Contacts of the helix formed by residues 325 - 354 (chain A) in PDB entry 7A62
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 ASP 325 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 2.7 55.6 + - - +
320A VAL 4.7 2.0 + - - +
323A LYS* 3.8 13.0 - - + +
324A GLY* 1.3 74.2 - - - +
326A ALA* 1.3 62.5 + - - +
327A GLY 2.9 9.5 + - - -
328A LEU* 3.1 22.8 + - + +
329A ARG* 3.0 30.7 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLY 4.0 2.0 + - - -
325A ASP* 1.3 70.3 + - - +
327A GLY* 1.3 66.1 + - - +
329A ARG* 3.6 26.0 - - - +
330A GLU* 2.9 29.9 + - - +
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Residues in contact with GLY 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 3.7 11.1 - - - +
197A LEU* 3.2 19.8 - - - +
325A ASP* 2.9 9.5 + - - -
326A ALA* 1.3 80.4 - - - +
328A LEU* 1.3 61.0 + - - +
330A GLU* 3.4 5.5 + - - +
331A ALA* 3.1 17.8 + - - +
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ARG* 4.1 15.0 - - + +
196A LEU* 4.1 27.1 - - + -
197A LEU* 3.7 38.3 - - + +
200A LEU* 4.5 5.6 - - + +
319A PHE* 4.4 15.0 - - + -
320A VAL* 3.6 17.7 - - + +
323A LYS* 4.5 11.9 - - + -
325A ASP* 3.1 37.1 + - + +
327A GLY* 1.3 76.3 - - - +
329A ARG* 1.3 58.7 + - - +
331A ALA* 3.3 2.2 + - - +
332A TYR* 2.8 30.8 + - - +
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Residues in contact with ARG 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A VAL* 3.7 19.2 + - + +
321A LEU* 4.9 9.8 - - - +
324A GLY* 3.6 11.7 - - - -
325A ASP 3.0 40.2 + - - +
326A ALA* 3.6 28.1 - - - +
328A LEU* 1.3 75.7 - - - +
330A GLU* 1.3 58.8 + - - +
332A TYR* 3.6 1.4 - - - +
333A ASP* 2.8 35.9 + - - +
400A LEU* 3.7 30.3 - - + -
401A LYS 3.7 21.5 + - - +
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Residues in contact with GLU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 5.3 0.9 - - + -
326A ALA* 2.9 19.6 + - - +
327A GLY* 3.8 5.6 - - - +
329A ARG* 1.3 76.3 - - - +
331A ALA* 1.3 58.2 + - - +
333A ASP* 3.4 7.2 + - - +
334A ALA* 2.9 27.4 + - + +
337A LYS* 6.0 0.8 + - - +
337C LYS* 3.6 26.8 + - - +
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Residues in contact with ALA 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 4.0 13.0 - - + -
200A LEU* 3.9 20.0 - - + +
201A LEU* 3.7 34.5 - - + -
327A GLY 3.1 16.8 + - - +
328A LEU* 3.8 3.4 - - - +
330A GLU* 1.3 76.2 - - - +
332A TYR* 1.3 65.2 + - - +
334A ALA* 3.2 11.1 + - - +
335A CYS* 3.3 17.2 + - - -
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Residues in contact with TYR 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A LEU* 4.2 9.7 - - + +
277A LEU* 2.6 50.3 + - + +
316A VAL* 4.2 14.8 - - + -
317A ARG* 3.0 43.3 + - + +
320A VAL* 4.1 18.2 - - + -
328A LEU 2.8 20.3 + - - +
329A ARG 3.6 2.7 - - - +
331A ALA* 1.3 73.6 - - - +
333A ASP* 1.3 72.5 + - - +
335A CYS* 3.1 11.7 + - - +
336A VAL* 3.0 39.8 + - + +
398A SER* 4.0 3.6 - - - -
400A LEU* 3.6 26.5 - - + -
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Residues in contact with ASP 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A ARG 2.8 21.9 + - - +
330A GLU* 3.6 7.6 - - - +
332A TYR* 1.3 78.2 - - - +
334A ALA* 1.3 61.9 + - - +
336A VAL* 3.0 4.8 + - - +
337A LYS* 2.7 46.9 + - - +
399A LEU* 3.7 16.6 - - + +
400A LEU* 2.8 30.2 + - - +
401A LYS* 2.9 29.3 + - - +
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Residues in contact with ALA 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A LEU* 4.4 10.8 - - + -
204A ALA* 3.5 23.8 - - + +
330A GLU 2.9 15.0 + - - +
331A ALA* 3.2 13.4 + - - +
333A ASP* 1.3 75.4 - - - +
335A CYS* 1.3 62.8 + - - +
337A LYS* 4.1 9.2 - - - +
338A ALA* 3.1 20.1 + - - +
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Residues in contact with CYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200A LEU* 3.1 41.5 - - - -
203A ILE* 3.7 23.8 - - + -
204A ALA* 3.7 9.0 - - - +
207A LEU* 4.3 5.5 - - + +
276A LEU* 6.3 0.2 - - - -
277A LEU* 3.8 23.7 - - + +
331A ALA 3.3 8.7 + - - -
332A TYR 3.1 8.3 + - - +
334A ALA* 1.3 75.2 - - - +
336A VAL* 1.3 65.9 + - - +
338A ALA* 3.4 3.2 + - - +
339A LEU* 3.2 22.0 + - - +
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Residues in contact with VAL 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A LEU* 4.0 16.2 - - + -
279A ILE* 4.6 7.6 - - + -
332A TYR* 3.0 46.3 + - + +
333A ASP* 3.0 7.3 + - - +
335A CYS* 1.3 76.7 - - - +
337A LYS* 1.3 61.4 + - - +
339A LEU* 3.2 7.3 + - - +
340A VAL* 3.1 20.7 + - + +
395A THR* 3.7 24.2 - - - +
398A SER* 4.3 5.2 - - - +
399A LEU* 3.7 28.9 - - + +
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Residues in contact with LYS 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 4.9 0.4 - - - +
330A GLU* 6.3 0.8 - - - +
333A ASP* 2.7 34.1 + - - +
334A ALA* 4.1 7.7 - - - +
336A VAL* 1.3 73.5 - - - +
338A ALA* 1.3 57.3 + - - +
340A VAL* 2.9 11.5 + - - +
341A SER* 2.8 32.4 + - - +
399A LEU* 3.6 27.1 - - + -
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Residues in contact with ALA 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ALA* 4.0 11.4 - - - +
207A LEU* 3.8 25.9 - - + +
208A GLU* 3.6 28.3 + - + +
211A LEU* 5.8 0.3 - - - +
334A ALA 3.1 19.3 + - - +
335A CYS 3.8 4.5 - - - +
337A LYS* 1.3 75.1 - - - +
339A LEU* 1.3 57.4 + - - +
341A SER* 3.3 3.7 + - - -
342A LEU* 3.0 33.6 + - - +
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Residues in contact with LEU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A LEU* 4.5 6.6 - - + +
270A PHE* 4.3 30.3 - - + +
273A PHE* 4.0 31.6 - - + +
274A ASP* 3.7 21.5 - - - +
277A LEU* 4.3 5.2 - - + -
279A ILE* 4.1 15.0 - - + -
335A CYS 3.2 11.1 + - - +
336A VAL 3.4 9.2 - - - +
337A LYS 3.1 0.4 - - - -
338A ALA* 1.3 75.3 - - - +
340A VAL* 1.3 63.4 + - - +
342A LEU* 3.4 10.9 + - + +
343A ARG* 3.1 39.6 + - - +
395A THR* 4.1 4.3 - - + -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A VAL* 3.1 14.8 + - + +
337A LYS* 2.9 12.6 + - - +
339A LEU* 1.3 76.4 - - - +
341A SER* 1.3 52.8 + - - +
343A ARG* 3.0 7.6 + - - +
344A SER* 2.7 43.7 + - - +
392A ARG* 4.4 13.6 - - + +
395A THR* 3.7 22.7 - - + +
396A GLU* 3.8 34.8 - - + +
399A LEU* 5.5 3.6 - - + -
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLU* 3.9 12.4 + - - -
211A LEU* 3.8 23.6 - - - +
337A LYS* 2.8 19.4 + - - +
338A ALA 3.6 8.3 - - - -
340A VAL* 1.3 74.6 - - - +
342A LEU* 1.3 58.4 + - - +
344A SER* 3.7 6.9 - - - -
345A TYR* 2.9 31.2 + - - +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A VAL* 5.7 3.8 - - + -
207A LEU* 4.1 35.4 - - + +
210A ALA* 4.3 8.5 - - + +
211A LEU* 3.7 37.7 - - + +
214A PHE* 4.5 16.0 - - + -
269A VAL* 5.8 2.0 - - + -
270A PHE* 4.0 29.6 - - + -
338A ALA 3.0 18.0 + - - +
339A LEU* 3.7 15.7 - - + +
340A VAL 3.2 0.2 - - - -
341A SER* 1.3 77.5 - - - +
343A ARG* 1.3 58.7 + - - +
345A TYR* 3.8 1.0 - - - +
346A HIS* 2.8 31.6 + - - +
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Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A PHE* 3.3 30.4 - - + +
271A GLN* 4.7 0.6 - - - +
274A ASP* 3.0 36.2 + - - -
292A LEU* 5.6 0.8 - - - +
339A LEU* 3.1 24.3 + - + +
340A VAL* 3.0 7.9 + - - +
342A LEU* 1.3 78.4 - - - +
344A SER* 1.3 57.9 + - - +
346A HIS* 3.5 9.2 + - + +
347A LEU* 3.0 30.8 + - - +
388A LEU 5.3 1.6 - - - +
391A VAL* 3.2 20.5 - - - +
392A ARG* 4.1 24.0 - - + +
395A THR* 2.9 25.4 + - - +
502A HEM 2.4 43.4 + - - +
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Residues in contact with SER 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A VAL* 2.7 29.0 + - - +
341A SER* 3.7 7.6 - - - -
343A ARG* 1.3 69.8 - - - +
345A TYR* 1.3 65.4 + - - +
347A LEU* 3.1 20.3 + - - +
348A GLN* 3.2 18.0 + - - +
392A ARG* 3.3 31.7 + - - +
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Residues in contact with TYR 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 3.5 15.7 - - + -
214A PHE* 3.9 38.8 - + + -
215A HIS* 3.3 42.2 - + - -
218A HIS* 2.9 35.1 + - - -
341A SER 2.9 17.4 + - - +
342A LEU 3.8 1.8 - - - +
344A SER* 1.3 76.6 - - - +
346A HIS* 1.3 64.6 + - - +
348A GLN* 2.8 41.8 + - + +
349A ILE* 3.0 28.9 + - + -
219D ASP* 4.5 3.8 + - - -
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Residues in contact with HIS 346 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 4.0 15.2 - + + -
270A PHE* 4.6 9.4 - + + -
342A LEU 2.8 22.4 + - - +
343A ARG* 3.7 10.2 + - - +
345A TYR* 1.3 73.3 - - - +
347A LEU* 1.3 58.0 + - - +
349A ILE* 3.3 10.5 + - + +
350A VAL* 3.0 36.3 + - + +
388A LEU* 4.0 14.4 - - + +
502A HEM 2.3 96.1 + + + +
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Residues in contact with LEU 347 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A ARG 3.0 14.8 + - - +
344A SER 3.2 10.1 - - - +
345A TYR 2.9 0.8 + - - -
346A HIS* 1.3 77.0 - - - +
348A GLN* 1.3 65.3 + - + +
350A VAL* 3.3 2.7 + - - +
351A THR* 3.0 25.7 + - - -
385A MET* 3.5 38.6 - - + -
388A LEU* 3.9 28.0 - - + +
389A LYS* 3.9 24.0 - - + +
392A ARG* 3.9 36.1 - - + +
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Residues in contact with GLN 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 6.3 0.7 - - + -
344A SER* 3.2 15.6 + - - +
345A TYR* 2.8 33.0 + - + +
347A LEU* 1.3 77.1 - - + +
349A ILE* 1.3 60.4 + - + +
351A THR* 3.4 9.0 + - - +
352A LYS* 3.0 29.1 + - - +
219D ASP* 5.2 5.2 - - - +
----------------------------------------------------------
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Residues in contact with ILE 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PHE* 3.9 13.9 - - + -
217A ILE* 3.8 17.5 - - + -
218A HIS* 3.7 34.8 - - + +
345A TYR* 3.0 33.9 + - + +
346A HIS* 3.4 10.5 - - - +
347A LEU 3.2 0.2 - - - -
348A GLN* 1.3 79.5 - - + +
350A VAL* 1.3 59.0 + - + +
352A LYS* 3.2 1.3 + - - -
353A TYR* 2.9 39.8 + - + +
502A HEM 3.5 39.3 - - + -
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Residues in contact with VAL 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A HIS* 3.0 32.1 + - + +
347A LEU 3.3 4.2 + - - +
349A ILE* 1.3 73.0 - - - +
351A THR* 1.3 61.5 + - - +
353A TYR 4.5 0.2 - - - +
354A ILE* 2.9 36.0 + - + +
355A LEU* 3.2 6.8 + - + -
384A LEU* 4.1 25.4 - - + -
385A MET* 4.4 10.8 - - - -
388A LEU* 3.9 16.6 - - + -
502A HEM 3.8 36.3 - - + -
----------------------------------------------------------
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Residues in contact with THR 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU 3.0 14.8 + - - -
348A GLN* 3.5 12.6 - - - +
350A VAL* 1.3 77.9 - - - +
352A LYS* 1.3 64.0 + - + +
355A LEU* 3.4 25.7 - - + +
356A ILE* 3.1 44.1 + - + +
385A MET* 3.8 9.2 - - - +
----------------------------------------------------------
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Residues in contact with LYS 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A HIS* 2.8 42.4 + - + +
223A PRO* 3.9 24.1 - - + +
348A GLN 3.0 17.0 + - - +
349A ILE* 3.8 3.6 - - - +
351A THR* 1.3 79.7 - - + +
353A TYR* 1.3 88.8 + - + +
356A ILE* 4.3 10.9 - - + +
357A PRO* 3.2 20.3 - - - +
146D GLU* 4.6 9.7 + - - -
216D GLN* 6.1 0.2 - - - +
219D ASP* 4.4 9.5 + - - +
220D HIS* 4.6 10.1 + - - -
----------------------------------------------------------
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Residues in contact with TYR 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ILE* 3.3 31.6 + - + -
218A HIS* 3.7 10.2 - - - -
221A VAL* 2.8 52.4 + - + -
223A PRO* 3.7 25.0 - - + +
226A PHE* 3.5 27.0 - - + -
227A PHE* 3.6 13.9 + - - +
349A ILE* 2.9 37.8 + - + +
352A LYS* 1.3 104.9 + - + +
354A ILE* 1.3 65.8 + - - +
357A PRO* 3.8 5.6 - - - +
502A HEM 3.9 17.3 - - + -
----------------------------------------------------------
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Residues in contact with ILE 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PHE* 4.0 9.2 - - + -
227A PHE* 3.5 13.8 - - + -
231A ARG* 4.6 9.9 - - + +
350A VAL* 2.9 16.0 + - + +
352A LYS 3.5 0.2 - - - -
353A TYR* 1.3 87.0 - - - +
355A LEU* 1.3 68.7 + - + +
356A ILE 3.4 1.1 - - - -
357A PRO* 3.4 1.6 - - - +
358A ALA* 2.9 27.2 + - + +
379A THR* 3.9 30.3 - - + -
384A LEU* 4.4 11.9 - - + -
502A HEM 3.7 53.6 - - + -
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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