Contacts of the helix formed by residues 228 - 249 (chain E) in PDB entry 1FPY
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 228 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108E ALA* 3.5 39.3 - - + +
111E ALA* 4.2 7.2 - - + -
112E GLU* 3.9 18.6 + - + +
124E VAL* 3.0 16.4 + - + -
126E PHE* 3.4 43.3 - - + -
226E ASN 3.2 2.5 + - - -
227E THR* 1.3 70.2 - - - +
229E THR* 1.3 62.1 + - - +
231E LYS* 3.3 3.1 + - - +
232E ALA* 3.2 17.3 + - - +
371E PHE* 3.5 30.8 - - + +
372E ALA* 3.7 23.3 - - + +
375E LEU* 4.0 12.8 - - + -
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Residues in contact with THR 229 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105E ARG* 4.6 24.7 - - + +
108E ALA* 3.5 32.5 + - + +
109E LYS* 3.8 23.9 + - + -
112E GLU* 3.1 24.9 + - - +
227E THR* 3.0 1.8 + - - -
228E MET* 1.3 70.2 - - - +
230E LYS* 1.3 67.7 + - - +
231E LYS 3.2 0.5 + - - -
232E ALA* 3.2 8.2 + - - +
233E ASP* 3.2 21.7 + - - +
368E TYR* 4.0 4.7 - - + -
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Residues in contact with LYS 230 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226E ASN* 3.3 34.3 - - - +
227E THR* 3.0 27.4 + - - +
229E THR* 1.3 77.0 - - - +
231E LYS* 1.3 57.8 + - - +
233E ASP* 3.0 19.1 - - + +
234E GLU* 3.0 38.0 + - + +
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Residues in contact with LYS 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E PHE* 3.5 22.4 - - + +
128E PRO* 3.3 37.2 - - + -
204E LEU* 5.0 1.0 - - - +
223E THR* 3.3 28.2 + - - -
224E ARG 2.7 28.9 + - - +
225E PHE* 4.3 1.3 - - - +
226E ASN* 4.0 14.7 - - + +
227E THR 2.9 12.0 + - - +
228E MET 3.6 8.3 - - - +
229E THR 3.1 0.2 - - - -
230E LYS* 1.3 74.8 - - - +
232E ALA* 1.3 60.4 + - - +
234E GLU* 3.0 30.2 + - + +
235E ILE* 2.8 32.4 + - + +
371E PHE* 4.1 5.2 - - + -
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Residues in contact with ALA 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108E ALA* 5.9 0.2 - - + -
228E MET* 3.2 6.4 + - + +
229E THR 3.2 2.9 + - - +
231E LYS* 1.3 76.6 - - - +
233E ASP* 1.3 62.0 + - - +
235E ILE* 3.4 5.0 + - - +
236E GLN* 3.3 22.7 + - - +
367E PRO* 3.4 21.3 - - + +
368E TYR* 3.2 39.0 + - + +
371E PHE* 3.6 20.5 - - + -
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Residues in contact with ASP 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E THR* 4.4 5.4 - - - +
88E ARG* 3.4 16.4 + - - +
105E ARG* 2.9 36.7 + - - -
229E THR* 3.2 13.3 + - - +
230E LYS* 3.0 22.1 + - + +
232E ALA* 1.3 76.1 - - - +
234E GLU* 1.3 59.1 + - + +
236E GLN* 2.9 23.9 + - - +
237E ILE* 3.0 19.2 + - + +
368E TYR* 2.6 33.1 + - - -
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Residues in contact with GLU 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203E GLY 4.3 12.0 - - - +
204E LEU* 3.5 40.5 - - + +
205E VAL 5.1 1.4 + - - -
224E ARG 3.8 5.4 - - - +
226E ASN* 3.4 23.7 + - - +
230E LYS* 3.0 20.2 + - + +
231E LYS* 3.0 39.0 + - + +
233E ASP* 1.3 82.0 - - + +
235E ILE* 1.3 53.1 + - - +
237E ILE* 3.2 5.9 + - + +
238E TYR* 2.7 35.7 + - - +
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Residues in contact with ILE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E PRO* 4.2 13.5 - - + -
130E PRO* 3.9 16.6 - - + -
223E THR* 5.6 2.0 - - - +
231E LYS* 2.8 21.6 + - - +
232E ALA* 3.4 9.4 - - - +
233E ASP 3.0 0.2 - - - -
234E GLU* 1.3 74.3 - - - +
236E GLN* 1.3 65.9 + - - +
238E TYR* 3.1 10.4 + - + +
239E LYS* 2.9 40.8 + - + +
268E MET* 3.4 34.5 - - + -
367E PRO* 3.3 25.4 - - + -
371E PHE* 4.2 15.9 - - + -
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Residues in contact with GLN 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E THR* 3.1 32.9 + - - +
26E GLY 2.9 28.7 + - - +
28E GLU* 3.5 24.9 - - - +
88E ARG* 3.6 19.3 - - - +
232E ALA 3.4 13.7 - - - +
233E ASP 2.9 7.7 + - - +
235E ILE* 1.3 77.1 - - - +
237E ILE* 1.3 63.4 + - - +
239E LYS* 3.4 18.5 + - - +
240E TYR* 3.0 23.4 + - - +
367E PRO* 3.8 19.1 - - - +
368E TYR* 4.2 6.7 - - + +
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Residues in contact with ILE 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E GLU* 5.3 2.2 - - - +
73E THR 6.0 1.1 - - - +
75E VAL* 5.3 7.0 - - + -
88E ARG* 4.0 18.6 - - - +
199E MET* 5.2 0.9 - - - +
202E MET* 4.0 50.0 - - + +
204E LEU* 3.6 23.1 - - + -
233E ASP* 3.0 20.6 + - + +
234E GLU* 3.5 11.4 - - + +
235E ILE 3.2 0.2 - - - -
236E GLN* 1.3 75.2 - - - +
238E TYR* 1.3 55.5 + - - +
240E TYR* 3.0 8.3 + - - +
241E VAL* 2.8 37.8 + - + +
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Residues in contact with TYR 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E PRO* 2.9 43.2 + - + -
132E PHE* 3.5 7.0 - + - -
199E MET* 3.2 33.6 - - + +
204E LEU* 4.2 6.3 - - + -
221E VAL* 2.9 48.7 + - + +
223E THR* 4.3 17.3 - - + -
234E GLU 2.7 17.3 + - - +
235E ILE* 3.1 14.8 - - + +
237E ILE* 1.3 73.8 - - - +
239E LYS* 1.3 58.7 + - + +
241E VAL* 3.1 2.7 + - - +
242E VAL* 2.8 46.2 + - + +
255E PHE* 3.7 21.8 - + - -
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Residues in contact with LYS 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26E GLY 5.0 5.1 + - - -
27E LYS* 6.1 1.3 - - - +
130E PRO* 6.2 0.9 - - + -
235E ILE* 2.9 39.4 + - + +
236E GLN* 3.8 19.3 + - - +
238E TYR* 1.3 75.8 - - + +
240E TYR* 1.3 58.4 + - - +
242E VAL* 3.7 0.2 - - - +
243E HIS* 2.7 43.6 + - + +
255E PHE* 3.6 44.0 - - + -
268E MET* 6.1 0.7 - - + -
363E PRO* 3.3 25.7 + - - -
364E ALA 5.0 1.8 + - - -
365E ALA 4.3 8.3 + - - -
367E PRO* 5.0 1.0 - - - +
468K VAL* 3.4 26.8 + - - +
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Residues in contact with TYR 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182D VAL* 4.2 17.3 - - + -
183D PRO* 3.5 20.2 - - + -
20E ARG* 3.4 25.4 + - - +
28E GLU* 4.1 7.6 - - - +
77E ASP* 2.6 32.7 + - - -
79E PHE* 3.4 26.0 - + - -
80E PHE* 3.2 21.3 - - - -
202E MET* 4.5 17.0 - - + -
236E GLN 3.0 14.3 + - - +
237E ILE* 3.0 9.8 + - - +
239E LYS* 1.3 77.1 - - - +
241E VAL* 1.3 64.5 + - - +
243E HIS* 3.6 3.5 - - - +
244E ASN* 2.9 51.6 + - - +
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Residues in contact with VAL 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 3.8 9.4 - - + -
195E MET* 3.6 28.9 - - - +
198E VAL* 3.6 27.1 - - + -
199E MET* 3.7 18.6 - - + -
202E MET* 3.5 30.5 - - - -
237E ILE* 2.8 24.3 + - + +
238E TYR 3.5 6.1 - - - +
240E TYR* 1.3 70.6 - - + +
242E VAL* 1.3 58.3 + - - +
245E VAL* 2.8 33.8 + - + +
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Residues in contact with VAL 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132E PHE* 3.9 23.8 - - + -
195E MET* 3.3 22.5 - - + +
199E MET* 3.6 19.5 - - + -
238E TYR* 2.8 41.0 + - + +
239E LYS 3.7 0.4 - - - +
241E VAL* 1.3 72.7 - - - +
243E HIS* 1.3 64.6 + - - +
246E ALA* 3.0 26.3 + - - +
253E ALA* 3.8 18.6 - - + -
255E PHE* 3.6 21.5 - - + -
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Residues in contact with HIS 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171D HIS* 3.8 21.3 - + - -
184D PRO* 4.1 22.1 - - + +
27E LYS* 3.9 20.5 + - - -
239E LYS* 2.7 31.1 + - + +
240E TYR* 3.6 4.6 - - - +
242E VAL* 1.3 73.6 - - - +
244E ASN* 1.3 59.1 + - - +
246E ALA* 3.5 3.3 - - - +
247E HIS* 3.1 24.8 + - - +
252E THR* 5.7 0.3 - - - -
253E ALA* 3.2 37.6 + - + -
254E THR* 4.5 2.2 - - - -
255E PHE* 3.7 19.0 - + - -
467K SER 4.4 2.5 + - - -
468K VAL 3.4 24.9 + - - -
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Residues in contact with ASN 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D PRO* 3.3 18.6 - - - +
184D PRO* 3.7 23.0 - - - +
79E PHE* 3.5 33.6 - - + +
80E PHE* 5.9 0.6 - - - -
240E TYR* 2.9 54.8 + - - +
243E HIS* 1.3 72.4 - - - +
245E VAL* 1.3 66.1 + - - +
246E ALA 3.1 1.1 - - - -
247E HIS* 3.2 9.1 + - - +
248E ARG* 2.8 27.4 + - + +
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Residues in contact with VAL 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E PHE* 3.6 21.5 - - + -
191E ILE* 4.2 5.2 - - + +
194E GLU* 4.0 13.2 - - + +
195E MET* 3.6 29.4 - - + -
198E VAL* 4.2 14.6 - - + -
241E VAL* 2.8 36.7 + - + +
242E VAL 4.1 0.2 - - - +
244E ASN* 1.3 70.3 - - - +
246E ALA* 1.3 64.3 + - - +
248E ARG* 3.1 10.3 + - - +
249E PHE* 3.0 47.7 + - + -
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Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E LEU* 3.8 28.0 - - + -
191E ILE* 5.1 3.1 - - - -
195E MET* 4.0 5.1 - - + +
242E VAL 3.0 18.5 + - - +
243E HIS 3.5 5.6 - - - +
245E VAL* 1.3 78.0 - - - +
247E HIS* 1.3 57.5 + - - +
249E PHE* 2.9 10.5 + - - -
251E LYS* 2.7 38.0 + - + +
253E ALA* 3.8 14.8 - - + +
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Residues in contact with HIS 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169D LYS* 4.8 20.5 - - + +
171D HIS* 5.7 3.4 - - + -
184D PRO* 4.1 26.3 - - + +
243E HIS 3.1 14.2 + - - +
244E ASN* 3.4 14.6 - - - +
246E ALA* 1.3 79.3 - - - +
248E ARG* 1.3 62.0 + - + +
250E GLY* 2.8 24.8 + - - -
251E LYS 3.3 13.3 + - - +
252E THR* 6.1 0.2 - - - -
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Residues in contact with ARG 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E PRO 5.5 2.2 + - - -
79E PHE* 4.1 30.1 - - + +
194E GLU* 3.3 25.9 + - - -
198E VAL* 5.5 1.6 - - - +
244E ASN 2.8 14.7 + - - +
245E VAL* 3.5 16.9 - - - +
247E HIS* 1.3 82.8 - - + +
249E PHE* 1.3 76.6 + - + +
250E GLY 3.1 1.5 + - - -
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Residues in contact with PHE 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190E ASP* 4.5 7.2 - - + -
191E ILE* 3.8 45.3 - - + -
194E GLU* 3.7 28.9 - - + -
245E VAL* 3.0 30.0 + - + +
246E ALA* 2.9 9.9 + - - +
248E ARG* 1.3 99.8 - - + +
250E GLY* 1.3 62.9 + - - +
251E LYS* 3.1 11.5 + - + +
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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
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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