Contacts of the helix formed by residues 318 - 344 (chain A) in PDB entry 2PG0
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 ILE 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLN* 3.1 23.9 + - + +
250A LEU* 5.8 0.2 - - + -
308A VAL* 3.3 45.5 - - + +
311A GLU* 3.5 35.2 - - + +
312A HIS* 3.5 11.9 - - + +
316A LYS* 3.7 8.7 - - + +
317A GLN* 1.3 77.0 - - - +
319A VAL* 1.3 65.8 + - - +
320A THR 3.3 2.2 - - - -
321A GLU* 3.3 28.7 + - + +
322A VAL* 3.0 22.6 + - + +
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Residues in contact with VAL 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A MET 6.2 0.4 - - - +
246A GLN* 3.7 15.9 + - + +
249A ARG* 5.7 5.6 - - - +
317A GLN* 3.5 29.0 + - + +
318A ILE* 1.3 75.6 - - - +
320A THR* 1.3 61.5 + - - +
322A VAL* 3.4 9.2 - - + +
323A SER* 2.9 31.1 + - - +
378A ILE* 3.9 23.3 - - + -
382A GLN* 4.3 19.3 - - - +
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Residues in contact with THR 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE 3.3 0.8 - - - -
319A VAL* 1.3 77.9 - - - +
321A GLU* 1.3 70.8 + - - +
323A SER* 3.2 6.6 + - - -
324A MET* 3.0 54.9 + - + +
378A ILE* 5.4 0.7 - - - -
379A ILE* 4.2 12.6 - - + +
382A GLN* 3.2 41.4 + - + +
383A LEU* 6.4 1.8 - - + -
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Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 3.3 23.1 - - + -
308A VAL* 3.9 20.2 - - + -
311A GLU* 6.4 0.7 - - + -
317A GLN 4.8 0.2 - - - +
318A ILE* 3.3 40.3 + - + +
320A THR* 1.3 86.9 - - - +
322A VAL* 1.3 58.0 + - - +
324A MET* 3.4 12.2 - - - +
325A ALA* 2.9 24.3 + - - +
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Residues in contact with VAL 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A GLN* 3.4 35.0 - - + +
249A ARG* 3.8 10.4 - - + +
250A LEU* 3.3 47.1 - - + +
308A VAL* 4.4 9.8 - - + +
318A ILE* 3.0 16.7 + - + +
319A VAL* 3.4 14.8 - - + +
321A GLU* 1.3 74.0 - - - +
323A SER* 1.3 65.6 + - - +
325A ALA* 3.6 5.5 - - + +
326A LYS* 2.9 29.3 + - - +
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Residues in contact with SER 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 4.7 4.0 + - - -
319A VAL* 2.9 21.2 + - - +
320A THR 3.2 4.7 + - - -
322A VAL* 1.3 80.3 - - - +
324A MET* 1.3 64.4 + - - +
326A LYS* 3.5 0.5 + - - +
327A TRP* 3.1 26.0 + - - -
375A MET* 3.6 34.6 - - - +
378A ILE* 3.6 19.8 - - - +
379A ILE* 4.0 16.8 - - - -
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A PHE* 4.0 22.9 - - + -
320A THR* 3.0 38.7 + - + +
321A GLU* 3.4 14.1 - - - +
323A SER* 1.3 73.1 - - - +
325A ALA* 1.3 64.9 + - - +
327A TRP* 3.7 11.2 - - - +
328A TRP* 3.0 30.9 + - - +
379A ILE* 3.8 26.9 - - + +
383A LEU* 6.0 4.3 - - + -
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Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A LEU* 5.5 0.4 - - + -
253A ALA* 4.0 16.4 - - + -
304A PHE* 3.7 22.4 - - + -
305A VAL* 5.0 5.8 - - + -
308A VAL* 4.7 7.0 - - + -
321A GLU 2.9 21.0 + - - +
322A VAL* 3.6 9.6 - - + +
324A MET* 1.3 72.9 - - - +
326A LYS* 1.3 62.6 + - - +
328A TRP* 5.2 0.7 - - - -
329A ILE* 3.0 39.5 + - + +
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Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ARG* 3.8 30.3 - - + +
252A VAL* 4.0 15.0 - - + -
253A ALA* 4.1 9.1 - - - +
322A VAL 2.9 17.4 + - - +
323A SER 3.8 4.3 - - - +
324A MET 3.3 0.4 - - - -
325A ALA* 1.3 76.2 - - - +
327A TRP* 1.3 59.4 + - - +
330A THR* 2.8 33.6 + - - +
365A SER 2.9 24.1 + - - -
366A ALA 3.5 6.1 - - - -
368A TYR 3.2 20.0 + - - -
369A ALA* 4.4 4.3 - - - -
370A GLY 2.8 22.8 + - - -
372A ASN* 2.8 21.3 + - - +
375A MET* 3.8 15.5 - - + -
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Residues in contact with TRP 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A SER 3.1 24.2 + - - -
324A MET* 3.7 11.5 + - - +
326A LYS* 1.3 78.5 - - - +
328A TRP* 1.3 94.8 + + + +
330A THR* 3.1 2.6 + - - -
331A GLU* 3.1 43.9 + - + +
335A ARG* 6.1 0.4 - - - -
372A ASN* 3.3 31.0 + - + +
375A MET* 3.7 16.4 - - + -
376A LYS* 3.6 40.6 - - + +
379A ILE* 3.5 26.1 - - + +
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Residues in contact with TRP 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 3.7 23.8 - - + -
300A LEU* 4.2 19.3 - - + -
301A GLY* 4.0 14.1 - - - -
324A MET* 3.0 17.8 + - + +
325A ALA* 4.5 0.7 - - - +
327A TRP* 1.3 114.0 - + + +
329A ILE* 1.3 69.4 + - + +
331A GLU* 3.5 2.1 + - + +
332A MET* 2.9 65.9 + - + +
335A ARG* 4.1 20.9 + - - +
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Residues in contact with ILE 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A ALA* 3.7 13.2 - - + +
256A ALA* 3.9 4.3 - - + +
257A GLN* 3.5 45.8 - - - +
301A GLY* 3.7 26.0 - - - +
304A PHE* 5.3 2.7 - - + -
305A VAL* 3.8 20.2 - - + +
325A ALA* 3.0 33.9 + - + +
326A LYS 4.7 0.4 - - - +
328A TRP* 1.3 88.9 - - + +
330A THR* 1.3 60.4 + - - +
332A MET* 3.3 6.8 + - + +
333A ALA* 2.8 27.9 + - - +
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Residues in contact with THR 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A VAL* 4.0 12.3 - - + +
253A ALA* 5.4 0.7 - - - -
256A ALA* 3.7 16.6 - - + -
326A LYS* 2.8 24.7 + - + +
327A TRP 3.1 0.9 + - - -
329A ILE* 1.3 76.8 - - - +
331A GLU* 1.3 59.4 + - - +
333A ALA* 3.3 3.3 + - - +
334A LYS* 3.0 29.3 + - - +
365A SER* 3.3 47.5 + - - +
366A ALA 4.1 1.3 - - - -
372A ASN* 2.9 29.3 + - - -
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Residues in contact with GLU 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TRP* 3.1 41.1 + - + +
328A TRP* 3.9 2.9 - - + +
330A THR* 1.3 75.9 + - - +
332A MET* 1.3 63.8 - - - +
334A LYS* 3.0 39.0 + - - +
335A ARG* 3.0 40.8 + - - +
366A ALA* 3.7 1.9 - - - +
372A ASN* 2.9 25.1 + - - +
376A LYS* 5.8 1.3 - - - +
342B GLN* 4.8 4.9 - - - +
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Residues in contact with MET 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A GLN* 4.2 13.2 - - - +
260A ALA* 3.9 19.1 - - + -
297A GLU* 2.9 57.2 - - + +
298A ILE* 3.9 26.2 - - + -
301A GLY* 4.7 1.3 - - - -
328A TRP* 2.9 40.1 + - + +
329A ILE* 3.5 8.3 - - + +
330A THR 3.3 0.2 - - - -
331A GLU* 1.3 75.4 - - - +
333A ALA* 1.3 59.0 + - - +
335A ARG* 3.2 18.5 + - - +
336A VAL* 2.9 34.2 + - + +
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Residues in contact with ALA 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256A ALA* 3.6 23.8 - - + +
260A ALA* 4.0 19.5 - - + +
263A MET* 3.6 4.6 - - + +
329A ILE 2.8 16.6 + - - +
330A THR 3.7 3.8 - - - +
332A MET* 1.3 72.9 - - - +
334A LYS* 1.3 60.6 + - - +
336A VAL* 3.3 3.4 + - - +
337A ALA* 2.9 28.6 + - - +
362A ILE* 3.7 23.3 - - + -
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Residues in contact with LYS 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A THR 3.0 19.0 + - - +
331A GLU* 3.0 40.6 + - - +
333A ALA* 1.3 77.4 - - - +
335A ARG* 1.3 60.7 + - + +
337A ALA* 3.3 3.5 + - - +
338A ALA* 3.1 22.9 + - - +
359A TYR* 5.7 0.5 - - - -
362A ILE* 4.3 15.9 - - + +
363A PRO* 3.9 34.3 + - + -
366A ALA* 3.6 24.4 - - + +
338B ALA* 5.1 15.7 + - - +
342B GLN* 4.0 14.5 + - - +
359B TYR* 5.8 0.9 - - - -
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Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A GLU* 2.7 37.8 + - - +
327A TRP* 6.1 0.8 - - - -
328A TRP* 4.1 16.8 + - - +
331A GLU* 3.0 34.1 + - + +
332A MET* 3.5 26.3 - - - +
334A LYS* 1.3 71.5 - - + +
336A VAL* 1.3 68.6 + - + +
338A ALA* 3.3 7.8 + - - +
339A GLU* 3.1 29.8 + - + +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A ALA* 3.7 29.6 - - + +
263A MET* 3.8 17.0 - - + -
264A PHE* 4.2 8.7 - - - +
294A MET* 4.4 23.9 - - + +
297A GLU* 5.8 1.8 - - + +
298A ILE* 4.3 22.0 - - + -
332A MET* 2.9 24.2 + - + +
333A ALA* 3.5 10.3 - - - +
335A ARG* 1.3 76.9 - - + +
337A ALA* 1.3 56.0 + - - +
339A GLU* 3.3 7.5 + - - +
340A ALA* 2.8 28.2 + - + +
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A MET* 3.5 28.5 - - - -
333A ALA 2.9 11.6 + - - +
334A LYS 3.3 8.5 + - - +
336A VAL* 1.3 75.7 - - - +
338A ALA* 1.3 57.4 - - - +
340A ALA* 3.3 3.7 + - - +
341A MET 2.9 25.8 + - - -
355A ILE* 5.1 0.7 - - - +
359A TYR* 3.6 24.8 - - + +
362A ILE* 3.5 19.7 - - + -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A LYS 3.1 13.1 + - - +
335A ARG* 3.7 9.6 - - - +
336A VAL 3.3 0.2 - - - -
337A ALA* 1.3 75.7 - - - +
339A GLU* 1.3 63.0 + - + +
341A MET* 3.6 2.3 + - - +
342A GLN* 3.2 22.9 + - - +
359A TYR* 4.1 16.3 - - + +
334B LYS* 5.1 16.4 + - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 2.9 59.9 + - - +
294A MET* 3.8 28.0 - - + +
335A ARG* 3.1 16.8 + - + +
336A VAL 3.6 6.5 - - - +
338A ALA* 1.3 75.3 - - + +
340A ALA* 1.3 59.8 + - - +
342A GLN* 3.3 2.6 + - - +
343A LEU* 2.9 37.4 + - + +
----------------------------------------------------------
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Residues in contact with ALA 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A MET* 4.3 5.4 - - + +
267A THR* 3.1 30.1 - - - +
294A MET* 5.1 1.5 - - - -
336A VAL* 2.8 21.3 + - + +
337A ALA* 3.5 5.4 - - - +
339A GLU* 1.3 69.8 - - - +
341A MET* 1.3 64.2 + - - +
343A LEU* 3.4 1.9 + - - -
344A HIS* 2.7 33.0 + - - -
355A ILE* 3.5 26.5 - - + -
----------------------------------------------------------
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Residues in contact with MET 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A ALA 2.9 18.2 + - - +
338A ALA 4.1 3.8 - - - +
340A ALA* 1.3 72.1 - - - +
342A GLN* 1.3 65.0 + - - +
344A HIS* 3.1 17.8 + - - +
345A GLY 3.6 8.1 + - - +
348A GLY* 3.5 32.3 - - - +
349A TYR* 4.0 23.1 - - + +
355A ILE* 4.2 5.7 - - + +
359A TYR* 3.5 46.7 - - + -
208B VAL* 4.2 9.4 - - + -
363B PRO* 3.6 32.1 - - + +
367B ILE* 4.4 9.8 - - + +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ARG* 3.8 10.5 - - - +
338A ALA 3.2 16.2 + - - +
339A GLU* 3.7 4.3 - - - +
341A MET* 1.3 77.9 - - - +
343A LEU* 1.3 53.6 + - - +
345A GLY* 3.1 12.5 + - - -
331B GLU* 4.8 3.6 - - - +
334B LYS* 3.9 10.8 + - - +
363B PRO 4.6 1.0 - - - +
366B ALA* 3.1 44.6 + - - +
367B ILE* 3.5 17.2 - - - +
371B THR* 4.0 4.4 - - - -
372B ASN* 3.8 5.8 - - - +
373B GLU* 2.9 41.0 + - - +
401B FAD 2.4 25.8 + - - -
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Residues in contact with LEU 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A THR* 3.8 30.1 - - + -
270A TYR* 4.0 4.3 - - - -
271A VAL* 3.9 19.0 - - + +
287A VAL* 4.2 29.8 - - + -
290A ARG* 3.7 40.8 - - + +
291A LEU* 4.9 5.4 - - + -
294A MET* 3.8 23.3 - - + -
339A GLU* 2.9 20.4 + - - +
340A ALA 3.4 0.6 + - - +
341A MET 3.3 0.2 - - - -
342A GLN* 1.3 75.8 - - - +
344A HIS* 1.3 57.0 + - - +
345A GLY 3.3 1.3 - - - -
401B FAD 3.4 28.1 - - + +
----------------------------------------------------------
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Residues in contact with HIS 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A LEU* 4.0 9.4 + - + +
267A THR* 3.8 33.1 - - - +
270A TYR* 3.6 45.7 + + + +
340A ALA 2.7 23.1 + - - -
341A MET 3.1 8.1 + - - +
343A LEU* 1.3 78.5 - - - +
345A GLY* 1.3 63.1 + - - +
347A TYR* 3.4 23.3 + - - +
348A GLY* 3.4 18.6 - - - +
353A TYR* 4.4 15.4 - + - -
355A ILE* 3.9 30.4 - - + +
401B FAD 4.1 2.7 - - - +
----------------------------------------------------------
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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