Contacts of the helix formed by residues 228 - 249 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108G ALA* 3.5 39.9 - - + +
111G ALA* 4.2 7.2 - - + -
112G GLU* 3.9 16.8 + - + +
124G VAL* 3.0 16.4 + - + -
126G PHE* 3.4 43.3 - - + -
226G ASN 3.2 2.8 + - - -
227G THR* 1.3 69.9 - - - +
229G THR* 1.3 61.2 - - - +
231G LYS* 3.3 2.6 + - - +
232G ALA* 3.2 18.4 + - - +
371G PHE* 3.5 30.6 - - + +
372G ALA* 3.7 23.6 - - + +
375G LEU* 4.0 12.6 - - + -
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Residues in contact with THR 229 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105G ARG* 4.6 24.0 - - + +
108G ALA* 3.5 32.3 + - + +
109G LYS* 3.8 25.3 + - + -
112G GLU* 3.1 23.7 + - - +
227G THR* 3.0 1.8 + - - -
228G MET* 1.3 71.8 - - - +
230G LYS* 1.3 66.8 + - - +
231G LYS 3.2 0.5 + - - -
232G ALA* 3.2 7.6 + - - +
233G ASP* 3.2 20.9 + - - +
368G TYR* 4.6 4.9 - - + -
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Residues in contact with LYS 230 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ASN* 3.3 35.2 - - - +
227G THR* 3.0 27.2 + - - +
229G THR* 1.3 78.5 - - - +
231G LYS* 1.3 56.2 + - - +
233G ASP* 3.0 18.1 - - + +
234G GLU* 3.0 37.7 + - + +
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Residues in contact with LYS 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G PHE* 3.5 21.8 - - + +
128G PRO* 3.3 37.5 - - + -
204G LEU* 5.0 1.2 - - - +
223G THR* 3.3 27.4 + - - -
224G ARG 2.7 29.7 + - - +
225G PHE* 4.3 1.1 - - - +
226G ASN* 4.0 14.5 - - + +
227G THR 2.9 12.0 + - - +
228G MET 3.6 8.5 - - - +
230G LYS* 1.3 74.9 - - - +
232G ALA* 1.3 60.2 + - - +
234G GLU* 3.0 30.5 + - + +
235G ILE* 2.8 33.0 + - + +
371G PHE* 4.1 4.5 - - + -
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Residues in contact with ALA 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G MET 3.2 6.0 + - - +
229G THR* 3.2 3.3 + - - +
231G LYS* 1.3 78.4 - - - +
233G ASP* 1.3 63.6 + - - +
235G ILE* 3.4 5.2 + - - +
236G GLN* 3.3 22.7 + - - +
367G PRO* 3.4 21.6 - - + +
368G TYR* 3.2 39.4 + - + +
371G PHE* 3.6 19.8 - - + -
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Residues in contact with ASP 233 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G THR* 4.4 4.9 - - - +
88G ARG* 3.4 16.3 + - - +
105G ARG* 2.9 37.1 + - - -
229G THR* 3.2 13.8 + - - +
230G LYS* 3.0 21.9 + - + +
231G LYS 3.0 0.2 - - - -
232G ALA* 1.3 76.0 - - - +
234G GLU* 1.3 61.0 + - + +
236G GLN* 2.9 24.6 + - - +
237G ILE* 3.0 19.0 + - + +
368G TYR* 2.6 32.7 + - - -
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Residues in contact with GLU 234 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203G GLY 4.3 12.0 - - - +
204G LEU* 3.5 40.1 - - + +
205G VAL 5.1 1.4 + - - -
224G ARG 3.8 5.9 - - - +
226G ASN* 3.4 24.5 + - - +
230G LYS* 3.0 19.2 + - + +
231G LYS* 3.0 37.6 + - + +
233G ASP* 1.3 81.1 - - + +
235G ILE* 1.3 52.8 + - - +
237G ILE* 3.2 6.4 + - + +
238G TYR* 2.7 35.2 + - - +
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Residues in contact with ILE 235 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G PRO* 4.2 13.5 - - + +
130G PRO* 3.9 16.8 - - + -
223G THR* 5.6 1.3 - - - +
231G LYS* 2.8 23.4 + - - +
232G ALA 3.4 8.7 - - - +
233G ASP 3.0 0.2 + - - -
234G GLU* 1.3 74.3 - - - +
236G GLN* 1.3 67.3 + - - +
238G TYR* 3.1 9.9 + - + +
239G LYS* 2.9 41.0 + - + +
268G MET* 3.4 34.5 - - + -
367G PRO* 3.3 25.1 - - + -
371G PHE* 4.2 16.8 - - + -
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Residues in contact with GLN 236 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22G THR* 3.1 32.2 + - - +
26G GLY 2.9 29.1 + - - +
28G GLU* 3.5 23.5 - - - +
88G ARG* 3.6 19.7 - - - +
232G ALA 3.3 14.6 + - - +
233G ASP 2.9 7.7 + - - +
235G ILE* 1.3 76.3 - - - +
237G ILE* 1.3 63.1 + - - +
239G LYS* 3.4 18.8 + - - +
240G TYR* 3.0 23.4 + - - +
367G PRO* 3.8 19.4 - - - +
368G TYR* 4.2 7.2 - - + +
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Residues in contact with ILE 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28G GLU* 5.3 2.2 - - - +
73G THR 6.0 1.8 - - - +
75G VAL* 5.3 7.2 - - + -
88G ARG* 4.0 19.1 - - - +
199G MET* 5.2 1.3 - - - +
202G MET* 4.0 51.1 - - + +
204G LEU* 3.6 23.6 - - + -
233G ASP* 3.0 20.8 + - + +
234G GLU* 3.5 11.7 - - + +
236G GLN* 1.3 74.8 - - - +
238G TYR* 1.3 54.2 + - - +
240G TYR* 3.0 8.3 + - - +
241G VAL* 2.8 36.7 + - + +
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Residues in contact with TYR 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130G PRO* 2.9 42.6 + - + -
132G PHE* 3.5 6.6 - + - -
199G MET* 3.2 32.3 - - + +
204G LEU* 4.2 6.7 - - + +
221G VAL* 2.9 50.0 + - + +
223G THR* 4.3 17.3 - - + -
234G GLU 2.7 17.9 + - - +
235G ILE* 3.1 15.9 - - + +
237G ILE* 1.3 74.3 - - - +
239G LYS* 1.3 56.5 - - + +
241G VAL* 3.1 3.1 + - - +
242G VAL* 2.8 46.8 + - + +
255G PHE* 3.7 22.0 - + - -
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Residues in contact with LYS 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A VAL* 3.4 25.1 + - - +
26G GLY* 5.0 6.1 + - - -
27G LYS* 6.1 1.3 - - - +
130G PRO* 6.2 1.3 - - + -
235G ILE* 2.9 39.4 + - + +
236G GLN* 3.8 19.4 + - - +
238G TYR* 1.3 75.5 - - + +
240G TYR* 1.3 57.4 + - - +
242G VAL* 3.7 0.2 - - - +
243G HIS* 2.7 43.0 + - + +
255G PHE* 3.6 46.0 - - + -
268G MET* 6.1 1.1 - - + -
363G PRO* 3.3 25.5 + - - -
364G ALA 5.0 2.0 - - - -
365G ALA 4.3 8.7 + - - -
367G PRO* 5.0 0.6 - - - +
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Residues in contact with TYR 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20G ARG* 3.4 25.9 + - - +
28G GLU* 4.1 7.2 - - - +
77G ASP* 2.6 31.5 + - - -
79G PHE* 3.4 26.1 - + - +
80G PHE* 3.2 20.8 - - - -
202G MET* 4.5 16.6 - - + -
236G GLN 3.0 14.7 + - - +
237G ILE* 3.3 10.5 - - - +
239G LYS* 1.3 78.1 - - - +
241G VAL* 1.3 65.2 + - - +
243G HIS* 3.6 3.3 - - - +
244G ASN* 2.9 51.4 + - - +
182H VAL* 4.2 18.6 - - + -
183H PRO* 3.5 20.2 - - + -
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Residues in contact with VAL 241 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79G PHE* 3.8 9.0 - - + -
195G MET* 3.6 28.7 - - - +
198G VAL* 3.6 27.4 - - + -
199G MET* 3.7 18.6 - - + -
202G MET* 3.5 30.7 - - - -
237G ILE* 2.8 23.6 + - + +
238G TYR 3.5 6.3 - - - +
240G TYR* 1.3 72.3 - - - +
242G VAL* 1.3 57.4 + - - +
245G VAL* 2.8 33.5 + - + +
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Residues in contact with VAL 242 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G PHE* 3.9 24.2 - - + -
195G MET* 3.3 23.8 - - + +
199G MET* 3.6 19.1 - - + -
221G VAL* 5.7 0.2 - - + -
238G TYR* 2.8 41.9 + - + +
239G LYS 3.7 0.2 - - - +
241G VAL* 1.3 71.6 - - - +
243G HIS* 1.3 65.8 + - - +
246G ALA* 3.0 26.9 + - - +
253G ALA* 3.8 18.6 - - + -
255G PHE* 3.6 22.2 - - + -
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Residues in contact with HIS 243 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A SER 4.3 2.5 + - - -
468A VAL 3.3 25.6 + - - -
27G LYS* 3.9 20.7 + - - -
239G LYS* 2.7 30.0 + - + +
240G TYR* 3.6 4.8 - - - +
242G VAL* 1.3 72.2 - - - +
244G ASN* 1.3 57.2 + - - +
246G ALA* 3.5 3.1 - - - +
247G HIS* 3.1 25.1 + - - +
252G THR* 5.7 0.3 - - - -
253G ALA* 3.2 39.1 + - + -
254G THR* 4.5 2.0 - - - -
255G PHE* 3.7 18.2 - + - -
171H HIS* 3.8 20.7 - + - -
182H VAL* 6.3 0.2 - - - +
183H PRO 5.2 0.4 - - - +
184H PRO* 4.0 24.0 - - + +
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Residues in contact with ASN 244 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.5 34.2 - - + +
80G PHE* 5.9 0.4 - - - -
240G TYR* 2.9 53.6 + - - +
243G HIS* 1.3 71.2 - - - +
245G VAL* 1.3 66.8 + - - +
246G ALA 3.1 1.1 - - - -
247G HIS* 3.2 9.4 + - - +
248G ARG* 2.8 27.2 + - - +
183H PRO* 3.2 28.7 - - - +
184H PRO* 3.7 12.6 - - - +
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Residues in contact with VAL 245 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G PHE* 3.6 22.4 - - + -
191G ILE* 4.2 4.9 - - + +
194G GLU* 4.0 12.8 - - + +
195G MET* 3.6 29.6 - - + +
198G VAL* 4.2 13.9 - - + -
241G VAL* 2.8 35.2 + - + +
242G VAL 4.1 0.2 - - - +
244G ASN* 1.3 71.6 - - - +
246G ALA* 1.3 64.5 + - - +
248G ARG* 3.1 9.2 + - - +
249G PHE* 3.0 48.0 + - + -
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Residues in contact with ALA 246 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134G LEU* 3.8 28.0 - - + -
191G ILE* 5.1 3.4 - - - -
195G MET* 4.0 5.3 - - + +
242G VAL 3.0 18.3 + - - +
243G HIS 3.5 5.6 - - - +
245G VAL* 1.3 77.4 - - - +
247G HIS* 1.3 57.3 + - - +
249G PHE* 2.9 10.3 + - - -
251G LYS* 2.7 39.0 + - - +
253G ALA* 3.8 15.5 - - + +
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Residues in contact with HIS 247 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243G HIS 3.1 13.4 + - - +
244G ASN* 3.4 16.8 - - - +
246G ALA* 1.3 79.7 - - - +
248G ARG* 1.3 62.6 + - + +
250G GLY* 2.8 25.8 + - - -
251G LYS 3.3 14.6 + - - +
252G THR* 5.4 0.4 - - - +
169H LYS* 4.9 18.8 - - + +
171H HIS* 5.8 3.2 - - + -
184H PRO* 4.1 25.9 - - + +
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Residues in contact with ARG 248 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78G PRO 5.5 2.4 + - - -
79G PHE* 4.1 29.0 - - + +
194G GLU* 3.3 25.7 + - - -
198G VAL* 5.5 1.4 - - - +
244G ASN 2.8 14.3 + - - +
245G VAL* 3.5 16.9 - - - +
247G HIS* 1.3 84.2 - - + +
249G PHE* 1.3 77.0 - - + +
250G GLY 3.1 1.3 + - - -
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Residues in contact with PHE 249 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190G ASP* 4.5 8.3 - - + -
191G ILE* 3.8 46.4 - - + -
194G GLU* 3.7 28.7 - - + -
245G VAL* 3.0 30.4 + - + +
246G ALA* 2.9 10.1 + - - +
248G ARG* 1.3 97.9 - - + +
250G GLY* 1.3 64.1 + - - +
251G LYS* 3.1 11.4 + - + +
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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