Contacts of the helix formed by residues 178 - 208 (chain E) in PDB entry 5UQ9
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 GLY 178 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106E TYR* 3.7 23.7 - - - +
109E THR* 3.6 32.0 + - - +
110E THR* 4.4 0.2 - - - -
125E GLY 4.9 1.6 - - - -
144E GLY 4.5 1.8 - - - -
145E GLY* 3.5 16.7 - - - -
176E ASP 3.4 0.2 - - - -
177E GLU* 1.3 77.6 - - - +
179E ALA* 1.3 62.7 + - - +
180E GLY 3.1 4.2 + - - -
181E HIS* 3.7 6.5 + - - +
182E PHE 3.8 0.3 + - - -
351E TRP* 4.1 2.2 - - - -
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Residues in contact with ALA 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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145E GLY 4.6 2.4 - - - +
174E VAL* 3.6 15.0 - - + -
175E GLY* 3.9 13.9 - - - -
176E ASP 3.5 7.9 + - - +
177E GLU 3.4 2.2 - - - -
178E GLY* 1.3 76.5 - - - +
180E GLY* 1.3 58.6 + - - +
182E PHE* 3.5 3.9 + - - +
183E VAL* 3.1 29.6 + - - +
351E TRP* 3.5 37.6 - - + -
353E LEU* 4.0 8.9 - - + +
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Residues in contact with GLY 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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125E GLY 4.0 4.9 - - - -
127E GLY 4.6 0.4 - - - -
142E MET* 3.4 28.2 - - - +
144E GLY* 4.2 3.6 - - - -
174E VAL* 3.4 16.9 - - - +
178E GLY* 3.1 2.4 - - - -
179E ALA* 1.3 75.6 - - - +
181E HIS* 1.3 53.8 + - - +
183E VAL* 2.9 7.0 + - - +
184E LYS* 2.7 34.9 + - - +
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Residues in contact with HIS 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ASP* 3.2 37.0 + - + -
102E GLY 3.2 21.1 + - - -
103E ASN* 5.3 1.3 - - - -
104E SER* 3.4 23.0 + - - +
106E TYR* 4.3 12.2 + - - -
109E THR* 2.4 37.6 + - + +
125E GLY* 3.5 21.7 + - - -
126E SER 3.3 18.3 + - - -
127E GLY* 3.9 4.5 - - - -
178E GLY 3.7 3.9 + - - +
179E ALA 3.5 0.2 - - - -
180E GLY* 1.3 76.1 - - - +
182E PHE* 1.3 56.1 + - - +
184E LYS* 3.7 6.9 - - + +
185E MET* 2.8 28.1 + - - +
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Residues in contact with PHE 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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106E TYR* 3.4 44.0 - + + +
178E GLY 3.8 3.6 + - - +
179E ALA 3.5 10.4 + - - +
180E GLY 3.2 0.4 - - - -
181E HIS* 1.3 78.3 - - - +
183E VAL* 1.3 58.8 + - + +
185E MET* 3.2 15.2 + - + +
186E VAL* 3.0 43.1 + - + +
270E SER* 3.4 17.9 - - - -
274E TYR* 5.4 1.6 - + - -
341E LEU* 3.6 31.0 - - + -
342E LEU* 4.1 11.4 - - + -
345E ALA* 3.5 29.8 - - + -
349E PHE* 4.6 3.4 - + - -
351E TRP* 3.9 18.6 - + + -
353E LEU* 5.8 1.8 - - + -
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Residues in contact with VAL 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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142E MET* 3.8 19.1 - - + -
174E VAL* 4.6 8.7 - - + -
179E ALA 3.1 16.4 + - - +
180E GLY* 2.9 11.3 + - - +
182E PHE* 1.3 75.3 - - + +
184E LYS* 1.3 58.9 + - - +
186E VAL* 3.4 0.9 + - - -
187E HIS* 2.9 27.0 + - - +
342E LEU* 4.1 15.5 - - + -
353E LEU* 4.9 7.9 - - + -
358E ILE* 3.9 33.4 - - + -
361E MET* 4.8 3.6 - - + -
362E TRP* 3.5 26.3 - - + +
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Residues in contact with LYS 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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102E GLY 6.0 0.2 - - - +
103E ASN* 2.8 43.7 + - - +
127E GLY* 3.9 19.1 - - - -
128E VAL 3.2 30.7 + - - +
129E SER* 4.0 6.7 - - - +
142E MET* 3.7 24.4 - - + -
180E GLY 2.7 18.9 + - - +
181E HIS* 3.8 9.9 - - + +
183E VAL* 1.3 73.5 - - - +
185E MET* 1.3 62.2 + - - +
187E HIS* 3.3 17.9 + - - +
188E ASN* 3.1 43.9 + - - +
263E THR* 5.7 0.2 - - + -
501F 8HS 4.6 7.0 - - - -
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Residues in contact with MET 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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106E TYR* 4.2 17.5 - - + -
181E HIS 2.8 18.3 + - - +
182E PHE* 3.2 47.5 + - + +
184E LYS* 1.3 76.6 - - - +
186E VAL* 1.3 72.0 + - + +
188E ASN* 3.2 5.2 + - - +
189E GLY 3.0 11.1 + - - -
263E THR* 3.9 19.6 - - + +
266E TRP* 3.6 39.0 - - + +
267E THR* 2.8 34.6 + - + +
270E SER* 4.1 9.2 - - - -
341E LEU* 4.9 0.7 - - + -
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Residues in contact with VAL 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 PHE* 3.0 39.9 + - + +
183E VAL 3.9 3.6 - - - +
185E MET* 1.3 82.5 - - + +
187E HIS* 1.3 57.4 + - - +
189E GLY* 3.2 0.7 + - - -
190E ILE* 2.8 45.0 + - + +
267E THR* 4.0 11.7 - - + -
281E ILE* 5.2 1.3 - - + -
338E GLY* 3.7 25.4 - - - +
341E LEU* 4.1 13.5 - - + -
342E LEU* 3.8 16.4 - - + -
362E TRP* 4.4 3.4 - - + -
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Residues in contact with HIS 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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129E SER* 3.0 30.9 + - - -
142E MET* 4.2 4.0 - - + -
183E VAL 2.9 18.5 + - - +
184E LYS* 3.3 14.4 - - - +
186E VAL* 1.3 77.2 - - - +
188E ASN* 1.3 69.9 + - - +
190E ILE* 3.2 7.9 + - - +
191E GLU* 2.8 46.5 + - - +
362E TRP* 3.8 21.5 - - + +
366E CYS* 3.4 31.0 - - - +
367E ILE* 4.0 4.2 + - + -
368E ILE* 3.5 27.0 - - + +
501F 8HS 5.9 0.7 - - - -
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Residues in contact with ASN 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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103E ASN* 3.3 6.9 - - - +
184E LYS* 3.1 31.3 + - - +
185E MET 3.8 0.4 - - - +
187E HIS* 1.3 82.4 + - - +
189E GLY* 1.3 55.8 + - - +
191E GLU* 2.9 25.4 + - - +
192E TYR* 2.7 48.0 + - + -
263E THR* 3.2 41.0 + - + +
501F 8HS 3.9 21.1 + - - -
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Residues in contact with GLY 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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185E MET 3.0 10.9 + - - -
186E VAL 3.2 3.6 + - - -
188E ASN* 1.3 77.1 - - - +
190E ILE* 1.3 60.2 + - - +
192E TYR* 3.3 5.5 + - - +
193E GLY 3.2 16.1 + - - -
264E GLY* 4.4 4.6 - - - -
267E THR* 3.7 13.6 + - - -
281E ILE* 3.3 39.0 - - - +
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Residues in contact with ILE 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 VAL* 2.8 31.8 + - + +
187E HIS 3.5 4.5 - - - +
189E GLY* 1.3 72.8 - - - +
191E GLU* 1.3 57.2 + - - +
193E GLY* 3.1 2.0 + - - +
194E ASP* 2.9 31.1 + - - +
281E ILE* 3.6 14.6 - - + +
334E SER* 4.9 9.5 + - - +
335E TYR* 3.4 52.0 - - + +
338E GLY* 4.6 12.1 - - - -
339E PHE* 5.0 2.0 - - + -
362E TRP* 3.6 33.2 - - + -
368E ILE* 3.9 7.9 - - + -
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Residues in contact with GLU 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 HIS* 2.8 25.0 + - - +
188E ASN* 2.9 34.5 + - - +
190E ILE* 1.3 75.0 - - - +
192E TYR* 1.3 65.5 + - + +
194E ASP* 4.1 2.1 - - - +
195E MET* 3.1 47.8 + - + +
232E LEU* 5.0 0.9 - - + -
288E ARG* 5.4 0.3 + - - -
367E ILE* 4.2 14.5 - - + +
368E ILE* 3.6 18.8 - - + -
447F ARG* 5.7 0.3 - - - +
450F PHE* 3.2 30.8 - - - -
501F 8HS 3.9 18.2 - - - +
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Residues in contact with TYR 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 ASN* 2.7 37.9 + - + -
189E GLY* 3.3 10.3 + - - +
191E GLU* 1.3 75.7 - - + +
193E GLY* 1.3 62.0 + - - +
195E MET* 4.1 1.0 - - - +
196E GLN* 3.1 18.7 + - - +
260E GLN* 4.1 18.1 - - + +
261E LYS 4.3 0.7 + - - -
263E THR* 4.5 1.4 + - - -
264E GLY* 3.8 27.2 + - - -
265E LYS 5.0 1.1 + - - -
281E ILE* 4.9 0.9 - - + -
284E ALA* 3.4 19.2 - - + +
285E VAL* 3.9 30.3 - - + -
288E ARG* 3.1 57.3 + - + +
443F ILE* 5.5 0.5 - - - +
501F 8HS 2.5 34.9 + - - -
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Residues in contact with GLY 193 (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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189E GLY 3.2 8.7 + - - -
190E ILE 3.1 7.1 + - - -
192E TYR* 1.3 76.3 - - - +
194E ASP* 1.3 61.3 + - - +
196E GLN* 3.3 1.4 + - - +
197E LEU* 2.9 35.4 + - - +
280E LEU* 3.6 27.0 - - - +
281E ILE* 5.2 1.3 - - - -
284E ALA* 3.9 8.7 - - - +
334E SER* 4.7 1.6 - - - -
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Residues in contact with ASP 194 (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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190E ILE* 2.9 17.9 + - - +
191E GLU* 4.1 1.8 - - - +
193E GLY* 1.3 76.3 - - - +
195E MET* 1.3 61.8 + - - +
197E LEU* 3.5 8.2 + - - +
198E ILE* 3.2 28.6 + - + +
232E LEU* 3.6 22.6 - - + +
327E LEU* 5.5 0.2 - - - +
331E LYS* 3.2 25.6 - - + +
334E SER* 4.4 6.9 + - - -
335E TYR* 2.8 39.0 + - - -
368E ILE* 4.1 10.0 - - - +
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Residues in contact with MET 195 (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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191E GLU* 3.1 41.5 + - - +
192E TYR 4.1 2.7 - - - +
194E ASP* 1.3 74.7 - - - +
196E GLN* 1.3 63.0 + - - +
198E ILE* 3.3 7.0 + - - +
199E CYS* 3.1 26.2 + - - -
232E LEU* 4.0 20.2 - - + -
288E ARG* 3.5 26.2 - - - +
443F ILE* 3.5 28.0 - - + +
446F GLN* 3.3 33.4 - - + +
447F ARG* 3.8 17.5 - - + +
450F PHE* 4.7 5.2 - - + -
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Residues in contact with GLN 196 (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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192E TYR 3.1 19.8 + - - +
193E GLY 3.9 2.9 - - - +
195E MET* 1.3 73.6 - - - +
197E LEU* 1.3 65.3 + - - +
199E CYS* 3.3 11.7 + - - +
200E GLU* 3.0 44.3 + - - +
284E ALA* 3.9 12.1 - - + +
287E ALA* 3.6 31.0 - - + +
288E ARG* 5.3 2.9 + - - +
419E PRO 5.4 0.2 + - - -
421E PRO* 4.2 7.0 - - + +
422E CYS* 3.5 22.7 - - - -
439F PRO* 5.4 5.1 - - - +
440F ALA* 5.8 2.8 - - - +
443F ILE* 4.1 13.6 - - + +
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Residues in contact with LEU 197 (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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193E GLY 2.9 24.2 + - - +
194E ASP* 3.7 11.0 - - - +
196E GLN* 1.3 77.2 - - - +
198E ILE* 1.3 61.6 + - - +
200E GLU* 3.2 7.1 + - - +
201E ALA* 3.0 22.0 + - - +
280E LEU* 4.4 7.9 - - + -
327E LEU* 3.5 20.8 - - + +
330E SER* 3.6 26.2 - - - +
331E LYS* 3.9 31.6 - - + +
334E SER* 4.9 1.1 - - - -
422E CYS* 3.6 26.7 - - + -
423E PHE* 3.8 20.6 - - + -
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Residues in contact with ILE 198 (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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194E ASP* 3.2 15.7 + - + +
195E MET* 3.3 7.8 + - - +
197E LEU* 1.3 77.1 - - - +
199E CYS* 1.3 53.4 + - - +
201E ALA* 3.2 7.8 + - - +
202E TYR* 2.7 33.1 + - - +
220E PHE* 3.8 10.4 - - + -
232E LEU* 3.9 23.8 - - + +
233E ILE* 3.7 28.5 - - + -
236E THR* 3.5 44.4 - - + +
327E LEU* 5.0 7.4 - - + -
442F LEU* 3.9 4.7 - - + -
446F GLN* 3.7 11.4 - - - +
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Residues in contact with CYS 199 (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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195E MET 3.1 18.4 + - - -
196E GLN* 3.6 15.3 - - - +
197E LEU 3.3 0.4 - - - -
198E ILE* 1.3 77.5 - - - +
200E GLU* 1.3 56.7 + - - +
202E TYR* 3.2 5.3 + - - +
203E HIS* 2.8 31.4 + - - +
439F PRO* 3.2 46.2 - - + +
442F LEU* 3.7 18.6 - - - -
443F ILE* 3.5 24.7 - - - -
446F GLN* 4.9 0.4 - - - -
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Residues in contact with GLU 200 (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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196E GLN* 3.0 34.7 + - - +
197E LEU* 3.2 7.1 + - - +
199E CYS* 1.3 75.5 - - - +
201E ALA* 1.3 61.6 + - - +
203E HIS* 3.6 6.0 + - - +
204E LEU* 3.1 28.4 + - - +
418E ILE* 5.1 1.0 - - - +
419E PRO 4.1 16.2 - - - +
420E MET* 3.8 3.1 - - + +
421E PRO* 3.0 17.4 - - - +
422E CYS* 2.6 37.4 + - - +
423E PHE* 3.0 45.6 + - + -
439F PRO* 5.1 1.8 - - + -
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Residues in contact with ALA 201 (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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197E LEU 3.0 12.9 + - - +
198E ILE* 3.2 8.9 + - - +
200E GLU* 1.3 75.5 - - - +
202E TYR* 1.3 59.9 + - - +
204E LEU* 3.2 3.2 + - - +
205E MET* 3.0 43.5 + - + +
220E PHE* 4.5 2.9 - - + -
223E TRP* 4.2 9.9 - - + -
323E ILE* 3.8 27.5 - - + +
327E LEU* 4.5 8.5 - - + -
423E PHE* 4.0 6.6 - - + -
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Residues in contact with TYR 202 (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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198E ILE 2.7 21.4 + - - +
199E CYS 3.2 2.2 + - - +
201E ALA* 1.3 71.4 - - - +
203E HIS* 1.3 59.9 + - - +
205E MET* 3.4 11.9 + - - +
206E LYS* 3.0 59.9 + - + +
213E GLN* 3.3 14.5 + - - -
216E MET* 3.7 28.7 - - + +
220E PHE* 4.3 6.5 - + + -
240E LEU* 3.8 30.3 - - + -
251E LEU* 3.4 22.9 - - + +
252E PRO* 5.6 1.0 - - - +
439F PRO* 3.7 27.6 - - + -
441F SER* 5.6 0.9 - - - -
442F LEU* 4.0 20.4 - - + -
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Residues in contact with HIS 203 (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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199E CYS 2.8 20.2 + - - +
200E GLU* 3.9 6.3 - - - +
202E TYR* 1.3 75.3 - - - +
204E LEU* 1.3 60.8 + - - +
206E LYS* 4.3 13.0 + - - +
207E ASP* 2.6 61.6 + - + +
418E ILE* 3.6 19.0 - - + +
419E PRO* 3.7 30.3 + - + +
435F HIS* 3.9 21.4 + + - -
437F MET 4.6 6.1 + - - -
438F LEU* 4.7 0.4 - - + -
439F PRO* 3.7 28.7 - - + +
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Residues in contact with LEU 204 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E GLU 3.1 23.0 + - - +
201E ALA 3.2 2.9 + - - +
203E HIS* 1.3 76.9 - - - +
205E MET* 1.3 58.2 + - - +
208E VAL* 3.1 53.3 + - + +
209E LEU* 3.3 4.0 + - - +
319E PHE* 5.1 3.8 - - + -
323E ILE* 3.7 33.2 - - + +
409E ALA* 4.7 12.8 - - + +
413E GLY* 4.1 15.3 - - - +
418E ILE* 3.8 22.2 - - + -
420E MET* 4.1 12.3 - - + -
423E PHE* 4.0 21.1 - - + -
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Residues in contact with MET 205 (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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201E ALA 3.0 28.6 + - - +
202E TYR* 3.8 1.8 - - - +
203E HIS 3.3 0.2 - - - -
204E LEU* 1.3 76.6 - - - +
206E LYS* 1.3 58.8 + - - +
209E LEU* 4.0 4.9 - - + +
210E GLY 3.6 2.8 + - - -
211E MET* 3.0 43.1 + - - +
216E MET* 3.6 23.3 - - + -
219E ALA* 3.9 18.6 - - - -
220E PHE* 3.5 35.9 - - + -
223E TRP* 3.6 20.2 - - + -
320E LEU* 3.5 32.1 - - + -
323E ILE* 4.3 7.0 - - + -
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Residues in contact with LYS 206 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202E TYR* 3.0 47.4 + - + +
203E HIS* 3.9 14.4 + - - +
204E LEU 3.2 0.2 - - - -
205E MET* 1.3 79.2 - - - +
207E ASP* 1.3 83.1 + - - +
210E GLY* 3.7 17.1 - - - -
211E MET 4.3 7.2 - - - +
213E GLN* 5.2 1.6 - - - +
216E MET* 4.0 17.3 - - + -
437F MET* 5.1 16.8 + - - +
438F LEU 5.9 3.8 - - - -
439F PRO* 5.9 1.2 - - - +
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Residues in contact with ASP 207 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203E HIS* 2.6 43.1 + - - +
206E LYS* 1.3 101.1 - - - +
208E VAL* 1.3 64.0 + - - +
210E GLY* 4.3 3.0 + - - -
416E ALA* 5.8 1.2 - - - +
418E ILE* 3.7 19.2 - - + +
435F HIS* 4.4 6.2 + - - -
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Residues in contact with VAL 208 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204E LEU* 3.1 35.7 + - + +
207E ASP* 1.3 81.4 - - - +
209E LEU* 1.3 61.9 + - - +
210E GLY 3.3 0.6 + - - -
310E PHE* 4.8 6.7 - - + -
312E PHE* 3.7 31.7 - - + +
316E LYS* 5.4 0.2 - - - +
319E PHE* 3.7 25.6 - - + -
412E THR* 4.0 16.6 - - + -
413E GLY* 5.0 2.0 - - - -
416E ALA* 4.1 14.8 - - + -
418E ILE* 3.8 17.0 - - + -
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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