Contacts of the helix formed by residues 327 - 351 (chain A) in PDB entry 6CMO
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 327 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLN* 4.2 2.0 - - - -
325A CYS* 3.5 12.0 - - - -
326A SER* 1.3 89.6 + - - +
328A ASP* 1.3 66.7 + - + +
329A THR* 3.1 27.5 + - - +
330A LYS* 3.1 30.1 + - - +
331A ASN* 3.9 5.7 + - - -
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Residues in contact with ASP 328 (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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52A GLN* 3.1 54.1 + - + +
53A MET* 3.3 27.7 - - - +
327A THR* 1.3 70.1 - - + +
329A THR* 1.3 59.7 + - - +
330A LYS 3.2 0.2 - - - -
331A ASN* 3.0 31.3 + - - +
332A VAL* 3.2 18.9 + - - +
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Residues in contact with THR 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 5.2 11.2 - - + -
327A THR* 3.1 19.1 - - - +
328A ASP* 1.3 77.5 - - - +
330A LYS* 1.3 68.3 + - + +
332A VAL* 3.3 16.7 - - + +
333A GLN* 3.3 27.6 - - - +
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Residues in contact with LYS 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A HIS* 4.4 10.3 + - + -
325A CYS* 3.6 36.1 - - + -
326A SER* 5.8 0.6 + - - -
327A THR* 3.1 23.2 + - - +
329A THR* 1.3 83.4 - - + +
331A ASN* 1.3 64.6 + - - +
333A GLN* 3.4 31.4 + - - +
334A PHE* 3.7 3.1 + - - +
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Residues in contact with ASN 331 (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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52A GLN* 3.3 32.9 + - - +
267A PHE* 5.3 8.6 - - + -
322A HIS* 3.7 24.3 + - - -
323A PHE 4.4 0.9 - - - +
324A THR* 5.3 0.5 - - - -
325A CYS* 3.9 19.7 + - - +
327A THR 4.0 4.6 + - - -
328A ASP* 3.0 21.3 + - - +
330A LYS* 1.3 77.2 - - - +
332A VAL* 1.3 62.5 + - + +
334A PHE* 3.2 15.6 + - - +
335A VAL* 3.5 15.0 + - - +
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Residues in contact with VAL 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 4.9 14.6 - - + -
189A PHE* 5.2 11.2 - - + -
191A PHE* 3.7 41.4 - - + -
196A PHE* 5.5 5.6 - - + -
328A ASP* 3.2 24.0 + - - +
329A THR* 3.3 20.9 - - - +
331A ASN* 1.3 73.4 - - + +
333A GLN* 1.3 59.1 + - - +
335A VAL* 3.6 10.4 + - + +
336A PHE* 2.9 29.5 + - - +
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Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 4.8 12.6 - - + -
329A THR* 3.3 30.1 + - - +
330A LYS* 3.5 24.9 - - - +
331A ASN 3.2 0.4 - - - -
332A VAL* 1.3 78.6 - - - +
334A PHE* 1.3 56.8 + - - +
336A PHE* 3.1 7.7 + - - +
337A ASP* 2.9 34.6 + - - +
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Residues in contact with PHE 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ILE* 4.0 23.6 - - + -
267A PHE* 4.0 11.0 - + + -
320A TYR* 3.6 28.0 - + + -
321A THR 3.3 25.1 - - - -
322A HIS* 3.3 45.1 - + + +
330A LYS 3.7 2.5 + - - +
331A ASN 3.2 10.3 + - - +
333A GLN* 1.3 74.5 - - - +
335A VAL* 1.3 62.2 + - - +
337A ASP* 2.8 17.4 - - - +
338A ALA* 2.8 27.3 + - + +
239R GLU* 4.8 8.7 - - - -
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Residues in contact with VAL 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A LEU* 4.3 18.8 - - + -
196A PHE* 4.2 22.0 - - + -
222A ILE* 5.5 11.7 - - + -
265A ILE* 5.3 6.1 - - + -
267A PHE* 4.3 22.9 - - + -
331A ASN 3.5 12.3 + - - +
332A VAL* 3.8 11.9 - - + +
333A GLN 3.3 0.4 - - - -
334A PHE* 1.3 76.1 - - + +
336A PHE* 1.3 58.2 + - - +
338A ALA* 4.2 3.6 - - - -
339A VAL* 2.9 41.3 + - + +
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Residues in contact with PHE 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 4.0 23.1 - + + -
192A LYS* 3.3 47.8 - - + -
194A LEU* 3.7 24.2 - - + -
196A PHE* 4.9 6.5 - + + -
332A VAL 2.9 19.7 + - - +
333A GLN* 3.1 8.7 + - - +
335A VAL* 1.3 77.9 - - - +
337A ASP* 1.3 59.5 + - + +
339A VAL* 3.4 6.0 - - - +
340A THR* 2.6 47.1 + - + -
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Residues in contact with ASP 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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333A GLN 2.9 16.9 + - - +
334A PHE* 2.8 32.5 - - - +
336A PHE* 1.3 77.9 - - + +
338A ALA* 1.3 61.7 + - - +
340A THR* 3.8 7.7 - - - -
341A ASP* 2.9 30.5 + - - +
236R GLN* 5.2 17.3 - - + +
237R GLN* 5.9 1.7 - - - +
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Residues in contact with ALA 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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265A ILE* 4.3 13.9 - - + -
320A TYR* 4.0 34.0 - - + -
334A PHE* 2.8 24.0 + - + +
335A VAL* 3.6 5.6 - - - +
337A ASP* 1.3 83.2 + - - +
339A VAL* 1.3 59.0 + - - +
341A ASP* 3.2 4.9 + - - +
342A VAL* 3.0 28.9 + - - +
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Residues in contact with VAL 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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34A VAL* 5.0 10.1 - - + -
36A LEU* 4.7 11.7 - - + -
194A LEU* 4.3 19.1 - - + -
196A PHE* 4.4 12.3 - - + -
219A THR* 5.4 4.7 - - + -
220A ALA* 4.6 20.9 - - + -
222A ILE* 6.4 0.2 - - + -
265A ILE* 5.0 4.5 - - + -
335A VAL* 2.9 37.3 + - + +
336A PHE* 3.4 9.4 - - - +
338A ALA* 1.3 72.0 - - + +
340A THR* 1.3 63.3 + - - +
342A VAL* 3.3 9.0 - - + +
343A ILE* 3.0 42.4 + - + +
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Residues in contact with THR 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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194A LEU* 4.4 9.3 - - - +
336A PHE* 2.6 41.2 + - + -
337A ASP* 3.8 9.4 - - + -
339A VAL* 1.3 78.3 - - - +
341A ASP* 1.3 57.2 + - - +
343A ILE* 3.4 9.1 + - - +
344A ILE* 3.0 47.9 + - + +
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Residues in contact with ASP 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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320A TYR* 3.5 12.8 + - + +
337A ASP 2.9 20.3 + - - +
338A ALA* 3.2 5.4 + - - +
340A THR* 1.3 77.0 - - - +
342A VAL* 1.3 57.3 + - - +
344A ILE* 3.2 14.8 + - - +
345A LYS* 2.9 56.4 + - - +
233R ALA* 4.7 10.6 - - - +
237R GLN* 4.1 24.6 - - + +
243R THR* 4.1 15.2 + - - +
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Residues in contact with VAL 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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219A THR* 4.2 27.6 - - + +
220A ALA* 5.3 3.6 - - + -
263A SER* 4.6 22.4 - - - +
320A TYR* 5.4 7.9 - - + +
338A ALA 3.0 16.8 + - - +
339A VAL* 3.3 18.4 - - + +
341A ASP* 1.3 74.5 + - - +
343A ILE* 1.3 62.5 + - - +
345A LYS* 3.3 18.1 + - + +
346A ASN* 2.9 28.6 + - + +
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Residues in contact with ILE 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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34A VAL* 4.8 19.7 - - + -
194A LEU* 5.8 6.3 - - + -
219A THR* 4.8 13.5 - - + -
339A VAL* 3.0 31.0 + - + +
340A THR* 3.7 7.9 - - - +
341A ASP 3.3 0.2 - - - -
342A VAL* 1.3 76.3 - - + +
344A ILE* 1.3 60.6 + - + +
346A ASN* 3.2 7.0 + - - +
347A ASN* 2.9 48.9 + - - +
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Residues in contact with ILE 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 THR* 3.0 37.6 + - + +
341A ASP* 3.5 15.7 - - - +
343A ILE* 1.3 76.5 - - + +
345A LYS* 1.3 56.9 + - + +
347A ASN* 3.4 6.8 + - - +
348A LEU* 2.9 46.7 + - + +
139R VAL* 5.2 9.8 - - + +
229R THR* 6.0 5.6 - - + -
230R VAL* 5.6 8.3 - - + -
233R ALA* 4.8 20.9 - - + -
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Residues in contact with LYS 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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316A THR 5.6 6.3 + - - +
317A LYS* 6.1 1.6 - - - +
318A GLU* 5.1 7.1 + - - +
320A TYR* 3.3 20.6 + - - -
341A ASP* 2.9 35.9 + - - +
342A VAL* 3.5 20.1 - - + +
343A ILE 3.3 0.2 - - - -
344A ILE* 1.3 76.2 - - + +
346A ASN* 1.3 57.3 + - - +
348A LEU* 3.4 10.3 + - + +
349A LYS* 3.0 39.7 + - + +
354A PHE* 5.4 2.8 - - + -
240R SER* 3.5 17.0 + - - -
242R THR* 4.5 19.4 - - + -
243R THR* 4.1 15.7 - - - +
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Residues in contact with ASN 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 VAL* 2.9 17.2 + - + +
343A ILE* 3.2 8.5 + - + +
345A LYS* 1.3 77.5 - - - +
347A ASN* 1.3 58.6 + - - +
349A LYS* 3.4 8.7 + - - +
350A ASP* 2.9 30.4 + - - +
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Residues in contact with ASN 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 ILE* 2.9 40.1 + - - +
344A ILE* 3.9 5.5 + - - +
346A ASN* 1.3 74.1 - - - +
348A LEU* 1.3 61.0 + - - +
350A ASP* 3.2 11.4 + - - +
351A CYS* 2.9 35.4 + - - -
138R VAL* 5.0 18.5 + - + +
139R VAL* 4.3 22.5 - - + +
148R PHE* 5.7 5.9 - - - -
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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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344A ILE* 2.9 39.1 + - + +
345A LYS* 3.7 9.6 - - + +
346A ASN 3.3 0.2 - - - -
347A ASN* 1.3 77.9 - - - +
349A LYS* 1.3 61.4 + - - +
351A CYS* 3.4 13.7 + - + +
352A GLY 3.4 8.5 + - - -
353A LEU* 3.7 26.3 + - + +
354A PHE* 3.7 20.4 + - + -
139R VAL* 4.3 17.5 - - + -
226R LEU* 6.6 0.4 - - + -
230R VAL* 5.1 21.1 - - + -
246R ALA* 4.4 22.9 - - + -
250R VAL* 5.7 8.5 - - + -
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Residues in contact with LYS 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A ASP* 5.6 6.1 + - - +
316A THR* 3.4 24.4 + - - +
345A LYS* 3.0 25.4 + - + +
346A ASN* 3.9 9.9 - - - +
348A LEU* 1.3 75.6 - - - +
350A ASP* 1.3 61.1 + - - +
352A GLY* 3.6 7.1 + - - -
354A PHE* 3.9 37.7 - - + +
311R LYS* 4.0 9.0 + - - +
312R GLN* 4.6 12.0 + - - -
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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 ASN* 2.9 22.8 + - - +
347A ASN* 3.5 15.1 + - - +
348A LEU 3.2 0.2 - - - -
349A LYS* 1.3 78.2 - - - +
351A CYS* 1.3 64.2 + - - +
352A GLY* 3.4 0.5 + - - -
70R THR* 5.2 5.7 + - - -
72R LEU* 5.0 10.8 - - - +
148R PHE* 4.7 16.5 - - - -
312R GLN* 5.7 2.9 + - - +
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Residues in contact with CYS 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A ASN 2.9 21.9 + - - +
348A LEU* 3.4 7.8 + - + +
350A ASP* 1.3 77.4 - - - +
352A GLY* 1.3 60.9 + - - +
353A LEU* 3.3 25.9 + - + +
72R LEU* 4.1 25.6 - - + +
135R ARG* 4.9 17.2 + - + -
138R VAL* 4.2 25.8 - - - -
139R VAL* 4.5 16.4 - - - -
309R MET* 5.8 0.5 - - - +
310R ASN* 5.3 2.0 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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