Contacts of the helix formed by residues 170 - 192 (chain E) in PDB entry 3A68
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 TYR 170 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLU* 4.2 6.7 - - - -
94E HIS* 2.7 52.3 + + + -
97E LYS* 3.3 20.2 - - + +
98E LEU* 3.3 24.8 + - + +
147E LEU* 3.8 33.7 - - + +
165E PHE* 3.5 35.0 - + - -
166E VAL* 3.0 17.9 + - + +
168E THR 3.5 0.4 - - - -
169E GLU* 1.3 95.1 - - + +
171E LEU* 1.3 59.7 + - - +
172E GLY 3.4 2.2 - - - -
173E GLU* 3.4 5.0 + - - +
174E GLN* 2.8 32.7 + - - +
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Residues in contact with LEU 171 (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 ASN* 4.4 9.1 - - - +
147E LEU* 3.8 30.3 - - + -
148E LEU* 4.0 23.8 - - + -
151E HIS* 4.3 7.4 - - + -
166E VAL* 3.0 23.6 + - + +
167E GLU* 3.6 23.8 + - + +
170E TYR* 1.3 76.1 - - - +
172E GLY* 1.3 62.5 + - - +
174E GLN* 3.3 3.8 + - - +
175E VAL* 3.1 26.2 + - - +
160V VAL* 3.6 31.4 - - + -
161V GLN* 3.8 19.0 - - + +
164V ASP* 6.1 0.4 - - + +
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Residues in contact with GLY 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167E GLU 3.9 6.8 + - - -
170E TYR 3.4 0.2 - - - -
171E LEU* 1.3 75.4 - - - +
173E GLU* 1.3 69.8 + - - +
175E VAL* 3.2 5.1 + - - +
176E GLU* 3.0 29.0 + - - +
161V GLN* 3.7 22.1 - - - +
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Residues in contact with GLU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E HIS* 6.0 7.2 - - + +
168E THR 3.5 3.5 - - - +
169E GLU* 3.3 31.9 - - - +
170E TYR* 3.6 7.5 + - - +
172E GLY* 1.3 76.5 + - - +
174E GLN* 1.3 57.4 + - - +
176E GLU* 3.3 10.7 + - + +
177E ALA* 2.9 29.2 + - - +
215E CA 2.6 29.1 - - - -
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Residues in contact with GLN 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94E HIS* 5.6 2.1 + - - -
140E GLU* 2.6 55.7 + - - +
143E THR* 3.9 7.5 - - - +
144E ASN* 3.5 35.2 - - + +
147E LEU* 3.9 18.0 - - + +
170E TYR* 2.8 17.9 + - - +
171E LEU* 3.7 5.6 - - - +
172E GLY 3.2 0.2 - - - -
173E GLU* 1.3 74.9 - - - +
175E VAL* 1.3 65.2 + - - +
177E ALA* 3.3 4.2 + - - +
178E ILE* 3.0 31.8 + - + +
214E CA 4.1 12.3 - - - -
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Residues in contact with VAL 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144E ASN* 5.2 11.0 - - - +
171E LEU 3.1 14.1 + - - +
172E GLY* 3.2 9.4 + - - +
174E GLN* 1.3 76.3 - - - +
176E GLU* 1.3 63.0 + - + +
178E ILE* 3.3 8.7 + - + +
179E LYS* 3.0 21.7 + - - +
101V TYR* 5.2 2.7 - - + -
104V LYS* 3.8 38.5 - - + +
105V ARG* 3.8 23.6 - - + +
161V GLN* 3.8 26.0 - - + +
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Residues in contact with GLU 176 (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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172E GLY 3.0 20.4 + - - +
173E GLU* 3.5 9.2 - - - +
174E GLN 3.2 0.2 - - - -
175E VAL* 1.3 77.8 - - + +
177E ALA* 1.3 57.8 + - - +
179E LYS* 3.3 6.1 + - - +
180E ARG* 2.9 29.0 + - - +
104V LYS* 3.3 42.3 + - + +
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Residues in contact with ALA 177 (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 GLU* 4.3 21.1 - - - +
173E GLU 2.9 17.6 + - - +
174E GLN* 3.3 8.9 + - - +
176E GLU* 1.3 76.0 - - - +
178E ILE* 1.3 63.3 + - - +
180E ARG* 3.3 9.6 + - - +
181E ILE* 3.1 33.1 + - + +
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Residues in contact with ILE 178 (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 LEU* 3.8 17.1 - - + +
140E GLU* 3.8 37.9 - - + +
141E LYS* 4.0 7.4 - - + +
144E ASN* 3.9 15.3 - - + +
174E GLN* 3.0 22.6 + - + +
175E VAL* 3.8 6.7 - - + +
176E GLU 3.3 0.2 - - - -
177E ALA* 1.3 74.9 - - - +
179E LYS* 1.3 64.1 + - - +
181E ILE* 5.0 0.2 - - - -
182E SER* 2.8 29.5 + - - -
37V ALA* 3.6 35.0 - - + +
39V GLN* 3.6 23.3 - - + +
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Residues in contact with LYS 179 (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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175E VAL 3.0 14.1 + - - +
176E GLU* 3.3 8.7 + - - +
178E ILE* 1.3 76.6 - - - +
180E ARG* 1.3 64.3 + - - +
182E SER* 3.3 5.6 + - - -
183E GLU* 2.9 47.0 + - - +
71L ASP* 3.0 48.4 + - - -
73L ASP* 3.9 17.9 - - + +
37V ALA* 4.3 3.8 - - + +
100V GLU 5.2 0.2 + - - -
103V ASN* 3.9 20.8 - - - +
104V LYS* 3.9 31.4 - - + +
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Residues in contact with ARG 180 (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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83E PHE* 3.5 29.0 - - - -
86E GLU* 5.7 2.4 + - - -
87E SER* 5.6 0.6 + - - -
90E GLU* 5.0 9.9 + - - -
176E GLU 2.9 16.6 + - - +
177E ALA* 3.5 10.1 - - - +
178E ILE 3.3 0.2 - - - -
179E LYS* 1.3 78.3 - - - +
181E ILE* 1.3 64.0 + - + +
183E GLU* 3.3 15.3 + - - +
184E TYR* 2.8 56.7 + - + +
204E LEU* 5.1 0.8 - - - +
207E GLU* 4.3 5.3 + - - -
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Residues in contact with ILE 181 (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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63E TYR* 4.2 8.7 - - - +
83E PHE* 4.4 22.2 - - + -
133E MET* 3.5 35.9 - - - +
136E ALA* 4.2 7.2 - - + +
137E LEU* 3.6 18.6 - - + +
140E GLU* 3.4 35.0 - - + +
177E ALA* 3.1 17.2 + - + +
178E ILE 4.2 2.0 - - - +
180E ARG* 1.3 77.7 - - + +
182E SER* 1.3 66.3 + - - +
184E TYR* 3.1 10.0 + - + +
185E VAL* 2.9 20.4 + - - +
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Residues in contact with SER 182 (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 LEU* 3.3 21.5 - - - +
178E ILE 2.8 24.1 + - - -
179E LYS 3.5 4.5 - - - -
181E ILE* 1.3 76.5 - - - +
183E GLU* 1.3 57.4 + - - +
185E VAL* 3.2 1.7 + - - -
186E ALA* 2.9 24.8 + - - +
73L ASP* 3.5 27.8 - - - -
36V LEU* 3.4 19.1 - - - +
37V ALA* 3.3 18.1 + - - -
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Residues in contact with GLU 183 (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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179E LYS* 2.9 48.1 + - - +
180E ARG* 3.5 15.9 - - - +
181E ILE 3.2 0.2 - - - -
182E SER* 1.3 76.4 - - - +
184E TYR* 1.3 63.8 + - + +
186E ALA* 3.3 1.4 + - - +
187E GLN* 3.0 41.3 + - - +
71L ASP* 4.5 3.8 - - - +
72L ARG 5.1 0.5 - - - +
73L ASP* 3.7 23.6 - - + +
76L ALA* 3.9 11.4 - - + +
78L ARG* 4.7 20.7 - - - +
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Residues in contact with TYR 184 (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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83E PHE* 3.7 25.4 - + - -
133E MET* 3.4 32.1 - - + -
180E ARG* 2.8 50.7 + - + +
181E ILE* 3.1 12.4 + - - +
183E GLU* 1.3 75.0 - - + +
185E VAL* 1.3 67.3 + - - +
187E GLN* 3.3 13.9 + - - +
188E LEU* 3.0 30.0 + - - +
200E PHE* 3.7 25.2 - + + -
203E MET* 4.9 0.9 - - + -
204E LEU* 3.5 14.1 - - + +
207E GLU* 2.7 37.8 + - - -
78L ARG* 6.1 0.2 - - - -
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Residues in contact with VAL 185 (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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130E LEU* 3.9 14.1 - - + +
133E MET* 3.6 35.2 - - + +
134E GLU* 4.0 13.5 - - + +
137E LEU* 4.4 13.0 - - + -
181E ILE 2.9 17.1 + - - +
182E SER* 3.5 7.6 - - - +
184E TYR* 1.3 76.6 - - - +
186E ALA* 1.3 62.5 + - - +
188E LEU* 3.3 3.3 + - - +
189E ARG* 3.0 49.6 + - - +
28V VAL* 5.5 0.2 - - + -
36V LEU* 3.9 16.2 - - + -
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Residues in contact with ALA 186 (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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182E SER 2.9 8.9 + - - +
183E GLU 3.7 4.5 - - - +
184E TYR 3.3 0.2 - - - -
185E VAL* 1.3 77.0 - - - +
187E GLN* 1.3 57.5 + - - +
189E ARG* 3.4 9.2 + - - +
190E ARG* 3.0 28.6 + - - +
73L ASP 3.4 25.1 - - - +
74L ASN* 3.8 21.8 - - - +
75L VAL 4.8 2.2 - - - +
76L ALA* 3.8 7.9 - - + -
36V LEU* 4.0 7.6 - - + +
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Residues in contact with GLN 187 (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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183E GLU* 3.0 37.6 + - - +
184E TYR* 3.8 17.2 - - - +
186E ALA* 1.3 74.3 - - - +
188E LEU* 1.3 60.8 + - - +
190E ARG* 3.1 8.2 + - - +
191E VAL* 2.9 34.7 + - - +
200E PHE* 3.8 12.8 - - + -
203E MET* 3.8 5.2 - - - +
76L ALA* 3.8 21.4 - - + +
78L ARG* 2.9 37.6 + - - +
198L TRP* 2.8 36.4 + - + +
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Residues in contact with LEU 188 (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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80E LEU* 5.6 0.7 - - + -
129E ALA* 3.8 34.1 - - + +
130E LEU* 4.0 18.0 - - + +
133E MET* 3.6 31.9 - - + -
184E TYR 3.0 20.3 + - - +
185E VAL 3.8 3.4 - - - +
187E GLN* 1.3 76.5 - - - +
189E ARG* 1.3 62.5 + - - +
191E VAL* 3.6 4.6 - - + +
192E GLY* 3.2 22.5 + - - -
197E VAL* 4.0 21.6 - - + +
200E PHE* 3.5 38.6 - - + -
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Residues in contact with ARG 189 (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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126E LYS* 5.4 1.8 - - - +
130E LEU* 3.9 20.8 - - + +
134E GLU* 2.9 28.1 + - - -
185E VAL* 3.0 27.6 + - - +
186E ALA* 3.6 8.3 - - - +
188E LEU* 1.3 78.7 - - - +
190E ARG* 1.3 62.2 + - - +
192E GLY* 3.9 6.8 + - - -
28V VAL* 3.6 15.4 - - - +
29V PRO 3.0 30.7 + - - -
30V THR* 4.3 16.7 + - - +
31V VAL 4.8 6.1 + - - -
32V PRO* 5.8 1.2 - - - +
36V LEU* 3.5 19.9 - - - +
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Residues in contact with ARG 190 (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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186E ALA 3.0 14.6 + - - +
187E GLN* 3.1 10.5 + - - +
189E ARG* 1.3 79.2 - - - +
191E VAL* 1.3 62.6 + - + +
192E GLY 3.6 0.2 + - - -
74L ASN 5.0 2.0 + - - -
75L VAL* 3.0 28.9 + - - +
76L ALA 5.2 0.8 + - - -
77L LEU* 3.6 30.6 - - - +
128L ASP* 3.1 38.6 + - - -
194L GLY* 3.2 46.0 - - - +
197L VAL* 3.9 10.5 - - - +
198L TRP* 4.1 13.9 - - + +
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Residues in contact with VAL 191 (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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187E GLN 2.9 22.7 + - - +
188E LEU* 3.6 12.3 - - + +
190E ARG* 1.3 77.5 - - - +
192E GLY* 1.3 67.4 + - - +
193E LYS 4.9 0.5 - - - +
196E GLY* 3.5 37.7 + - - +
197E VAL* 3.8 4.7 - - - +
200E PHE* 4.4 5.6 - - + -
195L HIS* 3.7 26.3 + - + +
198L TRP* 3.5 50.0 - - + -
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Residues in contact with GLY 192 (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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188E LEU 3.2 14.7 + - - -
189E ARG 4.4 5.2 - - - -
190E ARG 3.4 2.8 - - - -
191E VAL* 1.3 78.4 - - - +
193E LYS* 1.3 68.1 + - - +
196E GLY* 3.6 0.2 - - - -
197E VAL* 3.1 28.7 + - - +
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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
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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