Contacts of the helix formed by residues 260 - 285 (chain H) in PDB entry 5MGX
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 THR 260 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154F GLN* 4.3 3.4 - - - -
238F VAL* 5.5 10.8 - - - +
239F LEU* 5.7 2.8 - - - +
259H MET* 1.3 75.7 - - - +
261H PHE* 1.3 63.7 + - - +
262H GLU* 2.7 29.6 + - + +
263H GLU* 2.8 46.3 + - + +
264H GLU* 3.1 21.1 + - - +
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Residues in contact with PHE 261 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147F LEU* 6.0 0.2 - - + -
148F GLY* 3.7 29.6 - - - -
150F CYS* 3.5 20.6 - - - -
154F GLN* 3.6 40.4 + - + +
157F ASP* 3.6 33.9 - - + -
158F LEU* 3.9 26.7 - - + -
239F LEU* 5.8 4.3 - - + +
260H THR* 1.3 76.3 + - - +
262H GLU* 1.3 73.2 + - + +
264H GLU* 3.2 4.1 + - - +
265H ALA* 3.0 40.1 + - + +
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Residues in contact with GLU 262 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150F CYS* 5.6 1.6 - - - -
242F ASN* 4.4 15.2 + - - +
260H THR* 2.7 35.2 + - + +
261H PHE* 1.3 92.4 + - + +
263H GLU* 1.3 56.9 + - + +
265H ALA* 3.8 5.0 + - - +
266H GLN* 3.1 29.7 + - - +
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Residues in contact with GLU 263 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213H THR* 5.3 1.2 + - - -
214H GLY* 3.8 20.5 + - - -
215H GLN* 3.2 40.2 + - - +
218H VAL* 5.1 1.3 - - + +
259H MET* 3.3 16.6 - - + +
260H THR* 2.8 45.2 + - + +
261H PHE 3.2 0.4 - - - -
262H GLU* 1.3 75.8 - - + +
264H GLU* 1.4 57.7 + - - +
266H GLN* 3.4 11.7 + - - +
267H LEU* 3.0 38.6 + - + +
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Residues in contact with GLU 264 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F LEU* 3.7 20.6 - - + +
99F ASN* 5.4 1.6 + - - -
154F GLN* 3.9 14.4 - - - +
158F LEU* 4.3 15.9 - - + -
176F LYS* 3.1 28.6 + - - -
177F TYR* 3.1 23.8 + - + -
254H SER* 5.6 5.7 - - - -
259H MET* 4.1 11.0 - - + +
260H THR 3.1 18.8 + - - +
261H PHE* 3.2 8.3 + - - +
263H GLU* 1.4 74.4 - - - +
265H ALA* 1.3 56.7 + - - +
267H LEU* 3.3 10.9 + - - +
268H LEU* 3.0 32.4 + - - +
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Residues in contact with ALA 265 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158F LEU* 4.9 2.8 - - + +
261H PHE* 3.0 32.0 + - + +
262H GLU* 4.0 5.8 - - - +
264H GLU* 1.3 73.2 - - - +
266H GLN* 1.4 58.6 + - - +
268H LEU* 3.0 14.7 + - + +
269H GLN* 3.0 35.2 + - + +
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Residues in contact with GLN 266 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215H GLN* 4.9 9.5 + - - -
218H VAL* 3.9 35.4 - - + +
262H GLU 3.1 20.5 + - - +
263H GLU* 3.4 11.0 + - - +
265H ALA* 1.4 73.1 - - - +
267H LEU* 1.3 62.1 + - - +
269H GLN* 3.4 11.2 + - + +
270H LEU* 3.2 21.8 + - - +
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Residues in contact with LEU 267 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214H GLY* 4.2 20.2 - - - +
217H ARG* 3.8 42.6 - - + +
218H VAL* 3.9 13.7 - - + +
251H ILE* 3.6 43.3 - - + +
259H MET* 5.7 3.6 - - + -
263H GLU* 3.0 27.8 + - + +
264H GLU* 3.7 9.0 - - - +
266H GLN* 1.3 74.1 - - - +
268H LEU* 1.4 59.3 + - - +
269H GLN 3.4 0.2 - - - -
270H LEU* 3.4 8.8 + - + +
271H LYS* 3.0 27.9 + - - +
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Residues in contact with LEU 268 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96F ILE* 3.5 32.8 - - + +
97F LEU* 3.8 25.6 - - + -
158F LEU* 4.1 19.5 - - + +
251H ILE* 5.6 0.2 - - - -
264H GLU 3.0 16.5 + - - +
265H ALA* 3.0 13.0 + - - +
267H LEU* 1.4 74.2 - - - +
269H GLN* 1.4 69.0 + - - +
271H LYS* 3.3 18.6 + - - +
272H VAL* 3.1 28.5 + - - +
301H HIS* 4.5 15.9 - - + -
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Residues in contact with GLN 269 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265H ALA* 3.0 19.0 + - + +
266H GLN* 3.5 11.4 - - - +
268H LEU* 1.4 80.5 - - - +
270H LEU* 1.3 57.8 + - - +
272H VAL* 2.9 20.3 - - - +
273H LYS* 3.3 22.4 + - - +
302H GLN* 3.6 25.6 + - - +
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Residues in contact with LEU 270 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218H VAL* 3.8 16.8 - - + +
221H ALA* 3.8 27.1 - - + -
222H ASN* 3.5 41.5 - - - +
225H ARG* 4.2 13.2 - - - +
251H ILE* 4.0 11.4 - - + -
266H GLN 3.2 11.3 + - - +
267H LEU* 3.5 12.1 - - + +
268H LEU 3.2 0.4 - - - -
269H GLN* 1.3 78.4 - - - +
271H LYS* 1.3 58.9 + - - +
273H LYS* 3.3 12.9 + - + +
274H CYS* 3.0 36.5 + - - -
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Residues in contact with LYS 271 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95F ASP 4.0 3.8 + - - -
96F ILE 3.2 18.3 + - - -
97F LEU 3.3 3.3 - - - +
98F GLY* 3.2 35.8 - - - +
248H ILE* 4.6 10.3 - - + +
251H ILE* 3.7 23.3 - - + +
252H THR* 3.9 21.0 - - + +
267H LEU 3.0 17.7 + - - +
268H LEU* 3.3 17.9 + - + +
270H LEU* 1.3 75.3 - - - +
272H VAL* 1.4 52.9 + - - +
274H CYS* 3.3 4.4 + - - +
275H LEU* 2.8 50.4 + - + +
301H HIS* 4.6 13.7 + - - -
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Residues in contact with VAL 272 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H LEU* 3.1 17.0 + - + +
269H GLN* 2.9 29.8 - - - +
271H LYS* 1.4 71.3 - - + +
273H LYS* 1.4 62.3 + - + +
275H LEU* 3.4 6.5 + - + -
276H ASN* 3.0 30.0 + - - +
298H VAL* 3.6 22.5 - - + +
301H HIS* 3.6 43.1 - - + +
302H GLN* 3.5 31.2 - - - +
305H ASN* 5.7 1.8 - - - +
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Residues in contact with LYS 273 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225H ARG* 4.7 17.3 - - - +
269H GLN* 3.3 20.7 + - - +
270H LEU* 3.3 21.6 + - + +
272H VAL* 1.4 78.6 - - + +
274H CYS* 1.3 55.1 - - - +
276H ASN* 3.5 6.3 + - - +
277H ASN* 3.0 38.7 + - - +
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Residues in contact with CYS 274 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221H ALA 4.8 1.6 - - - -
225H ARG* 4.0 24.7 - - - -
244H TYR* 3.8 11.7 - - + +
247H ALA* 3.7 24.5 - - - -
248H ILE* 3.8 21.1 - - + -
251H ILE* 4.5 7.6 - - - -
270H LEU* 3.0 29.8 + - - +
271H LYS* 3.6 5.2 - - - +
273H LYS* 1.3 73.2 - - - +
275H LEU* 1.4 54.1 + - - +
277H ASN* 3.3 9.5 + - - +
278H LEU* 2.8 32.9 + - - +
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Residues in contact with LEU 275 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H ILE* 3.9 24.0 - - + -
271H LYS* 2.8 44.6 + - + +
272H VAL* 4.7 2.5 - - - -
274H CYS* 1.4 69.2 - - - +
276H ASN* 1.3 60.0 + - - +
278H LEU* 3.4 7.3 + - + +
279H ALA* 3.0 24.1 + - - +
294H SER* 3.4 33.1 - - - +
297H LEU* 4.1 36.6 - - + -
298H VAL* 3.6 19.3 - - + +
301H HIS* 4.9 6.1 - - + -
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Residues in contact with ASN 276 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272H VAL 3.0 18.3 + - - +
273H LYS* 3.5 9.1 - - - +
275H LEU* 1.3 72.3 - - - +
277H ASN* 1.3 61.8 + - - +
279H ALA* 3.5 6.5 + - - +
280H ALA 3.1 18.2 + - - -
295H CYS* 5.8 0.8 - - - +
298H VAL* 3.6 7.8 - - + +
305H ASN* 3.9 11.7 + - - +
307H LYS* 3.4 19.5 - - - +
308H ALA* 3.4 37.8 - - - +
311H ARG* 3.0 43.9 + - - +
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Residues in contact with ASN 277 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D GLU* 3.7 29.1 + - - +
225H ARG* 4.0 15.0 - - - +
229H ASN* 3.1 27.8 + - - +
232H TYR* 4.9 0.9 - - - -
244H TYR* 3.4 27.9 - - + -
273H LYS* 3.0 23.9 + - - +
274H CYS 3.5 6.1 - - - +
276H ASN* 1.3 78.3 - - - +
278H LEU* 1.3 60.3 + - - +
280H ALA* 3.5 7.6 - - - +
281H SER* 3.0 27.7 + - - -
311H ARG* 4.8 1.9 + - - -
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Residues in contact with LEU 278 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H ALA* 3.4 39.7 - - + +
244H TYR* 3.8 11.6 - - + -
245H ASP* 4.3 16.8 - - + +
248H ILE* 3.8 22.2 - - + -
274H CYS 2.8 16.2 + - - +
275H LEU* 3.5 10.5 - - + +
277H ASN* 1.3 73.0 - - - +
279H ALA* 1.4 53.8 + - - +
281H SER* 3.1 4.3 + - - -
282H GLN* 2.8 59.6 + - - +
294H SER* 3.7 14.1 - - - +
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Residues in contact with ALA 279 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H LEU 3.0 16.3 + - - +
276H ASN* 3.7 7.6 - - - +
278H LEU* 1.4 74.3 - - - +
280H ALA* 1.4 54.7 + - - +
282H GLN* 3.3 12.6 + - - +
283H LEU* 2.8 37.7 + - - +
291H ALA* 3.6 24.0 - - + +
294H SER* 3.8 5.2 - - - -
295H CYS* 3.7 20.4 - - - +
311H ARG* 4.9 4.7 - - - -
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Residues in contact with ALA 280 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
707D GLU* 5.8 1.1 - - + -
232H TYR* 3.9 21.2 + - + +
276H ASN 3.1 8.0 + - - +
277H ASN* 3.5 12.6 - - - +
279H ALA* 1.4 74.8 - - - +
281H SER* 1.4 60.3 + - - +
283H LEU* 3.7 9.0 + - - +
284H LYS* 3.4 27.0 + - - +
311H ARG* 3.5 41.4 - - - +
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Residues in contact with SER 281 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232H TYR* 3.5 18.0 - - - -
237H PHE* 3.8 22.7 - - - +
240H ALA* 3.7 4.3 - - - +
241H ALA* 4.0 12.8 - - - -
244H TYR* 3.3 17.0 - - - -
277H ASN 3.0 13.6 + - - -
278H LEU* 3.1 9.5 + - - -
280H ALA* 1.4 73.4 - - - +
282H GLN* 1.4 62.4 + - - +
284H LYS* 3.3 14.0 + - - +
285H LEU* 3.3 19.2 + - - +
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Residues in contact with GLN 282 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241H ALA* 5.1 5.6 - - + +
278H LEU* 2.8 47.6 + - + +
279H ALA* 3.4 5.1 + - - +
281H SER* 1.4 68.9 - - - +
283H LEU* 1.3 59.9 + - - +
285H LEU* 3.2 11.7 + - + -
287H HIS* 2.8 44.8 + - + +
290H ALA* 3.5 26.3 + - + +
291H ALA* 3.4 20.1 - - + -
294H SER* 3.0 23.1 + - - -
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Residues in contact with LEU 283 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D GLU* 5.9 2.0 - - - +
279H ALA 2.8 21.3 + - - +
280H ALA* 3.7 7.9 - - - +
282H GLN* 1.3 71.3 - - - +
284H LYS* 1.4 63.4 + - + +
286H ASP* 2.9 27.1 + - - +
287H HIS 4.8 1.1 - - - +
288H TYR* 4.1 5.4 - - + -
291H ALA* 3.8 5.8 - - + +
311H ARG* 4.1 30.7 - - + +
314H LYS* 4.2 24.7 - - + +
315H VAL* 3.7 28.3 - - + -
318H GLN* 3.4 33.5 - - - +
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Residues in contact with LYS 284 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
706D GLU* 2.9 30.7 + - - +
232H TYR* 3.5 17.7 + - - +
237H PHE* 3.6 48.7 - - + -
280H ALA 3.4 13.6 + - - +
281H SER 3.3 11.9 + - - +
283H LEU* 1.4 80.9 - - + +
285H LEU* 1.3 59.4 + - - +
286H ASP* 3.3 7.5 + - - +
314H LYS* 5.6 4.5 - - - +
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Residues in contact with LEU 285 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237H PHE* 3.7 39.9 - - + +
238H VAL* 3.7 28.5 - - + +
241H ALA* 4.8 6.1 - - + -
281H SER 3.3 13.2 + - - +
282H GLN* 3.2 12.2 + - + +
283H LEU 3.1 1.2 - - - -
284H LYS* 1.3 75.9 - - - +
286H ASP* 1.3 66.7 + - - +
287H HIS* 3.0 12.2 + - + +
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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