Contacts of the helix formed by residues 203 - 226 (chain D) in PDB entry 4O9U
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 MET 203 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D ALA* 3.7 29.4 - - - -
138D LYS* 3.7 39.3 - - + -
139D LEU* 3.8 27.1 - - + -
195D THR* 4.4 4.7 - - - +
198D ILE* 3.8 27.6 - - + +
199D GLY 3.3 20.1 + - - +
200D GLY* 4.1 11.2 - - - +
201D GLY 2.5 9.4 + - - +
202D ASP* 1.3 69.5 - - - +
204D PRO* 1.4 62.5 - - + +
206D ALA* 2.8 10.5 + - - -
207D ILE* 2.7 41.3 + - + +
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Residues in contact with PRO 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 6.2 0.3 - - - +
139D LEU* 5.3 1.1 - - + -
201D GLY 2.9 25.8 - - - +
203D MET* 1.4 81.6 - - + +
205D VAL* 1.3 60.4 + - - +
206D ALA 3.4 0.7 + - - -
207D ILE* 4.5 8.2 - - + +
208D SER* 3.7 17.7 + - - -
248D MET* 3.8 17.7 - - + +
252D MET* 3.6 12.1 - - + -
336D ARG 4.1 9.0 - - - +
337D MET* 3.6 24.9 - - + -
338D PRO* 3.6 28.6 - - + +
500D NAP 3.6 14.1 - - + -
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Residues in contact with VAL 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ASP 2.9 11.3 + - - +
204D PRO* 1.3 75.4 - - - +
206D ALA* 1.3 57.0 + - - +
209D PHE* 3.2 18.9 - - + +
245D THR* 3.3 17.7 - - + +
248D MET* 3.3 26.9 - - - +
249D ALA* 3.7 22.9 - - + -
252D MET* 3.5 23.6 - - + -
254D ARG* 5.8 0.9 - - + -
255D SER 5.0 4.5 - - - +
256D VAL* 5.1 8.5 - - + -
259D VAL* 4.3 23.1 - - + -
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Residues in contact with ALA 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135D ALA* 5.8 0.4 - - + -
195D THR* 6.1 0.4 - - - +
198D ILE* 4.2 22.2 - - + -
202D ASP 3.4 3.9 + - - +
203D MET* 2.8 22.8 + - - +
205D VAL* 1.3 79.9 - - - +
207D ILE* 1.3 53.6 + - + +
208D SER 3.4 0.7 - - - -
209D PHE* 3.1 9.2 - - + +
210D TYR* 2.7 54.3 + - + -
259D VAL* 5.5 2.0 - - + -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 4.7 7.6 - - - -
82D PRO* 3.3 31.2 - - + +
85D VAL* 3.8 29.6 - - + -
86D ALA* 3.7 31.2 - - + +
89D ASN* 2.9 13.9 + - - +
135D ALA* 4.8 11.2 - - + -
139D LEU* 4.3 17.9 - - + -
203D MET* 2.7 26.2 + - + +
204D PRO* 3.8 6.7 + - + +
206D ALA* 1.3 70.5 - - + +
208D SER* 1.3 54.4 + - - +
210D TYR* 3.1 6.4 + - + -
211D ASN* 2.5 30.1 + - - +
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Residues in contact with SER 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 5.3 6.7 - - - -
204D PRO 3.7 14.5 + - - -
206D ALA 3.4 0.2 - - - -
207D ILE* 1.3 76.6 - - - +
209D PHE* 1.3 58.2 + - - +
211D ASN* 3.5 10.0 - - - +
212D ALA* 2.7 31.7 + - - +
241D GLY* 3.1 10.4 + - - -
244D LEU* 3.7 20.0 - - - +
245D THR* 2.8 35.5 + - - -
248D MET* 4.7 8.7 - - - -
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Residues in contact with PHE 209 (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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194D MET* 4.5 22.2 - - + -
205D VAL* 3.2 18.4 - - + +
206D ALA* 3.1 16.7 - - + +
208D SER* 1.3 78.9 - - - +
210D TYR* 1.3 68.1 + + - +
212D ALA* 3.8 3.1 + - - +
213D PHE* 3.2 69.6 + + - -
245D THR* 3.3 18.7 + - + +
256D VAL* 5.4 10.5 - - + -
260D LEU* 4.8 24.2 - - + -
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Residues in contact with TYR 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D ASN* 3.2 17.9 - - - +
127D VAL* 3.9 20.2 - - + -
128D ALA* 3.7 20.7 - - + +
131D GLY* 3.7 19.3 - - - -
132D SER* 3.5 18.2 - - - +
135D ALA* 5.0 5.4 - - + -
191D GLY 3.5 9.9 + - - -
194D MET* 3.5 26.3 - - + -
195D THR* 3.3 28.8 - - - -
198D ILE* 5.8 0.6 - - + +
206D ALA* 2.7 41.7 + - + +
207D ILE* 3.4 2.9 - - - +
209D PHE* 1.3 81.0 - + - +
211D ASN* 1.3 54.3 - - - +
213D PHE* 3.4 8.6 - + + +
214D THR* 2.7 37.1 + - - -
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Residues in contact with ASN 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C MET* 4.5 4.8 + - + +
38C SER* 2.9 29.7 + - - -
39C ASN* 3.8 8.0 - - - +
42C HIS* 2.8 34.8 - - - -
85D VAL* 5.0 4.0 - - + -
89D ASN* 3.2 12.1 - - + +
207D ILE* 2.5 21.9 + - + +
208D SER* 3.0 12.0 + - - +
210D TYR* 1.3 72.0 - - - +
212D ALA* 1.3 63.2 + - - +
214D THR* 3.5 3.5 + - - -
215D GLY* 3.1 17.3 + - - -
237D VAL* 4.2 7.4 - - - +
241D GLY* 4.6 6.8 - - - -
244D LEU* 4.5 13.5 - - - +
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Residues in contact with ALA 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208D SER 2.7 19.3 + - - +
209D PHE* 4.0 4.9 - - - +
211D ASN* 1.3 70.6 - - - +
213D PHE* 1.3 63.2 + - + +
215D GLY* 3.1 3.1 + - - -
216D MET* 2.8 29.5 + - + +
238D GLY* 3.3 30.6 - - - +
241D GLY* 3.5 17.2 - - - +
242D THR* 3.5 10.1 - - - +
245D THR* 4.5 2.0 - - - +
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Residues in contact with PHE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D LEU* 5.7 4.5 - - + -
124D ILE* 2.9 42.6 - - + +
127D VAL* 4.6 20.2 - - + -
128D ALA* 3.9 7.9 - - + -
194D MET* 4.9 7.0 - - + -
209D PHE* 3.2 61.0 + + - +
210D TYR* 3.4 11.0 - + - +
211D ASN 3.3 0.2 - - - -
212D ALA* 1.3 78.4 - - + +
214D THR* 1.3 60.5 + - - +
216D MET* 3.0 14.7 + - + +
217D ALA 2.8 26.5 + - - -
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Residues in contact with THR 214 (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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42C HIS* 3.9 24.5 - - + -
89D ASN* 2.6 35.6 + - - +
92D GLY 3.7 7.4 - - - +
93D GLY* 3.5 28.3 - - - +
96D ALA* 5.4 0.4 - - + -
128D ALA* 3.5 11.3 - - - +
210D TYR 2.7 15.4 + - - -
211D ASN 3.7 3.6 - - - -
212D ALA 3.4 0.2 - - - -
213D PHE* 1.3 71.9 - - - +
215D GLY* 1.3 56.5 + - - +
217D ALA* 3.5 6.4 + - - +
218D VAL* 3.0 39.1 + - + +
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Residues in contact with GLY 215 (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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42C HIS* 5.0 1.6 - - - -
211D ASN 3.1 9.7 + - - -
212D ALA 3.1 8.2 + - - -
214D THR* 1.3 73.8 - - - +
216D MET* 1.3 53.3 + - - +
218D VAL* 3.3 3.5 + - - -
219D GLY 2.8 29.3 + - - -
234D GLY* 3.0 28.9 - - - +
237D VAL* 4.0 10.2 - - - +
238D GLY* 3.7 9.6 - - - -
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Residues in contact with MET 216 (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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124D ILE* 4.1 10.3 - - + -
212D ALA* 2.8 17.9 + - + +
213D PHE* 3.0 19.7 + - + +
215D GLY* 1.3 67.4 - - - +
217D ALA* 1.3 67.7 + - - +
219D GLY* 3.1 3.0 + - - -
220D PHE* 2.9 56.1 + - + -
234D GLY 4.9 1.1 - - - -
235D THR* 5.9 1.6 - - - +
238D GLY* 4.1 8.0 - - - -
242D THR* 4.7 15.5 - - + +
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Residues in contact with ALA 217 (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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96D ALA* 4.0 14.1 - - + -
121D GLY* 3.3 30.0 - - - +
124D ILE* 3.8 4.8 - - + +
125D GLY* 3.7 15.7 - - - +
213D PHE 2.8 15.7 + - - +
214D THR* 3.5 11.0 - - - +
216D MET* 1.3 73.1 - - - +
218D VAL* 1.3 63.1 + - - +
220D PHE* 3.4 1.7 + - - +
221D GLU* 3.1 29.8 + - - +
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Residues in contact with VAL 218 (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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42C HIS* 4.3 13.2 - - + +
44C VAL* 4.8 11.0 - - + -
45C VAL* 4.0 29.2 - - + -
96D ALA* 4.4 7.9 - - + -
214D THR* 3.0 28.4 + - + +
215D GLY* 3.7 4.7 - - - +
217D ALA* 1.3 72.5 - - - +
219D GLY* 1.3 65.8 + - - +
221D GLU* 3.6 6.1 + - - +
222D GLY 3.2 15.1 + - - -
230D LEU* 3.0 38.6 - - + +
234D GLY* 3.8 15.9 - - - +
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Residues in contact with GLY 219 (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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215D GLY 2.8 15.8 + - - -
216D MET* 3.1 4.5 + - - -
218D VAL* 1.3 79.3 - - - +
220D PHE* 1.3 60.8 + - - +
222D GLY* 3.2 7.6 + - - -
223D PHE* 2.9 28.3 + - - -
230D LEU 3.3 12.1 - - - +
231D MET* 4.0 3.3 - - - -
234D GLY* 3.6 7.1 - - - -
235D THR* 4.0 8.3 - - - -
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Residues in contact with PHE 220 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C PHE* 4.8 22.0 - + - -
117D LEU* 3.4 42.8 - - + +
120D LEU* 5.1 11.2 - - + -
121D GLY* 4.2 7.0 - - - +
124D ILE* 3.7 26.2 - - + -
216D MET* 2.9 52.1 + - + +
217D ALA 4.0 2.7 - - - +
219D GLY* 1.3 72.5 - - - +
221D GLU* 1.3 56.6 + - - +
223D PHE* 3.2 16.7 + + - +
224D ALA* 3.0 26.5 + - - +
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Residues in contact with GLU 221 (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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96D ALA* 3.7 23.0 - - + +
99D ILE* 3.5 24.8 - - + +
100D ALA* 3.2 22.5 + - - +
118D ALA* 2.7 33.1 - - - +
121D GLY* 3.3 3.9 - - - -
122D GLY 3.0 16.8 + - - -
217D ALA 3.1 24.0 + - - +
218D VAL* 4.0 6.7 - - - +
220D PHE* 1.3 76.1 - - - +
222D GLY* 1.3 56.5 + - - +
224D ALA* 3.1 7.0 + - - +
225D VAL* 2.9 36.2 + - - +
230D LEU* 4.9 2.0 - - + -
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Residues in contact with GLY 222 (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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218D VAL 3.2 10.3 + - - -
219D GLY 3.2 5.1 + - - -
221D GLU* 1.3 73.6 - - - +
223D PHE* 1.3 58.2 + - - +
225D VAL* 3.9 6.1 - - - -
226D GLY* 3.0 9.2 + - - -
227D ASN 2.7 39.5 + - - +
230D LEU* 3.7 17.4 - - - +
231D MET* 3.4 9.6 - - - +
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Residues in contact with PHE 223 (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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8C ALA* 3.8 26.0 - - + -
9C LEU* 5.5 0.2 - - - -
11C ILE* 5.6 0.7 - - + -
12C PHE* 3.6 43.1 - + + -
114D LEU* 4.2 14.1 - - - +
117D LEU* 4.3 19.7 - - + +
219D GLY* 2.9 34.1 + - - -
220D PHE* 3.2 18.5 + + - +
222D GLY* 1.3 75.2 - - - +
224D ALA* 1.3 60.7 + - - +
225D VAL 3.7 0.2 + - - -
226D GLY* 3.8 6.4 + - - -
231D MET* 3.7 49.5 - - + +
235D THR* 5.0 1.3 - - + -
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Residues in contact with ALA 224 (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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109D PHE* 3.3 23.5 - - + -
114D LEU* 3.9 20.6 - - - +
117D LEU* 4.2 2.2 - - - +
118D ALA* 3.8 35.2 - - + +
220D PHE 3.0 12.9 + - - +
221D GLU* 3.1 11.0 + - - +
223D PHE* 1.3 79.3 - - - +
225D VAL* 1.3 61.6 + - + +
226D GLY 3.4 0.2 - - - -
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Residues in contact with VAL 225 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET 5.1 5.2 + - - -
48C GLY* 6.1 3.8 - - - -
51C VAL* 6.5 1.6 - - + -
49D TRP* 5.7 5.7 - - - -
99D ILE* 3.9 27.1 - - + +
103D GLU* 4.9 14.6 - - + -
109D PHE* 5.5 3.8 - - + -
221D GLU* 2.9 24.2 + - - +
222D GLY* 3.7 2.7 - - - +
224D ALA* 1.3 80.5 - - + +
226D GLY* 1.3 61.3 + - - +
227D ASN* 3.3 30.1 - - + +
230D LEU* 5.5 3.6 - - + -
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Residues in contact with GLY 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C MET* 3.8 35.6 - - - +
3C PHE* 4.9 8.1 - - - -
49D TRP* 5.7 2.0 - - - -
222D GLY 3.0 6.1 + - - -
223D PHE 3.8 6.7 + - - -
224D ALA 3.4 3.2 - - - -
225D VAL* 1.3 80.0 - - - +
227D ASN* 1.3 58.3 + - - +
228D PRO* 3.4 11.6 - - - +
231D MET* 4.5 7.4 - - - -
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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