Contacts of the helix formed by residues 178 - 208 (chain D) 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 D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106D TYR* 3.7 14.2 - - - +
109D THR* 3.5 30.9 + - - +
110D THR* 4.7 0.2 - - - -
113D CYS* 4.9 0.2 - - - +
125D GLY 4.8 1.3 - - - -
144D GLY 4.6 2.0 - - - -
145D GLY* 3.6 13.7 - - - -
176D ASP 3.4 0.6 - - - -
177D GLU* 1.3 76.8 - - - +
179D ALA* 1.3 62.8 + - - +
180D GLY 3.2 4.2 + - - -
181D HIS* 3.6 4.3 + - - +
182D PHE* 3.6 14.4 + - - +
351D TRP* 4.2 1.7 - - - -
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D GLY 4.7 1.8 - - - +
174D VAL* 3.8 3.6 - - + -
175D GLY* 3.9 15.0 - - - -
176D ASP 3.4 12.0 + - - +
178D GLY* 1.3 75.2 - - - +
180D GLY* 1.3 59.6 + - - +
181D HIS 3.4 0.2 - - - -
182D PHE* 3.4 3.3 + - - +
183D VAL* 3.0 30.7 + - - +
351D TRP* 3.6 33.0 - - + -
353D LEU* 3.6 21.4 - - + +
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125D GLY 4.1 5.1 + - - -
127D GLY 4.7 0.7 - - - -
142D MET* 3.4 30.6 - - - +
144D GLY* 4.4 3.6 - - - -
174D VAL* 3.9 18.2 - - - +
178D GLY* 3.2 2.0 - - - -
179D ALA* 1.3 75.8 - - - +
181D HIS* 1.3 62.1 + - - +
183D VAL* 3.2 4.2 + - - +
184D LYS* 2.9 27.5 + - - +
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Residues in contact with HIS 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100D ASP* 3.3 30.9 + - - -
102D GLY 3.2 19.0 + - - -
103D ASN* 5.3 0.7 - - - -
104D SER* 3.7 27.7 - - - +
106D TYR* 4.0 12.5 + - - +
109D THR* 2.4 37.9 + - + +
125D GLY* 3.6 15.3 + - - -
126D SER 3.1 30.7 + - - -
127D GLY* 4.3 3.8 - - - -
178D GLY 3.6 5.1 + - - +
179D ALA 3.4 0.2 - - - -
180D GLY* 1.3 72.2 - - - +
182D PHE* 1.3 64.9 + - - +
184D LYS* 3.5 8.1 + - + +
185D MET* 3.1 21.1 + - - +
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Residues in contact with PHE 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D TYR* 3.6 40.4 - + + +
178D GLY 3.6 6.6 + - - +
179D ALA 3.4 10.0 + - - +
180D GLY 3.2 0.8 - - - -
181D HIS* 1.3 77.0 - - - +
183D VAL* 1.3 64.5 + - + +
185D MET* 3.1 31.5 + - + +
186D VAL* 3.0 34.3 + - + +
270D SER* 3.7 18.4 - - - -
274D TYR* 4.1 5.4 - + - -
341D LEU* 4.0 17.3 - - + -
342D LEU* 3.7 18.8 - - + -
345D ALA* 3.5 31.9 - - + -
351D TRP* 4.3 11.9 - + + -
353D LEU* 5.7 2.9 - - + -
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142D MET* 3.7 10.5 - - - -
174D VAL* 3.6 18.8 - - + -
179D ALA 3.0 19.2 + - - +
180D GLY* 3.2 9.8 + - - +
182D PHE* 1.3 74.8 - - + +
184D LYS* 1.3 52.9 + - - +
186D VAL 3.2 1.6 + - - -
187D HIS* 2.6 33.3 + - - +
342D LEU* 4.1 17.9 - - + -
353D LEU* 5.0 3.6 - - + -
358D ILE* 3.7 27.1 - - + -
361D MET* 4.8 4.3 - - + -
362D TRP* 3.4 34.0 - - + +
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Residues in contact with LYS 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASN* 3.5 26.5 + - - +
127D GLY* 3.5 26.7 - - - -
128D VAL 3.9 20.6 + - - +
129D SER* 4.5 3.9 - - - +
142D MET* 3.6 19.7 - - + -
180D GLY 2.9 12.2 + - - +
181D HIS* 3.7 11.4 - - + +
183D VAL* 1.3 77.3 - - - +
185D MET* 1.3 61.9 + - - +
187D HIS* 3.3 23.6 + - + +
188D ASN* 3.0 55.9 + - - +
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Residues in contact with MET 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLU* 4.8 9.4 - - - +
106D TYR* 3.6 20.6 - - + +
181D HIS 3.1 13.8 + - - +
182D PHE* 3.1 43.5 + - + +
184D LYS* 1.3 78.3 - - - +
186D VAL* 1.3 63.4 + - - +
188D ASN* 3.3 18.2 + - - +
189D GLY 3.3 1.2 + - - -
263D THR 5.5 2.0 - - - +
266D TRP* 3.2 37.0 - - + +
267D THR* 2.4 39.8 + - - +
270D SER* 3.9 11.4 - - - +
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Residues in contact with VAL 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D PHE* 3.0 39.4 + - + +
183D VAL 3.8 4.9 - - - +
185D MET* 1.3 77.3 - - - +
187D HIS* 1.3 65.5 + - - +
189D GLY* 3.1 1.9 + - - -
190D ILE* 3.0 26.1 + - + +
267D THR* 3.8 13.0 - - + +
281D ILE* 5.3 0.2 - - + -
338D GLY* 3.9 29.6 - - - +
341D LEU* 3.8 18.4 - - + -
342D LEU* 3.7 15.0 - - + -
362D TRP* 4.4 10.5 - - + -
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Residues in contact with HIS 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D SER* 3.4 29.7 + - - -
142D MET* 4.3 3.4 - - + -
183D VAL 2.6 22.7 + - - +
184D LYS* 3.4 17.7 + - - +
185D MET 3.2 0.2 - - - -
186D VAL* 1.3 73.2 - - - +
188D ASN* 1.3 85.1 + - - +
190D ILE* 3.7 4.3 + - - +
191D GLU* 3.2 31.1 + - - +
362D TRP* 3.7 26.4 - + - +
366D CYS* 3.7 21.1 - - - +
367D ILE* 4.6 4.1 + - + -
368D ILE* 3.5 28.6 - - + +
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Residues in contact with ASN 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103D ASN* 5.5 2.4 + - - +
184D LYS* 3.0 34.6 + - - +
185D MET* 3.7 9.9 - - - +
186D VAL 3.2 0.2 - - - -
187D HIS* 1.3 95.7 + - - +
189D GLY* 1.3 65.5 + - - +
191D GLU* 3.2 13.1 + - - +
192D TYR* 3.1 31.1 + - + -
263D THR* 4.5 23.4 + - + +
264D GLY* 4.6 12.1 - - - -
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Residues in contact with GLY 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185D MET 3.3 5.7 + - - -
186D VAL 3.1 5.1 + - - -
188D ASN* 1.3 76.4 - - - +
190D ILE* 1.3 64.8 + - - +
192D TYR* 3.1 14.7 + - - +
193D GLY 3.2 8.8 + - - -
264D GLY* 4.2 7.2 - - - -
267D THR* 3.3 23.9 + - - -
281D ILE* 3.5 22.1 - - - +
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Residues in contact with ILE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D VAL* 3.0 18.8 + - + +
187D HIS 4.0 3.6 - - - +
189D GLY* 1.3 75.2 - - - +
191D GLU* 1.3 63.3 + - - +
193D GLY* 3.1 2.5 + - - +
194D ASP* 3.0 24.1 + - - +
281D ILE* 3.6 18.1 - - + +
334D SER* 4.7 9.1 + - - +
335D TYR* 3.4 55.0 - - + +
338D GLY* 4.4 18.4 - - - -
339D PHE* 5.2 0.9 - - + -
362D TRP* 3.5 30.7 - - + -
368D ILE* 4.0 11.2 - - + -
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Residues in contact with GLU 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450C PHE* 4.1 9.5 - - - -
187D HIS* 3.2 25.1 + - + +
188D ASN* 3.3 19.3 - - - +
189D GLY 3.2 0.4 - - - -
190D ILE* 1.3 77.3 - - - +
192D TYR* 1.3 70.4 + - + +
194D ASP* 3.5 0.9 + - - +
195D MET* 3.1 48.9 + - + +
232D LEU* 5.4 0.4 - - + -
288D ARG* 5.7 0.2 + - - -
367D ILE* 3.1 37.8 - - + +
368D ILE* 3.6 22.4 - - + -
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Residues in contact with TYR 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C ILE* 5.2 1.2 - - - +
447C ARG* 5.2 2.3 + - - -
188D ASN* 3.1 22.0 - - + -
189D GLY* 3.1 11.1 + - - +
191D GLU* 1.3 87.6 - - + +
193D GLY* 1.3 61.9 + - - +
195D MET* 3.9 1.6 - - - +
196D GLN* 3.1 25.5 + - - +
259D GLY 5.3 0.4 + - - -
262D GLY* 3.9 9.5 - - - -
263D THR* 3.2 32.7 + - + +
264D GLY* 3.4 20.6 + - - -
281D ILE* 5.3 0.2 - - + -
284D ALA* 3.6 12.1 - - + +
285D VAL* 3.8 31.4 - - + -
288D ARG* 3.0 60.7 + - + +
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Residues in contact with GLY 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189D GLY 3.2 6.7 + - - -
190D ILE 3.1 6.8 + - - -
192D TYR* 1.3 80.7 - - - +
194D ASP* 1.3 58.4 + - - +
196D GLN* 3.4 1.4 + - - +
197D LEU* 2.8 38.0 + - - +
280D LEU* 3.6 25.2 - - - +
281D ILE* 5.3 1.3 - - - -
284D ALA* 3.8 8.5 - - - +
334D SER* 4.8 2.7 - - - -
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Residues in contact with ASP 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D ILE* 3.0 15.5 + - - +
191D GLU* 4.1 3.1 - - - +
193D GLY* 1.3 78.1 - - - +
195D MET* 1.3 62.6 + - - +
197D LEU* 3.4 10.2 + - - +
198D ILE* 3.1 29.3 + - + +
232D LEU* 3.8 20.5 - - + +
331D LYS* 3.5 26.7 - - - +
334D SER* 4.7 3.6 + - - -
335D TYR* 2.7 39.7 + - - -
368D ILE* 4.0 11.8 - - + +
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Residues in contact with MET 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443C ILE* 3.7 31.9 - - + +
446C GLN* 3.2 36.7 - - + +
447C ARG* 3.7 19.7 - - + +
450C PHE* 4.7 6.7 - - + -
191D GLU* 3.1 33.7 + - - +
192D TYR 3.9 2.9 - - - +
194D ASP* 1.3 77.2 - - - +
196D GLN* 1.3 61.2 + - - +
198D ILE* 3.2 7.0 + - - +
199D CYS* 3.1 27.7 + - - -
232D LEU* 3.7 21.3 - - + -
288D ARG* 3.4 23.6 - - - +
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Residues in contact with GLN 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C PRO* 5.3 5.7 - - - +
440C ALA* 5.8 3.3 - - - +
443C ILE* 3.9 19.3 - - + +
192D TYR 3.1 17.9 + - - +
193D GLY 3.9 2.5 - - - +
195D MET* 1.3 77.3 - - - +
197D LEU* 1.3 63.5 + - - +
199D CYS* 3.1 12.3 + - - +
200D GLU* 3.0 50.9 + - - +
284D ALA* 4.0 10.8 - - + +
287D ALA* 3.5 31.5 - - + +
288D ARG 5.2 0.2 + - - -
421D PRO* 4.1 8.1 - - - +
422D CYS* 3.5 22.9 - - - -
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Residues in contact with LEU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193D GLY 2.8 27.5 + - - +
194D ASP* 3.7 11.7 - - - +
195D MET 3.3 0.2 - - - -
196D GLN* 1.3 77.6 - - - +
198D ILE* 1.3 60.7 + - - +
200D GLU* 3.5 5.3 + - - +
201D ALA 3.1 17.2 + - - -
280D LEU* 4.3 8.3 - - + -
327D LEU* 3.4 24.0 - - + +
330D SER* 3.6 15.7 - - - +
331D LYS* 3.8 36.6 - - + +
334D SER* 4.8 1.3 - - - -
422D CYS* 3.6 26.5 - - + -
423D PHE* 3.5 28.4 - - + -
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Residues in contact with ILE 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442C LEU* 4.1 3.4 - - + -
446C GLN* 3.9 11.0 - - - +
194D ASP* 3.1 15.2 + - + +
195D MET 3.2 7.6 + - - +
197D LEU* 1.3 74.1 - - - +
199D CYS* 1.3 59.4 + - - +
201D ALA* 3.4 6.0 + - - +
202D TYR* 2.8 27.5 + - - +
220D PHE* 3.7 11.1 - - + -
230D SER* 5.0 0.4 - - - +
232D LEU* 3.6 33.0 - - + -
233D ILE* 3.7 24.9 - - + -
236D THR* 3.4 37.0 - - + +
327D LEU* 4.5 9.4 - - + -
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Residues in contact with CYS 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C PRO* 3.2 45.1 - - + +
442C LEU* 3.9 16.8 - - - -
443C ILE* 3.5 27.8 - - - -
446C GLN* 4.9 0.7 - - - -
195D MET 3.1 17.8 + - - -
196D GLN* 3.1 15.7 + - - +
198D ILE* 1.3 78.1 - - - +
200D GLU* 1.3 56.9 + - - +
202D TYR* 3.3 5.1 + - - +
203D HIS* 2.8 29.8 + - - +
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Residues in contact with GLU 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439C PRO* 5.0 2.5 - - + -
196D GLN* 3.0 36.6 + - - +
197D LEU* 3.9 4.5 - - - +
199D CYS* 1.3 74.9 - - - +
201D ALA* 1.3 58.1 + - - +
203D HIS* 3.2 8.0 + - - +
204D LEU* 3.0 32.9 + - - +
418D ILE* 5.2 0.7 - - - +
419D PRO 4.3 8.7 - - - +
420D MET* 3.8 4.9 - - + +
421D PRO* 3.0 21.2 - - + +
422D CYS* 2.7 35.2 + - - +
423D PHE* 3.0 46.3 + - + +
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Residues in contact with ALA 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D LEU 3.1 16.6 + - - +
198D ILE 3.7 3.8 - - - +
200D GLU* 1.3 73.7 - - - +
202D TYR* 1.3 65.7 + - - +
204D LEU* 3.3 2.8 + - - +
205D MET* 3.2 29.4 + - - +
220D PHE* 4.4 1.8 - - + -
223D TRP* 4.0 17.9 - - + -
323D ILE* 3.8 25.6 - - + +
327D LEU* 4.2 12.6 - - + -
423D PHE* 4.3 7.7 - - + -
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Residues in contact with TYR 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C PRO* 4.0 26.5 - - + -
441C SER* 5.6 2.9 + - - -
442C LEU* 4.1 20.4 - - + -
198D ILE 2.8 18.3 + - - +
199D CYS 3.3 1.1 + - - +
201D ALA* 1.3 75.0 - - - +
203D HIS* 1.3 63.6 + + - +
205D MET* 3.4 13.1 + - + +
206D LYS* 3.1 56.3 + - + +
213D GLN* 3.9 11.1 + - - -
216D MET* 3.5 26.7 - - + -
220D PHE* 4.1 8.6 - - + -
240D LEU* 3.5 33.9 - - + -
251D LEU* 4.1 16.6 - - + +
252D PRO* 5.8 1.4 - - - +
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Residues in contact with HIS 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C HIS* 4.1 16.4 - + - -
437C MET 4.6 4.3 + - - -
438C LEU* 4.6 1.1 - - + -
439C PRO* 3.6 32.1 - - + +
199D CYS 2.8 20.2 + - - +
200D GLU* 3.6 7.9 - - - +
201D ALA 3.2 0.2 - - - -
202D TYR* 1.3 76.1 - + - +
204D LEU* 1.3 62.5 - - - +
206D LYS* 4.5 12.4 + - - +
207D ASP* 2.7 52.4 + - + +
418D ILE* 3.6 18.7 - - + +
419D PRO* 3.5 35.2 + - + +
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200D GLU 3.0 16.3 + - - +
201D ALA 3.8 2.7 - - - +
202D TYR 3.3 0.2 - - - -
203D HIS* 1.3 77.0 - - - +
205D MET* 1.3 62.8 + - - +
208D VAL* 3.1 47.3 + - + +
209D LEU* 3.6 2.4 + - - +
319D PHE* 4.9 4.3 - - + -
323D ILE* 3.6 34.5 - - + +
409D ALA* 4.4 13.0 - - + +
413D GLY* 4.2 7.4 - - - +
418D ILE* 3.9 18.6 - - + -
420D MET* 3.9 27.4 - - + -
423D PHE* 3.9 27.6 - - + -
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Residues in contact with MET 205 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D ALA 3.2 9.7 + - - +
202D TYR* 3.8 13.0 - - + -
203D HIS 3.4 0.2 - - - -
204D LEU* 1.3 76.3 - - - +
206D LYS* 1.3 59.4 + - - +
209D LEU* 3.6 6.8 - - - +
210D GLY 3.4 5.7 + - - -
211D MET* 3.1 44.5 + - - +
216D MET* 3.6 29.2 - - + -
219D ALA* 4.0 19.7 - - - -
220D PHE* 3.4 30.7 - - + -
223D TRP* 3.8 24.2 - - + -
320D LEU* 4.1 9.4 - - + -
323D ILE* 4.2 13.9 - - + -
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Residues in contact with LYS 206 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437C MET* 5.3 13.1 + - - +
438C LEU 5.9 3.8 + - - -
439C PRO* 6.0 0.8 - - - +
202D TYR* 3.1 51.8 + - + +
203D HIS* 4.0 11.6 + - - +
204D LEU 3.2 0.4 - - - -
205D MET* 1.3 79.1 - - - +
207D ASP* 1.3 81.0 + - - +
210D GLY* 3.6 18.4 - - - -
211D MET 4.5 6.0 - - - +
213D GLN* 4.4 9.2 - - - +
216D MET* 3.8 17.7 - - + -
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Residues in contact with ASP 207 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C HIS* 4.5 7.3 + - - -
203D HIS* 2.7 38.2 + - - +
206D LYS* 1.3 100.3 - - - +
208D VAL* 1.3 62.1 + - - +
210D GLY* 4.4 2.2 - - - -
310D PHE* 5.6 2.6 - - - -
416D ALA* 5.8 0.7 - - - +
418D ILE* 3.6 23.7 - - + +
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Residues in contact with VAL 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204D LEU* 3.1 30.0 + - + +
207D ASP* 1.3 81.2 - - - +
209D LEU* 1.3 58.6 + - - +
210D GLY 3.5 0.4 - - - -
310D PHE* 4.5 8.6 - - + -
312D PHE* 3.9 30.5 - - + +
316D LYS* 5.4 1.0 - - - -
319D PHE* 3.6 28.7 - - + -
412D THR* 4.1 13.7 - - + -
416D ALA* 3.9 13.7 - - + -
418D ILE* 3.8 25.6 - - + -
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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