Contacts of the helix formed by residues 194 - 221 (chain D) in PDB entry 4IL6
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 ASN 194 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 4.4 8.9 - - - +
189D HIS 6.0 0.2 - - - +
190D ASN 4.0 1.2 + - - +
191D TRP* 3.1 47.1 + - + +
193D LEU* 1.3 78.0 - - - +
195D PRO* 1.3 63.4 - - - +
196D PHE* 3.1 36.6 + - - +
197D HIS* 3.1 4.3 + - - +
198D MET* 3.0 27.0 + - - +
285D GLY* 4.5 5.0 + - - -
289D LEU* 4.3 10.5 - - - +
293D LEU 4.7 1.2 + - - -
294D ARG* 4.5 0.8 - - - +
295D SER* 3.6 30.9 + - - +
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Residues in contact with PRO 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B PHE* 3.9 13.7 - - + -
193D LEU 3.5 6.7 - - - +
194D ASN* 1.3 89.0 - - - +
196D PHE* 1.3 60.5 + - + +
198D MET* 3.5 13.3 - - - +
199D MET* 3.0 34.7 + - - +
295D SER* 3.3 16.4 - - - +
30L LEU* 4.0 11.3 - - + +
31L PHE* 3.8 31.6 - - + -
34L TYR* 3.8 23.3 - - + -
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Residues in contact with PHE 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324B LEU* 4.0 24.7 - - + -
453B PHE* 5.4 3.6 - + - -
607B CLA 3.9 32.1 - - + -
622B LMG 4.1 18.4 - - + -
194D ASN* 3.1 17.2 + - - +
195D PRO* 1.3 77.3 - - + +
197D HIS* 1.3 65.8 + - - +
199D MET* 3.5 23.6 + - + -
200D GLY 3.2 15.6 + - - -
281D MET* 3.3 29.4 - - - +
282D SER* 3.4 13.9 + - - -
284D ILE* 3.7 24.5 - - + -
285D GLY* 3.6 18.6 - - - -
31L PHE* 4.2 12.1 - + - -
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Residues in contact with HIS 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D TRP* 3.1 65.8 + + + +
192D THR* 4.3 9.9 + - - -
194D ASN 3.1 10.6 + - - +
196D PHE* 1.3 77.9 - - - +
198D MET* 1.3 58.0 + - - +
200D GLY* 3.2 3.0 + - - +
201D VAL* 2.9 46.8 + - + +
282D SER* 4.7 2.5 - - - +
402D CLA 2.2 67.1 + + + -
403D CLA 4.5 7.6 + - + +
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Residues in contact with MET 198 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.9 7.0 - - + -
176A ILE* 3.9 15.9 - - + -
180A PHE* 3.8 16.2 - - + -
192D THR 3.3 21.8 - - - +
193D LEU 3.6 5.4 - - - +
194D ASN 3.0 12.1 + - - +
195D PRO* 3.5 13.9 - - + +
196D PHE 3.3 0.4 - - - -
197D HIS* 1.3 77.9 - - - +
199D MET* 1.3 56.7 + - - +
201D VAL* 3.3 3.5 + - - +
202D ALA 3.0 21.8 + - - -
403D CLA 3.5 40.2 - - - +
407D PL9 3.4 15.1 - - + +
30L LEU* 3.7 19.3 - - + -
34L TYR* 3.3 26.7 - - - +
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Residues in contact with MET 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B CLA 4.2 6.1 - - + -
195D PRO 3.0 18.6 + - - +
196D PHE* 3.5 33.4 - - + +
197D HIS 3.3 0.4 - - - -
198D MET* 1.3 73.0 - - - +
200D GLY* 1.3 60.1 + - - +
202D ALA* 3.3 3.3 + - - +
203D GLY 2.9 24.9 + - - -
278D GLY* 3.8 3.2 - - - -
281D MET* 3.8 30.1 - - + -
407D PL9 3.6 38.6 - - + +
27L LEU* 3.8 27.4 - - - -
30L LEU* 3.7 15.0 - - + -
31L PHE* 3.8 18.2 - - + -
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Residues in contact with GLY 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196D PHE 3.2 10.4 + - - -
197D HIS 3.2 8.1 + - - -
199D MET* 1.3 75.9 - - - +
201D VAL* 1.3 55.2 + - - +
203D GLY* 3.2 1.7 + - - -
204D VAL* 3.0 33.6 + - - +
278D GLY* 3.2 24.2 + - - -
282D SER* 4.2 1.8 - - - -
402D CLA 3.5 17.3 - - - -
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Residues in contact with VAL 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197D HIS* 2.9 42.7 + - + +
198D MET 3.6 3.6 - - - +
199D MET 3.3 0.2 - - - -
200D GLY* 1.3 73.8 - - - +
202D ALA* 1.3 57.3 + - - +
204D VAL 3.3 0.3 + - - -
205D LEU* 2.9 52.9 + - + +
402D CLA 3.7 30.5 - - + -
403D CLA 3.5 44.4 - - + +
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Residues in contact with ALA 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B LHG 3.9 7.0 - - + -
198D MET 3.0 11.6 + - - +
199D MET 3.3 7.6 + - - +
201D VAL* 1.3 77.7 - - - +
203D GLY* 1.3 53.4 + - - +
206D GLY* 2.8 32.4 + - - -
403D CLA 3.4 25.9 - - + +
407D PL9 3.6 42.0 - - + +
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Residues in contact with GLY 203 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D MET 2.9 12.6 + - - -
200D GLY 3.2 3.6 + - - -
202D ALA* 1.3 78.2 - - - +
204D VAL* 1.3 55.8 + - - +
207D GLY* 2.8 21.7 + - - -
274D VAL* 3.6 22.5 - - - +
275D PRO* 3.3 20.0 - - - +
278D GLY* 4.0 4.5 - - - -
407D PL9 3.8 10.0 - - - +
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Residues in contact with VAL 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.7 27.1 - - + +
206A PHE* 4.2 11.9 - - + -
209A ALA* 3.7 9.6 - - + +
200D GLY 3.0 19.5 + - - +
201D VAL 3.9 2.7 - - - +
203D GLY* 1.3 74.9 - - - +
205D LEU* 1.3 59.4 - - - +
207D GLY* 3.3 0.9 + - - -
208D ALA* 2.9 28.1 + - - +
279D LEU* 3.6 28.5 - - + -
402D CLA 3.8 38.4 - - + -
404D PHO 4.5 7.6 - - + -
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Residues in contact with LEU 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A VAL* 3.9 21.3 - - + -
1005A CLA 3.7 27.4 - - + -
1007A PHO 3.7 39.7 - - + +
201D VAL* 2.9 36.6 + - + +
204D VAL* 1.3 72.8 - - - +
206D GLY* 1.3 60.5 + - - +
208D ALA* 3.4 4.4 + - - +
209D LEU* 2.9 29.1 + - - +
402D CLA 3.6 28.5 - - + -
403D CLA 3.7 21.3 - - + +
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Residues in contact with GLY 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D ALA 2.8 20.4 + - - -
205D LEU* 1.3 76.7 - - - +
207D GLY* 1.3 56.4 + - - +
209D LEU* 3.4 6.0 + - - +
210D LEU* 2.9 33.7 + - - +
274D VAL* 4.0 7.4 - - - -
403D CLA 3.5 13.2 - - - -
407D PL9 4.1 16.2 - - - +
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Residues in contact with GLY 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY 4.0 2.0 - - - -
209A ALA* 4.1 5.4 - - - -
212A CYS* 3.2 32.8 - - - +
203D GLY 2.8 21.6 + - - -
204D VAL 3.7 1.1 - - - -
205D LEU 3.3 0.2 - - - -
206D GLY* 1.3 73.3 - - - +
208D ALA* 1.3 58.4 + - - +
210D LEU* 3.2 1.3 + - - -
211D CYS* 2.9 24.4 + - - +
274D VAL* 3.8 5.9 - - - +
275D PRO* 4.4 2.9 - - - -
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Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A GLY 4.4 1.3 - - - +
205A VAL* 3.8 29.2 - - + +
208A GLY* 3.8 15.5 - - - -
209A ALA 3.9 1.4 - - - +
279A PRO* 3.9 2.4 - - + +
1007A PHO 3.6 22.3 - - + +
204D VAL 2.9 16.7 + - - +
205D LEU 3.7 5.2 - - - +
207D GLY* 1.3 74.0 - - - +
209D LEU* 1.3 62.0 + - - +
211D CYS* 3.4 2.4 + - - +
212D ALA* 3.0 25.1 + - - +
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Residues in contact with LEU 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1007A PHO 3.5 71.3 - - + +
205D LEU 2.9 17.8 + - - +
206D GLY 3.4 5.4 - - - +
207D GLY 3.3 0.2 - - - -
208D ALA* 1.3 76.7 - - - +
210D LEU* 1.3 61.6 + - - +
212D ALA* 3.3 2.4 + - - +
213D ILE* 2.9 45.3 + - + +
403D CLA 4.0 25.1 - - + -
407D PL9 3.9 30.1 - - + -
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Residues in contact with LEU 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A CYS* 3.7 16.8 - - - -
206D GLY 2.9 20.5 + - - +
207D GLY 3.2 4.5 + - - +
209D LEU* 1.3 73.0 - - + +
211D CYS* 1.3 64.4 + - - +
213D ILE* 3.7 7.7 - - + +
214D HIS* 3.0 30.2 + - + +
261D PHE* 4.6 8.1 - - + -
267D LEU* 6.5 0.2 - - + -
270D PHE* 3.9 22.4 - - + +
271D MET* 3.9 13.6 - - + +
274D VAL* 3.9 33.2 - - + -
407D PL9 4.0 40.4 - - + -
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Residues in contact with CYS 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY* 3.3 36.1 - - - +
211A PHE* 3.9 11.7 - - - -
212A CYS* 4.0 4.7 - - + -
275A LEU* 3.2 58.5 - - - +
279A PRO* 4.1 4.7 - - + -
207D GLY 2.9 8.8 + - - +
208D ALA 3.4 6.1 - - - +
210D LEU* 1.3 76.2 - - - +
212D ALA* 1.3 61.6 + - - +
214D HIS* 4.2 0.7 - - - +
215D GLY 3.1 18.7 + - - -
271D MET* 4.2 11.1 - - - +
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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
----------------------------------------------------------
146A ALA* 4.6 0.3 - - - +
275A LEU 3.7 9.6 + - - -
276A ALA* 3.9 5.9 - - - +
279A PRO* 3.7 12.8 - - + +
280A VAL* 3.9 16.6 - - + -
1007A PHO 3.9 26.2 - - + -
208D ALA 3.0 17.2 + - - +
209D LEU 3.8 2.7 - - - +
211D CYS* 1.3 76.7 - - - +
213D ILE* 1.3 56.6 + - - +
216D ALA* 2.9 32.6 + - - +
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Residues in contact with ILE 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 5.5 0.7 - - + -
1007A PHO 3.2 57.9 - - + +
209D LEU* 2.9 31.6 + - + +
210D LEU* 3.7 15.5 - - + +
212D ALA* 1.3 71.0 - - - +
214D HIS* 1.3 64.0 + - + +
216D ALA* 3.9 2.9 - - + +
217D THR* 2.7 37.4 + - - +
253D TRP* 3.4 35.7 - - + -
407D PL9 4.0 24.9 - - + -
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Residues in contact with HIS 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A HIS* 3.5 15.9 - + - -
272A HIS* 3.2 16.3 + + - -
275A LEU* 4.4 1.8 - - + -
1002A FE2 2.1 31.4 - - - -
210D LEU* 3.0 21.0 + - + +
211D CYS 4.2 0.2 - - - +
213D ILE* 1.3 76.3 - - + +
215D GLY* 1.3 67.0 + - - +
217D THR 3.3 0.5 + - - -
218D VAL* 3.0 37.6 + - + +
244D TYR* 4.0 5.2 - - - -
267D LEU* 3.6 22.6 - - + +
268D HIS* 3.1 3.7 + + - -
271D MET* 3.8 17.3 - - + -
401D BCT 3.3 12.6 - - - -
407D PL9 2.8 28.1 + - + +
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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
----------------------------------------------------------
272A HIS* 3.1 30.5 - - - +
275A LEU* 4.1 5.1 - - - +
276A ALA* 3.7 6.7 - - - -
211D CYS 3.1 16.8 + - - -
214D HIS* 1.3 78.9 - - - +
216D ALA* 1.3 61.1 + - - +
218D VAL* 3.6 2.1 + - - +
219D GLU* 3.1 28.6 + - - +
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Residues in contact with ALA 216 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 4.0 16.2 - - + -
146A ALA* 3.7 24.7 - - + -
276A ALA* 3.5 6.9 - - - +
212D ALA 2.9 19.8 + - - +
213D ILE* 4.0 4.0 - - - +
215D GLY* 1.3 75.9 - - - +
217D THR* 1.3 57.3 + - - +
219D GLU 3.5 0.5 + - - -
220D ASN* 2.7 39.5 + - - +
411D LHG 4.2 14.1 - - + -
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Residues in contact with THR 217 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A ILE* 3.9 9.1 - - + +
213D ILE 2.7 24.5 + - - -
214D HIS 3.3 0.4 + - - -
216D ALA* 1.3 73.6 - - - +
218D VAL* 1.3 59.3 + - - +
220D ASN 3.2 1.7 + - - -
221D THR* 2.7 36.5 + - + +
244D TYR* 5.7 0.2 - - + -
249D ALA* 3.7 20.2 - - + -
252D PHE* 6.0 0.2 - - + -
253D TRP* 2.8 37.2 + - - +
407D PL9 3.3 35.9 - - + +
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Residues in contact with VAL 218 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A SER 5.1 0.7 - - - +
269A ARG* 5.5 0.4 - - - -
272A HIS* 3.5 44.4 - - + +
214D HIS* 3.0 36.5 + - + +
215D GLY 3.9 1.1 - - - +
217D THR* 1.3 76.5 - - - +
219D GLU* 1.3 64.0 + - - +
220D ASN 3.2 1.0 + - - -
221D THR* 3.3 15.0 + - - -
222D LEU* 3.3 24.3 + - + +
243D THR* 4.9 4.5 - - + -
244D TYR* 3.6 40.1 - - + +
407D PL9 4.9 0.9 - - - +
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Residues in contact with GLU 219 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A ARG* 2.8 33.6 + - - -
269A ARG* 3.0 40.0 - - - +
272A HIS* 4.1 1.3 - - + -
273A PHE* 3.7 22.1 - - + +
215D GLY 3.1 20.5 + - - +
216D ALA 3.9 1.8 - - - +
217D THR 3.3 0.2 - - - -
218D VAL* 1.3 78.7 - - - +
220D ASN* 1.3 59.6 + - - +
221D THR 3.6 0.2 - - - -
222D LEU* 3.6 19.4 - - - +
231D THR* 4.7 0.3 + - - -
232D PHE* 3.8 7.4 - - - -
411D LHG 3.5 49.5 - - + +
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Residues in contact with ASN 220 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 3.3 11.5 - - + +
140A ARG* 3.0 48.5 + - - +
141A PRO 3.3 0.5 - - - -
142A TRP* 2.7 38.2 + - - +
143A ILE* 3.7 26.7 - - + +
216D ALA* 2.7 29.7 + - - +
217D THR 3.6 1.6 - - - +
218D VAL 3.2 0.4 - - - -
219D GLU* 1.3 76.0 - - - +
221D THR* 1.3 60.1 + - - +
222D LEU 3.6 1.6 - - - -
411D LHG 2.9 24.5 + - - -
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Residues in contact with THR 221 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A MET* 3.8 24.9 - - + -
459C ILE* 3.8 15.9 - - - +
217D THR* 2.7 24.6 + - + +
218D VAL 3.3 4.5 + - - -
220D ASN* 1.3 81.4 - - - +
222D LEU* 1.3 66.4 + - - +
223D PHE 3.6 0.2 + - - -
244D TYR* 3.5 19.8 - - - -
245D SER 2.9 30.0 + - - -
248D THR* 4.3 1.3 - - + -
249D ALA* 3.8 28.6 - - + +
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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) + - + + + + + -
------------------------------------------------------------
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