Contacts of the helix formed by residues 228 - 249 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I ALA* 3.5 39.5 - - + +
111I ALA* 4.2 7.2 - - + -
112I GLU* 3.9 17.5 + - + +
124I VAL* 3.0 16.8 + - + -
126I PHE* 3.4 43.3 - - + -
226I ASN 3.2 2.8 + - - -
227I THR* 1.3 69.7 - - - +
229I THR* 1.3 61.5 + - - +
231I LYS* 3.3 2.8 + - - +
232I ALA* 3.2 18.2 + - + +
371I PHE* 3.5 31.1 - - + +
372I ALA* 3.7 24.0 - - + +
375I LEU* 4.0 12.6 - - + -
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Residues in contact with THR 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I ARG* 4.6 24.7 - - + +
108I ALA* 3.5 32.8 + - + +
109I LYS* 3.8 23.9 + - + -
112I GLU* 3.1 26.0 + - - +
227I THR 3.0 1.6 + - - -
228I MET* 1.3 70.5 - - - +
230I LYS* 1.3 66.4 + - - +
231I LYS 3.2 0.7 + - - -
232I ALA* 3.2 7.8 + - - +
233I ASP* 3.2 21.5 + - - +
368I TYR* 4.0 4.7 - - + -
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Residues in contact with LYS 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226I ASN* 3.3 34.3 - - - +
227I THR* 3.0 27.2 + - - +
229I THR* 1.3 76.8 - - - +
231I LYS* 1.3 56.7 + - - +
233I ASP* 3.0 18.7 - - + +
234I GLU* 3.0 37.3 + - + +
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Residues in contact with LYS 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE* 3.5 21.8 - - + +
128I PRO* 3.3 37.2 - - + -
204I LEU* 5.0 0.8 - - - +
223I THR* 3.3 28.2 + - - -
224I ARG 2.7 28.3 + - - +
225I PHE* 4.3 1.6 - - - +
226I ASN* 4.0 14.3 - - + +
227I THR 2.9 11.6 + - - +
228I MET 3.6 8.3 - - - +
229I THR 3.1 0.2 - - - -
230I LYS* 1.3 73.8 - - - +
232I ALA* 1.3 61.1 + - - +
234I GLU* 3.0 31.2 + - + +
235I ILE* 2.8 32.6 + - - +
371I PHE* 4.1 4.9 - - + -
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Residues in contact with ALA 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228I MET 3.2 6.6 + - - +
229I THR 3.2 3.3 + - - +
231I LYS* 1.3 78.0 - - - +
233I ASP* 1.3 62.4 + - - +
235I ILE* 3.4 5.4 + - - +
236I GLN* 3.3 22.7 + - - +
367I PRO* 3.4 22.0 - - + +
368I TYR* 3.2 39.0 - - + +
371I PHE* 3.6 19.8 - - + -
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Residues in contact with ASP 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73I THR* 4.4 5.6 - - - +
88I ARG* 3.4 15.4 + - - +
105I ARG* 2.9 37.3 + - - -
229I THR* 3.2 13.8 + - - +
230I LYS* 3.0 21.8 + - + +
232I ALA* 1.3 76.9 - - - +
234I GLU* 1.3 59.6 + - + +
236I GLN* 2.9 24.4 + - - +
237I ILE* 3.0 18.8 + - + +
368I TYR* 2.6 33.0 + - - -
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Residues in contact with GLU 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203I GLY 4.3 12.0 - - - +
204I LEU* 3.5 40.6 - - + +
205I VAL 5.1 1.8 + - - -
224I ARG 3.8 5.4 - - - +
226I ASN* 3.4 23.7 + - - +
230I LYS* 3.0 19.8 + - + +
231I LYS* 3.0 38.6 + - + +
233I ASP* 1.3 80.4 - - + +
235I ILE* 1.3 53.3 + - - +
237I ILE* 3.2 6.1 + - + +
238I TYR* 2.7 35.4 + - - +
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Residues in contact with ILE 235 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128I PRO* 4.2 12.8 - - + +
130I PRO* 3.9 17.0 - - + -
223I THR* 5.6 1.6 - - - +
231I LYS* 2.8 23.0 + - - +
232I ALA* 3.4 8.7 - - - +
233I ASP 3.0 0.2 + - - -
234I GLU* 1.3 75.2 - - - +
236I GLN* 1.3 66.5 + - - +
238I TYR* 3.1 10.5 + - + +
239I LYS* 2.9 40.4 + - + +
268I MET* 3.4 33.0 - - + -
363I PRO 6.0 0.2 - - - +
367I PRO* 3.3 26.5 - - + -
371I PHE* 4.2 15.9 - - + -
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Residues in contact with GLN 236 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I THR* 3.1 32.1 + - - +
26I GLY 2.9 28.4 + - - +
28I GLU* 3.5 24.4 - - - +
88I ARG* 3.6 20.0 - - - +
232I ALA 3.4 14.1 - - - +
233I ASP 2.9 7.9 + - - +
235I ILE* 1.3 76.2 - - - +
237I ILE* 1.3 63.4 + - - +
239I LYS* 3.4 18.2 + - - +
240I TYR* 3.0 23.0 + - - +
367I PRO* 3.8 19.6 - - - +
368I TYR* 4.2 7.2 - - + +
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Residues in contact with ILE 237 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I GLU* 5.3 2.2 - - - +
73I THR 6.0 1.6 - - - +
75I VAL* 5.3 7.0 - - + -
88I ARG* 4.0 18.6 - - - +
199I MET* 5.2 1.1 - - - +
202I MET* 4.0 51.6 - - + +
204I LEU* 3.6 23.6 - - + -
233I ASP* 3.0 19.9 + - + +
234I GLU* 3.5 11.9 - - + +
236I GLN* 1.3 74.3 - - - +
238I TYR* 1.3 55.1 + - - +
240I TYR* 3.0 8.3 + - - +
241I VAL* 2.8 37.1 + - + +
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Residues in contact with TYR 238 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130I PRO* 2.9 43.9 + - + -
132I PHE* 3.5 6.3 - + - -
199I MET* 3.2 32.7 - - + +
204I LEU* 4.2 6.1 - - + -
221I VAL* 2.9 48.9 + - + +
223I THR* 4.3 17.9 - - + -
234I GLU 2.7 18.5 + - - +
235I ILE* 3.1 15.0 - - + +
237I ILE* 1.3 73.6 - - - +
239I LYS* 1.3 58.8 + - + +
241I VAL* 3.1 3.1 + - - +
242I VAL* 2.8 46.3 + - + +
255I PHE* 3.7 21.8 - + - -
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Residues in contact with LYS 239 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468C VAL* 3.4 26.9 + - - +
26I GLY* 5.0 5.3 + - - -
27I LYS* 6.1 1.8 - - - +
130I PRO* 6.2 0.9 - - + -
235I ILE* 2.9 38.6 + - + +
236I GLN* 3.8 20.3 + - - +
238I TYR* 1.3 76.7 - - + +
240I TYR* 1.3 58.0 + - - +
242I VAL* 3.7 0.2 - - - +
243I HIS* 2.7 43.0 + - + +
255I PHE* 3.6 46.4 - - + -
268I MET* 6.1 0.7 - - + -
363I PRO* 3.3 25.5 + - - -
364I ALA 5.0 1.6 + - - -
365I ALA 4.3 8.5 + - - -
367I PRO* 5.0 0.8 - - - +
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Residues in contact with TYR 240 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20I ARG* 3.4 25.6 + - - +
28I GLU* 4.1 7.8 + - - +
77I ASP* 2.6 31.7 + - - -
79I PHE* 3.4 26.2 - + - -
80I PHE* 3.2 21.0 - - - -
202I MET* 4.5 17.5 - - + -
236I GLN 3.0 13.6 + - - +
237I ILE* 3.3 11.2 - - - +
239I LYS* 1.3 77.3 - - - +
241I VAL* 1.3 66.4 + - - +
243I HIS* 4.5 3.1 - - - -
244I ASN* 2.9 52.2 + - - +
182J VAL* 4.2 19.3 - - + -
183J PRO* 3.6 20.6 - - + +
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Residues in contact with VAL 241 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I PHE* 3.8 9.0 - - + -
195I MET* 3.6 28.7 - - - +
198I VAL* 3.6 26.9 - - + -
199I MET* 3.7 18.2 - - + -
202I MET* 3.5 31.0 - - - -
237I ILE* 2.8 24.3 + - + +
238I TYR 3.5 5.6 - - - +
240I TYR* 1.3 71.2 - - + +
242I VAL* 1.3 57.4 + - - +
245I VAL* 2.8 33.6 + - + +
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Residues in contact with VAL 242 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I PHE* 3.9 24.0 - - + -
195I MET* 3.3 23.0 - - + +
199I MET* 3.6 19.1 - - + -
221I VAL* 5.7 0.2 - - + -
238I TYR* 2.8 43.2 + - + +
239I LYS 3.7 0.2 - - - +
241I VAL* 1.3 71.7 - - - +
243I HIS* 1.3 65.9 + - - +
246I ALA* 3.0 26.5 + - - +
253I ALA* 3.8 18.2 - - + -
255I PHE* 3.6 21.5 - - + -
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Residues in contact with HIS 243 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466C TYR 4.8 0.8 + - - -
467C SER 4.5 1.5 + - - -
468C VAL 3.4 24.5 + - - -
27I LYS* 3.9 20.1 + - - -
239I LYS* 2.7 31.5 + - + +
240I TYR* 3.6 4.6 - - - +
242I VAL* 1.3 73.2 - - - +
244I ASN* 1.3 57.7 - - - +
246I ALA* 3.5 3.3 - - - +
247I HIS* 3.1 24.8 + - - +
252I THR* 5.7 0.2 - - - -
253I ALA* 3.2 38.6 + - + -
254I THR* 4.5 2.4 - - - -
255I PHE* 3.7 20.4 - + - -
171J HIS* 3.8 20.8 - + - -
182J VAL* 6.2 0.6 - - - +
183J PRO 5.2 0.2 - - - +
184J PRO* 3.9 22.3 - - + +
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Residues in contact with ASN 244 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I PHE* 3.5 33.3 - - + +
80I PHE* 5.9 0.4 - - - -
240I TYR* 2.9 53.7 + - - +
243I HIS* 1.3 72.4 - - - +
245I VAL* 1.3 66.8 + - - +
246I ALA 3.1 1.3 - - - -
247I HIS* 3.4 8.7 - - - +
248I ARG* 2.8 27.4 + - + +
183J PRO* 3.2 31.4 - - - +
184J PRO* 3.7 10.0 - - - +
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Residues in contact with VAL 245 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79I PHE* 3.6 22.0 - - + -
191I ILE* 4.2 5.8 - - + +
194I GLU* 4.0 12.8 - - + +
195I MET* 3.6 28.3 - - + +
198I VAL* 4.2 14.6 - - + -
241I VAL* 2.8 35.5 + - + +
244I ASN* 1.3 70.3 - - - +
246I ALA* 1.3 64.2 + - - +
248I ARG* 3.1 9.7 + - - +
249I PHE* 3.0 47.8 + - + -
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Residues in contact with ALA 246 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I LEU* 3.8 28.5 - - + -
191I ILE* 5.1 3.4 - - - -
195I MET* 4.0 4.9 - - + +
242I VAL 3.0 18.7 + - - +
243I HIS 3.5 5.4 - - - +
245I VAL* 1.3 76.6 - - - +
247I HIS* 1.3 56.9 + - - +
249I PHE* 2.9 11.1 + - - -
251I LYS* 2.7 38.7 + - + +
253I ALA* 3.8 14.8 - - + +
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Residues in contact with HIS 247 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243I HIS 3.1 14.4 + - - +
244I ASN* 3.4 15.3 - - - +
246I ALA* 1.3 79.6 - - - +
248I ARG* 1.3 61.8 + - + +
250I GLY* 2.8 25.5 + - - -
251I LYS 3.3 13.9 + - - +
252I THR* 5.4 0.4 - - - +
169J LYS* 4.9 18.6 - - + +
171J HIS* 5.8 2.8 - - + -
184J PRO* 4.0 26.8 - - + +
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Residues in contact with ARG 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I PRO 5.5 2.6 + - - -
79I PHE* 4.1 28.9 - - + +
194I GLU* 3.3 25.7 + - - -
198I VAL* 5.5 2.2 - - - +
244I ASN 2.8 14.3 + - - +
245I VAL* 3.1 17.1 + - - +
247I HIS* 1.3 83.0 - - + +
249I PHE* 1.3 75.9 + - + +
250I GLY 3.1 2.1 + - - -
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Residues in contact with PHE 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190I ASP* 4.5 8.1 - - + -
191I ILE* 3.8 45.5 - - + -
194I GLU* 3.7 29.4 - - + -
245I VAL* 3.0 30.8 + - + +
246I ALA* 2.9 10.5 + - - +
248I ARG* 1.3 99.0 - - + +
250I GLY* 1.3 63.4 + - - +
251I LYS* 3.1 11.2 + - + +
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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