Contacts of the helix formed by residues 228 - 249 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108K ALA* 3.3 38.1 - - + +
111K ALA* 4.1 7.9 - - + -
112K GLU* 3.8 20.0 + - + +
124K VAL* 3.0 14.9 + - + -
126K PHE* 3.5 41.7 - - + -
226K ASN 3.5 0.8 + - - -
227K THR* 1.3 74.1 - - - +
229K THR* 1.3 65.3 + - - +
231K LYS* 3.2 2.9 + - - +
232K ALA* 3.1 16.8 + - - +
371K PHE* 3.6 35.3 - - + +
372K ALA* 3.7 16.4 - - - +
375K LEU* 4.2 13.5 - - + -
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Residues in contact with THR 229 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105K ARG* 4.3 14.6 - - + +
108K ALA* 3.4 37.7 + - + +
109K LYS* 3.7 26.1 + - + -
112K GLU* 3.1 21.9 + - - +
228K MET* 1.3 75.3 - - - +
230K LYS* 1.3 64.6 + - - +
232K ALA* 3.1 7.8 + - - +
233K ASP* 3.1 22.9 + - - +
368K TYR* 4.3 11.7 - - + -
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Residues in contact with LYS 230 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72K SER* 5.7 7.2 + - - -
112K GLU* 4.6 0.2 + - - -
226K ASN* 3.4 29.4 - - - +
227K THR* 3.2 20.7 + - - +
229K THR* 1.3 77.3 - - - +
231K LYS* 1.3 58.0 + - - +
233K ASP* 3.1 19.0 - - + +
234K GLU* 2.9 35.8 + - + +
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Residues in contact with LYS 231 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126K PHE* 3.4 25.4 - - + +
128K PRO* 3.3 36.1 - - + -
204K LEU* 5.0 0.8 - - - +
223K THR* 3.1 26.6 + - - -
224K ARG 2.8 22.2 + - - +
226K ASN* 4.0 16.7 - - + +
227K THR 2.8 16.5 + - - +
228K MET 3.5 5.2 - - - +
230K LYS* 1.3 77.9 - - - +
232K ALA* 1.3 57.2 + - - +
234K GLU* 2.8 34.8 + - + +
235K ILE* 2.9 31.8 + - - +
371K PHE* 4.1 2.0 - - + -
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Residues in contact with ALA 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228K MET 3.1 7.8 + - - +
229K THR* 3.1 5.1 + - - +
231K LYS* 1.3 74.4 - - - +
233K ASP* 1.3 63.8 + - - +
235K ILE* 3.3 3.9 + - - +
236K GLN* 3.2 25.8 + - - +
367K PRO* 3.7 21.9 - - + +
368K TYR* 3.3 37.7 - - + +
371K PHE* 3.8 18.7 - - + -
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Residues in contact with ASP 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73K THR* 4.3 6.0 - - + +
88K ARG* 3.4 20.2 + - - +
105K ARG* 2.9 34.3 + - - -
229K THR* 3.1 15.2 + - - +
230K LYS* 3.1 19.3 + - + +
232K ALA* 1.3 78.1 - - - +
234K GLU* 1.3 63.8 + - + +
236K GLN* 3.0 15.5 + - - +
237K ILE* 3.0 20.9 + - + +
368K TYR* 2.6 34.0 + - - -
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Residues in contact with GLU 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203K GLY 4.0 14.1 - - - +
204K LEU* 3.8 30.6 - - + +
205K VAL 5.3 1.2 + - - -
224K ARG* 3.9 4.9 + - - +
226K ASN* 3.0 27.8 + - - -
230K LYS* 2.9 22.9 + - + +
231K LYS* 2.8 40.8 + - + +
233K ASP* 1.3 77.1 - - + +
235K ILE* 1.3 51.3 + - - +
237K ILE* 3.1 13.0 + - + +
238K TYR* 2.6 36.6 + - - +
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Residues in contact with ILE 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128K PRO* 3.9 30.7 - - + -
130K PRO* 3.8 30.7 - - + -
223K THR* 5.8 1.3 - - - +
231K LYS* 2.9 20.2 + - + +
232K ALA 3.5 8.1 - - - +
233K ASP 3.2 0.2 - - - -
234K GLU* 1.3 75.5 - - - +
236K GLN* 1.3 63.8 + - - +
238K TYR* 3.3 8.3 - - + +
239K LYS* 2.8 44.9 + - + +
268K MET* 4.2 10.5 - - + -
365K ALA 5.7 0.4 - - - +
367K PRO* 3.8 23.8 - - + -
371K PHE* 4.2 10.3 - - + -
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Residues in contact with GLN 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22K THR* 2.8 29.4 + - - +
26K GLY 3.1 27.7 + - - +
28K GLU* 3.2 35.3 - - - +
88K ARG* 3.7 17.9 - - - +
232K ALA 3.2 13.0 + - - +
233K ASP 3.0 8.5 + - - +
235K ILE* 1.3 79.0 - - - +
237K ILE* 1.3 55.9 + - - +
239K LYS* 3.5 21.6 + - - +
240K TYR* 3.0 22.0 + - - +
367K PRO* 3.7 16.5 - - + +
368K TYR* 4.1 10.8 - - + +
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Residues in contact with ILE 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28K GLU* 5.1 1.8 - - - +
73K THR 5.9 1.1 - - - +
75K VAL* 5.0 12.1 - - + -
88K ARG* 3.8 21.1 - - - +
199K MET* 5.2 0.4 - - - +
202K MET* 3.8 49.4 - - + +
204K LEU* 3.6 25.6 - - + -
233K ASP* 3.0 21.2 + - + +
234K GLU* 3.5 11.0 - - + +
236K GLN* 1.3 72.1 - - - +
238K TYR* 1.3 59.4 + - - +
240K TYR* 3.2 7.3 + - - +
241K VAL* 2.9 32.6 + - + +
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Residues in contact with TYR 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130K PRO* 2.9 44.4 + - + -
132K PHE* 3.6 6.6 - + - -
199K MET* 3.5 31.8 - - + +
204K LEU* 4.2 7.2 - - + -
221K VAL* 2.9 46.3 + - + -
223K THR* 4.0 17.5 - - + -
234K GLU 2.6 21.3 + - - +
235K ILE* 3.3 13.5 - - + +
237K ILE* 1.3 73.8 - - - +
239K LYS* 1.3 67.6 + - + +
241K VAL* 3.2 2.6 + - - +
242K VAL* 2.9 36.9 + - + +
255K PHE* 3.8 22.9 - + - -
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Residues in contact with LYS 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468E VAL* 3.3 31.4 + - - +
26K GLY* 4.1 9.5 + - - -
27K LYS* 6.1 0.4 - - - +
235K ILE* 2.8 31.7 + - + +
236K GLN* 3.8 28.8 + - - +
238K TYR* 1.3 72.9 - - + +
240K TYR* 1.3 58.3 + - - +
242K VAL* 3.8 0.3 - - - +
243K HIS* 2.9 43.6 + - + +
255K PHE* 3.7 36.6 - - + -
268K MET* 6.4 0.4 - - - -
363K PRO* 3.2 27.7 + - - -
364K ALA 5.0 2.4 + - - -
365K ALA 4.0 11.9 + - - -
367K PRO* 4.5 1.0 - - - +
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Residues in contact with TYR 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K ARG* 3.4 28.0 + - - +
28K GLU* 3.9 6.9 + - - +
77K ASP* 2.6 32.5 + - - -
79K PHE* 3.4 26.1 - + - +
80K PHE* 3.2 20.3 - - - -
202K MET* 4.3 17.7 - - + -
236K GLN 3.0 15.8 + - - +
237K ILE* 3.2 10.1 + - - +
239K LYS* 1.3 76.7 - - - +
241K VAL* 1.3 60.1 + - - +
243K HIS* 3.8 3.5 - - - +
244K ASN* 2.9 58.5 + - - +
182L VAL* 4.1 12.8 - - + -
183L PRO* 3.7 24.5 - - + -
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Residues in contact with VAL 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K PHE* 4.1 8.3 - - + -
195K MET* 3.6 28.7 - - + +
198K VAL* 3.8 15.7 - - + -
199K MET* 3.8 18.6 - - + -
202K MET* 3.6 29.2 - - - -
237K ILE* 2.9 21.2 + - + +
238K TYR 3.8 3.1 - - - +
240K TYR* 1.3 76.1 - - + +
242K VAL* 1.3 59.6 + - - +
245K VAL* 2.8 52.7 + - + +
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Residues in contact with VAL 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132K PHE* 3.8 32.1 - - + -
195K MET* 3.7 13.9 - - + +
199K MET* 3.6 20.4 - - + -
238K TYR* 2.9 37.8 + - + +
239K LYS 3.8 3.4 - - - +
241K VAL* 1.3 75.2 - - - +
243K HIS* 1.3 64.9 + - - +
246K ALA* 3.0 27.5 + - - +
253K ALA* 3.7 19.5 - - + -
255K PHE* 3.7 17.9 - - + -
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Residues in contact with HIS 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467E SER 4.3 0.7 - - - -
468E VAL 3.5 23.8 + - - -
27K LYS* 3.8 21.7 + - - -
239K LYS* 2.9 29.6 + - + +
240K TYR* 3.8 4.6 - - - +
242K VAL* 1.3 74.1 - - - +
244K ASN* 1.3 58.0 + - - +
246K ALA* 3.5 3.1 - - - +
247K HIS* 3.0 26.8 + - - +
252K THR* 5.8 0.3 - - - -
253K ALA* 3.2 36.3 + - + -
254K THR* 4.6 1.6 - - - -
255K PHE* 3.7 20.7 - + - -
171L HIS* 3.7 20.5 - + - -
183L PRO 5.1 0.4 - - - +
184L PRO* 3.8 24.7 - - + +
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Residues in contact with ASN 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K PHE* 3.5 35.0 - - + +
80K PHE* 6.0 0.4 - - - -
240K TYR* 2.9 39.9 + - - +
243K HIS* 1.3 75.3 - - - +
245K VAL* 1.3 58.9 + - - +
246K ALA 3.2 0.9 - - - -
247K HIS* 3.6 10.3 - - - +
248K ARG* 3.0 28.2 + - - +
183L PRO* 3.2 30.0 - - - +
184L PRO* 3.6 21.3 - - - +
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Residues in contact with VAL 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K PHE* 3.8 17.5 - - + -
191K ILE* 4.1 4.7 - - + +
194K GLU* 4.1 12.3 - - + +
195K MET* 3.7 28.7 - - + -
198K VAL* 4.4 10.1 - - + -
241K VAL* 2.8 41.8 + - + +
242K VAL 4.3 0.2 - - - +
244K ASN* 1.3 70.1 - - - +
246K ALA* 1.3 67.6 + - - +
248K ARG* 3.2 10.3 + - - +
249K PHE* 3.0 45.3 + - + -
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Residues in contact with ALA 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134K LEU* 3.8 26.9 - - + -
191K ILE* 5.0 1.8 - - - -
195K MET* 4.2 5.5 - - + +
242K VAL 3.0 18.7 + - - +
243K HIS 3.5 4.7 - - - +
245K VAL* 1.3 77.6 - - - +
247K HIS* 1.3 64.3 + - - +
249K PHE* 2.9 10.6 + - - -
251K LYS* 2.9 34.8 + - + +
253K ALA* 3.9 16.4 - - + +
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Residues in contact with HIS 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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243K HIS 3.0 15.4 + - - +
244K ASN* 3.6 13.9 - - - +
245K VAL 3.2 0.2 - - - -
246K ALA* 1.3 79.4 - - - +
248K ARG* 1.3 59.9 + - - +
250K GLY* 3.0 20.6 + - - -
251K LYS 3.4 13.2 + - - +
252K THR* 5.3 0.2 - - - +
169L LYS* 4.7 21.3 - - + +
171L HIS* 6.1 1.6 - - - -
184L PRO* 4.2 26.0 - - + +
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Residues in contact with ARG 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78K PRO* 4.2 11.1 + - - +
79K PHE* 3.7 33.1 - - + +
194K GLU* 2.9 31.5 + - - -
198K VAL* 4.5 9.1 - - - +
244K ASN 3.0 18.1 + - - +
245K VAL* 3.2 10.6 + - - +
247K HIS* 1.3 79.1 - - + +
249K PHE* 1.3 75.5 + - - +
250K GLY 3.4 0.6 + - - -
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Residues in contact with PHE 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190K ASP* 4.4 10.3 - - + -
191K ILE* 3.7 41.1 - - + -
194K GLU* 3.7 28.7 - - + -
245K VAL* 3.0 35.9 + - + +
246K ALA 2.9 11.0 + - - +
248K ARG* 1.3 93.3 - - + +
250K GLY* 1.3 62.2 + - - +
251K LYS* 3.6 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