Contacts of the helix formed by residues 228 - 249 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108L ALA* 3.5 38.8 - - + +
111L ALA* 4.2 7.2 - - + -
112L GLU* 3.9 18.2 + - + +
124L VAL* 3.0 16.8 + - + -
126L PHE* 3.4 44.9 - - + -
226L ASN 3.2 2.3 + - - -
227L THR* 1.3 69.9 - - - +
229L THR* 1.3 62.9 + - - +
231L LYS* 3.3 3.1 + - - +
232L ALA* 3.2 16.8 + - - +
371L PHE* 3.5 30.9 - - + +
372L ALA* 3.7 23.8 - - + +
375L LEU* 4.0 12.6 - - + -
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Residues in contact with THR 229 (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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105L ARG* 4.6 24.2 - - + +
108L ALA* 3.5 32.2 + - + +
109L LYS* 3.8 24.3 + - + -
112L GLU* 3.1 24.0 + - - +
227L THR* 3.0 1.8 + - - -
228L MET* 1.3 71.2 - - - +
230L LYS* 1.3 67.5 + - - +
231L LYS 3.2 0.5 + - - -
232L ALA* 3.2 7.6 + - - +
233L ASP* 3.2 20.9 + - - +
368L TYR* 4.6 4.9 - - + -
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Residues in contact with LYS 230 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226L ASN* 3.3 34.5 - - - +
227L THR* 3.0 26.6 + - - +
229L THR* 1.3 77.0 - - - +
231L LYS* 1.3 56.4 + - - +
233L ASP* 3.0 18.4 - - + +
234L GLU* 3.0 37.2 + - + +
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Residues in contact with LYS 231 (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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126L PHE* 3.5 21.3 - - + +
128L PRO* 3.3 37.9 - - + -
204L LEU* 5.0 0.6 - - - +
223L THR* 3.3 28.2 + - - -
224L ARG 2.7 28.4 + - - +
225L PHE* 4.3 1.1 - - - +
226L ASN* 4.0 14.7 - - + +
227L THR 2.9 11.6 + - - +
228L MET 3.6 8.3 - - - +
230L LYS* 1.3 75.4 - - - +
232L ALA* 1.3 59.9 + - - +
234L GLU* 3.0 29.4 + - + +
235L ILE* 2.8 32.6 + - - +
371L PHE* 4.1 4.7 - - + -
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Residues in contact with ALA 232 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228L MET 3.2 6.4 + - - +
229L THR* 3.2 3.6 + - - +
231L LYS* 1.3 77.2 - - - +
233L ASP* 1.3 62.8 + - - +
235L ILE* 3.4 5.4 + - - +
236L GLN* 3.3 23.2 + - - +
367L PRO* 3.4 21.4 - - + +
368L TYR* 3.2 38.5 + - + +
371L PHE* 3.6 19.6 - - + -
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Residues in contact with ASP 233 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73L THR* 4.4 5.2 - - - +
88L ARG* 3.4 16.1 + - - +
105L ARG* 2.9 36.2 + - - -
229L THR* 3.2 13.9 + - - +
230L LYS* 3.0 22.2 + - + +
232L ALA* 1.3 75.9 - - - +
234L GLU* 1.3 60.2 + - + +
236L GLN* 2.9 24.1 + - - +
237L ILE* 3.0 19.4 + - + +
368L TYR* 2.6 33.0 + - - -
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Residues in contact with GLU 234 (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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203L GLY 4.3 12.6 - - - +
204L LEU* 3.5 41.7 - - + +
205L VAL 5.1 1.3 + - - -
224L ARG 3.8 5.5 - - - +
226L ASN* 3.4 24.7 + - - +
230L LYS* 3.0 18.4 + - + +
231L LYS* 3.0 39.3 + - + +
233L ASP* 1.3 80.9 - - + +
235L ILE* 1.3 52.7 + - - +
237L ILE* 3.5 6.2 - - + +
238L TYR* 2.7 35.4 + - - +
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Residues in contact with ILE 235 (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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128L PRO* 4.1 13.9 - - + -
130L PRO* 3.9 17.0 - - + -
223L THR* 5.6 1.6 - - - +
231L LYS* 2.8 23.1 + - - +
232L ALA* 3.4 8.7 - - - +
233L ASP 3.0 0.4 - - - -
234L GLU* 1.3 74.1 - - - +
236L GLN* 1.3 66.6 + - - +
238L TYR* 3.1 10.8 + - + +
239L LYS* 2.9 40.7 + - + +
268L MET* 3.4 33.2 - - + -
363L PRO 6.0 0.2 - - - +
367L PRO* 3.3 25.6 - - + -
371L PHE* 4.2 16.4 - - + -
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Residues in contact with GLN 236 (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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22L THR* 3.1 32.2 + - - +
26L GLY 2.9 28.6 + - - +
28L GLU* 3.6 23.6 - - - +
88L ARG* 3.6 19.7 - - - +
232L ALA 3.3 13.9 + - - +
233L ASP 2.9 7.7 + - - +
235L ILE* 1.3 76.4 - - - +
237L ILE* 1.3 63.7 + - - +
239L LYS* 3.4 18.7 + - - +
240L TYR* 3.0 23.0 + - - +
367L PRO* 3.8 19.8 - - - +
368L TYR* 4.2 7.4 - - + +
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Residues in contact with ILE 237 (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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28L GLU* 5.3 2.0 - - - +
73L THR 6.0 1.1 - - - +
75L VAL* 5.3 7.9 - - + -
88L ARG* 4.0 19.1 - - - +
199L MET* 5.2 1.1 - - - +
202L MET* 4.0 50.7 - - + +
204L LEU* 3.6 23.6 - - + -
233L ASP* 3.0 20.8 + - + +
234L GLU* 3.5 11.2 - - + +
236L GLN* 1.3 74.6 - - - +
238L TYR* 1.3 55.1 + - - +
240L TYR* 3.0 8.6 + - - +
241L VAL* 2.8 37.9 + - + +
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Residues in contact with TYR 238 (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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130L PRO* 2.9 43.7 + - + -
132L PHE* 3.5 7.2 - + - -
199L MET* 3.2 31.8 - - + +
204L LEU* 4.2 6.7 - - + +
221L VAL* 2.9 49.6 + - + +
223L THR* 4.3 17.0 - - + -
234L GLU 2.7 16.9 + - - +
235L ILE* 3.1 15.5 - - + +
237L ILE* 1.3 75.0 - - - +
239L LYS* 1.3 58.5 + - + +
241L VAL* 3.1 2.7 + - - +
242L VAL* 2.8 45.7 + - + +
255L PHE* 3.7 22.2 - + - -
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Residues in contact with LYS 239 (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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468F VAL* 3.4 25.9 + - - +
26L GLY* 5.0 5.7 + - - -
27L LYS* 6.1 1.3 - - - +
130L PRO* 6.2 1.3 - - + -
235L ILE* 2.9 38.1 + - + +
236L GLN* 3.8 20.8 + - - +
238L TYR* 1.3 75.0 - - + +
240L TYR* 1.3 56.7 + - - +
242L VAL* 3.7 0.3 - - - +
243L HIS* 2.7 43.5 + - + +
255L PHE* 3.6 44.9 - - + -
268L MET* 6.1 1.1 - - + -
363L PRO* 3.3 25.7 + - - -
364L ALA 5.0 1.8 + - - -
365L ALA 4.3 8.1 + - - -
367L PRO* 5.0 0.8 - - - +
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Residues in contact with TYR 240 (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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182G VAL* 4.2 18.2 - - + -
183G PRO* 3.5 20.4 - - + -
20L ARG* 3.4 27.3 + - - +
28L GLU* 4.1 6.7 - - - +
77L ASP* 2.6 33.0 + - - -
79L PHE* 3.4 24.8 - + - -
80L PHE* 3.2 20.6 - - - -
202L MET* 4.5 17.5 - - + -
236L GLN 3.0 15.0 + - - +
237L ILE* 3.3 10.5 - - - +
239L LYS* 1.3 77.9 - - - +
241L VAL* 1.3 64.4 + - - +
243L HIS* 3.6 3.1 - - - +
244L ASN* 2.9 51.3 + - - +
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Residues in contact with VAL 241 (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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79L PHE* 3.8 8.1 - - + -
195L MET* 3.6 28.5 - - - +
198L VAL* 3.6 26.7 - - + -
199L MET* 3.7 17.7 - - + -
202L MET* 3.5 30.7 - - - -
237L ILE* 2.8 23.8 + - + +
238L TYR 3.5 6.3 - - - +
240L TYR* 1.3 71.6 - - + +
242L VAL* 1.3 58.4 + - - +
245L VAL* 2.8 33.9 + - + +
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Residues in contact with VAL 242 (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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132L PHE* 3.9 23.6 - - + -
195L MET* 3.3 23.4 - - + +
199L MET* 3.6 19.3 - - + -
238L TYR* 2.8 41.6 + - + +
239L LYS 3.7 0.2 - - - +
241L VAL* 1.3 71.8 - - - +
243L HIS* 1.3 65.8 + - - +
246L ALA* 3.0 26.9 + - - +
253L ALA* 3.8 18.8 - - + -
255L PHE* 3.6 22.2 - - + -
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Residues in contact with HIS 243 (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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466F TYR 4.8 0.6 + - - -
467F SER 4.5 2.0 + - - -
468F VAL 3.4 24.5 + - - -
171G HIS* 3.7 21.5 - + - -
182G VAL* 6.3 0.4 - - - +
183G PRO 5.2 0.4 - - - +
184G PRO* 4.0 22.7 - - + +
27L LYS* 3.9 20.2 + - - -
239L LYS* 2.7 29.6 + - + +
240L TYR* 3.6 4.4 - - - +
242L VAL* 1.3 72.2 - - - +
244L ASN* 1.3 58.4 + - - +
246L ALA* 3.5 3.6 - - - +
247L HIS* 3.1 25.1 + - - +
252L THR* 5.7 0.3 - - - -
253L ALA* 3.2 38.5 + - + -
254L THR* 4.5 1.8 - - - -
255L PHE* 3.7 19.7 - + - -
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Residues in contact with ASN 244 (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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183G PRO* 3.2 28.4 - - - +
184G PRO* 3.6 13.9 - - - +
79L PHE* 3.5 33.6 - - + +
80L PHE* 5.9 0.6 - - - -
240L TYR* 2.9 53.7 + - - +
243L HIS* 1.3 72.5 - - - +
245L VAL* 1.3 66.3 + - - +
246L ALA 3.1 0.9 - - - -
247L HIS* 3.4 8.5 - - - +
248L ARG* 2.8 27.4 + - + +
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Residues in contact with VAL 245 (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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79L PHE* 3.6 22.4 - - + -
191L ILE* 4.2 5.2 - - + +
194L GLU* 4.0 12.8 - - + +
195L MET* 3.6 28.7 - - + +
198L VAL* 4.2 14.4 - - + -
241L VAL* 2.8 33.9 + - + +
244L ASN* 1.3 71.5 - - - +
246L ALA* 1.3 65.4 + - - +
248L ARG* 3.1 10.1 + - - +
249L PHE* 3.0 48.6 + - + -
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Residues in contact with ALA 246 (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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134L LEU* 3.8 28.5 - - + -
191L ILE* 5.1 3.4 - - - -
195L MET* 4.0 4.9 - - + +
242L VAL 3.0 18.1 + - - +
243L HIS 3.5 5.6 - - - +
245L VAL* 1.3 77.8 - - - +
247L HIS* 1.3 58.1 + - - +
249L PHE* 2.9 10.7 + - - -
251L LYS* 2.7 38.3 + - + +
253L ALA* 3.8 15.0 - - + +
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Residues in contact with HIS 247 (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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169G LYS* 4.8 20.6 - - + +
171G HIS* 5.8 3.3 - - + -
184G PRO* 4.1 25.4 - - + +
243L HIS 3.1 13.8 + - - +
244L ASN* 3.4 15.9 - - - +
246L ALA* 1.3 80.6 - - - +
248L ARG* 1.3 62.8 + - + +
250L GLY* 2.8 25.6 + - - -
251L LYS 3.3 13.2 + - - +
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Residues in contact with ARG 248 (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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78L PRO 5.5 2.2 + - - -
79L PHE* 4.1 28.7 - - + +
194L GLU* 3.3 25.5 + - - -
198L VAL* 5.5 1.6 - - - +
244L ASN* 2.8 15.0 + - + +
245L VAL* 3.5 16.9 - - - +
247L HIS* 1.3 82.9 - - + +
249L PHE* 1.3 77.0 + - + +
250L GLY 3.1 1.9 + - - -
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Residues in contact with PHE 249 (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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190L ASP* 4.5 8.1 - - + -
191L ILE* 3.8 45.8 - - + -
194L GLU* 3.7 29.6 - - + -
245L VAL* 3.0 29.7 + - + +
246L ALA* 2.9 10.3 + - - +
248L ARG* 1.3 98.6 - - + +
250L GLY* 1.3 63.0 + - - +
251L LYS* 3.1 12.4 + - + +
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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