Contacts of the helix formed by residues 198 - 220 (chain L) in PDB entry 1XFB
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 ASP 198 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196L ASP 3.8 1.0 + - - -
197L HIS* 1.3 77.9 - - - +
199L LEU* 1.3 66.3 + - - +
200L LYS* 3.1 36.4 + - - +
201L ARG* 3.2 26.7 + - - +
202L CYS 3.3 8.0 + - - -
236L PRO* 4.1 2.7 - - - -
240L CYS* 4.0 15.7 - - - -
242L ILE* 4.3 8.7 - - + +
244L TYR* 3.4 14.9 + - - +
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Residues in contact with LEU 199 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198L ASP* 1.3 73.7 - - - +
200L LYS* 1.3 65.3 + - - +
202L CYS* 3.1 4.3 + - - +
203L GLN* 3.0 21.0 + - - +
234L VAL* 3.3 20.0 - - + +
235L THR* 3.2 33.7 - - - -
236L PRO* 3.8 12.8 - - + +
244L TYR* 3.3 43.3 + - + -
248L GLU* 3.7 28.5 - - + +
249L ILE* 4.4 5.6 - - + -
252L ALA* 3.9 13.0 - - + -
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Residues in contact with LYS 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I SER* 5.7 0.9 - - - -
6I PRO* 4.0 25.0 - - - +
198L ASP* 3.1 20.9 + - - +
199L LEU* 1.3 78.9 - - - +
201L ARG* 1.3 63.3 + - - +
203L GLN* 3.1 10.3 + - - +
204L TYR* 3.0 21.4 + - - +
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Residues in contact with ARG 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I HIS* 2.5 54.9 + - - +
4I SER* 3.7 19.1 + - - +
157J ARG* 3.6 14.0 - - - +
154L ILE* 3.4 19.5 - - + +
155L SER 3.3 24.7 + - - -
156L GLU* 4.6 0.6 + - - +
158L THR 5.5 0.2 - - - +
159L PRO* 4.8 1.6 - - - +
197L HIS* 3.7 24.2 - - + +
198L ASP* 3.2 20.0 + - - +
200L LYS* 1.3 79.3 - - - +
202L CYS* 1.3 64.3 + - - +
204L TYR* 3.1 7.6 + - - +
205L VAL* 2.9 33.4 + - + +
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Residues in contact with CYS 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154L ILE* 4.1 18.1 - - - +
191L ILE* 5.2 4.5 - - - -
192L LEU 6.1 0.2 - - - -
197L HIS* 4.0 12.2 - - + -
198L ASP 3.3 3.0 + - - +
199L LEU 3.1 9.0 + - - +
201L ARG* 1.3 78.4 - - - +
203L GLN* 1.3 57.9 - - - +
205L VAL* 4.0 0.5 - - - +
206L THR* 2.8 41.4 + - - -
232L ASN* 4.2 6.7 - - - -
233L MET 4.4 0.4 - - - -
234L VAL* 3.5 11.2 - - - -
235L THR 3.2 44.0 - - - +
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Residues in contact with GLN 203 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199L LEU* 3.0 11.8 + - - +
200L LYS* 3.4 12.7 - - - +
202L CYS* 1.3 77.5 - - - +
204L TYR* 1.3 57.1 + - - +
206L THR* 3.2 3.3 + - - -
207L GLU* 2.6 58.7 + - - +
234L VAL* 3.8 16.7 - - + +
252L ALA* 3.4 37.1 + - + +
255L THR* 3.7 15.0 - - - +
256L ALA* 3.9 6.2 - - + +
259L ARG* 3.2 16.4 - - - +
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Residues in contact with TYR 204 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I HIS* 3.0 50.1 + + + +
4I SER* 3.4 32.8 - - - -
5I TYR 5.2 0.4 - - - -
221I HIS* 2.8 36.1 - + + -
118J GLY 5.3 0.3 + - - -
200L LYS 3.0 12.0 + - - +
201L ARG* 3.3 9.0 - - - +
203L GLN* 1.3 76.9 - - - +
205L VAL* 1.3 67.7 + - - +
207L GLU* 3.1 12.2 + - - +
208L LYS* 3.0 54.0 + - + +
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Residues in contact with VAL 205 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I HIS* 3.6 28.0 - - + +
154L ILE* 3.9 24.9 - - + -
159L PRO* 3.6 31.0 - - + -
164L ILE* 6.0 0.4 - - + -
191L ILE* 3.7 15.7 - - + -
201L ARG* 2.9 26.3 + - + +
202L CYS 4.0 0.2 - - - +
204L TYR* 1.3 78.1 - - + +
206L THR* 1.3 64.0 + - - +
208L LYS* 3.2 5.9 + - + +
209L VAL* 2.9 25.7 + - + +
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Residues in contact with THR 206 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191L ILE* 3.4 16.4 - - + +
202L CYS* 2.8 28.4 + - - -
203L GLN* 3.5 5.8 - - - -
205L VAL* 1.3 75.5 - - - +
207L GLU* 1.3 64.8 + - - +
209L VAL* 3.8 0.7 - - - +
210L LEU* 2.9 45.0 + - + +
231L PRO* 5.8 2.2 - - + -
232L ASN* 3.3 28.3 + - - +
234L VAL* 4.4 9.5 - - + +
256L ALA* 4.1 15.5 - - + -
257L LEU* 5.9 1.3 - - + -
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Residues in contact with GLU 207 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218I SER* 5.3 0.9 - - - -
203L GLN* 2.6 51.3 + - - +
204L TYR* 3.1 12.1 + - + +
206L THR* 1.3 78.1 - - - +
208L LYS* 1.3 62.8 + - + +
210L LEU* 4.8 0.4 - - - -
211L ALA* 2.9 30.7 + - - +
256L ALA* 3.7 23.7 - - - +
259L ARG* 3.0 31.3 + - - +
260L THR* 3.4 15.8 - - + +
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Residues in contact with LYS 208 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215I LYS* 5.5 0.7 - - - -
218I SER* 2.4 45.3 + - - +
219I ASP* 4.5 3.3 - - - +
221I HIS* 3.0 21.9 + - - +
164L ILE* 4.7 13.5 - - + +
204L TYR* 3.0 61.3 + - + +
205L VAL* 3.7 6.7 - - - +
207L GLU* 1.3 75.7 - - - +
209L VAL* 1.3 67.6 + - + +
211L ALA* 3.4 6.4 + - - +
212L ALA* 3.1 21.7 + - - +
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Residues in contact with VAL 209 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152L LEU* 3.3 36.6 - - + -
159L PRO* 4.8 0.7 - - + -
164L ILE* 4.4 21.9 - - + +
189L PRO* 4.2 15.0 - - + +
191L ILE* 3.6 19.1 - - + -
205L VAL* 2.9 28.2 + - + +
206L THR 3.8 3.1 - - - +
208L LYS* 1.3 76.1 - - - +
210L LEU* 1.3 66.0 + - + +
212L ALA* 3.0 5.7 + - - +
213L VAL* 2.9 36.9 + - + +
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Residues in contact with LEU 210 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189L PRO* 4.0 17.5 - - + -
191L ILE* 6.5 0.2 - - + -
206L THR* 2.9 38.7 + - + +
207L GLU 4.0 0.4 - - - +
209L VAL* 1.3 76.9 - - + +
211L ALA* 1.3 64.9 + - - +
213L VAL* 2.9 16.0 + - + +
214L TYR* 2.9 24.2 + - + -
229L LEU* 3.9 33.4 - - + -
231L PRO* 4.7 7.0 - - + -
256L ALA 5.0 0.9 - - - +
257L LEU* 3.8 26.5 - - + -
260L THR* 3.5 28.7 - - + +
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Residues in contact with ALA 211 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LYS* 3.7 13.7 - - + +
218I SER* 3.4 32.1 - - - +
207L GLU 2.9 19.6 + - - +
208L LYS 3.6 4.5 - - - +
209L VAL 3.3 0.2 - - - -
210L LEU* 1.3 76.6 - - - +
212L ALA* 1.3 61.9 + - - +
214L TYR* 3.8 3.8 + - - +
215L LYS* 3.3 21.1 + - - +
260L THR* 4.1 15.8 - - + +
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Residues in contact with ALA 212 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215I LYS* 3.7 20.4 - - - +
164L ILE* 3.5 29.2 - - + -
165L LEU* 6.1 0.4 - - - -
168L ALA* 4.1 9.9 - - + +
208L LYS 3.1 7.2 + - - +
209L VAL 3.0 9.7 + - - +
211L ALA* 1.3 75.3 - - - +
213L VAL* 1.3 67.6 + - - +
215L LYS* 3.2 3.3 + - - +
216L ALA* 3.0 23.6 + - - +
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Residues in contact with VAL 213 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ALA* 4.0 16.3 - - + +
171L LEU* 4.2 12.8 - - + -
187L VAL* 3.9 27.6 - - + -
189L PRO* 4.1 17.9 - - + -
209L VAL* 2.9 35.2 + - + +
210L LEU* 3.3 12.1 - - + +
212L ALA* 1.3 75.9 - - - +
214L TYR* 1.3 65.4 - - + +
216L ALA* 3.3 4.4 + - - +
217L LEU* 3.0 35.2 + - + +
229L LEU* 5.3 1.1 - - + -
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Residues in contact with TYR 214 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L VAL* 5.7 1.6 - - - +
210L LEU* 2.9 26.0 + - + +
211L ALA* 4.5 2.5 - - - +
213L VAL* 1.3 78.3 - - + +
215L LYS* 1.3 66.2 + - - +
217L LEU* 3.2 16.3 + - + +
218L SER* 2.9 22.2 + - - -
224L LEU* 3.6 36.4 - - + +
227L THR* 5.1 2.9 + - - -
228L LEU 5.2 0.7 - - - -
229L LEU* 3.4 40.2 - - + +
260L THR 3.9 16.8 - - - +
261L VAL* 3.7 22.4 - - + +
262L PRO* 3.7 19.1 - - + -
265L VAL* 3.5 24.9 - - + +
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Residues in contact with LYS 215 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208I LYS 5.6 0.4 - - - -
211I ALA* 3.8 23.6 - - + +
212I ALA* 3.9 26.9 - - - +
215I LYS* 3.9 30.1 - - + -
211L ALA 3.3 16.4 + - - +
212L ALA 3.2 5.6 + - - +
214L TYR* 1.3 77.4 - - - +
216L ALA* 1.3 58.1 + - - +
218L SER* 3.2 4.9 + - - -
219L ASP* 2.9 67.6 + - - +
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Residues in contact with ALA 216 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ALA* 3.4 35.2 - - + +
169L ASN* 4.3 4.3 - - - +
172L ALA* 3.8 6.1 - - + -
212L ALA 3.0 12.0 + - - +
213L VAL 3.4 8.1 - - - +
215L LYS* 1.3 75.5 - - - +
217L LEU* 1.3 67.9 + - - +
219L ASP* 2.9 10.8 + - - +
220L HIS* 2.9 29.4 + - + -
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Residues in contact with LEU 217 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168L ALA 5.8 0.2 - - - +
171L LEU 4.8 0.2 - - - -
172L ALA* 3.7 21.8 - - + +
175L ALA* 3.9 9.0 - - + -
187L VAL* 4.4 17.9 - - + -
213L VAL* 3.0 27.9 + - + +
214L TYR* 3.5 39.3 - - + +
216L ALA* 1.3 75.9 - - - +
218L SER* 1.3 63.3 + - - +
220L HIS 3.2 1.6 + - - -
221L HIS 3.1 3.8 + - - -
222L VAL* 3.0 59.9 + - + -
224L LEU* 4.0 15.5 - - + -
227L THR* 5.5 2.0 - - + +
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Residues in contact with SER 218 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207I GLU 5.0 0.3 + - - -
208I LYS* 2.5 43.4 + - - +
211I ALA* 3.5 29.6 - - - +
214L TYR 2.9 13.1 + - - -
215L LYS* 3.3 10.8 - - - -
217L LEU* 1.3 76.1 - - - +
219L ASP* 1.3 59.8 + - - +
221L HIS* 2.9 13.1 + - - +
222L VAL 5.0 2.9 - - - +
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Residues in contact with ASP 219 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208I LYS* 4.7 3.6 - - - +
162K LEU* 3.2 25.1 - - + +
165K LEU* 3.7 25.4 - - + +
215L LYS* 2.9 52.6 + - - +
216L ALA* 2.9 11.2 + - - +
218L SER* 1.3 77.3 + - - +
220L HIS* 1.3 66.7 + - + +
221L HIS* 3.4 12.4 + - - -
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Residues in contact with HIS 220 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116K LEU* 5.3 3.7 - - + +
117K ALA 3.7 5.5 - - - +
162K LEU* 3.6 30.0 - - + +
165K LEU* 4.2 2.6 - - - +
166K GLU* 3.9 12.1 - - + -
169L ASN* 2.8 28.7 + - - -
172L ALA* 3.4 29.3 - - + +
173L ARG* 3.8 35.2 + - + +
176L SER* 3.7 18.4 + - - -
216L ALA* 2.9 22.9 + - - +
217L LEU 3.9 2.9 - - - +
218L SER 3.1 0.4 - - - -
219L ASP* 1.3 80.1 - - + +
221L HIS* 1.3 74.0 + - - +
222L VAL* 3.3 3.4 + - + -
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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) + - + + + + + -
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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