Contacts of the helix formed by residues 236 - 259 (chain B) in PDB entry 1I4S
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 TYR 236 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LYS 3.4 6.7 - - - +
224B ALA* 3.3 21.5 - - - +
226B THR 3.0 25.3 + - - -
227B HIS* 3.6 41.0 - + + -
228B VAL* 5.2 2.0 - - + -
235B HIS* 1.3 78.0 - - + +
237B GLU* 1.3 67.8 + - - +
238B THR 3.3 1.7 + - - -
239B LEU* 3.3 6.5 + - - -
240B GLU* 2.9 39.4 + - + +
293B ILE* 6.0 0.7 - - + -
304B ILE* 3.7 13.7 + - + +
307B ASP* 3.3 43.8 + - + -
308B VAL* 3.8 23.1 - - + -
311B ALA* 3.6 10.1 - - + -
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Residues in contact with GLU 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A LYS 4.0 2.7 - - - +
63A ARG* 3.4 15.2 - - - +
64A GLU* 2.8 43.2 + - + +
235B HIS* 3.3 38.4 + - + +
236B TYR* 1.3 82.1 - - - +
238B THR* 1.3 65.7 + - - +
240B GLU* 3.4 25.6 - - - +
241B PHE* 3.4 8.8 + - - +
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A VAL* 4.0 30.7 - - + +
62A LYS* 2.9 43.4 + - + +
67A LEU* 4.3 9.0 - - + -
223B LYS* 6.1 5.4 - - - +
235B HIS 5.0 1.2 + - - -
236B TYR 3.4 0.2 - - - -
237B GLU* 1.3 76.3 - - - +
239B LEU* 1.3 68.0 + - - +
240B GLU 3.1 1.6 - - - -
241B PHE* 3.2 13.1 + - - +
242B LEU* 3.3 13.0 + - - +
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220B LEU* 4.0 31.4 - - + -
223B LYS* 4.2 22.6 - - + +
224B ALA* 4.0 33.2 - - + +
236B TYR* 3.3 9.0 + - - +
238B THR* 1.3 78.7 - - - +
240B GLU* 1.3 53.0 + - - +
242B LEU* 3.4 2.6 + - + -
243B GLY* 2.7 30.8 + - - -
311B ALA* 3.7 15.9 - - + +
314B ALA* 2.9 13.5 - - + +
315B ALA* 4.3 14.8 - - + +
318B ILE* 4.4 19.1 - - + -
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B TYR* 2.9 29.1 + - + +
237B GLU* 3.4 14.0 - - - +
238B THR 3.1 0.2 - - - -
239B LEU* 1.3 78.3 - - - +
241B PHE* 1.3 59.6 - - - +
243B GLY 3.9 0.2 - - - -
244B ASP* 3.0 30.0 + - + +
307B ASP* 2.9 50.9 - - + +
310B GLU* 4.0 11.5 - - - +
311B ALA* 3.9 12.3 - - + +
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Residues in contact with PHE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A VAL* 3.6 23.3 - - + +
55A LEU* 4.0 13.2 - - + -
56A VAL* 3.6 19.5 - - + -
64A GLU* 4.5 15.9 - - + -
67A LEU* 3.3 45.1 - - + -
68A SER* 3.3 27.1 - - - -
71A LYS* 3.8 26.4 - - + +
237B GLU 3.4 8.2 + - - +
238B THR* 3.2 13.4 + - - +
240B GLU* 1.3 83.6 - - - +
242B LEU* 1.3 56.7 + - - +
244B ASP* 4.0 8.7 + - - +
245B ALA* 4.0 9.5 + - - +
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Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 4.7 8.7 - - + -
52A VAL* 3.8 18.8 - - + -
53A ASP* 4.0 23.1 - - + +
56A VAL* 4.6 17.3 - - + -
238B THR 3.3 8.8 + - - +
239B LEU* 3.5 10.3 - - + +
241B PHE* 1.3 76.7 - - - +
243B GLY* 1.3 59.7 + - - +
244B ASP 3.2 1.6 - - - -
245B ALA* 3.3 2.9 + - - +
246B LEU* 2.9 23.9 + - + +
314B ALA* 3.7 14.6 - - + -
317B TYR* 4.2 15.7 - - + -
318B ILE* 3.7 35.0 - - + -
322B ARG* 4.2 7.2 - - - +
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Residues in contact with GLY 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B LEU 2.7 15.7 + - - -
240B GLU 3.9 0.7 - - - -
242B LEU* 1.3 71.3 - - - +
244B ASP* 1.3 56.9 + - - +
246B LEU* 3.5 10.5 - - - -
247B VAL* 2.6 39.0 + - - +
310B GLU* 3.4 28.5 - - - -
314B ALA* 3.4 7.1 - - - +
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Residues in contact with ASP 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ASN* 5.5 1.4 + - - -
71A LYS* 5.8 4.0 - - - -
240B GLU* 3.0 18.9 + - + +
241B PHE* 4.1 8.8 - - - +
242B LEU 3.2 0.4 - - - -
243B GLY* 1.3 78.4 - - - +
245B ALA* 1.3 60.6 + - - +
247B VAL* 4.2 0.7 - - - +
248B ASN* 2.8 33.1 + - - +
275B ILE* 5.7 4.0 - - - +
310B GLU* 3.1 29.7 - - - +
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Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ALA 4.6 0.5 - - - +
48A ASN* 3.6 27.8 + - - +
49A PHE* 4.1 14.7 - - + +
52A VAL* 3.7 33.7 - - + -
71A LYS* 5.9 0.4 - - - -
241B PHE 4.0 2.3 + - - +
242B LEU 3.3 6.8 + - - +
243B GLY 3.2 0.2 - - - -
244B ASP* 1.3 78.6 - - - +
246B LEU* 1.3 65.9 + - - +
248B ASN* 3.4 2.6 + - - +
249B PHE* 3.0 23.9 + - - +
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Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A PHE* 3.7 36.5 - - + -
242B LEU* 2.9 19.2 + - + +
243B GLY* 3.4 7.9 - - - +
245B ALA* 1.3 77.0 - - - +
247B VAL* 1.3 62.6 + - - +
249B PHE* 3.2 8.9 + - + +
250B PHE* 3.1 63.7 + - + -
313B TRP* 3.4 35.4 - - + +
314B ALA* 4.1 1.6 - - - +
317B TYR* 3.8 24.2 - - + -
324B ALA* 5.8 0.4 - - + -
327B THR* 4.3 0.7 - - + -
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Residues in contact with VAL 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B GLY 2.6 25.6 + - - +
244B ASP* 4.2 1.6 - - - +
246B LEU* 1.3 71.9 - - + +
248B ASN* 1.3 65.9 + - - +
250B PHE* 3.9 8.7 - - + +
251B ILE* 3.2 44.8 + - + +
280B PHE* 3.5 23.6 - - + -
309B PHE* 4.7 4.0 - - + -
310B GLU* 4.3 12.6 - - + -
313B TRP* 3.8 34.5 - - + -
331B PHE* 4.3 13.5 - - + -
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Residues in contact with ASN 248 (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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45A ALA* 3.1 38.4 - - - +
48A ASN* 4.5 8.9 - - - +
244B ASP* 2.8 26.7 + - - +
245B ALA* 3.6 8.1 - - - +
247B VAL* 1.3 78.3 - - - +
249B PHE* 1.3 61.7 + - - +
251B ILE* 3.9 1.0 - - - +
252B VAL* 3.0 32.5 + - - +
271B LYS* 3.6 15.0 + - - +
275B ILE* 2.8 34.9 - - + +
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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
----------------------------------------------------------
42A LEU* 4.3 6.1 - - + -
45A ALA* 4.1 18.4 - - - +
46A LEU* 3.3 41.5 - - + -
49A PHE* 4.2 20.9 - + + -
117A TYR* 3.3 42.8 - + - -
124A ALA* 4.2 15.5 - - + -
245B ALA 3.0 12.4 + - - +
246B LEU* 3.2 7.8 + - + +
248B ASN* 1.3 77.5 - - - +
250B PHE* 1.3 90.3 + + - +
251B ILE 3.2 0.2 + - - -
252B VAL* 3.2 0.7 + - - +
253B ASP* 2.9 28.0 + - + +
324B ALA* 5.3 1.6 - - + -
328B ARG* 5.1 5.4 - - + -
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B LEU* 3.1 53.9 + - + -
247B VAL* 3.4 11.2 + - + +
249B PHE* 1.3 94.9 - + - +
251B ILE* 1.3 62.3 + - - +
253B ASP* 4.8 0.7 - - - -
254B LEU* 3.3 6.9 + - - +
313B TRP* 4.8 4.5 - + + -
324B ALA* 4.2 6.5 - - - -
327B THR* 3.9 18.6 - - + -
328B ARG* 3.4 42.6 - - + -
331B PHE* 3.7 39.9 - + + -
332B TYR* 2.6 33.3 + - + -
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Residues in contact with ILE 251 (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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247B VAL* 3.2 41.6 + - + +
248B ASN 4.1 1.3 - - - +
250B PHE* 1.3 78.1 - - - +
252B VAL* 1.3 69.0 + - + +
254B LEU* 3.2 8.9 + - - +
255B LEU* 2.9 24.1 + - + +
271B LYS* 5.1 0.9 - - - +
274B LEU* 3.6 42.0 - - + +
275B ILE* 4.1 16.4 - - + -
279B PHE* 5.8 0.4 - - + -
280B PHE* 3.9 18.4 - - + -
283B LEU* 5.2 2.7 - - + -
331B PHE* 4.0 22.0 - - + -
339B ILE* 4.4 12.3 - - + -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 3.8 36.1 - - + +
42A LEU* 3.9 17.0 - - + -
45A ALA* 3.9 20.0 - - + -
248B ASN* 3.0 27.9 + - - +
249B PHE 3.9 0.4 - - - +
251B ILE* 1.3 77.7 - - + +
253B ASP* 1.3 64.4 + - - +
255B LEU* 3.0 6.5 + - - +
256B VAL* 2.9 24.6 + - + +
271B LYS* 4.0 30.1 - - + -
275B ILE* 4.9 2.2 - - + -
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Residues in contact with ASP 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.9 18.6 - - + +
117A TYR* 2.6 34.1 + - - -
122A ARG* 2.6 38.1 + - - -
249B PHE* 2.9 23.8 + - + +
252B VAL* 1.3 76.5 - - - +
254B LEU* 1.3 54.9 + - - +
256B VAL* 4.2 0.8 - - - -
257B GLN* 2.8 29.8 + - - +
328B ARG* 4.6 3.1 + - - -
332B TYR* 3.7 15.3 + - - +
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Residues in contact with LEU 254 (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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250B PHE 3.3 5.7 + - - +
251B ILE* 3.2 9.8 + - - +
252B VAL 3.0 0.6 - - - -
253B ASP* 1.3 78.8 - - - +
255B LEU* 1.3 65.0 + - - +
257B GLN* 2.9 6.4 + - - +
258B TYR* 2.9 47.8 + - + +
332B TYR* 3.3 54.5 - - + +
336B LYS* 4.2 15.9 - - + -
339B ILE* 3.3 39.0 - - + -
340B LEU* 4.2 13.2 - - + -
343B ILE* 4.5 2.9 - - - -
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Residues in contact with LEU 255 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.0 15.0 - - + -
251B ILE* 2.9 11.4 + - + +
252B VAL* 3.2 12.1 - - - +
254B LEU* 1.3 73.4 - - - +
256B VAL* 1.3 57.5 - - + +
257B GLN 2.9 1.6 + - - -
259B SER* 2.7 42.2 + - - -
267B LEU* 3.8 10.3 - - + +
270B LEU* 3.3 36.3 - - + -
271B LYS* 3.3 44.6 - - + +
274B LEU* 3.7 14.6 - - + -
343B ILE* 3.7 17.1 - - + +
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Residues in contact with VAL 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A THR* 3.5 39.0 - - + +
41A PHE* 3.8 25.4 - - + -
42A LEU* 3.9 28.9 - - + +
118A ILE* 5.6 3.1 - - + -
122A ARG* 4.0 15.7 - - - +
252B VAL 2.9 12.2 + - - +
253B ASP 4.3 0.9 - - - +
255B LEU* 1.3 76.8 - - - +
257B GLN* 1.3 57.5 + - - +
259B SER* 5.1 0.4 - - - -
262B LYS* 3.3 24.3 + - - +
267B LEU* 4.0 5.4 - - + +
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Residues in contact with GLN 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A ARG* 2.8 49.7 + - - +
253B ASP* 2.8 33.1 + - - +
254B LEU* 2.9 10.5 + - - +
256B VAL* 1.3 81.9 - - - +
258B TYR* 1.3 91.8 + - + +
259B SER 3.7 0.4 - - - -
262B LYS* 4.0 10.8 + - - -
332B TYR* 5.7 2.0 - - - -
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Residues in contact with TYR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254B LEU* 2.9 23.6 + - + +
257B GLN* 1.3 105.1 + - + +
259B SER* 1.3 69.9 + - - +
260B PRO* 3.5 4.0 - - - +
336B LYS* 2.5 40.0 + - - -
340B LEU* 3.3 41.3 - - + -
343B ILE* 4.6 7.8 - - + +
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Residues in contact with SER 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255B LEU* 2.7 32.9 + - - -
257B GLN 3.7 0.2 - - - -
258B TYR* 1.3 80.1 - - - +
260B PRO* 1.3 65.5 - - - +
261B ASN 3.2 5.6 + - - -
262B LYS* 2.8 29.4 + - - +
266B PHE* 2.8 36.7 - - - -
267B LEU* 3.5 12.3 - - - +
343B ILE* 3.9 7.2 - - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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