Contacts of the helix formed by residues 326 - 357 (chain A) in PDB entry 2PFV
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 ASN 326 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A SER* 2.9 39.7 + - - +
280A ILE* 3.4 26.9 - - - +
281A SER* 3.8 13.9 - - - -
324A LEU* 3.9 3.9 - - - +
325A GLN* 1.3 76.3 + - + +
327A TYR* 1.3 58.7 + - - +
328A ASN* 3.0 15.7 + - - +
329A LEU* 3.2 34.1 + - + +
330A LEU 4.2 0.2 + - - -
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Residues in contact with TYR 327 (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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316A LYS* 4.3 22.6 + - + +
319A LEU* 4.5 17.5 - - + -
320A ARG* 5.2 4.7 + - - -
322A LYS 5.7 3.1 - - - -
324A LEU* 3.9 37.3 - - + +
325A GLN 3.4 4.6 + - - -
326A ASN* 1.3 76.7 - - - +
328A ASN* 1.3 61.8 + - - +
330A LEU* 3.1 32.5 + - + +
331A GLN* 3.3 42.6 + - + +
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Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A GLN 3.9 5.5 + - - -
326A ASN* 3.0 23.8 - - - +
327A TYR* 1.3 79.5 - - - +
329A LEU* 1.3 85.9 + - - +
331A GLN* 3.2 17.1 + - - +
332A ASP* 2.5 36.9 + - - +
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Residues in contact with LEU 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 4.9 3.8 - - + -
281A SER* 5.2 7.2 - - - +
284A ALA* 3.9 26.5 - - + -
326A ASN* 3.2 38.4 - - + +
327A TYR 3.2 0.4 - - - -
328A ASN* 1.3 104.8 - - - +
330A LEU* 1.3 61.9 + - - +
332A ASP* 3.2 6.5 + - + +
333A CYS* 3.0 28.6 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A ILE* 3.8 28.0 - - + +
283A TYR* 4.0 18.2 - - + -
284A ALA* 5.0 3.8 - - + -
312A ILE* 3.4 24.5 - - + +
315A VAL* 4.1 10.1 - - + -
316A LYS* 4.2 12.8 - - + -
319A LEU* 3.4 33.7 - - + -
324A LEU* 4.7 0.4 - - + -
326A ASN 4.9 1.1 - - - +
327A TYR* 3.1 26.5 + - + +
329A LEU* 1.3 78.1 - - - +
331A GLN* 1.3 57.4 + - + +
333A CYS* 3.0 6.3 + - - +
334A THR* 2.8 33.2 + - - -
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Residues in contact with GLN 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 3.4 39.1 - - + +
328A ASN* 3.2 23.8 + - - +
330A LEU* 1.3 76.0 - - - +
332A ASP* 1.3 65.7 + - - +
334A THR* 3.3 9.8 + - - -
335A GLN* 3.1 22.0 + - - +
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Residues in contact with ASP 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ASN* 2.5 33.2 + - - +
329A LEU* 3.6 6.5 - - + +
331A GLN* 1.3 78.9 - - - +
333A CYS* 1.3 60.5 - - - +
335A GLN* 3.4 7.0 + - - +
336A GLU* 2.9 29.3 + - - +
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Residues in contact with CYS 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A TYR* 5.8 0.2 - - - -
284A ALA* 4.2 24.9 - - - -
287A PHE* 3.4 37.5 - - + -
288A GLY* 5.0 3.4 - - - -
291A LEU* 5.6 0.2 - - - -
312A ILE* 4.5 7.2 - - + -
329A LEU* 3.0 22.9 + - - +
330A LEU* 3.0 13.2 + - - +
332A ASP* 1.3 75.7 - - - +
334A THR* 1.3 59.5 + - - +
336A GLU* 4.4 3.8 - - - +
337A VAL* 2.9 34.5 + - - +
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Residues in contact with THR 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A ILE* 3.5 18.9 - - + +
313A ASN* 5.1 11.4 + - - +
316A LYS* 4.7 6.4 - - - +
330A LEU 2.8 18.5 + - - -
331A GLN* 3.5 9.4 - - - -
333A CYS* 1.3 76.7 - - - +
335A GLN* 1.3 58.4 + - - +
337A VAL* 3.6 9.1 - - + +
338A ARG* 3.1 27.5 + - + +
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Residues in contact with GLN 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A GLN 3.1 14.8 + - - +
332A ASP* 3.7 8.1 - - - +
333A CYS 3.1 0.6 - - - -
334A THR* 1.3 76.9 - - - +
336A GLU* 1.3 64.9 + - - +
338A ARG* 3.3 5.0 + - - +
339A GLN* 3.2 24.6 + - - +
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Residues in contact with GLU 336 (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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291A LEU* 3.5 21.1 - - + +
332A ASP 2.9 18.2 + - - +
333A CYS* 3.9 4.3 - - - +
335A GLN* 1.3 78.8 - - - +
337A VAL* 1.3 57.5 + - - +
339A GLN* 3.3 13.5 - - - +
340A VAL* 3.2 24.3 - - - +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 3.6 17.0 - - + -
291A LEU* 3.8 15.7 - - + +
305A SER* 3.8 14.6 - - - +
308A LEU* 3.9 17.7 - - + -
309A VAL* 3.6 28.3 - - + +
312A ILE* 4.3 8.1 - - + -
333A CYS 2.9 20.5 + - - +
334A THR* 3.6 13.7 - - + +
336A GLU* 1.3 74.8 - - - +
338A ARG* 1.3 64.9 + - - +
339A GLN 3.4 0.7 - - - -
340A VAL* 3.9 2.1 - - - +
341A THR* 3.2 24.6 + - - +
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Residues in contact with ARG 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309A VAL* 5.6 1.6 - - - -
334A THR* 3.1 20.2 - - + +
335A GLN* 3.3 8.6 + - - +
337A VAL* 1.3 82.3 - - - +
339A GLN* 1.3 61.1 + - - +
341A THR* 3.2 17.5 + - - -
342A GLN* 3.2 16.9 + - - +
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Residues in contact with GLN 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN 3.2 12.1 + - - +
336A GLU* 3.3 14.9 - - - +
338A ARG* 1.3 74.7 - - - +
340A VAL* 1.3 81.4 + - - +
342A GLN* 3.3 15.3 + - - +
343A SER* 2.8 40.5 + - - -
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Residues in contact with VAL 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A LEU* 3.9 19.7 - - + +
294A VAL* 4.4 17.7 - - + -
295A ARG* 6.1 4.9 - - + -
298A LEU* 5.3 7.2 - - + -
302A GLY 5.1 2.2 - - - +
305A SER* 3.7 21.3 - - - +
336A GLU 3.2 16.1 + - - +
337A VAL* 3.9 6.7 - - - +
338A ARG 3.3 0.2 - - - -
339A GLN* 1.3 99.2 - - - +
341A THR* 1.3 62.9 + - - +
343A SER* 3.0 15.5 + - - -
344A LEU* 3.2 13.5 + - + +
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Residues in contact with THR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A SER* 3.2 27.8 - - - +
306A PHE* 4.3 17.7 - - + -
309A VAL* 3.6 21.0 - - + +
337A VAL 3.2 16.0 + - - +
338A ARG* 3.2 13.5 + - - -
340A VAL* 1.3 75.6 - - - +
342A GLN* 1.3 64.7 + - - +
344A LEU* 3.1 22.0 + - - +
345A PHE* 3.1 19.7 - - - -
392A ALA* 4.5 12.1 - - - +
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Residues in contact with GLN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A ARG 3.2 17.1 + - - +
339A GLN* 3.5 14.5 - - - +
341A THR* 1.3 83.2 + - - +
343A SER* 1.3 62.3 + - - +
344A LEU 3.3 0.5 + - - -
345A PHE* 3.6 9.9 + - - +
346A ARG* 3.5 17.5 + - - +
392A ALA* 6.0 2.9 - - - +
396A ILE* 5.9 6.7 - - + -
400A ASN* 3.9 37.6 + - + +
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Residues in contact with SER 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 6.4 2.2 - - - -
339A GLN* 2.8 35.5 + - - -
340A VAL* 3.0 8.5 + - - -
342A GLN* 1.3 75.3 - - - +
344A LEU* 1.3 59.2 + - - +
346A ARG* 4.0 8.3 - - - +
347A ASP* 2.8 33.6 + - - +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 4.4 13.7 - - + -
302A GLY* 3.5 32.5 - - - +
303A PHE* 4.5 4.9 - - + -
305A SER* 3.3 25.8 - - - +
306A PHE* 4.2 23.3 - - + -
340A VAL* 3.2 13.6 + - + +
341A THR* 3.1 15.9 + - - +
343A SER* 1.3 74.3 - - - +
345A PHE* 1.3 64.5 + - + +
347A ASP* 3.2 8.3 + - + +
348A ALA* 2.8 29.8 + - - +
378A ARG* 4.8 16.2 + - - +
382A PHE* 3.9 13.0 - - + -
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Residues in contact with PHE 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A PHE* 4.0 15.7 - + - -
341A THR 3.1 20.9 - - - -
342A GLN* 3.6 9.2 + - - +
344A LEU* 1.3 75.7 - - + +
346A ARG* 1.3 64.0 + - - +
348A ALA* 3.1 17.0 + - - +
349A ILE* 3.4 13.2 - - - +
382A PHE* 4.1 15.3 - + - -
389A CYS* 3.7 33.7 - - + -
392A ALA* 3.8 17.7 - - + -
393A MET* 3.4 30.3 - - + -
400A ASN 5.8 0.2 - - - +
401A TRP* 4.1 12.1 - + + -
427A LEU* 4.2 2.5 - - + -
430A PHE* 3.5 44.1 - + + -
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Residues in contact with ARG 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A GLN* 3.5 11.8 + - + +
343A SER* 4.0 7.4 - - - +
344A LEU 3.3 0.4 - - - -
345A PHE* 1.3 79.7 - - - +
347A ASP* 1.3 63.4 + - - +
349A ILE* 3.5 8.9 + - - +
350A ASP* 3.5 24.6 + - - +
399A GLU 2.9 26.9 + - - -
400A ASN* 3.3 23.5 + - - +
401A TRP* 3.4 24.6 - - - +
402A LEU 3.1 13.5 + - - -
403A PRO* 5.2 3.6 - - - +
404A SER 5.6 0.6 - - - +
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Residues in contact with ASP 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A LEU* 5.2 13.6 - - + +
343A SER* 2.8 21.5 + - - +
344A LEU* 3.4 8.8 - - + +
346A ARG* 1.3 77.6 - - - +
348A ALA* 1.3 57.8 + - - +
350A ASP* 3.0 8.7 + - - +
351A ARG* 2.7 52.3 + - - +
378A ARG* 4.8 8.3 + - - -
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU 2.8 16.7 + - - +
345A PHE 3.1 11.4 + - - +
347A ASP* 1.3 76.5 + - - +
349A ILE* 1.3 62.5 + - - +
351A ARG* 3.3 7.1 + - - +
352A ILE* 3.0 28.8 + - + +
378A ARG* 4.6 10.7 - - + +
379A LEU* 5.3 3.6 - - + -
382A PHE* 4.1 15.0 - - + -
430A PHE* 3.7 20.9 - - + -
434A CYS* 4.4 5.4 - - - -
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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
----------------------------------------------------------
345A PHE 3.4 15.0 + - - +
346A ARG 3.7 3.8 - - - +
347A ASP 3.1 0.6 - - - -
348A ALA* 1.3 78.1 - - - +
350A ASP* 1.3 62.1 + - - +
352A ILE* 2.8 27.5 + - - +
353A ILE* 2.9 33.2 + - + +
401A TRP* 3.5 31.4 - - + +
402A LEU* 5.1 4.0 - - + -
403A PRO* 3.8 19.5 - - + -
430A PHE* 3.5 24.7 - - + +
433A ASP 5.3 0.9 - - - +
434A CYS* 3.5 17.9 - - - +
437A THR* 4.5 17.5 - - + +
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Residues in contact with ASP 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A ARG* 3.5 29.5 + - - +
347A ASP* 3.0 11.0 + - - +
349A ILE* 1.3 84.1 - - - +
351A ARG* 1.3 57.9 + - - +
353A ILE* 3.8 17.8 - - - +
354A LYS* 2.9 31.9 + - - +
403A PRO* 5.1 5.6 - - - +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A GLU* 5.9 4.8 - - - +
347A ASP* 2.7 32.6 + - - +
348A ALA 3.4 5.4 - - - +
350A ASP* 1.3 73.7 - - - +
352A ILE* 1.3 60.0 + - - +
354A LYS* 3.9 3.6 - - - +
355A LYS* 3.0 48.6 + - + +
374A ASP* 2.8 40.8 + - - +
375A THR* 6.1 1.3 - - - +
378A ARG* 3.3 51.6 - - - +
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Residues in contact with ILE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 3.0 16.6 - - + +
349A ILE* 2.8 9.4 + - - +
351A ARG* 1.3 77.2 - - + +
353A ILE* 1.3 59.4 + - - +
355A LYS* 3.3 4.9 + - - +
356A ALA* 2.9 31.1 + - + +
371A ALA* 5.2 0.3 - - - +
375A THR* 3.7 33.9 - - + +
379A LEU* 5.0 2.7 - - + -
434A CYS* 3.5 42.4 - - + +
437A THR* 4.0 9.2 - - + +
438A LEU* 3.5 39.0 - - + +
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Residues in contact with ILE 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 2.9 19.7 + - + +
350A ASP* 3.8 17.3 - - - +
352A ILE* 1.3 75.6 - - - +
354A LYS* 1.3 60.3 + - - +
356A ALA* 4.1 0.2 - - - +
357A ASN* 2.6 36.3 + - - +
403A PRO* 3.7 30.3 - - + -
437A THR* 3.7 18.2 - - + -
441A ASN* 3.6 27.8 - - - +
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Residues in contact with LYS 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A ASP 2.9 18.5 + - - +
351A ARG* 4.0 4.5 - - - +
353A ILE* 1.3 76.7 - - - +
355A LYS* 1.3 59.2 + - + +
357A ASN* 3.5 3.6 + - - +
358A SER* 3.0 28.6 + - - -
----------------------------------------------------------
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Residues in contact with LYS 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A ARG* 3.0 38.2 + - + +
352A ILE* 3.8 5.6 - - - +
354A LYS* 1.3 75.6 - - + +
356A ALA* 1.3 63.4 + - - +
358A SER* 2.8 29.0 + - - +
359A ILE* 4.3 1.7 + - - +
370A GLU* 4.6 19.2 + - + +
371A ALA* 3.8 26.5 + - + +
374A ASP* 3.9 38.7 + - + +
375A THR* 5.4 0.2 - - - +
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 2.9 18.0 + - + +
353A ILE 4.1 1.1 - - - +
355A LYS* 1.3 77.3 - - - +
357A ASN* 1.3 59.5 + - - +
358A SER 3.4 0.8 + - - -
359A ILE 4.1 1.0 + - - +
371A ALA* 3.8 11.6 - - + +
438A LEU* 4.8 5.2 - - + +
441A ASN* 3.7 29.8 - - + -
442A LEU* 3.8 19.2 - - + +
445A LYS* 3.4 32.4 + - - +
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Residues in contact with ASN 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A ILE* 2.6 33.5 + - - +
354A LYS* 3.7 3.8 - - - +
355A LYS 3.2 0.2 - - - -
356A ALA* 1.3 76.3 - - - +
358A SER* 1.3 63.6 + - - +
359A ILE 3.4 5.2 - - - -
360A SER* 4.7 2.6 + - - -
441A ASN* 3.4 38.4 + - - +
444A ARG* 4.6 9.8 - - - +
445A LYS* 3.8 17.2 + - + +
448A ILE* 5.6 2.4 - - - +
----------------------------------------------------------
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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).
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