Contacts of the helix formed by residues 386 - 411 (chain A) in PDB entry 4CZ8
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 386 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ALA* 3.7 10.8 - - - +
382A SER 5.0 0.7 - - - +
384A LEU 4.6 3.3 + - - -
385A LEU* 1.3 79.7 - - - +
387A VAL* 1.3 75.3 + - + +
388A HIS* 3.4 10.1 - - + +
389A TRP* 3.4 29.9 - - - +
390A GLY* 3.0 17.2 + - - -
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Residues in contact with VAL 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A LEU* 3.5 21.4 - - + +
377A ALA* 3.8 26.2 - - + +
378A LEU* 3.7 24.2 - - + -
386A THR* 1.3 77.6 - - + +
388A HIS* 1.3 60.3 + - - +
390A GLY* 3.0 4.5 + - - -
391A GLU* 2.9 29.3 + - + +
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Residues in contact with HIS 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A VAL* 4.6 18.2 - - + +
321A ASN* 5.8 1.0 + - - -
386A THR* 3.4 8.3 - - + +
387A VAL* 1.3 80.3 - - - +
389A TRP* 1.3 67.1 + + + +
391A GLU* 3.1 12.4 + - - +
392A ILE* 2.9 61.6 + - + +
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Residues in contact with TRP 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 5.0 4.0 - + - -
112A PHE* 4.0 32.5 - + + -
113A ASN* 3.0 38.1 - - - -
114A SER* 4.3 7.6 - - - -
118A LEU* 4.3 27.1 - - + +
384A LEU 5.7 2.0 - - - -
385A LEU* 5.3 1.8 - - + -
386A THR* 3.4 37.2 + - - +
387A VAL 3.2 0.6 - - - -
388A HIS* 1.3 82.6 - + + +
390A GLY* 1.3 60.3 + - - +
392A ILE* 3.2 27.3 + - + +
393A ILE* 2.9 36.6 + - + +
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Residues in contact with GLY 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373A PRO* 4.4 12.7 - - - +
374A LEU* 4.1 29.1 - - - +
385A LEU* 6.0 0.8 - - - +
386A THR 3.0 10.9 + - - -
387A VAL 3.0 8.9 + - - -
389A TRP* 1.3 77.8 - - - +
391A GLU* 1.3 55.6 + - - +
393A ILE* 3.2 4.3 + - - +
394A MSE 2.9 30.7 + - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 2.4 43.7 + - - -
314A ASN* 3.0 28.5 + - - +
317A VAL* 3.9 20.3 - - + +
374A LEU* 3.7 16.1 - - + +
387A VAL* 2.9 21.4 + - + +
388A HIS* 3.1 15.7 + - - +
390A GLY* 1.3 76.4 - - - +
392A ILE* 1.3 56.9 + - + +
394A MSE 3.5 12.1 - - - +
395A ALA* 2.9 32.4 + - - +
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Residues in contact with ILE 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.5 25.4 - - + -
112A PHE* 4.1 7.2 - - + -
317A VAL* 4.1 16.2 - - + -
321A ASN* 3.6 28.7 - - + +
388A HIS* 2.9 50.1 + - + +
389A TRP* 3.2 33.8 + - + +
391A GLU* 1.3 77.0 - - - +
393A ILE* 1.3 53.8 + - - +
395A ALA* 3.7 4.2 - - - +
396A THR* 2.4 42.0 + - - +
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Residues in contact with ILE 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.9 20.6 - - + -
118A LEU* 4.3 26.9 - - + +
121A LEU* 3.7 26.5 - - + -
122A PHE* 4.3 11.2 - - + -
125A ILE* 4.0 20.0 - - + -
370A ALA 4.8 0.2 - - - +
373A PRO* 3.9 22.4 - - + -
385A LEU* 6.3 1.1 - - + -
389A TRP* 2.9 23.9 + - + +
390A GLY* 3.2 4.2 + - - +
392A ILE* 1.3 77.0 - - - +
394A MSE 1.3 58.8 + - - +
396A THR* 3.3 5.3 + - - -
397A VAL* 2.9 37.8 + - + +
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Residues in contact with MSE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ARG* 3.9 2.9 - - - +
309A LEU* 4.6 2.7 - - + -
312A GLU* 3.4 33.9 - - - +
313A MSE 3.6 18.8 - - + -
314A ASN* 4.3 2.7 - - - +
318A ILE* 5.7 0.4 - - + -
370A ALA* 3.2 33.1 + - + +
371A SER* 3.2 29.2 - - - +
374A LEU* 4.5 9.4 - - + -
390A GLY 2.9 16.9 + - - +
391A GLU* 3.5 25.6 - - - +
393A ILE* 1.3 75.3 - - - +
395A ALA* 1.3 65.5 + - + +
397A VAL* 3.3 4.7 + - - +
398A VAL* 2.9 39.0 + - + +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ASN* 5.9 0.2 - - - +
317A VAL* 4.0 17.0 - - + +
318A ILE* 3.6 32.5 - - + -
321A ASN* 6.3 2.5 - - + -
391A GLU 2.9 19.3 + - - +
392A ILE* 3.7 4.0 - - - +
394A MSE 1.3 79.3 - - + +
396A THR* 1.3 62.6 + - - +
398A VAL* 3.1 4.9 + - - +
399A ILE* 2.9 32.8 + - + +
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Residues in contact with THR 396 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A PHE* 3.5 17.5 - - + -
112A PHE* 4.3 4.9 - - + -
122A PHE* 3.5 27.1 - - + -
321A ASN* 6.1 0.5 - - - +
325A GLY* 4.3 10.7 - - - +
328A VAL* 3.7 28.0 - - + -
392A ILE* 2.4 31.1 + - - +
393A ILE 3.7 2.0 - - - -
395A ALA* 1.3 76.6 - - - +
397A VAL* 1.3 51.8 + - - +
399A ILE* 3.6 7.1 + - - +
400A THR* 2.4 38.0 + - - +
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Residues in contact with VAL 397 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.6 20.6 - - + -
125A ILE* 4.0 18.6 - - + -
126A ILE* 4.2 5.8 - - + -
309A LEU* 5.9 0.2 - - + -
366A PRO* 3.5 36.3 - - + +
367A SER* 5.1 0.4 - - - -
370A ALA* 3.6 12.8 - - + -
393A ILE* 2.9 29.5 + - + +
394A MSE 3.5 4.3 - - - +
395A ALA 3.2 0.2 - - - -
396A THR* 1.3 73.4 - - - +
398A VAL* 1.3 61.4 + - - +
400A THR* 3.2 7.1 + - - -
401A VAL* 2.9 35.7 + - + +
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ILE* 5.1 6.5 - - + +
309A LEU* 3.7 36.3 - - + -
313A MSE 3.7 37.0 - - + -
318A ILE* 4.8 4.7 - - + -
394A MSE 2.9 24.1 + - + +
395A ALA* 3.4 10.3 - - - +
397A VAL* 1.3 76.2 - - - +
399A ILE* 1.3 66.3 + - + +
401A VAL* 3.1 8.7 + - - +
402A LEU* 2.9 38.6 + - + +
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Residues in contact with ILE 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 4.4 20.9 - - + +
321A ASN 4.4 1.8 - - - +
322A LEU* 4.1 37.2 - - + +
325A GLY* 3.9 26.0 - - - +
326A LEU* 3.8 22.0 - - + -
329A ALA* 4.7 0.4 - - + -
395A ALA* 2.9 24.4 + - + +
396A THR 3.8 4.0 - - - +
398A VAL* 1.3 78.5 - - + +
400A THR* 1.3 63.4 + - - +
402A LEU* 3.4 6.7 + - + +
403A THR* 2.9 37.3 + - - +
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Residues in contact with THR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A PHE* 3.5 13.5 - - + -
126A ILE* 4.3 27.4 - - + -
325A GLY 5.1 0.2 + - - -
329A ALA* 3.9 27.8 + - + +
332A VAL* 5.2 6.5 - - + -
333A MSE 6.3 1.1 - - + -
362A ARG* 4.3 14.6 - - + -
396A THR* 2.4 30.1 + - - +
397A VAL* 3.3 8.3 - - - -
399A ILE* 1.3 77.1 - - - +
401A VAL* 1.3 57.4 + - - +
403A THR* 4.0 0.5 - - - -
404A SER* 2.9 37.8 + - - -
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Residues in contact with VAL 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 3.9 25.4 - - + -
36A ILE* 4.4 9.4 - - + -
126A ILE* 5.8 0.2 - - + -
309A LEU* 5.2 1.8 - - + -
362A ARG* 3.3 35.7 - - + +
363A GLY* 4.4 3.1 - - - +
366A PRO* 4.5 3.6 - - + -
367A SER* 4.1 22.4 - - - +
397A VAL* 2.9 30.8 + - + +
398A VAL* 3.5 9.4 - - - +
400A THR* 1.3 75.9 - - - +
402A LEU* 1.3 64.7 + - - +
404A SER* 4.8 0.2 - - - -
405A VAL* 2.9 30.7 + - - +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A VAL* 5.0 1.6 - - + -
33A PRO* 4.0 30.3 - - + +
36A ILE* 4.0 32.8 - - + -
313A MSE 5.8 4.0 - - + -
398A VAL* 2.9 30.7 + - + +
399A ILE* 3.8 7.0 - - + +
401A VAL* 1.3 76.1 - - - +
403A THR* 1.3 64.5 + - - +
405A VAL* 4.0 1.5 - - - +
406A ILE* 2.9 40.9 + - + +
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Residues in contact with THR 403 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.6 23.4 - - + +
329A ALA* 4.0 15.7 - - + +
330A LEU* 4.3 14.4 - - + -
333A MSE 3.6 19.7 - - - -
399A ILE* 2.9 24.9 + - - +
400A THR 4.0 0.2 - - - -
402A LEU* 1.3 72.4 - - - +
404A SER* 1.3 58.3 + - - +
406A ILE* 4.0 2.6 - - - +
407A VAL* 2.9 46.5 + - + +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MSE 3.7 22.8 - - - +
360A GLY 4.6 0.5 + - - -
361A PRO* 3.2 25.6 - - - +
362A ARG* 3.7 14.2 + - - +
400A THR* 2.9 26.5 + - - -
401A VAL 4.1 0.9 - - - -
403A THR* 1.3 72.9 - - - +
405A VAL* 1.3 58.7 + - - +
408A GLU* 2.9 46.1 + - - +
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Residues in contact with VAL 405 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 3.7 25.4 - - - +
32A VAL* 4.2 21.1 - - + -
33A PRO* 4.7 4.7 - - + -
130A ASP 5.8 0.4 - - - +
133A THR* 4.1 10.5 - - + -
361A PRO* 3.8 17.5 - - + -
362A ARG 3.3 22.4 - - - +
363A GLY* 4.8 1.6 - - - -
401A VAL* 2.9 31.5 + - + +
402A LEU* 4.0 2.2 - - - +
404A SER* 1.3 71.6 - - - +
406A ILE* 1.3 64.8 + - + +
409A THR* 2.5 37.2 + - - +
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Residues in contact with ILE 406 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 6.2 1.3 - - - -
33A PRO* 3.9 31.9 - - + -
402A LEU* 2.9 37.1 + - + +
403A THR* 4.0 3.1 - - - +
405A VAL* 1.3 74.4 - - - +
407A VAL* 1.3 63.8 + - + +
409A THR* 3.8 3.1 - - - -
410A LEU* 2.9 45.6 + - + +
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Residues in contact with VAL 407 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 5.9 2.9 - - + -
333A MSE 3.6 19.3 - - + -
403A THR* 2.9 36.7 + - + +
406A ILE* 1.3 76.8 - - + +
408A GLU* 1.3 55.8 + - - +
409A THR 3.1 0.2 - - - -
410A LEU* 2.9 5.3 + - - -
411A TRP* 2.7 66.6 + - + -
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Residues in contact with GLU 408 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LEU* 3.5 6.8 - - - +
333A MSE 3.9 31.0 - - + +
337A ARG* 5.8 1.9 - - - +
357A ALA 4.6 1.9 - - - +
358A LEU* 2.9 28.8 - - - +
359A GLU* 2.8 32.1 - - - +
360A GLY 2.9 27.9 + - - +
361A PRO* 3.0 18.9 - - + -
404A SER* 2.9 35.7 + - - +
405A VAL 4.5 0.2 - - - +
407A VAL* 1.3 74.0 - - - +
409A THR* 1.3 58.9 + - - +
411A TRP* 3.3 14.3 - - - +
412A ILE* 4.0 4.9 - - - +
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Residues in contact with THR 409 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER* 4.9 8.1 - - - -
133A THR* 3.3 39.4 + - - +
134A LEU* 3.4 17.6 - - + +
137A LEU* 3.4 22.5 - - + +
361A PRO* 5.1 0.2 - - - +
405A VAL* 2.5 31.1 + - - +
406A ILE* 4.0 2.9 - - - -
408A GLU* 1.3 77.0 - - - +
410A LEU* 1.3 62.5 + - - +
412A ILE* 3.2 18.0 - - - +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ILE* 2.9 29.6 + - + +
407A VAL* 2.9 4.8 + - - +
409A THR* 1.3 81.2 - - - +
411A TRP* 1.3 58.7 + - - +
412A ILE 3.3 0.9 - - - -
413A PRO* 3.4 19.6 - - - +
414A ILE* 5.1 3.6 - - - +
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Residues in contact with TRP 411 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MSE 4.3 13.7 - - + -
334A ILE* 4.6 18.6 - - + -
358A LEU* 3.0 54.7 - - + -
359A GLU* 2.6 23.8 + - - -
407A VAL* 2.7 43.0 + - + +
408A GLU* 3.3 22.4 - - + +
410A LEU* 1.3 72.9 - - + +
412A ILE* 1.3 64.6 + - - +
413A PRO* 3.4 2.0 - - - -
414A ILE* 3.2 18.0 + - + +
415A LEU* 2.9 35.6 + - + +
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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