Contacts of the helix formed by residues 228 - 249 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108C ALA* 3.5 39.0 - - + +
111C ALA* 4.2 7.0 - - + -
112C GLU* 3.9 18.6 + - + +
124C VAL* 3.0 16.8 + - + -
126C PHE* 3.4 44.9 - - + -
226C ASN 3.2 2.3 + - - -
227C THR* 1.3 71.0 - - - +
229C THR* 1.3 62.9 + - - +
231C LYS* 3.3 2.9 + - - +
232C ALA* 3.2 17.3 + - - +
371C PHE* 3.5 30.1 - - + +
372C ALA* 3.7 23.8 - - + +
375C LEU* 4.0 12.1 - - + -
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Residues in contact with THR 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 4.6 24.2 - - + +
108C ALA* 3.5 32.7 + - + +
109C LYS* 3.8 25.5 + - + -
112C GLU* 3.1 23.8 + - - +
227C THR* 3.0 1.8 + - - -
228C MET* 1.3 70.4 - - - +
230C LYS* 1.3 65.7 + - - +
231C LYS 3.2 0.9 + - - -
232C ALA* 3.2 7.6 + - - +
233C ASP* 3.2 21.6 + - - +
368C TYR* 4.6 4.7 - - + -
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Residues in contact with LYS 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226C ASN* 3.3 33.9 - - - +
227C THR* 3.0 26.8 + - - +
229C THR* 1.3 78.9 - - - +
231C LYS* 1.3 57.3 + - - +
233C ASP* 3.0 18.1 - - + +
234C GLU* 3.0 37.2 + - + +
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Residues in contact with LYS 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C PHE* 3.5 21.8 - - + +
128C PRO* 3.3 37.0 - - + -
204C LEU* 5.0 0.8 - - - +
223C THR* 3.3 27.8 + - - -
224C ARG 2.7 28.9 + - - +
225C PHE* 4.3 1.1 - - - +
226C ASN* 4.0 16.1 - - + +
227C THR 2.9 11.0 + - - +
228C MET 3.6 8.5 - - - +
229C THR 3.1 0.2 - - - -
230C LYS* 1.3 75.5 - - - +
232C ALA* 1.3 60.8 + - - +
234C GLU* 3.0 30.9 + - + +
235C ILE* 2.8 31.9 + - - +
371C PHE* 4.1 4.9 - - + -
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Residues in contact with ALA 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C ALA* 5.9 0.2 - - + -
228C MET 3.2 6.4 + - - +
229C THR 3.2 3.6 + - - +
231C LYS* 1.3 78.2 - - - +
233C ASP* 1.3 63.5 + - - +
235C ILE* 3.4 4.6 + - - +
236C GLN* 3.3 23.2 + - - +
367C PRO* 3.4 25.3 - - + +
368C TYR* 3.2 37.6 + - + +
371C PHE* 3.6 16.9 - - + -
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Residues in contact with ASP 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C THR* 4.4 5.0 - - - +
88C ARG* 3.4 16.6 + - - +
105C ARG* 2.9 37.7 + - - -
229C THR* 3.2 13.5 + - - +
230C LYS* 3.0 22.5 + - + +
231C LYS 3.0 0.2 - - - -
232C ALA* 1.3 76.2 - - - +
234C GLU* 1.3 60.1 + - + +
236C GLN* 2.9 23.7 + - - +
237C ILE* 3.0 18.6 + - + +
368C TYR* 2.6 33.3 + - - -
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Residues in contact with GLU 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203C GLY 4.3 12.3 - - - +
204C LEU* 3.5 41.2 - - + +
205C VAL 5.1 2.0 + - - -
224C ARG 3.8 5.2 - - - +
226C ASN* 3.4 24.7 + - - +
230C LYS* 3.1 19.6 - - + +
231C LYS* 3.0 38.4 + - + +
233C ASP* 1.3 81.6 - - + +
235C ILE* 1.3 52.0 + - - +
237C ILE* 3.2 6.6 + - + +
238C TYR* 2.7 35.7 + - - +
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Residues in contact with ILE 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C PRO* 4.1 13.5 - - + -
130C PRO* 3.9 18.2 - - + -
223C THR* 5.6 1.6 - - - +
231C LYS* 2.8 22.5 + - - +
232C ALA* 3.4 9.0 - - - +
233C ASP 3.0 0.4 - - - -
234C GLU* 1.3 74.3 - - - +
236C GLN* 1.3 66.3 + - - +
238C TYR* 3.1 10.4 + - + +
239C LYS* 2.9 40.4 + - + +
268C MET* 3.4 33.2 - - + -
367C PRO* 3.3 25.4 - - + -
371C PHE* 4.2 15.9 - - + -
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Residues in contact with GLN 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C THR* 3.1 32.7 + - - +
26C GLY 2.9 28.0 + - - +
28C GLU* 3.5 24.8 - - - +
88C ARG* 3.6 19.3 - - - +
232C ALA 3.4 13.5 - - - +
233C ASP 2.9 7.9 + - - +
235C ILE* 1.3 75.2 - - - +
237C ILE* 1.3 62.6 + - - +
239C LYS* 3.4 18.9 + - - +
240C TYR* 3.0 23.2 + - - +
367C PRO* 3.8 19.6 - - - +
368C TYR* 4.2 8.1 - - + +
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Residues in contact with ILE 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C GLU* 5.3 2.2 - - - +
73C THR 6.0 1.1 - - - +
75C VAL* 5.3 7.6 - - + -
88C ARG* 4.0 18.6 - - - +
199C MET* 5.2 0.9 - - - +
202C MET* 4.0 51.6 - - + +
204C LEU* 3.6 22.9 - - + -
233C ASP* 3.0 20.3 + - + +
234C GLU* 3.5 11.4 - - + +
236C GLN* 1.3 75.4 - - - +
238C TYR* 1.3 55.2 + - - +
240C TYR* 3.0 8.1 + - - +
241C VAL* 2.8 37.6 + - + +
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Residues in contact with TYR 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C PRO* 2.9 42.7 + - + -
132C PHE* 3.5 6.6 - + - -
199C MET* 3.2 32.3 - - + -
204C LEU* 4.2 7.0 - - + -
221C VAL* 2.9 50.1 + - + +
223C THR* 4.3 17.9 - - + -
234C GLU 2.7 17.3 + - - +
235C ILE* 3.1 14.8 - - + +
237C ILE* 1.3 74.0 - - - +
239C LYS* 1.3 57.9 + - + +
241C VAL* 3.1 3.3 + - - +
242C VAL* 2.8 45.9 + - + +
255C PHE* 3.7 21.5 - + - -
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Residues in contact with LYS 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C GLY* 5.0 5.7 + - - -
27C LYS* 6.1 1.6 - - - +
130C PRO* 6.2 0.9 - - + -
235C ILE* 2.9 39.2 + - + +
236C GLN* 3.8 19.1 + - - +
238C TYR* 1.3 75.6 - - + +
240C TYR* 1.3 58.1 + - - +
242C VAL* 3.7 0.2 - - - +
243C HIS* 2.7 43.9 + - + +
255C PHE* 3.6 44.4 - - + -
268C MET* 6.3 0.9 - - - -
363C PRO* 3.3 25.7 + - - -
364C ALA 5.0 2.0 + - - -
365C ALA 4.3 8.3 + - - -
367C PRO* 5.0 1.2 - - - +
468I VAL* 3.3 27.0 + - - +
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Residues in contact with TYR 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182B VAL* 4.2 18.8 - - + -
183B PRO* 3.5 19.5 - - + -
20C ARG* 3.4 26.1 + - - +
28C GLU* 4.1 7.4 - - - +
77C ASP* 2.6 31.6 + - - -
79C PHE* 3.4 26.2 - + - -
80C PHE* 3.2 20.4 - - - -
202C MET* 4.4 17.0 - - + -
236C GLN 3.0 14.4 + - - +
237C ILE* 3.0 10.5 + - - +
239C LYS* 1.3 78.0 - - - +
241C VAL* 1.3 65.3 + - - +
243C HIS* 3.6 3.3 - - - +
244C ASN* 2.9 50.9 + - - +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.8 9.2 - - + -
195C MET* 3.6 29.4 - - - +
198C VAL* 3.6 26.2 - - + -
199C MET* 3.7 18.2 - - + -
202C MET* 3.5 31.2 - - - -
237C ILE* 2.8 23.2 + - + +
238C TYR 3.5 6.1 - - - +
240C TYR* 1.3 70.8 - - - +
242C VAL* 1.3 58.4 + - - +
245C VAL* 2.8 34.3 + - + +
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Residues in contact with VAL 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132C PHE* 3.9 23.3 - - + -
195C MET* 3.3 23.7 - - + +
199C MET* 3.6 19.7 - - + -
238C TYR* 2.8 41.2 + - + +
239C LYS 3.7 0.2 - - - +
241C VAL* 1.3 72.8 - - - +
243C HIS* 1.3 65.5 + - - +
246C ALA* 3.0 26.5 + - - +
253C ALA* 3.8 18.8 - - + -
255C PHE* 3.6 20.4 - - + -
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Residues in contact with HIS 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B HIS* 3.8 20.9 - + - -
182B VAL* 6.3 0.6 - - - +
183B PRO 5.2 0.4 - - - +
184B PRO* 3.9 24.5 - - + +
27C LYS* 3.9 20.3 + - - -
239C LYS* 2.7 30.1 + - + +
240C TYR* 3.6 4.4 - - - +
242C VAL* 1.3 72.4 - - - +
244C ASN* 1.3 58.8 - - - +
246C ALA* 3.5 3.5 - - - +
247C HIS* 3.1 24.9 + - - +
252C THR* 5.7 0.2 - - - -
253C ALA* 3.2 39.1 + - + -
254C THR* 4.5 1.8 - - - -
255C PHE* 3.7 18.1 - + - -
467I SER 4.3 2.1 + - - -
468I VAL 3.3 27.2 + - - -
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Residues in contact with ASN 244 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B PRO* 3.2 29.9 - - - +
184B PRO* 3.7 10.8 - - - +
79C PHE* 3.5 33.3 - - + +
80C PHE* 5.9 0.4 - - - -
240C TYR* 2.9 54.2 + - - +
243C HIS* 1.3 73.1 - - - +
245C VAL* 1.3 66.4 + - - +
246C ALA 3.1 1.3 - - - -
247C HIS* 3.2 9.8 + - - +
248C ARG* 2.8 27.4 + - + +
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Residues in contact with VAL 245 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79C PHE* 3.6 22.2 - - + -
191C ILE* 4.2 5.6 - - + +
194C GLU* 4.0 13.0 - - + +
195C MET* 3.6 29.2 - - + +
198C VAL* 4.2 14.6 - - + -
241C VAL* 2.8 35.6 + - + +
244C ASN* 1.3 70.5 - - - +
246C ALA* 1.3 64.2 - - - +
248C ARG* 3.1 10.2 + - - +
249C PHE* 3.0 47.8 + - + -
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Residues in contact with ALA 246 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134C LEU* 3.8 27.8 - - + -
191C ILE* 5.1 3.4 - - - -
195C MET* 4.0 5.5 - - + +
242C VAL 3.0 18.9 + - - +
243C HIS 3.5 5.6 - - - +
245C VAL* 1.3 77.6 - - - +
247C HIS* 1.3 58.0 + - - +
249C PHE* 2.9 10.3 + - - -
251C LYS* 2.7 38.0 + - + +
253C ALA* 3.8 15.3 - - + +
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Residues in contact with HIS 247 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LYS* 4.9 18.3 - - + +
171B HIS* 5.9 2.6 - - + -
184B PRO* 4.1 25.9 - - + +
243C HIS 3.1 13.6 + - - +
244C ASN* 3.2 15.9 + - - +
246C ALA* 1.3 79.8 - - - +
248C ARG* 1.3 63.1 + - + +
250C GLY* 2.8 25.5 + - - -
251C LYS 3.3 13.5 + - - +
252C THR* 6.1 0.2 - - - -
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Residues in contact with ARG 248 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C PRO 5.5 2.0 + - - -
79C PHE* 4.1 29.0 - - + +
194C GLU* 3.3 25.7 + - - -
198C VAL* 5.5 1.6 - - - +
244C ASN* 2.8 14.5 + - + +
245C VAL* 3.5 17.1 - - - +
247C HIS* 1.3 83.1 - - + +
249C PHE* 1.3 78.0 + - + +
250C GLY 3.1 1.9 + - - -
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Residues in contact with PHE 249 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C ASP* 4.5 7.6 - - + -
191C ILE* 3.8 45.1 - - + -
194C GLU* 3.7 29.2 - - + -
245C VAL* 3.0 29.7 + - + +
246C ALA* 2.9 9.9 + - - +
248C ARG* 1.3 98.5 - - + +
250C GLY* 1.3 64.3 + - - +
251C LYS* 3.1 11.8 + - + +
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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