Contacts of the helix formed by residues 334 - 361 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A TYR* 5.6 1.7 + - - -
57B TYR 3.2 5.8 + - - +
59B ASP* 4.2 23.0 - - + +
333B PHE* 1.3 88.1 - - - +
335B ILE* 1.3 65.0 + - - +
336B ILE* 3.7 11.6 + - - +
337B PRO* 3.1 36.2 - - + +
338B THR* 2.6 28.2 + - - -
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Residues in contact with ILE 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 5.1 2.2 - - - +
333B PHE* 3.9 18.8 - - + -
334B ASN* 1.3 76.4 + - - +
336B ILE* 1.3 65.7 + - - +
338B THR* 4.4 2.5 - - - -
339B LEU* 3.0 44.9 + - + +
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Residues in contact with ILE 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 4.8 9.6 + - - +
49A TYR* 5.6 8.7 - - + +
50A VAL* 4.9 17.0 - - + -
54A ASN* 6.0 2.9 - - + -
334B ASN* 3.3 13.2 + - - +
335B ILE* 1.3 80.4 - - - +
337B PRO* 1.3 67.9 - - + +
339B LEU* 4.3 2.1 - - - +
340B LEU* 3.3 21.0 + - - +
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Residues in contact with PRO 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 3.8 19.5 - - - +
57B TYR 3.2 15.7 - - - +
58B GLN 4.3 10.1 - - - +
59B ASP* 4.7 2.0 - - + +
334B ASN* 3.1 38.1 - - + +
336B ILE* 1.3 96.3 - - + +
338B THR* 1.3 61.6 + - - +
340B LEU* 3.5 6.5 - - + +
341B ASN* 3.0 25.3 + - - +
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Residues in contact with THR 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B CYS* 5.7 5.2 - - - -
57B TYR* 3.1 31.1 - - + +
333B PHE* 3.4 17.1 - - + -
334B ASN 2.6 23.3 + - - -
335B ILE* 3.4 4.4 + - - -
337B PRO* 1.3 76.1 - - - +
339B LEU* 1.3 64.4 + - + +
341B ASN* 3.3 5.1 + - - +
342B ILE* 2.9 52.8 + - + +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A TYR* 3.4 32.5 - - + +
344A ALA* 4.9 2.6 - - - +
348A LEU* 5.3 13.0 - - + +
335B ILE* 3.0 30.1 + - + +
336B ILE 4.3 2.0 - - - +
338B THR* 1.3 79.5 - - + +
340B LEU* 1.3 54.9 + - - +
342B ILE* 3.8 14.8 - - + +
343B GLY* 2.8 32.4 + - - -
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A LEU* 3.9 22.2 - - + -
341A ASN* 3.5 35.0 - - + +
344A ALA* 3.5 26.5 - - + +
336B ILE 3.3 18.3 + - - +
337B PRO* 3.5 9.0 - - + +
339B LEU* 1.3 81.9 - - - +
341B ASN* 1.3 66.4 + - + +
343B GLY* 3.3 7.6 + - - -
344B ALA* 3.3 11.0 + - + +
340C LEU* 5.3 13.5 - - + +
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Residues in contact with ASN 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 4.5 9.1 - - - +
50B VAL* 2.9 45.0 + - - +
51B CYS* 3.9 12.5 - - - -
56B GLY* 4.7 11.3 - - - +
57B TYR* 6.3 0.2 - - - -
337B PRO 3.0 15.2 + - - +
338B THR* 3.9 3.8 - - - +
340B LEU* 1.3 81.6 - - + +
342B ILE* 1.3 66.3 + - + +
344B ALA* 3.4 4.9 + - - +
345B GLY* 3.1 18.0 + - - -
336C ILE 5.4 1.0 - - - +
340C LEU* 4.4 16.7 - - - +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B VAL* 5.5 14.5 - - + +
47B ILE* 5.8 10.1 - - + -
51B CYS* 5.8 6.1 - - - -
338B THR* 2.9 42.2 + - + +
339B LEU* 3.8 14.6 - - + +
341B ASN* 1.3 75.3 - - + +
343B GLY* 1.3 66.1 + - - +
345B GLY* 3.0 12.3 + - - +
346B LEU* 3.2 13.3 + - + +
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Residues in contact with GLY 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 4.4 13.5 - - - -
347A ALA* 3.3 31.4 - - - +
348A LEU* 4.9 5.8 - - - -
339B LEU 2.8 20.3 + - - -
340B LEU 3.7 2.9 - - - -
341B ASN 3.2 0.4 - - - -
342B ILE* 1.3 74.6 - - - +
344B ALA* 1.3 60.0 + - - +
346B LEU* 3.3 11.7 + - - +
347B ALA* 3.4 4.9 + - - +
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Residues in contact with ALA 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A ALA* 4.9 2.8 - - + +
340B LEU* 3.3 12.2 + - + +
341B ASN* 3.8 7.6 - - - +
342B ILE 3.3 0.2 - - - -
343B GLY* 1.3 74.6 - - - +
345B GLY* 1.3 60.0 + - - +
347B ALA* 3.4 2.0 + - - +
348B LEU* 2.8 31.3 + - - +
339C LEU 4.3 1.2 - - - +
340C LEU* 3.5 42.0 - - + +
343C GLY* 3.9 17.3 - - - -
344C ALA* 4.5 2.9 - - + +
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Residues in contact with GLY 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 4.1 10.8 - - - +
46B VAL* 3.8 30.3 - - - -
341B ASN 3.1 6.5 + - - -
342B ILE 3.0 9.3 + - - -
344B ALA* 1.3 77.3 - - - +
346B LEU* 1.3 56.0 + - - +
348B LEU* 3.6 8.0 + - - +
349B LEU* 3.2 24.4 + - - +
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Residues in contact with LEU 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA* 4.6 14.1 - - + +
342B ILE* 3.2 11.0 + - + +
343B GLY* 3.4 11.0 - - - +
344B ALA 3.2 0.2 - - - -
345B GLY* 1.3 74.0 - - - +
347B ALA* 1.3 64.8 + - - +
348B LEU 3.1 1.3 - - - -
349B LEU* 3.1 16.8 + - - +
350B GLY* 3.4 8.1 + - - -
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Residues in contact with ALA 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ALA* 4.9 7.8 - - + +
343B GLY 3.4 9.4 + - - +
344B ALA 3.4 2.0 + - - +
346B LEU* 1.3 78.9 - - - +
348B LEU* 1.3 60.9 + - - +
350B GLY* 3.2 11.2 + - - +
351B LEU 3.4 1.7 + - - -
343C GLY* 2.9 36.8 - - - +
346C LEU* 3.2 32.7 - - + +
347C ALA* 4.6 3.8 - - + +
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Residues in contact with LEU 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B VAL* 4.3 8.3 - - + +
45B TYR* 6.2 3.6 - - + -
344B ALA 2.8 19.6 + - - +
345B GLY* 3.7 9.9 - - - +
347B ALA* 1.3 75.5 - - - +
349B LEU* 1.3 59.4 + - - +
350B GLY 3.2 0.2 - - - -
351B LEU* 3.6 6.3 + - - +
352B VAL* 3.1 27.0 + - - +
339C LEU* 5.1 22.0 - - + +
343C GLY* 4.6 3.3 - - - -
346C LEU* 5.3 0.7 - - - -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 5.6 0.4 - - - -
39B GLN* 4.8 11.0 - - + -
42B VAL* 3.5 34.3 - - + +
345B GLY 3.2 7.5 + - - +
346B LEU* 3.1 13.3 + - - +
348B LEU* 1.3 73.9 - - - +
350B GLY* 1.3 63.2 + - - +
352B VAL* 3.7 2.7 - - - +
353B ASN* 3.0 32.6 + - - +
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Residues in contact with GLY 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B LEU 3.4 5.3 + - - -
347B ALA* 3.2 9.7 + - - -
349B LEU* 1.3 80.0 - - - +
351B LEU* 1.3 60.4 + - - +
353B ASN* 3.6 20.2 + - - +
354B VAL* 3.8 5.7 + - - +
346C LEU* 5.1 2.2 - - - -
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Residues in contact with LEU 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B ALA 3.4 5.6 + - - +
348B LEU* 4.2 7.2 - - - +
349B LEU 3.4 0.2 - - - -
350B GLY* 1.3 73.7 - - - +
352B VAL* 1.3 59.1 + - - +
353B ASN 3.2 0.4 - - - -
354B VAL* 2.9 25.7 + - + +
355B ILE* 3.0 12.5 + - - +
342C ILE* 6.1 3.8 - - + -
346C LEU* 4.0 21.2 - - + +
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Residues in contact with VAL 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B THR* 3.9 25.8 - - + +
41B LEU* 6.4 2.0 - - + -
42B VAL* 4.2 11.0 - - + -
348B LEU 3.1 18.8 + - - +
349B LEU* 3.7 10.8 - - - +
350B GLY 3.3 0.2 - - - -
351B LEU* 1.3 72.7 - - - +
353B ASN* 1.3 65.9 + - - +
355B ILE* 3.2 20.0 + - + +
356B CYS* 3.4 9.5 + - - -
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Residues in contact with ASN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ASN* 4.0 25.6 + - + +
38B THR* 2.8 30.3 + - - -
39B GLN* 5.5 1.0 - - - +
349B LEU* 3.0 16.3 + - - +
350B GLY* 3.6 12.9 + - - +
351B LEU 3.2 0.2 - - - -
352B VAL* 1.3 77.1 - - - +
354B VAL* 1.3 60.1 + - - +
356B CYS* 3.8 3.7 + - - +
357B ASP* 3.4 19.2 + - - +
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Residues in contact with VAL 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350B GLY 3.8 2.6 + - - +
351B LEU* 2.9 20.1 + - + +
353B ASN* 1.3 77.4 - - - +
355B ILE* 1.3 62.9 + - - +
357B ASP* 3.5 10.5 - - + +
358B TRP* 3.4 19.8 + - - +
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Residues in contact with ILE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B LEU 3.0 9.8 + - - +
352B VAL* 3.2 14.5 + - - +
354B VAL* 1.3 76.5 - - - +
356B CYS* 1.3 62.9 + - - +
357B ASP 3.2 0.2 - - - -
358B TRP* 3.6 5.6 + - - +
359B ILE* 3.3 22.5 + - - +
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Residues in contact with CYS 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 5.0 14.6 - - + -
37B PHE* 5.4 5.8 - - - -
38B THR* 3.3 32.8 - - + -
352B VAL 3.4 7.1 + - - +
353B ASN* 3.8 4.5 + - - +
355B ILE* 1.3 78.3 - - - +
357B ASP* 1.3 60.8 + - - +
359B ILE* 3.6 10.1 - - + +
360B VAL* 3.0 27.0 + - - +
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Residues in contact with ASP 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B ASN 3.4 14.4 + - - +
354B VAL* 3.5 15.3 - - - +
355B ILE 3.2 0.4 - - - -
356B CYS* 1.3 78.9 - - - +
358B TRP* 1.3 60.1 + - - +
360B VAL* 3.2 20.0 + - - +
361B LEU* 3.3 8.1 + - - +
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Residues in contact with TRP 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B VAL 3.4 12.0 + - - +
355B ILE* 3.6 6.3 + - - +
356B CYS 3.4 0.2 - - - -
357B ASP* 1.3 76.0 - - - +
359B ILE* 1.3 59.9 + - - +
361B LEU* 3.1 18.8 + - - +
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Residues in contact with ILE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B ILE 3.3 17.3 + - - +
356B CYS* 3.6 12.3 - - + +
357B ASP 3.2 0.4 - - - -
358B TRP* 1.3 75.6 - - - +
360B VAL* 1.3 61.5 + - - +
361B LEU* 3.5 2.3 + - - +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356B CYS 3.0 14.5 + - - +
357B ASP* 3.2 14.8 + - - +
359B ILE* 1.3 75.6 - - - +
361B LEU* 1.3 69.0 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASP 3.3 8.4 + - - +
358B TRP* 3.1 17.9 + - - +
359B ILE 3.2 2.6 - - - +
360B VAL* 1.3 85.8 - - - +
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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