Contacts of the helix formed by residues 178 - 208 (chain C) 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 C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C TYR* 4.0 13.9 - - - +
109C THR* 3.5 26.6 - - - +
113C CYS* 4.8 0.2 - - - +
125C GLY 4.6 2.0 - - - -
144C GLY 4.0 4.0 - - - -
145C GLY* 3.3 18.2 - - - -
177C GLU* 1.3 77.3 - - - +
179C ALA* 1.3 64.7 + - - +
180C GLY 3.1 3.9 + - - -
181C HIS* 3.5 10.2 + - - +
182C PHE 3.7 6.4 + - - -
351C TRP* 4.5 0.7 - - - -
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Residues in contact with ALA 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144C GLY* 4.4 2.2 - - - -
174C VAL* 3.6 8.5 - - + -
176C ASP 3.2 24.6 + - - +
178C GLY* 1.3 75.3 - - - +
180C GLY* 1.3 57.9 - - - +
181C HIS 3.4 0.2 - - - -
182C PHE* 3.3 3.6 + - - +
183C VAL* 2.9 30.8 + - - +
351C TRP* 3.5 30.3 - - + -
353C LEU* 3.6 21.8 - - + -
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Residues in contact with GLY 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C GLY 4.0 3.4 - - - -
127C GLY 4.7 2.0 - - - -
142C MET* 3.3 29.4 - - - +
144C GLY* 4.1 4.4 - - - -
174C VAL* 3.4 17.2 - - - +
178C GLY* 3.1 2.0 - - - -
179C ALA* 1.3 75.4 - - - +
181C HIS* 1.3 54.1 + - - +
183C VAL* 3.1 5.5 + - - +
184C LYS* 2.7 35.6 + - - +
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Residues in contact with HIS 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C ASP* 3.6 20.7 + - - -
102C GLY 2.9 27.0 + - - -
103C ASN* 4.9 1.6 - - - -
104C SER* 3.5 26.6 + - - +
106C TYR* 4.1 8.5 + - - -
109C THR* 2.7 32.3 + - + +
125C GLY* 3.4 29.5 + - - -
126C SER 3.3 20.0 + - - -
127C GLY* 4.3 4.7 - - - -
178C GLY 3.5 8.3 + - - +
179C ALA 3.4 0.2 - - - -
180C GLY* 1.3 75.1 - - - +
182C PHE* 1.3 57.5 + - - +
184C LYS* 3.5 7.5 + - + +
185C MET* 3.0 26.5 + - - +
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Residues in contact with PHE 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 3.5 50.9 - + + +
178C GLY 3.7 0.8 + - - -
179C ALA 3.3 8.9 + - - +
180C GLY 3.2 0.6 - - - -
181C HIS* 1.3 76.0 - - - +
183C VAL* 1.3 66.9 + - + +
185C MET* 3.1 25.6 + - + +
186C VAL* 3.0 41.5 + - + +
270C SER* 3.6 18.8 - - - -
274C TYR* 4.7 1.6 - + - -
341C LEU* 4.1 16.6 - - + -
342C LEU* 3.8 17.0 - - + -
345C ALA* 3.4 32.8 - - + -
351C TRP* 4.0 20.2 - + + -
353C LEU* 5.5 2.5 - - + -
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Residues in contact with VAL 183 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C MET* 4.1 11.7 - - + -
174C VAL* 4.5 6.3 - - + -
179C ALA 2.9 19.4 + - - +
180C GLY* 3.1 9.6 + - - +
182C PHE* 1.3 76.2 - - + +
184C LYS* 1.3 57.9 + - - +
186C VAL* 3.2 1.4 + - - +
187C HIS 2.9 23.7 + - - -
342C LEU* 3.8 17.9 - - + -
353C LEU* 4.4 11.0 - - + -
358C ILE* 3.7 39.7 - - + -
361C MET* 6.0 1.1 - - + -
362C TRP* 3.3 31.6 - - + +
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Residues in contact with LYS 184 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C ASN* 3.3 39.3 - - - +
127C GLY* 3.9 21.3 - - - -
128C VAL 3.8 7.7 + - - +
129C SER* 3.5 34.6 + - - +
142C MET* 4.0 17.2 - - + -
180C GLY 2.7 19.8 + - - +
181C HIS* 3.7 12.8 - - + +
183C VAL* 1.3 73.6 - - - +
185C MET* 1.3 62.5 + - - +
187C HIS* 3.2 17.0 + - - +
188C ASN* 3.0 40.8 + - - +
263C THR* 5.6 0.4 - - + -
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Residues in contact with MET 185 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C TYR* 4.1 18.4 - - + -
181C HIS 3.0 14.0 + - - +
182C PHE* 3.1 48.4 + - + +
184C LYS* 1.3 78.1 - - - +
186C VAL* 1.3 67.9 + - + +
188C ASN* 3.3 5.0 + - - +
189C GLY 3.1 9.0 + - - -
263C THR* 3.9 23.3 - - + +
266C TRP* 3.7 27.1 - - + +
267C THR* 2.8 32.7 + - - +
270C SER* 4.1 12.6 - - - -
341C LEU* 4.9 0.7 - - + -
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Residues in contact with VAL 186 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182C PHE* 3.0 28.1 + - + +
183C VAL 3.2 5.8 + - - +
185C MET* 1.3 76.2 - - + +
187C HIS* 1.3 60.0 + - - +
189C GLY* 3.2 1.0 + - - -
190C ILE* 2.9 36.7 + - + +
267C THR* 4.1 9.1 - - + +
281C ILE* 5.6 0.2 - - + -
338C GLY* 3.9 24.0 - - - +
341C LEU* 3.9 19.7 - - + -
342C LEU* 3.6 23.3 - - + -
362C TRP* 3.9 15.7 - - + -
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Residues in contact with HIS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C SER* 2.9 29.0 + - - -
142C MET* 4.6 3.1 - - + -
183C VAL 2.9 9.0 + - - +
184C LYS* 3.3 17.8 + - - +
185C MET 3.2 0.2 - - - -
186C VAL* 1.3 76.8 - - - +
188C ASN* 1.3 91.1 + - - +
190C ILE* 3.3 4.2 + - - +
191C GLU* 2.8 43.9 + - - +
362C TRP* 3.5 32.7 - + - +
366C CYS* 3.7 19.1 - - + +
367C ILE* 4.2 6.2 + - + -
368C ILE* 3.6 25.3 - - + +
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Residues in contact with ASN 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103C ASN* 4.2 0.3 - - - +
184C LYS* 3.0 37.1 + - - +
185C MET 3.3 3.1 + - - +
187C HIS* 1.3 101.3 + - - +
189C GLY* 1.3 61.1 + - - +
191C GLU* 3.3 13.8 + - - +
192C TYR* 3.0 38.0 + - + -
263C THR* 3.3 39.9 + - - +
267C THR* 4.6 0.2 - - - -
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Residues in contact with GLY 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185C MET 3.1 11.3 + - - -
186C VAL 3.2 2.8 + - - -
188C ASN* 1.3 73.7 - - - +
190C ILE* 1.3 63.3 + - - +
192C TYR* 3.1 13.9 + - - +
193C GLY 3.3 8.0 + - - -
263C THR 5.0 0.9 - - - -
264C GLY 5.1 1.3 - - - -
267C THR* 3.5 28.1 + - - -
281C ILE* 3.3 24.4 - - - +
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Residues in contact with ILE 190 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C VAL* 2.9 29.7 + - + +
187C HIS 3.7 4.5 - - - +
189C GLY* 1.3 74.2 - - - +
191C GLU* 1.3 61.9 + - - +
193C GLY* 3.1 2.1 + - - -
194C ASP* 3.1 24.6 + - - +
281C ILE* 3.5 17.7 - - + +
334C SER* 3.6 33.8 + - - +
335C TYR* 3.4 46.4 - - + +
338C GLY* 4.0 10.3 - - - -
339C PHE* 6.2 0.9 - - + -
362C TRP* 4.5 10.5 - - + -
368C ILE* 3.8 11.2 - - + -
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Residues in contact with GLU 191 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187C HIS* 2.8 40.3 + - - +
188C ASN* 3.3 19.0 + - - +
189C GLY 3.1 0.2 - - - -
190C ILE* 1.3 78.1 - - - +
192C TYR* 1.3 66.4 + - + +
194C ASP* 3.5 1.5 + - - +
195C MET* 3.2 44.9 + - + +
232C LEU* 5.4 0.4 - - + -
367C ILE* 4.2 17.5 - - + +
368C ILE* 3.5 19.3 - - + +
450D PHE* 3.6 27.5 - - - -
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Residues in contact with TYR 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C ASN* 3.0 31.5 + - + -
189C GLY* 3.1 9.8 + - - +
191C GLU* 1.3 81.9 - - + +
193C GLY* 1.3 62.6 + - - +
195C MET* 4.0 1.4 - - - +
196C GLN* 3.1 26.0 + - - +
260C GLN* 2.8 27.8 + - - -
261C LYS* 3.2 11.3 + - - -
262C GLY* 5.0 0.2 - - - -
263C THR* 4.6 2.6 + - - -
264C GLY* 3.5 31.7 + - - -
265C LYS 5.1 0.2 - - - -
281C ILE* 4.8 4.5 - - + -
284C ALA* 3.5 13.2 - - + +
285C VAL* 3.9 20.6 - - + -
288C ARG* 2.9 55.9 + - + +
443D ILE* 5.5 0.9 - - - +
447D ARG* 4.3 2.6 + - - -
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Residues in contact with GLY 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189C GLY 3.3 6.3 + - - -
190C ILE 3.1 7.0 + - - -
192C TYR* 1.3 77.4 - - - +
194C ASP* 1.3 62.0 + - - +
196C GLN* 3.3 1.6 + - - +
197C LEU* 2.8 36.2 + - - +
280C LEU* 3.6 25.0 - - - +
281C ILE* 4.9 1.5 - - - +
284C ALA* 4.1 8.5 - - - +
334C SER* 4.6 2.5 - - - -
422C CYS* 4.9 0.2 - - - -
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Residues in contact with ASP 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C ILE* 3.1 17.1 + - - +
191C GLU* 4.2 2.0 - - - +
193C GLY* 1.3 76.8 - - - +
195C MET* 1.3 61.9 + - - +
197C LEU* 3.4 9.0 + - - +
198C ILE* 3.1 31.7 + - + +
232C LEU* 3.9 19.4 - - + +
331C LYS* 3.3 28.8 + - + +
334C SER* 4.3 5.7 + - - -
335C TYR* 2.7 38.7 + - - -
368C ILE* 4.1 9.1 - - + +
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Residues in contact with MET 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C GLU* 3.2 41.5 + - - +
192C TYR 4.1 2.9 - - - +
194C ASP* 1.3 77.0 - - - +
196C GLN* 1.3 61.2 + - - +
198C ILE* 3.4 5.9 + - - +
199C CYS* 3.2 28.4 + - - -
232C LEU* 3.9 20.0 - - + -
288C ARG* 3.8 14.6 - - - +
443D ILE* 3.7 42.4 - - + +
446D GLN* 3.3 32.9 - - + +
447D ARG* 4.3 7.6 - - + +
450D PHE* 4.3 9.2 - - + -
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Residues in contact with GLN 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C TYR 3.1 19.0 + - - +
193C GLY 3.9 3.1 - - - +
195C MET* 1.3 73.2 - - - +
197C LEU* 1.3 60.0 + - - +
199C CYS* 3.2 11.2 + - - +
200C GLU* 3.0 55.7 + - - +
284C ALA* 3.9 17.0 + - + -
287C ALA* 3.7 27.4 - - + +
288C ARG 5.0 0.2 - - - +
421C PRO* 4.3 3.6 - - - +
422C CYS* 3.6 13.2 - - - -
439D PRO* 6.0 1.7 - - - +
440D ALA* 5.9 2.6 - - - +
443D ILE* 3.5 23.4 - - + +
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Residues in contact with LEU 197 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C GLY 2.8 28.6 + - - +
194C ASP* 3.6 10.3 - - - +
195C MET 3.3 0.2 - - - -
196C GLN* 1.3 77.3 - - - +
198C ILE* 1.3 61.3 + - - +
200C GLU* 3.3 5.5 + - - +
201C ALA* 3.1 18.0 + - - +
280C LEU* 4.2 9.6 - - + -
327C LEU* 3.4 22.7 - - + +
330C SER* 3.6 12.6 - - - +
331C LYS* 3.8 36.8 - - + +
334C SER* 4.8 0.2 - - - -
422C CYS* 3.6 26.0 - - + +
423C PHE* 3.5 32.1 - - + -
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Residues in contact with ILE 198 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194C ASP* 3.1 19.9 + - + +
195C MET* 3.7 5.6 - - - +
196C GLN 3.3 0.4 - - - -
197C LEU* 1.3 75.9 - - - +
199C CYS* 1.3 58.2 + - - +
201C ALA* 3.3 5.7 + - - +
202C TYR* 2.8 26.5 + - - +
220C PHE* 3.8 13.9 - - + -
232C LEU* 3.7 37.5 - - + -
233C ILE* 4.2 15.0 - - + -
236C THR* 3.6 37.7 - - + +
327C LEU* 4.3 14.4 - - + -
442D LEU* 4.2 2.5 - - + -
446D GLN* 3.7 11.0 - - - +
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Residues in contact with CYS 199 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195C MET 3.2 21.2 + - - -
196C GLN* 3.2 17.0 + - - +
198C ILE* 1.3 77.7 - - - +
200C GLU* 1.3 56.3 + - - +
202C TYR* 3.2 7.8 + - - +
203C HIS 2.8 24.3 + - - -
439D PRO* 3.3 46.1 - - + +
442D LEU* 3.8 18.6 - - - -
443D ILE* 3.5 23.1 - - - -
446D GLN* 4.9 1.3 - - - -
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Residues in contact with GLU 200 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196C GLN* 3.0 30.6 + - - +
197C LEU* 3.8 4.8 - - - +
198C ILE 3.3 0.4 - - - -
199C CYS* 1.3 75.6 - - - +
201C ALA* 1.3 62.2 + - - +
203C HIS* 3.5 7.6 + - - +
204C LEU* 3.4 26.7 + - - +
418C ILE* 5.2 0.2 - - - +
419C PRO 4.2 9.2 - - - +
420C MET* 3.8 4.6 - - + +
421C PRO* 3.0 26.3 - - + +
422C CYS* 2.6 39.8 + - - +
423C PHE* 2.8 45.3 + - + +
439D PRO* 5.3 0.7 - - - -
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Residues in contact with ALA 201 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C LEU 3.1 13.3 + - - +
198C ILE* 3.7 7.6 - - - +
199C CYS 3.3 0.2 - - - -
200C GLU* 1.3 75.9 - - - +
202C TYR* 1.3 64.1 + - - +
204C LEU* 3.3 4.7 + - - +
205C MET* 3.1 28.0 + - - +
220C PHE* 4.7 1.6 - - + -
223C TRP* 4.4 16.2 - - + -
323C ILE* 3.6 27.5 - - + +
327C LEU* 4.5 8.7 - - + -
423C PHE* 4.0 11.6 - - + -
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Residues in contact with TYR 202 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198C ILE 2.8 17.4 + - - +
199C CYS* 3.2 5.8 + - - +
201C ALA* 1.3 75.8 - - - +
203C HIS* 1.3 66.3 + + - +
205C MET* 3.4 5.8 + - - +
206C LYS* 3.2 40.2 + - + +
213C GLN* 3.2 19.6 + - - -
216C MET* 3.5 25.1 - - + -
220C PHE* 4.4 11.6 - + + -
240C LEU* 3.5 36.3 - - + -
251C LEU* 3.9 17.1 - - + +
252C PRO* 5.8 0.7 - - - +
439D PRO* 3.8 29.4 - - + -
441D SER* 5.9 2.0 - - - -
442D LEU* 4.1 14.6 - - + -
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Residues in contact with HIS 203 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199C CYS 2.8 10.0 + - - +
200C GLU* 3.8 8.5 - - - +
201C ALA 3.2 0.4 - - - -
202C TYR* 1.3 82.8 - + - +
204C LEU* 1.3 57.2 + - - +
206C LYS* 3.4 6.4 + - + -
207C ASP* 2.7 59.3 + - - +
418C ILE* 3.4 19.7 - - + +
419C PRO* 3.5 32.0 + - + +
435D HIS* 3.7 18.1 + + - -
437D MET 4.3 5.8 + - - -
438D LEU* 4.3 4.0 - - + -
439D PRO* 3.5 35.9 - - + +
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200C GLU 3.4 13.9 + - - +
201C ALA 3.3 5.0 + - - +
203C HIS* 1.3 75.9 - - - +
205C MET* 1.3 59.5 + - - +
208C VAL* 2.9 56.0 + - + +
209C LEU* 3.2 3.8 + - - +
319C PHE* 4.9 3.6 - - + -
323C ILE* 3.7 34.1 - - + -
409C ALA* 4.4 11.9 - - + +
413C GLY* 4.1 6.1 - - - +
418C ILE* 3.7 24.9 - - + -
420C MET* 4.0 31.0 - - + -
423C PHE* 4.4 11.0 - - + -
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Residues in contact with MET 205 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201C ALA 3.1 19.2 + - - +
202C TYR* 3.8 4.7 - - - +
203C HIS 3.3 0.2 - - - -
204C LEU* 1.3 76.9 - - - +
206C LYS* 1.3 57.4 + - - +
209C LEU* 3.8 4.4 - - + +
210C GLY 3.5 3.8 + - - -
211C MET* 2.9 39.5 + - + +
216C MET* 3.6 40.2 - - + +
219C ALA* 3.8 11.0 - - + -
220C PHE* 3.6 26.7 - - + -
223C TRP* 3.5 31.4 - - - -
320C LEU* 3.7 21.5 - - + -
323C ILE* 4.3 9.6 - - + -
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Residues in contact with LYS 206 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202C TYR* 3.2 41.9 + - + +
203C HIS* 4.0 6.5 - - + +
204C LEU 3.2 0.2 - - - -
205C MET* 1.3 79.0 - - - +
207C ASP* 1.3 73.9 + - - +
210C GLY* 3.3 19.9 - - - -
211C MET 4.2 8.6 - - - +
213C GLN* 4.8 9.4 - - - +
216C MET* 4.0 14.8 - - + -
437D MET* 6.4 2.0 - - - -
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Residues in contact with ASP 207 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203C HIS* 2.7 44.1 + - - +
206C LYS* 1.3 99.8 - - - +
208C VAL* 1.3 64.6 + - - +
210C GLY* 4.4 1.8 - - - -
310C PHE* 6.1 0.3 - - - -
416C ALA* 5.6 1.2 - - - +
418C ILE* 3.6 20.9 - - + +
435D HIS* 4.1 7.6 + - - -
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Residues in contact with VAL 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204C LEU* 2.9 42.0 + - + +
207C ASP* 1.3 78.3 - - - +
209C LEU* 1.3 63.3 + - + +
210C GLY 3.4 0.4 - - - -
310C PHE* 4.7 8.9 - - + -
312C PHE* 4.2 23.1 - - + +
319C PHE* 3.7 27.1 - - + -
412C THR* 4.1 15.9 - - + -
413C GLY* 4.9 2.2 - - - -
416C ALA* 3.7 25.6 - - + -
418C ILE* 3.7 7.6 - - + -
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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