Contacts of the helix formed by residues 228 - 249 (chain B) in PDB entry 1F1H
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA* 3.3 38.4 - - + +
111B ALA* 4.1 7.9 - - + -
112B GLU* 3.8 20.2 + - + +
124B VAL* 3.0 15.6 + - + -
126B PHE* 3.5 42.4 - - + -
226B ASN 3.5 0.6 + - - -
227B THR* 1.3 73.7 - - - +
229B THR* 1.3 63.5 + - - +
231B LYS* 3.2 3.3 + - - +
232B ALA* 3.1 16.0 + - + +
371B PHE* 3.6 35.0 - - + +
372B ALA* 3.7 17.0 - - - +
375B LEU* 4.2 13.9 - - + -
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Residues in contact with THR 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ARG* 4.3 15.3 - - + +
108B ALA* 3.4 37.4 + - + +
109B LYS* 3.7 25.4 + - + -
112B GLU* 3.1 22.1 + - - +
228B MET* 1.3 74.7 - - - +
230B LYS* 1.3 64.6 + - - +
232B ALA* 3.1 7.6 + - - +
233B ASP* 3.1 22.1 + - - +
368B TYR* 4.3 11.4 - - + -
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Residues in contact with LYS 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B SER* 5.7 7.4 + - - -
226B ASN* 3.4 29.6 - - - +
227B THR* 3.2 22.9 + - - +
229B THR* 1.3 76.8 - - - +
231B LYS* 1.3 57.6 + - - +
233B ASP* 3.1 19.4 - - + +
234B GLU* 2.9 36.1 + - + +
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Residues in contact with LYS 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.4 24.5 - - + +
128B PRO* 3.3 35.9 - - + -
204B LEU* 5.0 1.0 - - - +
205B VAL 6.1 0.2 - - - +
223B THR* 3.1 26.2 + - - -
224B ARG 2.8 22.3 + - - -
226B ASN* 4.0 15.8 - - + +
227B THR 2.8 17.6 + - - +
228B MET 3.5 4.9 - - - +
230B LYS* 1.3 78.0 - - - +
232B ALA* 1.3 55.6 + - - +
234B GLU* 2.8 35.2 + - - +
235B ILE* 2.9 32.0 + - - +
371B PHE* 4.1 2.2 - - + -
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Residues in contact with ALA 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B MET 3.1 7.8 + - - +
229B THR* 3.1 4.5 + - - +
231B LYS* 1.3 72.9 - - - +
233B ASP* 1.3 65.7 + - - +
235B ILE* 3.3 3.7 + - - +
236B GLN* 3.2 25.6 + - - +
367B PRO* 3.7 20.5 - - + +
368B TYR* 3.3 37.5 - - + +
371B PHE* 3.8 19.9 - - + -
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Residues in contact with ASP 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B THR* 4.3 6.4 - - + +
88B ARG* 3.4 19.4 + - - +
105B ARG* 2.9 34.6 + - - -
229B THR 3.1 15.0 + - - +
230B LYS* 3.1 20.0 + - + +
232B ALA* 1.3 76.6 - - - +
234B GLU* 1.3 63.9 + - + +
236B GLN* 3.0 15.7 + - - +
237B ILE* 3.0 21.4 + - + +
368B TYR* 2.6 33.6 + - - -
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Residues in contact with GLU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203B GLY 4.0 14.0 - - - +
204B LEU* 3.8 30.6 - - + +
205B VAL 5.3 1.8 + - - -
224B ARG* 3.9 4.9 + - - +
225B PHE 4.9 0.2 - - - +
226B ASN* 3.0 28.2 + - - -
230B LYS* 2.9 22.7 + - + +
231B LYS* 2.8 42.9 + - + +
233B ASP* 1.3 77.4 - - + +
235B ILE* 1.3 51.0 + - - +
237B ILE* 3.2 12.4 + - + +
238B TYR* 2.6 36.9 + - - +
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Residues in contact with ILE 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B PRO* 3.9 29.2 - - + -
130B PRO* 3.8 30.7 - - + -
223B THR* 5.8 1.6 - - - +
231B LYS* 2.9 20.4 + - + +
232B ALA 3.5 8.3 - - - +
233B ASP 3.2 0.2 - - - -
234B GLU* 1.3 74.8 - - - +
236B GLN* 1.3 62.2 - - - +
238B TYR* 3.3 8.7 + - + +
239B LYS* 2.8 44.0 + - + +
268B MET* 4.2 11.2 - - - -
365B ALA 5.7 0.4 - - - +
367B PRO* 3.8 24.0 - - + -
371B PHE* 4.2 9.9 - - + -
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Residues in contact with GLN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B THR* 2.8 29.4 + - - +
26B GLY 3.1 27.3 + - - +
28B GLU* 3.2 35.2 - - - +
88B ARG* 3.7 17.7 - - - +
232B ALA 3.2 13.7 + - - +
233B ASP 3.0 9.0 + - - +
235B ILE* 1.3 78.5 - - - +
237B ILE* 1.3 55.8 + - - +
239B LYS* 3.5 20.9 + - - +
240B TYR* 3.0 22.2 + - - +
367B PRO* 3.7 16.7 - - + +
368B TYR* 4.1 10.8 - - + +
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Residues in contact with ILE 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B GLU* 5.1 2.0 - - - +
73B THR 5.9 0.7 - - - +
75B VAL* 5.0 12.6 - - + -
88B ARG* 3.8 21.8 - - - +
199B MET* 5.2 0.7 - - - +
202B MET* 3.8 48.9 - - + +
204B LEU* 3.6 24.5 - - + -
233B ASP* 3.0 19.3 + - + +
234B GLU* 3.2 11.9 + - + +
236B GLN* 1.3 71.7 - - - +
238B TYR* 1.3 60.1 + - - +
240B TYR* 3.2 8.5 + - - +
241B VAL* 2.9 32.5 + - + +
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Residues in contact with TYR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B PRO* 2.9 43.1 + - + -
132B PHE* 3.6 6.9 - + - -
199B MET* 3.5 31.6 - - + +
204B LEU* 4.2 6.7 - - + -
221B VAL* 2.9 45.8 + - + -
223B THR* 4.0 18.4 - - + -
234B GLU 2.6 21.6 + - - +
235B ILE* 3.3 12.1 - - + +
237B ILE* 1.3 74.1 - - - +
239B LYS* 1.3 67.1 + - + +
241B VAL* 3.2 2.9 + - - +
242B VAL* 2.9 37.3 + - + +
255B PHE* 3.8 23.3 - + - -
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Residues in contact with LYS 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B GLY* 4.1 9.9 + - - +
27B LYS* 6.1 1.1 - - - +
130B PRO* 6.5 0.2 - - + -
235B ILE* 2.8 31.7 + - + +
236B GLN* 3.8 26.2 + - - +
238B TYR* 1.3 73.5 - - + +
240B TYR* 1.3 57.9 + - - +
242B VAL* 3.8 0.5 - - - +
243B HIS* 2.9 43.7 + - + +
255B PHE* 3.7 37.0 - - + -
268B MET* 6.4 0.2 - - - -
363B PRO* 3.2 28.1 + - - -
364B ALA 5.0 2.0 + - - -
365B ALA 4.0 11.5 + - - -
367B PRO* 4.5 1.2 - - - +
468H VAL* 3.3 29.4 + - - +
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Residues in contact with TYR 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A VAL* 3.9 20.2 - - + -
183A PRO* 3.7 16.1 - - + +
20B ARG* 3.4 27.5 + - - +
28B GLU* 3.9 7.2 - - - +
77B ASP* 2.6 33.4 + - - -
79B PHE* 3.4 26.7 - + - +
80B PHE* 3.2 20.6 - - - -
202B MET* 4.3 17.5 - - + -
236B GLN 3.0 14.5 + - - +
237B ILE* 3.2 10.3 + - - +
239B LYS* 1.3 76.5 - - - +
241B VAL* 1.3 58.6 + - - +
243B HIS* 3.5 3.9 + - - +
244B ASN* 2.9 57.9 + - - +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 4.1 8.3 - - + -
195B MET* 3.6 28.3 - - + +
198B VAL* 3.9 16.4 - - + -
199B MET* 3.8 20.0 - - + -
202B MET* 3.6 29.4 - - - -
237B ILE* 2.9 21.0 + - + +
238B TYR 3.8 3.1 - - - +
240B TYR* 1.3 74.4 - - + +
242B VAL* 1.3 58.7 + - - +
245B VAL* 2.8 52.5 + - + +
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Residues in contact with VAL 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 3.8 30.7 - - + -
195B MET* 3.7 13.7 - - + +
199B MET* 3.6 20.2 - - + -
238B TYR* 2.9 36.7 + - + +
239B LYS 3.8 3.4 - - - +
241B VAL* 1.3 76.1 - - - +
243B HIS* 1.3 64.6 + - - +
246B ALA* 3.0 27.7 + - - +
253B ALA* 3.7 20.0 - - + -
255B PHE* 3.7 17.9 - - + -
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Residues in contact with HIS 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A HIS* 3.8 20.0 - + - -
183A PRO 5.0 0.7 - - - +
184A PRO* 3.8 23.0 - - + +
27B LYS* 3.8 21.5 + - - -
239B LYS* 2.9 32.0 + - + +
240B TYR* 3.8 4.6 - - - +
242B VAL* 1.3 73.1 - - - +
244B ASN* 1.3 58.4 + - - +
246B ALA* 3.5 2.9 - - - +
247B HIS* 3.0 26.3 + - - +
252B THR* 5.8 0.3 - - - -
253B ALA* 3.2 36.9 + - + -
254B THR* 4.6 1.4 - - - -
255B PHE* 3.7 21.5 - + - -
466H TYR 5.0 0.2 + - - -
467H SER 4.4 1.9 + - - -
468H VAL 3.6 22.5 + - - -
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Residues in contact with ASN 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A PRO* 2.9 32.2 - - - +
184A PRO* 3.6 20.8 - - - +
79B PHE* 3.5 36.0 - - + +
80B PHE* 6.0 0.4 - - - -
240B TYR* 2.9 40.8 + - - +
243B HIS* 1.3 74.1 - - - +
245B VAL* 1.3 60.0 + - - +
246B ALA 3.2 0.9 - - - -
247B HIS* 3.6 9.1 - - - +
248B ARG* 3.0 28.2 + - - +
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Residues in contact with VAL 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B PHE* 3.8 16.8 - - + -
191B ILE* 4.1 4.7 - - + +
194B GLU* 4.1 11.2 - - + +
195B MET* 3.7 29.8 - - + -
198B VAL* 4.4 10.8 - - + -
241B VAL* 2.8 42.5 + - + +
244B ASN* 1.3 69.4 - - - +
246B ALA* 1.3 67.1 + - - +
248B ARG* 3.2 11.0 + - - +
249B PHE* 3.0 44.9 + - + -
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LEU* 3.8 26.5 - - + -
191B ILE* 5.0 2.0 - - - -
195B MET* 4.2 5.7 - - + +
242B VAL 3.0 19.6 + - - +
243B HIS 3.5 4.9 - - - +
245B VAL* 1.3 77.2 - - - +
247B HIS* 1.3 62.2 + - - +
249B PHE* 2.9 11.0 + - - -
250B GLY 3.3 0.2 + - - -
251B LYS* 2.9 33.6 + - + +
253B ALA* 3.9 16.2 - - + +
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Residues in contact with HIS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A LYS* 4.6 21.6 - - + +
171A HIS* 5.8 2.6 - - + -
184A PRO* 3.9 29.5 - - + +
243B HIS 3.0 14.1 + - - +
244B ASN* 3.6 13.2 - - - +
246B ALA* 1.3 79.7 - - - +
248B ARG* 1.3 59.5 + - - +
250B GLY* 3.0 21.0 + - - -
251B LYS 3.4 12.8 + - - +
252B THR* 5.3 0.2 - - - +
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Residues in contact with ARG 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B PRO* 4.2 10.7 + - - +
79B PHE* 3.8 33.2 - - + -
194B GLU* 2.9 31.3 + - - -
198B VAL* 4.5 8.5 - - - +
244B ASN 3.0 18.7 + - - +
245B VAL* 3.5 11.5 - - - +
247B HIS* 1.3 78.4 - - - +
249B PHE* 1.3 75.0 + - + +
250B GLY 3.4 0.6 + - - -
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Residues in contact with PHE 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B ASP* 4.4 9.9 - - + -
191B ILE* 3.7 42.4 - - + -
194B GLU* 3.7 28.9 - - + -
245B VAL* 3.0 34.7 + - + +
246B ALA 2.9 10.0 + - - +
248B ARG* 1.3 93.6 - - + +
250B GLY* 1.3 61.7 + - - +
251B LYS* 3.9 15.5 - - + +
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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