Contacts of the helix formed by residues 139 - 165 (chain E) in PDB entry 2B05
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 THR 139 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E VAL 4.5 6.1 - - - +
138E ALA* 1.3 80.4 - - - +
140E GLY* 1.3 68.7 + - - +
142E LYS* 3.5 11.6 + - - +
143E ARG* 3.1 17.8 + - - +
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Residues in contact with GLY 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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139E THR* 1.3 75.9 + - - +
141E GLU* 1.3 63.8 + - - -
143E ARG* 3.1 13.6 + - - +
144E ALA* 3.3 11.8 + - - +
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Residues in contact with GLU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140E GLY* 1.3 68.9 - - - -
142E LYS* 1.3 65.7 + - - +
144E ALA* 3.1 10.6 + - - +
145E THR* 2.9 29.6 + - - +
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Residues in contact with LYS 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E GLU* 3.1 37.5 + - - +
98E GLN* 6.1 3.3 - - - +
134E LEU* 5.9 5.4 - - - -
138E ALA* 3.6 22.0 - - + -
139E THR 3.5 9.6 + - - +
140E GLY 3.2 0.4 - - - -
141E GLU* 1.3 78.4 - - - +
143E ARG* 1.3 61.9 + - - +
145E THR* 3.4 7.7 + - - -
146E VAL* 3.2 30.7 + - + +
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Residues in contact with ARG 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135E ALA* 4.0 18.0 + - - +
138E ALA* 3.5 27.0 + - + +
139E THR* 3.1 20.4 + - - +
140E GLY 3.4 10.1 - - - +
142E LYS* 1.3 76.7 - - - +
144E ALA* 1.3 58.6 + - - +
145E THR 3.3 0.2 + - - -
146E VAL* 3.3 3.1 + - - +
147E VAL* 2.9 53.6 + - + +
185E GLU 4.6 3.0 + - - -
186E ILE* 2.7 45.4 + - - +
187E GLN* 5.9 0.2 + - - -
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Residues in contact with ALA 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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140E GLY 3.3 7.4 + - - +
141E GLU* 3.1 13.3 + - - +
143E ARG* 1.3 80.0 - - - +
145E THR* 1.3 62.4 + - - +
147E VAL* 3.5 5.8 + - - +
148E GLU* 3.0 27.3 + - - +
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Residues in contact with THR 145 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141E GLU* 2.9 17.9 + - - +
142E LYS* 3.6 8.6 - - - -
143E ARG 3.2 0.2 - - - -
144E ALA* 1.3 76.9 - - - +
146E VAL* 1.3 61.6 + - + +
148E GLU* 3.3 8.5 + - - +
149E SER* 3.0 33.3 + - - +
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Residues in contact with VAL 146 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98E GLN* 5.5 2.2 - - - +
131E TYR* 2.9 54.7 - - + +
134E LEU* 3.5 18.8 - - + -
135E ALA* 3.4 21.5 - - + +
138E ALA* 5.3 2.5 - - + -
142E LYS* 3.2 23.3 + - + +
143E ARG* 4.1 1.6 - - - +
145E THR* 1.3 81.2 - - + +
147E VAL* 1.3 60.4 + - - +
149E SER* 3.4 1.4 + - - -
150E SER* 3.0 27.7 + - - -
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Residues in contact with VAL 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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135E ALA* 3.9 12.3 - - + -
143E ARG* 2.9 47.0 + - + +
144E ALA* 3.8 6.5 - - - +
146E VAL* 1.3 73.9 - - - +
148E GLU* 1.3 66.3 + - + +
150E SER* 3.3 7.2 + - - -
151E GLU* 3.0 22.3 + - - +
182E PHE* 3.8 7.9 - - + -
186E ILE* 3.7 23.3 - - + -
187E GLN* 3.3 32.1 - - - +
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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 ALA 3.0 15.8 + - - +
145E THR* 3.3 10.3 + - - +
147E VAL* 1.3 76.5 - - + +
149E SER* 1.3 57.7 + - - +
151E GLU* 3.3 8.9 + - + +
152E LYS* 2.9 29.6 + - - +
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Residues in contact with SER 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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127E LYS* 5.4 0.7 - - - +
131E TYR* 3.6 45.7 + - - -
145E THR* 3.0 21.1 + - - +
146E VAL* 3.7 0.4 - - - -
147E VAL 3.3 0.2 - - - -
148E GLU* 1.3 73.1 - - - +
150E SER* 1.3 64.6 + - - +
152E LYS* 3.4 8.0 + - - +
153E ALA* 3.1 24.1 + - - +
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Residues in contact with SER 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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128E GLY* 2.8 23.7 + - - -
131E TYR* 3.6 16.7 - - - +
132E ARG* 3.6 8.0 + - - +
135E ALA* 5.8 0.2 - - - -
146E VAL 3.0 17.4 + - - -
147E VAL* 3.3 6.3 + - - -
149E SER* 1.3 75.9 - - - +
151E GLU* 1.3 61.4 + - - +
153E ALA* 3.3 3.8 + - - +
154E TYR* 3.0 39.4 + - - -
182E PHE* 3.6 15.3 - - - -
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Residues in contact with GLU 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 VAL 3.0 16.6 + - - +
148E GLU* 3.6 8.3 - - + +
150E SER* 1.3 77.9 - - - +
152E LYS* 1.3 58.9 + - - +
154E TYR* 3.9 3.4 - - - +
155E SER* 2.8 40.9 + - - -
179E TYR* 3.1 22.4 + - - -
182E PHE* 3.7 20.8 - - + -
183E TYR* 3.8 13.7 + - - -
187E GLN* 3.2 23.5 + - - +
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Residues in contact with LYS 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 2.9 17.0 + - - +
149E SER* 3.7 8.1 - - - +
150E SER 3.3 0.4 - - - -
151E GLU* 1.3 79.4 - - + +
153E ALA* 1.3 61.4 + - - +
155E SER* 3.8 4.9 - - - -
156E GLU* 3.1 24.7 + - + +
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Residues in contact with ALA 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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124E LEU* 3.5 33.3 - - + +
127E LYS* 3.7 22.9 - - + -
128E GLY* 3.6 15.3 - - - +
149E SER 3.1 16.5 + - - +
150E SER 3.7 2.2 - - - +
152E LYS* 1.3 74.6 - - - +
154E TYR* 1.3 64.5 + - - +
156E GLU* 3.5 1.4 + - - +
157E ALA* 3.1 23.0 + - - +
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Residues in contact with TYR 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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125E LYS* 3.8 13.2 - - + -
128E GLY* 3.5 16.8 - - - -
129E ASP* 2.6 33.5 + - - -
132E ARG* 2.9 20.4 + - - -
150E SER* 3.0 41.1 + - - +
151E GLU 3.9 0.7 - - - +
153E ALA* 1.3 74.8 - - - +
155E SER* 1.3 58.9 + - - +
157E ALA* 3.2 5.6 + - - +
158E HIS* 2.8 30.5 + - - +
175E LEU* 3.8 17.2 - - + +
178E ASN* 4.0 15.2 + - + -
179E TYR* 3.4 40.4 - + + -
182E PHE* 3.6 25.4 - + + -
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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 GLU* 2.8 27.9 + - - -
152E LYS* 3.8 6.5 - - - -
154E TYR* 1.3 78.4 - - - +
156E GLU* 1.3 62.5 + - - +
158E HIS* 3.3 4.2 + - - +
159E GLU* 3.2 27.8 + - - +
179E TYR* 3.6 19.3 + - - -
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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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124E LEU* 3.7 26.0 - - + +
152E LYS 3.1 17.5 + - - +
153E ALA 4.0 3.4 - - - +
154E TYR 3.3 0.2 - - - -
155E SER* 1.3 74.6 + - - +
157E ALA* 1.3 61.9 + - - +
159E GLU* 3.2 9.4 + - + +
160E ILE* 3.1 41.0 + - + +
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Residues in contact with ALA 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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121E VAL* 3.7 18.5 - - + +
124E LEU* 3.6 24.8 - - + +
125E LYS 4.2 2.9 - - - +
153E ALA 3.1 15.2 + - - +
154E TYR 3.5 8.1 - - - +
156E GLU* 1.3 75.7 - - - +
158E HIS* 1.3 56.7 + - - +
160E ILE* 3.4 0.7 + - - -
161E SER* 3.0 31.7 + - - -
175E LEU* 3.5 22.5 - - + +
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Residues in contact with HIS 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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154E TYR 2.8 16.6 + - - +
155E SER* 3.5 6.5 - - - +
156E GLU 3.2 0.2 - - - -
157E ALA* 1.3 78.2 - - - +
159E GLU* 1.3 60.4 + - - +
161E SER* 3.3 4.6 + - - -
162E LYS* 2.8 52.5 + - + +
172E ARG* 6.2 1.1 - - - -
175E LEU* 3.6 15.0 - - + +
176E ALA* 5.7 6.2 - - + +
179E TYR* 3.9 27.2 - + + -
196E LEU* 3.9 24.9 - - + +
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Residues in contact with GLU 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* 3.2 16.8 + - - +
156E GLU* 3.2 9.8 + - + +
158E HIS* 1.3 81.3 - - + +
160E ILE* 1.3 65.5 + - + +
162E LYS* 3.5 6.3 + - - +
163E GLU* 3.1 27.9 + - - +
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Residues in contact with ILE 160 (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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117E TYR* 4.5 17.7 - - + +
120E LYS* 4.4 15.0 - - + -
121E VAL* 3.9 17.7 - - + -
124E LEU* 3.9 24.0 - - + -
156E GLU* 3.1 32.4 + - + +
157E ALA* 5.0 0.2 - - - -
159E GLU* 1.3 76.7 - - + +
161E SER* 1.3 58.6 + - - +
163E GLU* 3.4 3.1 + - - -
164E HIS* 3.0 47.4 + - + +
165E MET* 6.2 0.2 - - - -
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Residues in contact with SER 161 (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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121E VAL* 3.8 22.8 - - - +
157E ALA 3.0 16.7 + - - -
158E HIS* 3.6 8.7 + - - -
160E ILE* 1.3 76.1 - - - +
162E LYS* 1.3 60.6 + - - +
165E MET* 2.9 48.9 + - - +
172E ARG* 3.4 26.1 + - - +
175E LEU* 3.9 9.6 - - - +
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Residues in contact with LYS 162 (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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158E HIS* 2.8 43.1 + - + +
159E GLU* 3.7 7.4 - - - +
161E SER* 1.3 78.2 + - - +
163E GLU* 1.3 62.4 + - - +
164E HIS 3.6 0.2 + - - -
165E MET 4.2 1.9 - - - +
172E ARG* 4.0 28.5 + - - +
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Residues in contact with GLU 163 (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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159E GLU* 3.1 16.8 + - - +
160E ILE* 3.9 1.1 - - - +
161E SER 3.2 0.2 - - - -
162E LYS* 1.3 82.6 - - + +
164E HIS* 1.3 92.5 + - + +
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Residues in contact with HIS 164 (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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114E GLU 5.9 2.5 - - - -
117E TYR* 4.0 31.3 - + + -
160E ILE* 3.0 34.2 + - + +
163E GLU* 1.3 114.2 + - + +
165E MET* 1.3 66.2 + - + +
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Residues in contact with MET 165 (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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117E TYR* 4.8 5.2 - - + +
118E GLU* 4.5 22.0 - - + +
121E VAL* 4.0 17.0 - - - -
161E SER* 2.9 28.7 + - - +
162E LYS 4.2 3.1 - - - +
163E GLU 3.9 0.2 - - - -
164E HIS* 1.3 86.8 - - + +
166E GLN* 1.3 59.9 + - - +
167E PRO* 4.1 0.7 - - - +
169E HIS* 3.3 41.5 - - + +
171E ILE* 3.6 13.7 - - + -
172E ARG* 2.6 55.7 + - + +
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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