Contacts of the helix formed by residues 228 - 249 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108J ALA* 3.5 40.2 - - + +
111J ALA* 4.2 7.2 - - + -
112J GLU* 3.9 16.8 + - + +
124J VAL* 3.0 16.9 + - + -
126J PHE* 3.4 45.1 - - + -
226J ASN 3.2 2.7 + - - -
227J THR* 1.3 70.6 - - - +
229J THR* 1.3 62.3 + - - +
231J LYS* 3.3 2.8 + - - +
232J ALA* 3.2 17.5 + - - +
371J PHE* 3.5 31.3 - - + +
372J ALA* 3.7 23.1 - - + +
375J LEU* 4.0 12.1 - - + -
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Residues in contact with THR 229 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105J ARG* 4.6 24.9 - - + +
108J ALA* 3.5 33.4 + - + +
109J LYS* 3.8 24.4 + - + -
112J GLU* 3.1 23.5 + - - +
227J THR* 3.0 1.4 + - - -
228J MET* 1.3 71.8 - - - +
230J LYS* 1.3 67.1 + - - +
231J LYS 3.2 0.9 + - - -
232J ALA* 3.2 7.6 + - - +
233J ASP* 3.2 20.2 + - - +
368J TYR* 4.0 4.2 - - + -
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Residues in contact with LYS 230 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226J ASN* 3.3 34.5 - - - +
227J THR* 3.0 27.5 + - - +
229J THR* 1.3 77.4 - - - +
231J LYS* 1.3 57.9 + - - +
233J ASP* 3.0 18.5 - - + +
234J GLU* 3.0 36.9 + - + +
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Residues in contact with LYS 231 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J PHE* 3.5 21.3 - - + +
128J PRO* 3.3 38.1 - - + -
204J LEU* 5.0 0.8 - - - +
223J THR* 3.4 27.2 + - - -
224J ARG 2.7 29.4 + - - +
225J PHE* 4.3 1.6 - - - +
226J ASN* 4.0 15.6 - - + +
227J THR 2.9 11.6 + - - +
228J MET 3.6 8.5 - - - +
230J LYS* 1.3 74.1 - - - +
232J ALA* 1.3 60.8 + - - +
234J GLU* 3.0 31.0 + - + +
235J ILE* 2.8 32.1 + - - +
371J PHE* 4.1 4.3 - - + -
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Residues in contact with ALA 232 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228J MET 3.2 5.9 + - - +
229J THR* 3.2 4.0 + - - +
231J LYS* 1.3 78.3 - - - +
233J ASP* 1.3 62.4 + - - +
235J ILE* 3.4 5.1 + - - +
236J GLN* 3.3 22.7 + - - +
367J PRO* 3.4 22.8 - - + +
368J TYR* 3.2 38.4 + - + +
371J PHE* 3.6 19.9 - - + -
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Residues in contact with ASP 233 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J THR* 4.4 5.0 - - - +
88J ARG* 3.4 15.4 + - - +
105J ARG* 2.9 37.0 + - - -
229J THR* 3.2 13.7 + - - +
230J LYS* 3.0 22.2 + - + +
232J ALA* 1.3 76.7 - - - +
234J GLU* 1.3 59.2 + - + +
236J GLN* 2.9 24.4 + - - +
237J ILE* 3.0 19.5 + - + +
368J TYR* 2.6 32.8 + - - -
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Residues in contact with GLU 234 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203J GLY 4.3 12.3 - - - +
204J LEU* 3.5 41.3 - - + +
205J VAL 5.1 1.2 + - - -
224J ARG 3.8 5.7 - - - +
226J ASN* 3.4 23.1 + - - +
230J LYS* 3.1 18.9 - - + +
231J LYS* 3.0 38.3 + - + +
233J ASP* 1.3 81.2 - - + +
235J ILE* 1.3 53.9 + - - +
237J ILE* 3.2 6.3 + - + +
238J TYR* 2.7 35.0 + - - +
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Residues in contact with ILE 235 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J PRO* 4.2 13.0 - - + -
130J PRO* 3.9 16.6 - - + -
223J THR* 5.6 1.3 - - - +
231J LYS* 2.8 22.3 + - - +
232J ALA* 3.4 8.7 - - - +
233J ASP 3.0 0.4 - - - -
234J GLU* 1.3 74.9 - - - +
236J GLN* 1.3 66.7 + - - +
238J TYR* 3.1 10.9 + - + +
239J LYS* 2.9 41.4 + - + +
268J MET* 3.4 33.7 - - + -
363J PRO 6.0 0.2 - - - +
367J PRO* 3.3 25.6 - - + -
371J PHE* 4.2 16.2 - - + -
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Residues in contact with GLN 236 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J THR* 3.1 32.2 + - - +
26J GLY 2.9 27.5 + - - +
28J GLU* 3.6 25.2 - - - +
88J ARG* 3.6 19.3 - - - +
232J ALA 3.4 13.7 - - - +
233J ASP 2.9 7.6 + - - +
235J ILE* 1.3 77.4 - - - +
237J ILE* 1.3 63.3 + - - +
239J LYS* 3.4 18.6 + - - +
240J TYR* 3.0 22.7 + - - +
367J PRO* 3.8 19.2 - - - +
368J TYR* 4.2 7.9 - - + +
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Residues in contact with ILE 237 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28J GLU* 5.3 2.2 - - - +
73J THR 6.0 1.6 - - - +
75J VAL* 5.3 7.0 - - + -
88J ARG* 4.0 19.1 - - - +
199J MET* 5.2 0.9 - - - +
202J MET* 4.0 51.6 - - + +
204J LEU* 3.6 23.8 - - + -
233J ASP* 3.0 19.9 + - + +
234J GLU* 3.5 12.1 - - + +
236J GLN* 1.3 75.4 - - - +
238J TYR* 1.3 54.1 + - - +
240J TYR* 3.0 8.5 + - - +
241J VAL* 2.8 37.3 + - + +
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Residues in contact with TYR 238 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130J PRO* 2.9 43.6 + - + -
132J PHE* 3.5 6.3 - + - -
199J MET* 3.2 33.0 - - + -
204J LEU* 4.2 7.2 - - + +
221J VAL* 2.9 48.9 + - + +
223J THR* 4.3 17.5 - - + -
234J GLU 2.7 17.1 + - - +
235J ILE* 3.1 16.6 - - + +
237J ILE* 1.3 74.2 - - - +
239J LYS* 1.3 57.1 + - + +
241J VAL* 3.1 3.0 + - - +
242J VAL* 2.8 46.6 + - + +
255J PHE* 3.7 21.3 - + - -
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Residues in contact with LYS 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468D VAL* 3.4 26.8 + - - +
26J GLY* 5.0 5.7 + - - -
27J LYS* 6.1 1.6 - - - +
130J PRO* 6.2 1.1 - - + -
235J ILE* 2.9 39.2 + - + +
236J GLN* 3.8 20.8 + - - +
238J TYR* 1.3 75.6 - - + +
240J TYR* 1.3 58.9 + - - +
242J VAL* 3.7 0.2 - - - +
243J HIS* 2.7 43.5 + - + +
255J PHE* 3.6 44.9 - - + -
268J MET* 6.3 0.4 - - - -
363J PRO* 3.3 25.7 + - - -
364J ALA 5.0 2.0 + - - -
365J ALA 4.3 8.3 + - - -
367J PRO* 5.0 0.8 - - - +
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Residues in contact with TYR 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20J ARG* 3.4 25.5 + - - +
28J GLU* 4.1 7.2 - - - +
77J ASP* 2.6 32.0 + - - -
79J PHE* 3.4 26.3 - + - -
80J PHE* 3.2 20.6 - - - -
202J MET* 4.4 17.5 - - + -
236J GLN 3.0 14.3 + - - +
237J ILE* 3.3 10.1 - - - +
239J LYS* 1.3 77.8 - - - +
241J VAL* 1.3 65.4 + - - +
243J HIS* 3.1 2.9 + - - -
244J ASN* 2.9 51.9 + - - +
182K VAL* 4.2 18.6 - - + -
183K PRO* 3.5 21.3 - - + -
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Residues in contact with VAL 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J PHE* 3.8 9.2 - - + -
195J MET* 3.6 28.9 - - - +
198J VAL* 3.6 25.8 - - + -
199J MET* 3.7 18.4 - - + -
202J MET* 3.5 31.2 - - - -
237J ILE* 2.8 23.9 + - + +
238J TYR 3.5 6.1 - - - +
240J TYR* 1.3 71.1 - - - +
242J VAL* 1.3 60.0 + - - +
245J VAL* 2.8 34.0 + - + +
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Residues in contact with VAL 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132J PHE* 3.9 23.8 - - + -
195J MET* 3.3 23.3 - - + +
199J MET* 3.6 19.1 - - + -
238J TYR* 2.8 41.8 + - + +
239J LYS 3.7 0.2 - - - +
241J VAL* 1.3 72.7 - - - +
243J HIS* 1.3 66.2 + - - +
246J ALA* 3.0 26.7 + - - +
253J ALA* 3.8 18.2 - - + -
255J PHE* 3.6 21.3 - - + -
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Residues in contact with HIS 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466D TYR 4.9 0.4 + - - -
467D SER 4.4 1.5 + - - -
468D VAL 3.4 25.4 + - - -
27J LYS* 3.9 20.4 + - - -
239J LYS* 2.7 30.1 + - + +
240J TYR* 3.6 4.6 - - - +
242J VAL* 1.3 73.4 - - - +
244J ASN* 1.3 58.5 + - - +
246J ALA* 3.5 3.3 - - - +
247J HIS* 3.1 24.9 + - - +
252J THR* 5.7 0.2 - - - -
253J ALA* 3.2 38.2 + - + -
254J THR* 4.5 1.8 - - - -
255J PHE* 3.7 19.0 - + - -
171K HIS* 3.8 21.6 - + - -
182K VAL* 6.3 0.4 - - - +
183K PRO 5.2 0.2 - - - +
184K PRO* 4.0 23.6 - - + +
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Residues in contact with ASN 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J PHE* 3.5 33.3 - - + +
80J PHE* 5.9 0.4 - - - -
240J TYR* 2.9 53.8 + - - +
243J HIS* 1.3 73.2 - - - +
245J VAL* 1.3 66.4 + - - +
246J ALA 3.1 1.3 - - - -
247J HIS* 3.2 9.5 + - - +
248J ARG* 2.8 27.4 + - - +
183K PRO* 3.2 29.1 - - - +
184K PRO* 3.7 11.8 - - - +
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Residues in contact with VAL 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79J PHE* 3.6 22.2 - - + -
191J ILE* 4.2 4.9 - - + +
194J GLU* 4.0 13.0 - - + +
195J MET* 3.6 29.4 - - + +
198J VAL* 4.2 14.6 - - + -
241J VAL* 2.8 35.2 + - + +
244J ASN* 1.3 70.9 - - - +
246J ALA* 1.3 64.3 + - - +
248J ARG* 3.1 9.7 + - - +
249J PHE* 3.0 48.0 + - + -
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Residues in contact with ALA 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134J LEU* 3.8 28.3 - - + -
191J ILE* 5.1 3.1 - - - -
195J MET* 4.0 5.3 - - + +
242J VAL 3.0 17.9 + - - +
243J HIS 3.5 5.4 - - - +
245J VAL* 1.3 77.0 - - - +
247J HIS* 1.3 57.0 + - - +
249J PHE* 2.9 10.3 + - - -
251J LYS* 2.7 40.2 + - + +
253J ALA* 3.8 15.3 - - + +
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Residues in contact with HIS 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243J HIS 3.1 14.2 + - - +
244J ASN* 3.4 15.3 - - - +
246J ALA* 1.3 79.3 - - - +
248J ARG* 1.3 61.3 + - + +
250J GLY* 2.8 25.3 + - - -
251J LYS 3.3 14.1 + - - +
252J THR* 6.1 0.2 - - - -
169K LYS* 4.9 19.6 - - + +
171K HIS* 5.9 3.2 - - + -
184K PRO* 4.1 26.3 - - + +
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Residues in contact with ARG 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78J PRO 5.5 2.2 + - - -
79J PHE* 4.1 29.3 - - + +
194J GLU* 3.3 25.3 + - - -
198J VAL* 5.5 1.8 - - - +
244J ASN* 2.8 14.7 + - + +
245J VAL* 3.5 16.5 - - - +
247J HIS* 1.3 82.4 - - + +
249J PHE* 1.3 76.1 + - + +
250J GLY 3.1 1.9 + - - -
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Residues in contact with PHE 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190J ASP* 4.5 7.9 - - + -
191J ILE* 3.8 45.8 - - + -
194J GLU* 3.7 28.9 - - + -
245J VAL* 3.0 30.8 + - + +
246J ALA* 2.9 9.3 + - - +
248J ARG* 1.3 97.6 - - + +
250J GLY* 1.3 63.3 + - - +
251J LYS* 3.1 11.6 + - + +
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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