Contacts of the helix formed by residues 334 - 359 (chain A) in PDB entry 3I5D
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A TYR 2.9 7.3 + - - +
59A ASP* 4.2 23.7 - - + +
333A PHE* 1.3 85.7 - - - +
335A ILE* 1.3 64.6 + - - +
336A ILE* 3.7 11.8 + - - +
337A PRO* 3.1 36.1 - - + +
338A THR* 2.6 28.3 + - - -
49C TYR* 5.2 5.0 + - - -
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Residues in contact with ILE 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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333A PHE* 3.9 19.4 - - + -
334A ASN* 1.3 76.6 + - - +
336A ILE* 1.3 65.7 + - - +
338A THR* 4.4 2.7 - - - -
339A LEU* 3.0 45.2 + - + +
45C TYR* 4.7 2.0 - - + +
49C TYR* 6.0 1.8 - - + +
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Residues in contact with ILE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A ASN* 3.7 14.1 + - - +
335A ILE* 1.3 81.7 - - - +
337A PRO* 1.3 67.6 - - + +
339A LEU* 4.3 1.6 - - - +
340A LEU* 3.3 21.0 + - - +
45C TYR* 4.4 10.0 + - - -
49C TYR* 4.9 14.5 + - + +
50C VAL* 4.7 20.2 - - + +
54C ASN* 5.6 4.9 - - + -
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Residues in contact with PRO 337 (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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56A GLY 3.8 18.8 - - - +
57A TYR 3.6 11.2 - - - +
58A GLN 4.4 9.9 - - - +
59A ASP* 4.9 1.8 - - + +
334A ASN* 3.1 40.6 - - + +
336A ILE* 1.3 96.6 - - + +
338A THR* 1.3 61.7 + - - +
340A LEU* 3.5 6.3 - - + +
341A ASN* 3.0 25.6 + - - +
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Residues in contact with THR 338 (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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51A CYS* 5.5 7.0 - - - -
56A GLY 5.7 0.2 - - - -
57A TYR* 3.2 29.0 - - + +
333A PHE* 3.4 16.9 - - + -
334A ASN 2.6 22.6 + - - -
335A ILE* 3.4 5.3 + - - -
337A PRO* 1.3 75.6 - - - +
339A LEU* 1.3 64.9 + - + +
341A ASN* 3.3 5.0 + - - +
342A ILE* 2.9 53.1 + - + +
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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
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335A ILE* 3.0 29.2 + - + +
336A ILE 4.3 0.9 - - - +
338A THR* 1.3 81.0 - - + +
340A LEU* 1.3 57.7 + - - +
342A ILE* 3.7 14.0 - - + +
343A GLY* 2.8 28.6 + - - -
45C TYR* 3.0 39.9 - - + +
344C ALA* 5.0 0.5 - - - +
348C LEU* 5.1 10.9 - - + +
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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
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336A ILE 3.3 18.2 + - - +
337A PRO* 3.5 9.4 - - + +
338A THR 3.2 0.2 - - - -
339A LEU* 1.3 80.9 - - - +
341A ASN* 1.3 63.3 + - + +
343A GLY 3.3 0.3 + - - -
344A ALA* 3.3 16.5 + - + +
340B LEU* 3.9 30.5 - - + -
340C LEU 4.3 3.6 - - - +
341C ASN* 2.9 40.6 - - + +
344C ALA* 3.6 26.8 - - + +
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Residues in contact with ASN 341 (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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45A TYR* 6.2 0.2 - - - -
46A VAL* 4.9 8.0 - - - +
50A VAL* 3.2 44.2 + - - +
51A CYS* 4.7 6.3 - - - -
56A GLY* 5.1 10.2 + - - +
337A PRO 3.0 14.4 + - - +
338A THR* 3.9 4.7 - - - +
340A LEU* 1.3 78.0 - - + +
342A ILE* 1.3 64.9 + - + +
344A ALA* 3.4 3.6 + - - +
345A GLY* 3.1 18.2 + - - -
340B LEU* 3.5 24.3 - - + +
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Residues in contact with ILE 342 (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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46A VAL* 5.4 17.7 - - + -
47A ILE* 6.1 5.4 - - + -
338A THR* 2.9 41.8 + - + +
339A LEU* 3.8 14.8 - - + +
341A ASN* 1.3 73.8 - - + +
343A GLY* 1.3 65.0 + - - +
345A GLY* 3.0 11.3 + - - +
346A LEU* 3.2 29.6 - - + +
351C LEU* 5.6 7.6 - - + -
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Residues in contact with GLY 343 (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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339A LEU 2.8 17.6 + - - -
340A LEU 3.7 2.7 - - - -
341A ASN 3.2 0.2 - - - -
342A ILE* 1.3 77.3 - - - +
344A ALA* 1.3 60.6 + - - +
346A LEU* 3.3 11.0 + - - +
347A ALA 3.4 0.9 + - - -
344C ALA* 3.9 20.0 - - - -
347C ALA* 2.9 31.6 - - - +
348C LEU* 4.5 7.0 - - - -
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Residues in contact with ALA 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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340A LEU 3.3 8.2 + - - +
341A ASN 3.8 2.5 - - - +
342A ILE 3.3 0.2 - - - -
343A GLY* 1.3 72.4 - - - +
345A GLY* 1.3 58.7 + - - +
346A LEU 3.2 0.2 - - - -
347A ALA* 3.4 8.2 + - - +
348A LEU* 2.8 31.1 + - - +
339B LEU 4.9 0.6 - - - +
340B LEU* 3.5 49.8 - - + +
343B GLY* 4.4 8.7 - - - -
344B ALA* 4.9 2.9 - - + +
344C ALA* 4.3 6.6 - - + +
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Residues in contact with GLY 345 (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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42A VAL* 4.7 10.4 - - - +
45A TYR* 6.3 0.9 - - - -
46A VAL* 4.5 18.4 - - - -
341A ASN 3.1 11.4 + - - -
342A ILE 3.0 9.3 + - - -
344A ALA* 1.3 78.1 - - - +
346A LEU* 1.3 59.9 + - - +
348A LEU* 3.6 7.0 + - - +
349A LEU* 3.2 24.9 + - - +
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Residues in contact with LEU 346 (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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342A ILE* 3.2 29.1 + - + +
343A GLY* 3.5 8.5 - - - +
344A ALA 3.2 0.4 - - - -
345A GLY* 1.3 75.7 - - - +
347A ALA* 1.3 66.3 + - - +
348A LEU 3.1 1.1 - - - -
349A LEU* 3.0 42.1 + - + +
350A GLY* 3.3 1.0 + - - -
347C ALA* 3.3 28.5 - - + +
348C LEU* 5.0 0.9 - - - -
350C GLY 4.9 0.7 - - - -
351C LEU* 3.3 32.5 - - + +
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Residues in contact with ALA 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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343A GLY 3.4 9.5 + - - +
344A ALA* 3.9 6.5 - - - +
346A LEU* 1.3 78.9 - - - +
348A LEU* 1.3 61.6 + - - +
350A GLY* 3.1 12.1 + - - +
351A LEU* 3.4 11.3 + - - +
343B GLY* 3.3 30.1 - - - +
346B LEU* 4.6 12.8 - - + +
347B ALA* 4.9 6.1 - - + +
347C ALA* 4.2 12.2 - - + +
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Residues in contact with LEU 348 (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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42A VAL* 5.5 4.0 - - + -
344A ALA 2.8 19.3 + - - +
345A GLY* 3.6 10.3 - - - +
346A LEU 3.1 0.2 - - - -
347A ALA* 1.3 78.5 - - - +
349A LEU* 1.3 56.0 + - - +
350A GLY 3.2 0.2 - - - -
351A LEU* 3.6 6.4 + - - +
352A VAL* 3.1 26.5 + - - +
339B LEU* 5.3 16.6 - - + +
343B GLY* 4.9 4.9 - - - -
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Residues in contact with LEU 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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38A THR* 5.5 5.6 + - - +
39A GLN* 4.9 14.6 - - + -
42A VAL* 4.3 30.5 - - + +
345A GLY 3.2 8.5 + - - +
346A LEU* 3.0 34.3 + - + +
348A LEU* 1.3 75.3 - - - +
350A GLY* 1.3 71.2 + - - +
351A LEU 3.4 0.2 - - - -
352A VAL* 3.8 8.6 - - + +
353A ASN* 3.2 25.8 + - - +
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Residues in contact with GLY 350 (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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346A LEU 3.3 1.5 + - - -
347A ALA* 3.1 10.0 + - - -
349A LEU* 1.3 90.7 - - - +
351A LEU* 1.3 56.9 + - - +
353A ASN* 4.3 1.1 - - - +
354A VAL* 3.1 31.4 + - - +
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Residues in contact with LEU 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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347A ALA 3.4 10.3 + - - +
348A LEU* 3.6 7.8 + - - +
350A GLY* 1.3 74.8 - - - +
352A VAL* 1.3 60.6 + - - +
353A ASN 3.4 0.2 - - - -
354A VAL* 4.6 3.1 - - - +
355A ILE* 3.0 37.1 + - + +
342B ILE* 6.3 3.6 - - + -
346B LEU* 6.1 4.3 - - + -
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Residues in contact with VAL 352 (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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38A THR* 5.4 10.3 - - + +
42A VAL* 5.2 9.2 - - + -
348A LEU 3.1 19.1 + - - +
349A LEU* 3.9 9.6 - - - +
350A GLY 3.3 0.2 - - - -
351A LEU* 1.3 78.5 - - - +
353A ASN* 1.3 58.4 + - + +
355A ILE* 5.2 0.2 - - - -
356A CYS* 2.9 33.3 + - - +
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Residues in contact with ASN 353 (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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38A THR* 4.6 15.7 - - + +
349A LEU* 3.2 17.8 + - + +
350A GLY* 4.5 2.0 - - - +
352A VAL* 1.3 78.5 - - - +
354A VAL* 1.3 58.6 + - - +
356A CYS* 4.0 7.1 - - - -
357A ASP* 3.2 26.5 + - - +
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Residues in contact with VAL 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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350A GLY 3.1 20.2 + - - +
351A LEU* 4.5 2.7 - - - +
353A ASN* 1.3 80.0 - - - +
355A ILE* 1.3 60.4 + - - +
356A CYS 3.6 0.2 - - - -
357A ASP* 3.9 3.8 + - - +
358A TRP* 3.5 19.8 + - - +
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Residues in contact with ILE 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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351A LEU* 3.0 22.6 + - + +
352A VAL* 4.9 0.4 - - - +
354A VAL* 1.3 77.8 - - - +
356A CYS* 1.3 58.5 + - - +
357A ASP 3.3 0.4 - - - -
358A TRP* 3.4 8.4 + - - +
359A ILE* 3.2 22.7 + - - +
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Residues in contact with CYS 356 (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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38A THR* 4.9 14.1 - - - -
352A VAL 2.9 29.3 + - - +
353A ASN* 4.0 8.3 - - - -
355A ILE* 1.3 75.5 - - - +
357A ASP* 1.3 66.4 + - - +
358A TRP 3.3 0.7 - - - -
359A ILE* 3.4 22.8 + - + +
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Residues in contact with ASP 357 (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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353A ASN 3.2 19.7 + - - +
354A VAL* 4.1 5.4 - - - +
355A ILE 3.3 0.2 - - - -
356A CYS* 1.3 82.6 - - - +
358A TRP* 1.3 60.6 - - - +
359A ILE 3.6 2.8 + - - -
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Residues in contact with TRP 358 (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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354A VAL 3.5 13.2 + - - +
355A ILE* 3.4 12.5 + - - +
356A CYS 3.3 0.4 - - - -
357A ASP* 1.3 78.5 - - - +
359A ILE* 1.3 59.8 + - - +
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Residues in contact with ILE 359 (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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355A ILE 3.2 13.4 + - - +
356A CYS* 3.4 19.7 + - + +
357A ASP 3.3 4.5 - - - -
358A TRP* 1.3 82.0 - - - +
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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) + - + + + + + -
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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