Contacts of the helix formed by residues 133 - 159 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E GLY 3.9 0.6 + - - -
132E GLN* 1.3 71.4 - - - +
134E THR* 1.3 64.1 + - - +
136E ILE* 3.3 11.0 + - - +
137E GLU* 3.0 24.2 + - - +
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Residues in contact with THR 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E GLN* 3.2 4.2 - - - +
133E ALA* 1.3 78.0 - - - +
135E GLU* 1.3 62.4 + - - +
137E GLU* 3.4 15.8 + - - +
138E ILE* 3.1 30.5 + - + +
171F ARG* 3.8 39.0 + - + +
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Residues in contact with GLU 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ALA* 5.0 0.8 - - - +
130E GLN 4.4 10.8 - - - +
131E GLY* 3.5 7.7 - - - -
132E GLN* 2.8 41.8 + - + +
134E THR* 1.3 73.8 - - - +
136E ILE* 1.3 65.6 + - - +
138E ILE* 3.4 9.8 + - + +
139E ALA* 3.2 21.3 + - - +
171F ARG* 3.7 30.5 + - - +
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Residues in contact with ILE 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ALA* 4.1 36.8 - - + +
130E GLN 4.4 1.1 - - - -
131E GLY 3.3 30.3 - - - +
132E GLN 2.9 16.5 + - - +
133E ALA* 3.8 9.4 - - - +
135E GLU* 1.3 69.0 - - - +
137E GLU* 1.3 61.3 + - - +
139E ALA* 3.2 3.3 + - - +
140E ALA* 2.8 32.7 + - + +
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Residues in contact with GLU 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133E ALA 3.0 12.9 + - - +
134E THR* 3.5 18.6 + - - +
136E ILE* 1.3 78.5 - - - +
138E ILE* 1.3 65.0 + - + +
140E ALA* 3.2 7.0 + - + +
141E ASN* 2.9 45.5 + - - +
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Residues in contact with ILE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E THR* 3.1 27.9 + - + +
135E GLU* 3.7 9.6 - - + +
136E ILE 3.3 0.2 - - - -
137E GLU* 1.3 80.1 - - + +
139E ALA* 1.3 61.6 + - - +
141E ASN* 3.2 8.7 + - - +
142E HIS* 3.0 22.0 + - - +
171F ARG* 3.8 31.2 - - + -
172F ASP* 3.8 33.2 - - + +
174F PHE* 4.3 14.4 - - + -
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Residues in contact with ALA 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLY 4.3 7.0 - - - +
129E ALA* 3.5 31.6 - - + -
135E GLU 3.2 10.7 + - - +
136E ILE 3.2 2.7 + - - +
138E ILE* 1.3 74.1 - - - +
140E ALA* 1.3 66.0 + - - +
142E HIS* 3.3 7.8 + - - +
143E ILE* 2.9 25.4 + - - +
174F PHE* 5.7 2.2 - - - -
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Residues in contact with ALA 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E ALA* 5.4 0.4 - - - +
136E ILE* 2.8 24.7 + - + +
137E GLU* 3.2 8.3 + - - +
139E ALA* 1.3 72.4 - - - +
141E ASN* 1.3 65.8 + - - +
143E ILE* 3.3 9.2 + - - +
144E LEU* 3.0 37.1 + - + +
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Residues in contact with ASN 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E GLU* 2.9 39.8 + - - +
138E ILE* 3.7 8.5 - - - +
140E ALA* 1.3 79.2 - - - +
142E HIS* 1.3 58.3 + - - +
144E LEU* 3.4 11.8 + - - +
145E LYS* 2.9 31.6 + - - +
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Residues in contact with HIS 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72E THR* 6.0 1.3 - - + -
138E ILE 3.0 16.3 + - - +
139E ALA* 3.6 5.9 + - - +
140E ALA 3.3 0.2 - - - -
141E ASN* 1.3 75.7 - - - +
143E ILE* 1.3 62.6 + - - +
145E LYS* 3.3 8.0 + - + +
146E THR* 2.9 41.9 + - - -
95F MET* 4.6 3.4 - - + -
119F GLU* 3.1 34.6 + - - -
174F PHE* 3.6 58.4 - + + -
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Residues in contact with ILE 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125E PRO* 3.9 24.6 - - + +
126E LEU 3.6 10.1 - - - +
127E GLY* 3.6 34.1 - - - +
128E GLY 5.2 0.4 - - - +
139E ALA 2.9 15.7 + - - +
140E ALA* 3.5 14.6 - - - +
142E HIS* 1.3 80.1 + - - +
144E LEU* 1.3 68.0 + - + +
146E THR* 3.3 8.0 + - - -
147E ARG* 3.0 26.5 + - - +
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Residues in contact with LEU 144 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E GLN* 6.3 1.1 - - - +
140E ALA* 3.0 28.9 + - + +
141E ASN* 3.8 11.9 - - - +
143E ILE* 1.3 80.5 - - + +
145E LYS* 1.3 63.2 + - - +
147E ARG* 3.2 17.0 + - + +
148E GLU* 3.1 30.0 + - - +
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Residues in contact with LYS 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141E ASN 2.9 18.3 + - - +
142E HIS* 3.7 10.1 - - + +
143E ILE 3.3 0.2 - - - -
144E LEU* 1.3 77.2 - - - +
146E THR* 1.3 60.8 + - - +
148E GLU* 3.3 17.3 + - + +
149E LYS* 3.1 23.1 + - - +
174F PHE 5.9 0.6 + - - -
176F THR* 4.0 25.4 - - + +
179F GLU* 4.1 15.0 + - - -
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Residues in contact with THR 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E VAL* 3.6 33.9 - - + -
75E PHE* 5.2 3.6 - - + -
125E PRO* 4.9 5.4 - - + -
142E HIS* 2.9 30.5 + - - -
143E ILE* 3.3 10.5 + - + -
145E LYS* 1.3 73.3 - - - +
147E ARG* 1.3 59.8 + - - +
149E LYS* 3.3 8.3 + - - +
150E LEU* 2.9 34.4 + - + +
119F GLU* 3.7 20.2 + - - +
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Residues in contact with ARG 147 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E GLN* 3.5 36.5 + - - +
125E PRO* 3.7 23.1 - - + +
143E ILE 3.0 12.8 + - - +
144E LEU* 3.2 19.6 + - + +
146E THR* 1.3 73.6 - - - +
148E GLU* 1.3 59.8 + - - +
150E LEU* 3.1 4.4 + - + +
151E ASN* 2.8 46.1 + - - +
166E GLN* 3.0 62.8 + - - +
169E THR* 3.1 29.9 + - - -
170E ASP* 3.7 10.1 + - - +
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Residues in contact with GLU 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E LEU* 3.1 17.1 + - - +
145E LYS* 3.5 20.1 - - - +
147E ARG* 1.3 74.4 - - + +
149E LYS* 1.3 59.1 + - - +
151E ASN* 3.3 6.0 + - - +
152E ARG* 2.8 36.2 + - - +
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Residues in contact with LYS 149 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PHE* 3.5 36.4 - - + -
145E LYS 3.1 10.8 + - - +
146E THR* 3.5 13.0 - - - +
148E GLU* 1.3 79.2 - - - +
150E LEU* 1.3 62.2 + - - +
152E ARG* 3.5 28.7 + - - +
153E ILE* 3.2 24.8 + - + +
117F ASN* 2.9 45.7 + - - +
118F ALA 4.7 0.6 + - - -
119F GLU* 3.3 30.4 + - - +
176F THR* 6.3 1.4 - - + +
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Residues in contact with LEU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E VAL* 4.3 4.5 - - + -
75E PHE* 3.7 23.8 - - + -
99E MET* 3.7 31.6 - - + -
102E PHE* 3.7 32.8 - - + -
125E PRO* 4.0 28.3 - - + -
146E THR* 2.9 28.3 + - + +
147E ARG* 3.1 5.4 + - + +
149E LYS* 1.3 76.4 - - - +
151E ASN* 1.3 62.1 + - - +
153E ILE 3.3 1.6 + - - -
154E LEU* 2.9 32.4 + - + +
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Residues in contact with ASN 151 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E ARG* 2.8 37.2 + - - +
148E GLU* 3.8 5.7 - - - +
150E LEU* 1.3 77.0 - - - +
152E ARG* 1.3 56.6 + - - +
154E LEU* 3.7 2.6 - - - +
155E SER* 2.8 31.5 + - - -
162E ILE* 4.3 16.0 + - + +
165E ILE* 3.5 28.7 - - + +
166E GLN* 3.0 41.4 + - - +
169E THR* 4.3 6.4 + - - +
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Residues in contact with ARG 152 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E GLU* 2.8 23.4 + - - +
149E LYS* 3.7 36.8 - - - +
150E LEU 3.3 0.2 - - - -
151E ASN* 1.3 72.2 - - - +
153E ILE* 1.3 71.3 + - - +
155E SER* 3.3 4.9 - - - -
156E GLU* 3.2 41.2 + - + +
162E ILE* 4.2 23.4 - - + +
117F ASN* 4.0 21.0 - - - +
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Residues in contact with ILE 153 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E PHE* 3.7 20.9 - - + -
78E TYR* 3.2 33.7 - - + +
102E PHE* 3.7 14.4 - - + -
149E LYS* 3.2 18.7 + - + +
150E LEU 4.0 2.7 - - - +
152E ARG* 1.3 88.6 - - - +
154E LEU* 1.3 62.7 + - - +
156E GLU* 3.2 25.3 + - - +
157E ARG* 3.2 21.2 - - + +
117F ASN* 3.5 37.0 - - - +
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Residues in contact with LEU 154 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E SER* 6.1 0.2 - - - +
102E PHE* 4.0 28.4 - - + +
105E ALA* 4.3 15.0 - - + -
122E ILE* 5.1 13.9 - - + -
150E LEU* 2.9 18.8 + - + +
151E ASN* 3.7 6.7 - - - +
153E ILE* 1.3 77.9 - - - +
155E SER* 1.3 56.0 + - - +
157E ARG* 3.1 4.8 + - + +
158E THR* 2.8 44.4 + - + +
165E ILE* 4.1 26.5 - - + -
169E THR* 5.3 5.6 - - + -
183E TYR* 5.7 0.4 - - + -
185E LEU* 4.1 24.5 - - + -
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Residues in contact with SER 155 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151E ASN 2.8 13.6 + - - -
152E ARG 3.3 11.2 - - - -
154E LEU* 1.3 75.2 - - - +
156E GLU* 1.3 57.8 + - - +
158E THR* 4.0 1.6 - - - -
159E GLY* 3.0 30.8 + - - -
160E GLN 2.8 24.2 + - - +
161E SER* 4.0 2.0 - - - -
162E ILE* 3.6 28.1 + - - +
165E ILE* 4.4 4.6 - - - +
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Residues in contact with GLU 156 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 5.2 1.7 + - - -
109E LYS* 3.7 11.3 + - - -
152E ARG* 3.2 33.1 + - + +
153E ILE* 3.2 24.5 + - - +
155E SER* 1.3 76.3 - - - +
157E ARG* 1.3 64.4 + - + +
158E THR 3.5 0.2 - - - -
159E GLY* 4.3 3.1 + - - -
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Residues in contact with ARG 157 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 3.3 28.1 + - - -
82E GLN* 3.6 32.0 + - - +
102E PHE* 5.8 0.7 - - - -
105E ALA* 3.5 35.6 + - + +
106E ALA* 4.1 8.9 + - - +
107E GLY 3.7 15.6 + - - -
108E ALA* 6.3 0.2 - - - +
109E LYS* 3.7 36.2 + - - +
112E ARG* 3.0 27.6 + - - +
153E ILE* 3.2 20.6 - - + +
154E LEU* 3.1 7.8 + - - +
156E GLU* 1.3 84.1 - - + +
158E THR* 1.3 61.7 + - - +
184E GLY 3.3 2.6 - - - +
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Residues in contact with THR 158 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ALA* 5.0 1.8 - - + -
154E LEU* 2.8 31.8 + - + +
155E SER* 3.7 1.2 + - - -
157E ARG* 1.3 80.7 - - - +
159E GLY* 1.3 57.9 + - - +
160E GLN* 3.2 21.9 + - - +
165E ILE* 4.0 2.8 - - - +
183E TYR* 3.5 27.0 - - + +
184E GLY* 3.4 29.9 - - - +
185E LEU* 3.7 25.8 - - + +
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Residues in contact with GLY 159 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155E SER 3.0 12.4 + - - -
156E GLU 4.3 3.0 + - - -
157E ARG 3.6 1.6 - - - +
158E THR* 1.3 76.9 - - - +
160E GLN* 1.3 62.2 + - - +
161E SER 4.0 0.5 + - - -
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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