARG* 1.3 89.0 - - - +
154F LEU* 1.3 62.3 + - - +
156F GLU* 3.2 17.1 + - - +
157F ARG* 3.2 27.5 + - + +
117G ASN* 3.4 39.7 - - - +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101F SER* 6.1 0.2 - - - +
102F PHE* 3.9 28.2 - - + -
105F ALA* 4.2 14.6 - - + -
122F ILE* 5.0 14.8 - - + -
150F LEU* 2.9 18.6 + - + +
151F ASN* 3.7 7.0 - - - +
153F ILE* 1.3 76.3 - - - +
155F SER* 1.3 63.1 + - - +
157F ARG* 3.2 3.2 + - + +
158F THR* 2.8 40.4 + - + +
165F ILE* 4.1 27.4 - - + -
169F THR* 5.3 5.6 - - + -
183F TYR* 5.8 0.7 - - + -
185F LEU* 4.2 23.3 - - + -
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Residues in contact with SER 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F ASN 2.8 17.3 + - - -
152F ARG 3.3 6.1 - - - -
154F LEU* 1.3 76.5 - - - +
156F GLU* 1.3 59.2 + - - +
158F THR* 3.9 2.0 - - - -
159F GLY* 2.9 31.7 + - - -
160F GLN 2.7 24.6 + - - -
161F SER* 4.1 1.1 - - - -
162F ILE* 3.6 29.2 + - - +
165F ILE* 4.5 4.2 - - - +
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Residues in contact with GLU 156 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F TYR* 5.3 1.7 + - - -
109F LYS* 3.7 11.0 + - - -
152F ARG* 3.2 33.6 + - + +
153F ILE* 3.4 22.9 - - - +
154F LEU 3.2 0.4 - - - -
155F SER* 1.3 78.3 - - - +
157F ARG* 1.3 61.9 + - + +
159F GLY* 4.3 3.1 + - - -
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Residues in contact with ARG 157 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78F TYR* 3.2 28.5 + - - -
82F GLN* 3.6 31.9 - - - +
102F PHE* 5.7 0.9 - - - -
105F ALA* 3.5 36.7 + - + +
106F ALA* 4.0 8.9 + - - +
107F GLY 3.7 16.2 + - - -
109F LYS* 3.8 36.1 + - - +
112F ARG* 3.0 27.5 + - - +
153F ILE* 3.2 20.2 - - + +
154F LEU* 3.2 6.3 + - - +
156F GLU* 1.3 82.4 + - + +
158F THR* 1.3 62.3 + - - +
184F GLY 3.4 2.1 - - - +
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Residues in contact with THR 158 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105F ALA* 5.1 1.1 - - + -
154F LEU* 2.8 32.1 + - + +
155F SER 3.6 0.7 + - - -
157F ARG* 1.3 78.8 - - + +
159F GLY* 1.3 62.1 + - - +
160F GLN* 3.1 22.6 + - - +
165F ILE* 4.1 1.7 - - - +
183F TYR* 3.6 27.5 - - + +
184F GLY* 3.4 25.4 - - - +
185F LEU* 3.8 28.3 - - + -
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Residues in contact with GLY 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155F SER 2.9 12.0 + - - -
156F GLU 4.3 3.6 + - - -
157F ARG 3.6 1.2 - - - -
158F THR* 1.3 77.6 - - - +
160F GLN* 1.3 64.0 + - - +
161F SER 4.1 0.2 + - - -
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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
------------------------------------------------------------
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