Contacts of the helix formed by residues 333 - 359 (chain A) in PDB entry 1HK8
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 333 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A SER* 3.0 22.3 + - - +
328A ILE* 3.8 23.1 - - + +
331A GLN 3.5 0.6 + - - +
332A PHE* 1.3 75.1 + - - +
334A GLU* 1.3 65.6 + - - +
335A GLN* 3.3 11.2 + - - +
336A LYS* 3.0 30.7 + - + +
337A PHE* 3.1 20.3 + - - +
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Residues in contact with GLU 334 (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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332A PHE* 3.9 25.1 + - + -
333A ASN* 1.3 72.6 - - - +
335A GLN* 1.3 63.8 + - - +
337A PHE* 3.2 7.4 + - + +
338A VAL* 3.1 28.3 + - + +
413A ARG* 3.7 28.6 + - - +
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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
----------------------------------------------------------
333A ASN* 3.2 12.3 + - - +
334A GLU* 1.3 77.4 - - - +
336A LYS* 1.3 64.4 + - - +
338A VAL* 3.2 18.3 + - - +
339A GLU* 3.1 44.9 + - - +
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Residues in contact with LYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ASP 4.2 6.5 + - - +
326A SER* 4.0 21.8 - - - +
328A ILE* 4.2 22.5 - - + +
333A ASN* 3.0 30.0 + - + +
335A GLN* 1.3 75.2 - - - +
337A PHE* 1.3 60.6 + - - +
339A GLU* 3.2 20.8 + - + +
340A LEU* 3.1 46.7 + - + +
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Residues in contact with PHE 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.7 31.4 - - + +
323A ALA* 3.8 11.9 - - + -
326A SER* 3.6 10.7 - - - +
332A PHE* 3.6 33.7 - + + -
333A ASN 3.1 5.7 + - - +
334A GLU* 3.4 13.0 - - + +
335A GLN 3.2 0.2 - - - -
336A LYS* 1.3 76.0 - - - +
338A VAL* 1.3 64.3 + - + +
340A LEU* 3.5 0.8 + - - +
341A PHE* 3.0 37.5 + + + +
407A LEU* 3.8 26.0 - - + -
411A VAL* 4.6 1.6 - - + -
415A ILE* 4.2 12.8 - - + -
419A ILE* 3.6 32.5 - - + -
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Residues in contact with VAL 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A GLU* 3.1 24.7 + - + +
335A GLN* 3.2 24.0 + - - +
337A PHE* 1.3 81.7 - - + +
339A GLU* 1.3 64.8 + - + +
341A PHE* 3.9 5.3 - - - +
342A ASN* 3.2 39.4 + - - +
422A LYS* 5.2 12.1 - - - +
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Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A GLN* 3.1 43.2 + - - +
336A LYS* 3.2 23.6 + - + +
338A VAL* 1.3 81.4 - - + +
340A LEU* 1.3 59.6 + - + +
342A ASN* 3.7 5.1 + - - +
343A GLU* 3.2 31.2 + - - +
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Residues in contact with LEU 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ILE* 3.8 22.9 - - + +
325A ASP* 3.6 41.1 - - + +
326A SER* 4.2 1.8 - - - +
336A LYS* 3.1 38.0 + - + +
339A GLU* 1.3 75.9 - - + +
341A PHE* 1.3 56.5 + - - +
343A GLU* 3.3 24.5 + - - +
344A ARG* 2.7 58.2 + - - +
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Residues in contact with PHE 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 4.9 2.7 - - + -
322A ILE* 4.0 25.9 - - + +
337A PHE* 3.0 25.4 + + + +
338A VAL* 3.9 5.4 - - - +
340A LEU* 1.3 76.5 - - - +
342A ASN* 1.3 69.9 + - - +
344A ARG* 3.2 2.3 + - - +
345A MET* 2.9 48.7 + - + +
419A ILE* 3.6 40.4 - - + -
422A LYS* 4.5 16.2 - - + -
423A MET* 3.7 35.9 - - + -
426A HIS* 3.9 21.5 - + - -
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Residues in contact with ASN 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A VAL* 3.2 30.0 + - - +
339A GLU* 4.0 5.4 - - - +
341A PHE* 1.3 94.9 - - - +
343A GLU* 1.3 63.9 + - - +
345A MET* 3.5 4.9 + - - +
346A ASP* 3.2 30.3 + - - +
426A HIS* 4.2 15.7 + - + -
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Residues in contact with GLU 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 3.2 18.8 + - - +
340A LEU* 3.6 25.9 - - - +
341A PHE 3.3 0.2 - - - -
342A ASN* 1.3 80.3 - - - +
344A ARG* 1.3 66.2 + - + +
346A ASP* 3.6 7.6 + - - +
347A LEU* 3.1 25.5 + - + +
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Residues in contact with ARG 344 (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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62A ILE* 3.4 45.1 + - + +
317A LEU* 4.1 16.2 - - + -
318A ASN 5.1 0.4 + - - -
321A ARG* 3.5 3.6 + - - +
322A ILE* 3.4 46.2 - - + +
325A ASP* 2.8 34.7 + - - +
340A LEU* 2.7 41.3 + - - +
341A PHE 3.8 3.1 - - - +
343A GLU* 1.3 80.2 + - + +
345A MET* 1.3 61.8 + - - +
347A LEU* 3.3 12.9 + - + +
348A CYS* 3.0 33.6 + - - -
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Residues in contact with MET 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A LEU* 4.1 8.7 - - + -
341A PHE* 2.9 43.0 + - + +
342A ASN 3.8 5.2 - - - +
344A ARG* 1.3 73.4 - - - +
346A ASP* 1.3 64.8 + - - +
348A CYS* 3.3 3.9 + - - +
349A PHE 3.1 9.5 + - - -
399A LEU* 3.7 25.6 - - + -
423A MET* 4.0 40.6 - - - +
426A HIS* 3.5 43.5 - - + +
427A LEU* 4.6 0.2 - - + -
430A TRP* 3.0 28.9 - - + -
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Residues in contact with ASP 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342A ASN* 3.2 14.9 + - - +
343A GLU* 3.6 10.5 - - - +
345A MET* 1.3 78.3 - - - +
347A LEU* 1.3 62.4 + - - +
349A PHE* 3.2 13.5 + - - +
350A GLU* 3.1 24.8 + - - +
426A HIS* 4.7 9.4 + - - -
430A TRP* 4.8 4.1 + - - +
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Residues in contact with LEU 347 (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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53A PHE* 3.5 44.2 - - + +
54A ILE* 4.2 9.8 - - + +
57A ALA* 3.8 24.2 - - + -
62A ILE* 4.1 11.2 - - + -
63A ILE* 3.9 23.3 - - + -
343A GLU* 3.1 14.0 + - + +
344A ARG* 3.4 15.3 - - + +
345A MET 3.2 0.4 - - - -
346A ASP* 1.3 79.1 - - - +
348A CYS* 1.3 62.6 + - - +
350A GLU* 3.0 9.8 + - - +
351A ALA* 3.0 20.1 + - - +
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Residues in contact with CYS 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ILE* 3.7 25.1 - - - -
315A VAL* 4.1 12.3 - - + +
317A LEU* 3.8 17.3 - - - -
344A ARG 3.0 16.8 + - - -
345A MET* 3.3 9.6 + - - +
347A LEU* 1.3 76.4 - - - +
349A PHE* 1.3 56.5 + - - +
351A ALA* 3.2 7.3 + - - +
352A LEU* 2.9 35.4 + - - +
399A LEU* 3.7 32.8 - - + -
430A TRP* 4.3 3.6 - - + -
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Residues in contact with PHE 349 (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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345A MET 3.1 5.3 + - - -
346A ASP* 3.4 12.8 - - - +
348A CYS* 1.3 74.9 - - - +
350A GLU* 1.3 76.9 + - - +
352A LEU* 4.0 2.6 - - - +
353A MET* 2.9 63.2 + - + +
430A TRP* 3.5 64.9 - + + +
433A ARG* 4.1 34.5 - - - -
434A THR* 3.9 26.5 - - + -
438A PHE* 4.3 4.0 - + - -
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A PRO* 6.4 0.2 - - + -
53A PHE* 3.6 29.4 - - + -
54A ILE* 3.6 11.5 - - + +
346A ASP* 3.1 12.8 + - - +
347A LEU* 3.0 11.5 + - - +
349A PHE* 1.3 96.9 - - - +
351A ALA* 1.3 58.3 + - - +
353A MET* 4.1 5.5 - - - +
354A CYS* 2.9 29.5 + - - +
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Residues in contact with ALA 351 (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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54A ILE* 3.9 30.3 - - + +
63A ILE* 4.4 13.0 - - + -
65A VAL* 4.4 5.2 - - + +
315A VAL* 4.0 17.9 - - + -
347A LEU 3.0 11.8 + - - +
348A CYS 3.2 7.8 + - - +
350A GLU* 1.3 76.7 - - - +
352A LEU* 1.3 65.4 + - - +
354A CYS* 3.3 16.0 + - - +
355A ARG* 3.4 12.6 + - - +
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A GLY 4.1 8.7 - - - +
314A VAL 4.1 1.1 - - - -
315A VAL* 3.5 31.0 - - + +
348A CYS 2.9 19.8 + - - +
349A PHE 4.0 2.5 - - - +
351A ALA* 1.3 78.0 - - - +
353A MET* 1.3 60.9 + - - +
355A ARG* 3.1 25.6 - - + +
356A ILE* 3.3 15.9 + - - +
397A VAL* 3.9 15.3 - - + -
398A SER 3.6 28.7 - - - +
399A LEU* 4.4 7.2 - - + -
430A TRP* 4.4 10.5 - - + -
438A PHE* 3.9 34.5 - - + -
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Residues in contact with MET 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A PHE* 2.9 54.1 + - + +
350A GLU* 4.1 7.9 - - - +
352A LEU* 1.3 74.6 - - - +
354A CYS* 1.3 66.5 + - - +
356A ILE* 3.3 19.6 + - + +
357A SER* 2.9 27.9 + - - +
360A LYS* 6.2 2.0 - - - +
434A THR* 4.1 22.7 - - + -
436A PHE* 4.8 10.8 - - + -
438A PHE* 3.9 22.2 - - + -
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Residues in contact with CYS 354 (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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49A MET 4.5 4.3 - - - -
50A VAL* 4.2 23.8 - - + -
51A PRO* 3.7 27.4 - - + -
54A ILE* 4.4 5.4 - - + -
72A PRO* 5.3 4.0 - - - +
350A GLU 2.9 20.2 + - - +
351A ALA* 3.3 11.4 - - - +
353A MET* 1.3 78.8 - - - +
355A ARG* 1.3 60.8 + - - +
357A SER* 3.4 8.3 - - - -
358A SER* 3.4 15.8 + - - -
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Residues in contact with ARG 355 (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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65A VAL* 3.7 17.6 - - - +
66A HIS* 3.0 29.7 + - - +
67A ASP* 3.9 1.6 + - - +
68A ILE* 4.4 0.6 - - - +
71A SER* 3.0 53.1 + - - +
72A PRO* 4.7 9.4 - - + +
124A TYR* 4.0 14.8 + - - -
312A LEU 5.1 10.3 - - - +
313A GLY* 4.4 1.9 - - - -
314A VAL 3.6 21.8 + - - +
315A VAL* 4.5 10.1 - - - -
351A ALA 3.5 10.5 - - - +
352A LEU* 3.1 27.6 - - + +
354A CYS* 1.3 77.5 - - - +
356A ILE* 1.3 66.6 + - + +
358A SER* 2.7 29.2 + - - -
359A LEU* 3.6 5.5 + - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A LEU* 4.2 22.0 - - + +
352A LEU 3.3 16.7 + - - +
353A MET* 3.8 29.4 - - + +
355A ARG* 1.3 78.7 - - + +
357A SER* 1.3 61.0 - - - +
359A LEU* 3.1 26.0 + - + +
360A LYS* 6.2 0.7 - - - -
387A ILE* 3.5 13.9 - - + +
397A VAL* 4.0 32.8 - - + -
436A PHE* 3.7 38.4 - - + -
438A PHE* 4.6 2.0 - - + -
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Residues in contact with SER 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A MET* 2.9 15.8 + - - +
354A CYS* 3.4 13.5 - - - -
356A ILE* 1.3 76.4 - - - +
358A SER* 1.3 65.6 + - - +
360A LYS* 3.1 49.7 + - - +
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Residues in contact with SER 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A MET* 4.4 11.4 - - - -
71A SER* 4.8 2.1 + - - -
72A PRO* 3.7 37.1 + - - +
75A PRO* 4.6 8.0 - - - +
354A CYS 3.4 5.6 + - - -
355A ARG 2.7 19.4 + - - -
357A SER* 1.3 78.7 - - - +
359A LEU* 1.3 68.1 + - - +
360A LYS 3.2 8.5 + - - +
362A VAL* 3.8 10.6 - - - +
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Residues in contact with LEU 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PRO* 3.4 42.0 - - + +
76A PHE 4.4 7.2 - - - +
77A THR* 4.9 4.5 - - + -
312A LEU* 4.2 19.5 - - + +
355A ARG 4.0 6.3 - - - +
356A ILE* 3.3 20.9 - - + +
357A SER 3.1 1.2 - - - -
358A SER* 1.3 81.6 + - - +
360A LYS* 1.3 63.1 + - - +
361A GLY 3.4 0.5 + - - -
362A VAL* 3.3 22.7 + - - +
386A ILE* 4.5 12.4 - - + +
387A ILE* 3.9 22.4 - - + +
390A PHE* 3.8 28.3 - - + -
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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