Contacts of the helix formed by residues 164 - 185 (chain E) in PDB entry 1Z6Z
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 TRP 164 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101E LEU* 4.9 7.0 - - + -
104E VAL* 3.6 22.9 - - + +
156E CYS* 3.5 33.2 - - - -
161E PHE* 3.1 31.5 + + + +
162E LYS 3.5 12.4 + - - -
163E GLY* 1.3 85.6 - - - +
165E ALA* 1.3 64.9 + - - +
166E LEU 3.4 2.5 - - - -
167E TYR* 3.3 15.2 + + + -
168E CYS* 2.9 28.9 + - - +
203E GLN* 5.9 3.6 - - - -
206E ALA* 3.7 29.6 - - + -
210E SER* 3.1 24.9 + - - -
215E MET* 5.5 7.4 - - + +
219E LEU* 4.1 19.5 - - + -
410E CL 4.6 9.6 - - + -
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Residues in contact with ALA 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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108E PHE* 3.9 29.4 - - + +
111E LEU* 3.9 17.0 - - + +
163E GLY 3.4 4.2 + - - -
164E TRP* 1.3 75.4 - - - +
166E LEU* 1.3 58.2 + - - +
168E CYS* 3.9 0.9 - - - +
169E ALA* 3.0 32.4 + - - +
177F LEU* 3.8 13.6 - - + +
180F VAL* 3.9 22.2 - - + +
184F GLU* 4.9 2.2 - - - +
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Residues in contact with LEU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101E LEU 4.9 3.4 - - - +
102E GLY* 5.2 7.0 - - - -
103E ASP 5.3 4.0 - - - +
111E LEU* 4.1 27.5 - - + +
116E GLN* 5.0 7.2 - - - +
117E VAL* 4.1 16.4 - - + -
120E TYR* 3.3 47.4 - - + -
121E TRP* 3.7 32.6 - - + -
164E TRP 3.4 0.4 - - - -
165E ALA* 1.3 78.0 - - - +
167E TYR* 1.3 57.5 + - - +
169E ALA* 3.9 0.9 - - - +
170E GLY 2.9 24.8 + - - -
129F LEU* 3.8 21.5 - - + -
177F LEU* 5.0 0.7 - - + -
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Residues in contact with TYR 167 (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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100E SER 3.5 23.6 - - - -
101E LEU* 3.7 32.6 + - + +
104E VAL* 5.6 0.2 - - + -
120E TYR* 3.3 8.6 + - - -
154E SER* 3.9 2.8 - - - -
156E CYS* 3.6 30.3 - - + -
164E TRP* 3.3 17.1 + + + +
166E LEU* 1.3 78.6 - - - +
168E CYS* 1.3 62.8 + - - +
170E GLY* 3.3 1.7 + - - -
171E LYS* 3.0 43.8 + - + +
202E MET* 4.0 12.8 - - - -
410E CL 2.9 33.9 - - + +
805E NAP 2.7 38.5 + - - -
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Residues in contact with CYS 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156E CYS* 3.5 33.7 - - - +
159E GLN 3.6 22.2 - - - -
160E PRO* 4.1 0.7 - - - -
161E PHE* 3.8 19.3 - - - -
164E TRP* 2.9 29.7 + - - +
165E ALA 4.0 2.0 - - - +
167E TYR* 1.3 74.4 - - - +
169E ALA* 1.3 58.4 + - - +
171E LYS 3.2 1.0 + - - -
172E ALA* 2.9 30.5 + - - +
176F MET* 3.6 17.3 - - + -
180F VAL* 4.2 4.7 - - + -
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Residues in contact with ALA 169 (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 TRP* 3.9 12.3 - - + -
165E ALA 3.0 19.5 + - - +
166E LEU 3.9 2.7 - - - +
168E CYS* 1.3 76.2 - - - +
170E GLY* 1.3 58.7 + - - +
172E ALA* 3.4 1.4 + - - +
173E ALA* 2.9 30.7 + - - +
173F ALA* 3.7 17.3 - - + +
176F MET* 3.7 11.8 - - - +
177F LEU* 3.8 29.8 - - + +
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Residues in contact with GLY 170 (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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120E TYR* 4.8 7.2 - - - -
121E TRP* 4.0 9.5 - - - -
124E ASN* 5.3 3.1 - - - -
125E LEU* 3.5 16.2 - - - +
166E LEU 2.9 17.8 + - - -
167E TYR 3.7 1.8 - - - -
169E ALA* 1.3 76.3 - - - +
171E LYS* 1.3 56.3 + - - +
173E ALA 3.3 1.0 + - - -
174E ARG* 2.9 38.8 + - - +
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Residues in contact with LYS 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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99E GLY* 5.3 3.6 - - - -
124E ASN* 5.5 2.4 + - - -
151E ASN* 5.0 0.2 + - - -
152E ILE 3.0 25.2 + - - +
153E SER* 4.3 14.1 - - - -
154E SER* 4.0 12.3 - - - -
156E CYS* 4.2 1.1 - - + -
157E ALA* 3.6 27.0 - - + +
167E TYR* 3.0 41.0 + - + +
168E CYS 3.2 2.0 + - - +
170E GLY* 1.3 72.8 - - - +
172E ALA* 1.3 65.3 + - - +
174E ARG* 3.4 26.7 + - + +
175E ASP* 3.0 26.7 + - - +
805E NAP 3.0 37.9 + - - -
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Residues in contact with ALA 172 (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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157E ALA* 3.6 24.0 - - - +
168E CYS 2.9 17.6 + - - +
169E ALA 3.7 3.6 - - - +
171E LYS* 1.3 77.1 - - - +
173E ALA* 1.3 61.2 + - - +
175E ASP* 3.5 4.2 + - - +
176E MET* 3.1 23.4 + - - +
172F ALA* 4.2 16.4 - - + +
176F MET* 4.0 21.3 - - + -
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Residues in contact with ALA 173 (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 LEU* 3.6 28.0 - - + -
169E ALA 2.9 17.4 + - - +
172E ALA* 1.3 74.1 - - - +
174E ARG* 1.3 60.3 + - - +
176E MET* 3.2 2.6 + - - +
177E LEU* 2.9 34.2 + - - +
169F ALA* 3.5 34.2 - - + +
172F ALA* 4.8 0.4 - - - -
173F ALA* 4.1 7.1 - - + +
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Residues in contact with ARG 174 (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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96E ASN* 3.2 26.9 + - - +
98E ALA 3.8 17.3 + - - -
123E LEU 5.1 1.0 + - - -
124E ASN* 2.9 42.2 + - - +
125E LEU* 3.9 5.4 - - + -
128E MET* 3.5 32.2 - - + +
151E ASN* 2.9 38.9 + - - +
152E ILE 3.5 8.1 + - - -
170E GLY 2.9 22.0 + - - +
171E LYS* 3.6 31.5 - - + +
173E ALA* 1.3 75.3 - - - +
175E ASP* 1.3 62.5 + - - +
177E LEU* 3.3 10.0 + - - +
178E PHE* 3.1 26.5 + - - +
805E NAP 4.5 1.2 + - - -
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Residues in contact with ASP 175 (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* 3.1 14.4 + - - -
153E SER* 2.6 25.9 + - - -
157E ALA* 3.7 12.2 - - + +
158E LEU* 4.7 5.1 - - + +
171E LYS 3.0 11.7 + - - +
172E ALA* 3.7 5.4 - - - +
173E ALA 3.3 0.2 - - - -
174E ARG* 1.3 76.1 - - - +
176E MET* 1.3 58.1 + - - +
178E PHE 3.4 0.7 + - - -
179E GLN* 2.9 39.7 + - - +
192E ASN* 3.4 19.7 + - - +
252E HIS* 2.8 32.1 + - - +
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Residues in contact with MET 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 ALA 3.1 17.2 + - - +
173E ALA 3.2 3.3 + - - +
175E ASP* 1.3 75.8 - - - +
177E LEU* 1.3 65.1 + - - +
179E GLN* 3.2 16.2 + - - +
180E VAL* 3.0 23.1 + - - +
156F CYS 3.7 7.0 - - - +
157F ALA 3.5 24.9 - - - +
158F LEU 3.7 22.9 - - - +
159F GLN 3.9 2.2 - - - +
160F PRO* 3.9 29.4 - - + -
168F CYS* 3.6 35.7 - - + +
169F ALA* 3.7 3.1 - - - +
172F ALA* 4.0 9.6 - - + -
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Residues in contact with LEU 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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125E LEU* 4.6 9.6 - - + +
128E MET* 4.1 22.4 - - - -
129E LEU* 4.1 36.6 - - + -
173E ALA 2.9 19.3 + - - +
174E ARG* 3.5 10.1 - - - +
176E MET* 1.3 73.7 - - - +
178E PHE* 1.3 65.2 + - + +
180E VAL* 3.2 8.8 + - - +
181E LEU 3.0 22.3 + - - -
108F PHE* 3.6 14.8 - - + -
121F TRP* 4.8 9.4 - - + -
165F ALA* 3.7 36.1 - - + +
166F LEU 4.6 0.4 - - - +
169F ALA* 3.7 10.9 - - + +
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Residues in contact with PHE 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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96E ASN* 3.4 23.6 - - - -
128E MET* 3.7 21.1 - - + -
132E THR* 3.6 30.1 - - + -
149E VAL* 3.7 17.5 - - + -
150E VAL 3.7 3.8 - - - -
151E ASN* 3.6 33.4 - - + -
174E ARG 3.1 11.1 + - - +
175E ASP 3.8 0.7 - - - +
177E LEU* 1.3 85.9 - - + +
179E GLN* 1.3 59.1 + - - +
181E LEU* 3.4 6.8 + - + +
182E ALA* 2.9 24.9 + - - +
190E VAL* 3.4 32.6 - - + +
191E LEU 4.2 2.0 - - - -
192E ASN* 3.4 22.0 - - - +
250E GLY* 5.1 0.2 - - - -
108F PHE* 4.5 5.6 - + - -
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Residues in contact with GLN 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 ASP* 2.9 31.9 + - - +
176E MET* 3.2 23.9 + - - +
178E PHE* 1.3 75.5 - - - +
180E VAL* 1.3 62.2 + - - +
182E ALA* 3.5 7.8 + - - +
183E LEU* 3.4 24.4 + - - +
192E ASN* 4.4 1.1 - - - +
250E GLY* 3.6 22.4 - - - +
158F LEU 5.0 2.5 + - - +
160F PRO* 3.9 30.3 - - + +
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Residues in contact with VAL 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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176E MET 3.0 19.0 + - - +
177E LEU 3.5 7.0 - - - +
179E GLN* 1.3 74.3 - - - +
181E LEU* 1.3 66.8 + - - +
183E LEU* 3.1 7.1 + - - +
184E GLU* 3.0 39.6 + - - +
108F PHE* 5.1 0.4 - - + -
160F PRO* 3.8 25.4 - - + -
161F PHE 3.4 22.4 - - - +
163F GLY 4.2 0.4 - - - +
165F ALA* 3.9 27.1 - - + +
168F CYS* 4.0 19.1 - - + -
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Residues in contact with LEU 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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132E THR* 3.9 19.3 - - + -
136E LEU* 3.8 13.9 - - + -
149E VAL* 3.7 30.3 - - + -
177E LEU 3.0 13.4 + - - +
178E PHE* 3.7 13.0 - - + +
180E VAL* 1.3 77.1 - - - +
182E ALA* 1.3 57.1 + - - +
184E GLU* 4.4 4.0 - - - -
185E GLU* 2.8 56.4 + - + +
188E VAL* 4.9 0.7 - - + -
190E VAL* 4.0 9.0 - - + -
108F PHE* 3.6 38.1 - - + -
109F VAL* 5.3 0.9 - - + -
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Residues in contact with ALA 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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178E PHE 2.9 17.8 + - - +
179E GLN 3.7 6.1 - - - +
180E VAL 3.3 0.4 - - - -
181E LEU* 1.3 76.2 - - - +
183E LEU* 1.3 62.3 + - + +
185E GLU 3.9 14.1 - - - +
186E PRO* 4.0 6.9 - - - +
190E VAL* 3.8 11.2 - - + +
249E SER* 3.6 28.2 + - - +
250E GLY* 3.7 20.2 - - - +
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Residues in contact with LEU 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 GLN 3.4 8.9 + - - +
180E VAL 3.1 9.2 + - - +
182E ALA* 1.3 80.9 - - + +
184E GLU* 1.3 61.9 + - - +
186E PRO* 4.1 11.3 - - - +
160F PRO* 3.5 42.6 - - + +
161F PHE* 4.4 6.7 - - + +
162F LYS* 3.6 34.1 - - + +
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Residues in contact with GLU 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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180E VAL* 3.0 28.5 + - - +
181E LEU* 3.8 4.7 - - - +
183E LEU* 1.3 77.5 - - - +
185E GLU* 1.3 75.9 + - + +
186E PRO* 3.3 8.4 - - - +
107F GLY* 3.5 8.7 - - - -
108F PHE* 3.1 37.4 + - + +
162F LYS* 3.7 16.8 - - + +
163F GLY* 2.8 38.8 + - - +
165F ALA* 4.9 1.0 - - - +
211F VAL* 5.9 0.2 - - - +
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Residues in contact with GLU 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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136E LEU* 5.3 0.7 - - + -
147E ARG* 3.8 17.4 + - - -
181E LEU* 2.8 32.1 + - + +
182E ALA 3.9 6.0 - - - +
184E GLU* 1.3 92.2 - - + +
186E PRO* 1.3 60.9 - - - +
187E ASN* 3.1 5.6 + - - +
188E VAL* 2.8 43.1 + - + +
108F PHE* 5.8 0.4 - - + -
109F VAL* 4.1 23.8 - - + +
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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