Contacts of the helix formed by residues 334 - 360 (chain A) in PDB entry 2G9Y
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).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TRP 5.3 0.2 - - - +
270A GLY 2.8 30.3 + - - +
271A PRO 3.6 13.3 + - - -
272A LYS* 3.9 5.4 - - - +
329A GLN* 3.0 33.6 + - - +
332A ALA* 3.9 8.3 - - + +
333A ALA* 1.3 76.6 - - - +
335A PRO* 1.3 63.7 - - - +
336A CYS* 3.5 6.4 + - - +
337A GLY* 2.8 27.4 + - - -
338A GLN* 2.9 21.3 + - - +
402A TYR* 3.9 3.5 + - - -
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Residues in contact with PRO 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PRO 4.4 2.7 - - - +
273A ALA 4.5 1.3 - - - +
286A CYS* 5.0 0.2 - - - -
333A ALA 3.3 11.2 - - - +
334A ASN* 1.3 83.6 - - - +
336A CYS* 1.3 57.7 + - - +
338A GLN* 3.2 2.4 + - + -
339A ILE* 2.8 38.0 + - - +
388A GLN* 3.5 40.2 - - + +
390A LEU* 3.7 21.3 - - + -
400A MET* 3.8 15.9 - - + -
402A TYR* 3.5 27.3 - - + +
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Residues in contact with CYS 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A TRP* 3.6 11.0 - - + +
269A LEU 3.7 20.0 - - - +
270A GLY* 3.8 12.8 - - - -
271A PRO 5.5 0.2 + - - -
284A VAL* 3.9 19.5 - - - -
286A CYS* 2.0 58.3 - - + -
334A ASN* 3.3 1.4 + - - +
335A PRO* 1.3 79.4 - - - +
337A GLY* 1.3 58.4 + - - +
339A ILE* 4.8 0.2 - - - -
340A GLY* 2.9 27.9 + - - -
388A GLN* 4.6 2.0 + - - +
390A LEU* 4.0 5.2 - - - -
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Residues in contact with GLY 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266A VAL* 4.9 4.0 - - - -
268A TRP* 3.8 16.7 + - - -
329A GLN* 3.4 22.2 - - - +
334A ASN* 2.8 19.9 + - - -
336A CYS* 1.3 73.0 - - - +
338A GLN* 1.3 61.6 + - - +
340A GLY* 4.0 0.2 - - - -
341A GLU* 3.2 31.7 + - - +
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Residues in contact with GLN 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLU* 3.6 20.0 + - + +
60A ALA* 4.9 1.4 - - - +
326A ILE* 3.7 26.5 - - + +
329A GLN* 3.3 12.9 - - + +
330A ASP* 3.0 30.0 - - - +
334A ASN 2.9 16.2 + - - +
335A PRO 3.5 3.8 - - - +
337A GLY* 1.3 74.7 - - - +
339A ILE* 1.3 65.9 + - - +
341A GLU* 3.4 5.5 + - - +
342A THR* 3.0 25.3 + - - +
374A SER* 3.1 20.0 + - - -
400A MET* 3.5 15.0 - - - +
402A TYR* 2.9 24.3 + - - -
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Residues in contact with ILE 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A ALA* 4.2 6.1 - - + +
61A ALA* 3.7 32.1 - - + +
64A TYR* 3.9 31.4 - - + -
268A TRP* 3.6 23.1 - - + -
286A CYS* 5.5 0.4 - - - -
335A PRO* 2.8 27.7 + - + +
336A CYS* 4.2 2.2 - - - +
338A GLN* 1.3 73.0 - - + +
340A GLY* 1.3 65.9 + - - +
342A THR* 3.0 9.4 + - - -
343A VAL* 3.0 23.1 + - + +
390A LEU* 4.6 4.5 - - + -
398A MET* 4.4 2.0 - - + -
400A MET* 3.8 31.0 - - + -
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Residues in contact with GLY 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 3.6 8.6 - - - -
268A TRP* 3.5 34.7 - - - -
336A CYS 2.9 15.7 + - - -
337A GLY 4.0 0.9 - - - -
339A ILE* 1.3 78.8 - - - +
341A GLU* 1.3 61.6 + - - +
343A VAL* 3.4 5.3 + - - +
344A ASP* 3.0 24.6 + - - +
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Residues in contact with GLU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.6 9.4 + - - +
264A MET 5.4 0.5 - - - +
265A PRO 4.5 3.1 - - - +
266A VAL* 3.8 13.8 - - + +
267A ARG* 2.9 34.5 + - - +
323A GLY* 5.3 4.4 - - - +
325A SER* 3.4 36.7 + - - +
326A ILE* 3.6 25.8 - - + +
337A GLY 3.2 18.1 + - - +
338A GLN 3.4 1.8 + - - +
339A ILE 3.2 0.4 - - - -
340A GLY* 1.3 73.9 - - - +
342A THR* 1.3 61.0 + - - +
344A ASP* 3.2 17.9 - - - +
345A LEU* 2.9 25.3 + - - +
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Residues in contact with THR 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A MET* 4.0 26.2 - - + +
57A GLU* 4.5 8.7 + - - +
58A ILE* 4.7 2.7 - - - -
61A ALA* 3.5 25.7 - - + +
72A PHE* 4.6 6.1 - - + -
75A ILE* 3.8 8.5 - - + +
326A ILE* 3.7 20.5 - - - +
338A GLN* 3.0 17.0 + - - +
339A ILE* 3.0 9.4 + - - -
341A GLU* 1.3 75.3 - - - +
343A VAL* 1.3 66.6 + - - +
345A LEU* 3.2 3.3 + - - +
346A ASP* 3.0 22.5 + - - +
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Residues in contact with VAL 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ALA* 3.7 30.7 - - + -
72A PHE* 4.6 11.4 - - + -
267A ARG* 3.9 25.6 - - - +
268A TRP* 3.9 19.7 - - + -
339A ILE* 3.0 18.8 + - + +
340A GLY* 3.5 7.9 - - - +
342A THR* 1.3 75.6 - - - +
344A ASP* 1.3 65.3 + - - +
346A ASP* 3.1 20.4 + - + +
347A GLU* 3.3 14.7 + - + +
658A SO4 4.9 1.8 - - - +
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Residues in contact with ASP 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 4.0 12.0 - - - +
267A ARG* 3.6 21.0 + - - +
292A ARG* 4.3 13.4 + - - -
298A THR* 4.7 0.9 - - - -
299A LEU* 3.4 39.4 + - - +
300A ALA 4.8 0.7 + - - -
323A GLY* 5.4 1.4 - - - -
340A GLY 3.0 15.0 + - - +
341A GLU* 3.2 26.2 - - - +
343A VAL* 1.3 76.9 - - - +
345A LEU* 1.3 62.6 + - - +
347A GLU* 3.1 18.4 + - - +
348A ALA* 3.4 9.9 + - - +
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Residues in contact with LEU 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 4.5 22.7 - - + -
49A ILE 4.0 14.6 - - - +
50A GLY* 3.6 21.1 - - - +
53A MET* 3.5 37.0 - - + -
75A ILE* 4.3 4.0 - - + -
299A LEU* 4.1 23.3 - - + +
321A VAL 5.0 0.9 - - - +
322A GLU 4.9 0.9 - - - -
323A GLY* 4.1 5.8 - - - +
326A ILE* 4.3 4.7 - - + -
341A GLU 2.9 13.5 + - - +
342A THR 3.2 8.5 + - - +
344A ASP* 1.3 75.8 + - - +
346A ASP* 1.3 64.4 + - - +
348A ALA* 3.0 4.2 + - - +
349A VAL* 2.9 28.9 + - + +
366A VAL* 4.9 3.1 - - + -
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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
----------------------------------------------------------
66A GLU* 5.3 2.4 - - - +
72A PHE* 3.2 28.6 - - + +
73A LYS 4.3 2.4 + - - -
74A GLY 2.8 26.1 + - - -
75A ILE* 3.0 30.3 + - + +
342A THR 3.0 13.1 + - - +
343A VAL* 3.1 13.0 + - + +
345A LEU* 1.3 75.3 - - - +
347A GLU* 1.3 63.6 + - - +
349A VAL* 3.3 2.7 + - - +
350A GLN* 2.8 46.0 + - - +
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Residues in contact with GLU 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267A ARG* 2.9 40.9 + - - -
292A ARG* 5.4 0.7 + - - -
298A THR* 5.2 6.2 + - - +
300A ALA* 3.9 20.4 - - + +
343A VAL* 3.5 15.8 - - + +
344A ASP* 3.1 10.8 + - - +
346A ASP* 1.3 74.1 - - - +
348A ALA* 1.3 66.7 + - - +
350A GLN* 3.1 19.0 + - - +
351A ARG* 3.1 27.7 + - - +
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Residues in contact with ALA 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 14.8 - - + +
299A LEU* 3.7 29.2 - - + +
300A ALA* 4.0 12.9 - - - +
303A THR* 3.7 22.5 - - - +
321A VAL* 4.5 0.2 - - + -
344A ASP 3.4 2.4 + - - +
345A LEU* 3.0 10.0 + - - +
347A GLU* 1.3 77.9 - - - +
349A VAL* 1.3 61.7 + - - +
351A ARG* 3.2 5.7 + - - +
352A ALA* 3.1 21.3 + - - +
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A LEU* 3.8 21.1 - - + -
74A GLY* 3.3 31.0 - - - +
75A ILE* 3.7 14.8 - - + +
78A LEU* 4.3 0.4 - - + -
345A LEU* 2.9 25.0 + - + +
346A ASP 3.5 7.6 - - - +
347A GLU 3.2 0.2 - - - -
348A ALA* 1.3 73.2 - - - +
350A GLN* 1.3 60.1 + - - +
352A ALA* 3.1 3.7 + - - +
353A LEU* 2.8 39.6 + - + +
364A VAL* 5.4 0.2 - - + -
366A VAL* 3.9 30.5 - - + -
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Residues in contact with GLN 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A LYS* 3.6 32.9 - - + +
74A GLY* 3.5 18.6 - - - +
346A ASP* 2.8 39.4 + - - +
347A GLU* 3.1 18.2 + - - +
349A VAL* 1.3 75.6 - - - +
351A ARG* 1.3 60.9 + - + +
353A LEU* 3.8 5.0 - - - +
354A GLU* 2.8 51.8 + - - +
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Residues in contact with ARG 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A ALA* 3.1 44.6 + - + +
301A GLN* 4.7 10.3 - - - +
303A THR* 4.3 9.4 - - + -
304A ASP* 2.8 45.0 + - - +
307A ILE* 4.2 3.9 - - - +
347A GLU* 3.1 16.1 + - - +
348A ALA 3.6 6.3 - - - +
349A VAL 3.2 0.2 - - - -
350A GLN* 1.3 76.6 - - - +
352A ALA* 1.3 63.0 + - - +
354A GLU* 3.7 20.7 + - - +
355A PHE* 3.1 23.2 + - - +
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Residues in contact with ALA 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.9 27.1 - - + +
48A LEU* 3.8 25.8 - - + -
303A THR* 4.6 3.7 - - + +
307A ILE* 4.2 5.4 - - - -
348A ALA 3.1 11.8 + - - +
349A VAL 3.1 8.6 + - - +
351A ARG* 1.3 76.3 - - - +
353A LEU* 1.3 57.8 + - - +
355A PHE* 3.3 2.8 + - - +
356A ALA* 2.8 32.1 + - - +
364A VAL* 4.1 7.9 - - + +
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Residues in contact with LEU 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A VAL* 4.2 19.5 - - + +
73A LYS 4.4 1.8 - - - +
74A GLY* 3.6 28.5 - - - +
77A ALA* 3.9 17.7 - - + -
78A LEU* 3.6 28.5 - - + -
349A VAL* 2.8 28.7 + - + +
350A GLN* 3.9 4.5 - - - +
352A ALA* 1.3 70.8 - - - +
354A GLU* 1.3 60.0 + - + +
356A ALA* 3.8 2.4 - - - +
357A LYS* 2.9 34.1 + - - +
364A VAL* 3.9 18.8 - - + -
422A TYR* 4.2 15.9 - - + -
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Residues in contact with GLU 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A GLN* 2.8 42.3 + - - +
351A ARG* 3.7 21.9 - - - +
353A LEU* 1.3 79.1 - - + +
355A PHE* 1.3 63.2 + - - +
357A LYS* 4.3 3.5 - - - +
358A LYS* 3.5 18.0 + - - +
----------------------------------------------------------
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Residues in contact with PHE 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 3.9 7.6 - - - -
46A ILE* 4.1 13.5 - - + -
304A ASP* 6.0 0.2 - - - +
307A ILE* 3.4 35.7 - - + -
311A SER* 4.3 13.5 - - - -
317A PHE* 3.9 22.9 - + - -
351A ARG 3.1 17.6 + - - +
352A ALA 3.6 2.0 - - - +
354A GLU* 1.3 77.9 - - - +
356A ALA* 1.3 62.2 + - - +
358A LYS* 3.2 7.8 + - + +
359A GLU* 2.9 50.9 + - + +
362A THR* 3.4 21.8 - - + -
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Residues in contact with ALA 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ALA 2.8 21.8 + - - +
353A LEU* 3.8 4.5 - - - +
355A PHE* 1.3 80.1 - - - +
357A LYS* 1.3 56.5 + - - +
359A GLU* 4.1 0.3 - - - +
360A GLY* 3.0 28.2 + - - -
362A THR* 3.9 20.5 + - + +
364A VAL* 3.4 25.8 - - + -
422A TYR* 3.9 17.5 + - + -
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Residues in contact with LYS 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR 3.9 0.5 - - - +
2A PRO* 3.0 51.6 - - + +
3A GLU 4.1 3.8 - - - +
4A MET 3.6 16.8 + - - -
5A PRO* 4.4 4.8 - - - +
6A VAL* 4.0 26.2 - - + +
353A LEU 2.9 20.3 + - - +
354A GLU* 4.3 4.0 - - - +
356A ALA* 1.3 74.5 - - - +
358A LYS* 1.3 61.8 + - - +
360A GLY* 3.9 5.2 + - - -
422A TYR* 3.3 20.5 + - - +
----------------------------------------------------------
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Residues in contact with LYS 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR* 2.8 28.3 + - - -
2A PRO* 4.5 11.2 - - + -
354A GLU 3.5 10.5 + - - +
355A PHE* 3.2 10.1 + - + +
357A LYS* 1.3 78.0 - - - +
359A GLU* 1.3 61.1 + - - +
----------------------------------------------------------
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Residues in contact with GLU 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR 3.9 6.2 + - - -
43A LYS* 2.9 32.3 + - - +
44A ASN* 3.8 7.9 - - - +
355A PHE* 2.9 43.7 + - + +
356A ALA 4.1 0.4 - - - +
358A LYS* 1.3 80.5 - - - +
360A GLY* 1.3 56.6 + - - +
361A ASN* 2.5 50.5 + - - -
362A THR* 2.9 22.0 + - - +
----------------------------------------------------------
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Residues in contact with GLY 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A THR 4.3 13.2 - - - -
4A MET* 5.4 3.8 - - - +
40A LYS* 2.7 33.0 + - - -
356A ALA 3.0 15.1 + - - -
357A LYS 3.9 6.5 + - - -
358A LYS 3.3 1.8 - - - -
359A GLU* 1.3 75.5 - - - +
361A ASN* 1.3 57.4 + - - +
362A THR 3.6 2.2 - - - -
422A TYR* 5.7 2.2 - - - -
424A PRO* 4.4 3.7 - - - +
----------------------------------------------------------
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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