Contacts of the helix formed by residues 334 - 360 (chain A) in PDB entry 6MXO
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 ARG 334 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 1.3 72.3 - - - +
335A GLU* 1.3 89.3 + - - +
337A VAL* 3.5 3.6 + - - +
338A GLN* 3.1 47.8 + - - +
400A PHE* 3.4 34.7 - - + -
407A ASN* 5.6 0.9 - - - +
412A GLN* 3.3 26.7 + - - +
413A THR* 2.8 30.4 + - - +
414A GLU 5.2 0.2 - - - +
415A TRP* 4.1 19.2 - - + +
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Residues in contact with GLU 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A THR* 3.2 9.8 - - - +
334A ARG* 1.3 108.4 + - + +
336A GLN* 1.3 57.4 + - - +
338A GLN* 3.5 12.9 + - - +
339A TRP* 3.0 27.0 + - - +
413A THR* 5.4 8.7 - - + -
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Residues in contact with GLN 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A THR 4.8 2.6 + - - -
330A ALA 4.7 3.3 + - - +
331A LEU* 3.8 28.8 - - + +
332A ALA* 3.1 21.9 + - - +
333A THR* 2.9 27.6 + - - +
335A GLU* 1.3 74.3 - - - +
337A VAL* 1.3 66.2 + - - +
338A GLN 3.2 0.2 - - - -
339A TRP* 3.2 6.0 + - + +
340A TRP* 3.1 39.5 + - + +
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Residues in contact with VAL 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LEU* 3.9 24.4 - - + +
333A THR 3.1 16.5 + - - +
334A ARG 3.7 5.2 - - - +
336A GLN* 1.3 78.4 - - - +
338A GLN* 1.3 55.5 + - - +
340A TRP 3.5 0.3 + - - -
341A LEU* 3.0 47.0 + - + +
400A PHE* 4.2 14.1 - - + -
403A ILE* 4.3 12.8 - - + -
415A TRP* 4.1 19.5 - - + -
419A LEU* 3.7 25.8 - - + -
422A LEU* 4.0 5.6 - - + +
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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
----------------------------------------------------------
334A ARG* 3.1 45.1 + - - +
335A GLU* 3.6 15.7 - - - +
336A GLN 3.2 0.2 - - - -
337A VAL* 1.3 77.2 - - - +
339A TRP* 1.3 59.0 + - - +
341A LEU* 3.3 8.2 + - - +
342A LEU* 2.9 28.9 + - - +
396A SER* 4.8 2.1 - - - -
397A HIS* 6.2 2.0 - - - -
400A PHE* 3.6 44.5 - - + -
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Residues in contact with TRP 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 4.9 5.8 - - - -
85A GLY* 6.0 0.7 - - - -
335A GLU 3.0 17.6 + - - +
336A GLN* 3.2 7.8 + - - +
338A GLN* 1.3 77.2 - - - +
340A TRP* 1.3 102.7 + + - +
342A LEU* 3.3 12.8 + - + +
343A GLN* 3.0 71.1 + - + +
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Residues in contact with TRP 340 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG 3.7 18.8 - - - -
85A GLY* 4.0 13.9 - - - -
86A LYS* 5.4 1.3 - - + -
323A LYS* 3.7 31.6 - - + -
325A PHE* 3.6 26.1 - + + -
331A LEU* 3.5 24.6 - - + +
336A GLN* 3.1 33.0 + - + +
337A VAL 4.0 0.2 - - - +
339A TRP* 1.3 106.7 - + - +
341A LEU* 1.3 67.8 + - - +
343A GLN* 3.0 11.4 + - + +
344A LEU* 2.9 29.6 + - + +
422A LEU* 3.6 22.2 - - + -
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Residues in contact with LEU 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A VAL* 3.0 35.2 + - + +
338A GLN* 3.6 6.3 - - - +
340A TRP* 1.3 74.9 - - - +
342A LEU* 1.3 56.5 - - - +
344A LEU* 3.4 5.7 + - + +
345A ALA* 2.8 30.5 + - - +
368A VAL* 4.6 7.9 - - + -
396A SER* 3.9 14.4 - - - +
399A ALA* 4.3 4.5 - - + -
400A PHE* 3.9 40.2 - - + +
403A ILE* 4.0 5.6 - - + -
422A LEU* 3.9 29.1 - - + +
423A PHE 5.6 0.4 - - - +
424A LEU* 3.9 28.5 - - + +
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Residues in contact with LEU 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLN 2.9 13.0 + - - +
339A TRP* 3.3 17.7 - - + +
340A TRP 3.1 0.2 - - - -
341A LEU* 1.3 74.5 - - - +
343A GLN* 1.3 78.5 + - - +
345A ALA* 3.2 0.4 + - - -
346A GLN* 2.9 45.8 + - + +
392A ALA 4.1 8.5 - - - +
393A HIS* 3.9 35.7 - - + +
396A SER* 3.5 24.8 - - - +
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Residues in contact with GLN 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.4 53.1 - - + +
86A LYS* 5.5 3.7 - - + +
339A TRP* 3.0 80.8 + - + +
340A TRP* 3.0 16.3 + - + +
342A LEU* 1.3 82.8 - - - +
344A LEU* 1.3 65.8 + - + +
346A GLN* 3.2 12.7 + - - +
347A GLU* 3.2 20.6 + - - +
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A LYS* 3.7 33.7 - - + -
321A CYS* 3.8 28.0 - - + +
322A SER 4.2 6.1 - - - +
323A LYS* 4.5 9.9 - - + +
325A PHE* 5.8 0.4 - - + -
340A TRP* 2.9 19.8 + - + +
341A LEU* 3.6 8.5 - - + +
343A GLN* 1.3 77.6 - - + +
345A ALA* 1.3 62.3 + - - +
347A GLU* 3.3 2.6 + - - -
348A LEU* 3.0 23.2 + - - +
422A LEU* 3.7 45.8 - - + +
423A PHE 4.4 1.1 - - - +
424A LEU* 3.9 18.2 - - + -
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Residues in contact with ALA 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A LEU 2.8 18.3 + - - +
342A LEU 3.7 4.0 - - - +
343A GLN 3.2 0.4 - - - -
344A LEU* 1.3 77.0 - - - +
346A GLN* 1.3 57.8 + - - +
348A LEU* 3.6 4.6 - - - +
349A GLU* 2.9 29.6 + - - +
392A ALA* 3.3 31.2 - - + +
395A MET* 4.0 7.9 - - + +
396A SER* 3.9 13.0 - - - +
424A LEU* 3.7 13.4 - - + +
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Residues in contact with GLN 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 3.4 35.4 + - - +
342A LEU* 2.9 37.7 + - + +
343A GLN* 3.2 14.4 + - - +
345A ALA* 1.3 75.2 - - - +
347A GLU* 1.3 66.2 + - - +
349A GLU* 3.6 4.4 + - - +
350A GLU* 3.3 25.1 + - - +
392A ALA* 3.6 19.0 - - + +
393A HIS* 4.9 9.1 - - - -
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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
----------------------------------------------------------
83A SER* 5.0 1.2 - - - +
84A ARG* 3.5 23.0 + - - +
86A LYS* 2.7 46.0 + - + +
87A ALA 4.3 1.1 - - - +
88A ASN* 4.3 21.8 - - - +
90A THR* 5.3 0.4 + - - +
93A ARG* 4.4 2.6 + - - -
321A CYS* 4.1 8.5 - - - -
343A GLN 3.2 9.3 + - - +
344A LEU* 3.3 6.9 + - - +
346A GLN* 1.3 78.5 - - - +
348A LEU* 1.3 65.0 + - - +
350A GLU* 3.2 10.7 + - - +
351A ARG* 3.0 50.4 + - + +
6T T 4.0 2.6 + - - -
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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
----------------------------------------------------------
319A ILE* 3.4 42.4 - - + +
320A GLY 4.6 0.4 - - - +
321A CYS* 3.7 18.1 - - - -
344A LEU 3.0 17.1 + - - +
345A ALA* 3.6 5.2 - - - +
347A GLU* 1.3 77.0 - - - +
349A GLU* 1.3 51.0 + - - +
351A ARG* 3.2 5.4 + - - +
352A LEU* 2.7 53.9 + - + +
366A LEU* 3.9 27.6 - - + -
395A MET* 4.2 12.8 - - - -
424A LEU* 4.2 20.4 - - + +
426A ALA* 4.4 7.9 - - + +
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Residues in contact with GLU 349 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A ALA 2.9 18.1 + - - +
346A GLN* 3.7 6.7 - - - +
348A LEU* 1.3 77.2 - - - +
350A GLU* 1.3 66.6 + - - +
352A LEU* 3.3 5.8 + - - +
353A THR* 3.0 37.2 + - - +
390A TYR* 3.6 30.5 - - + +
391A ASP* 4.2 1.0 - - - +
392A ALA* 3.1 26.3 + - + +
395A MET* 4.0 11.8 - - + +
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Residues in contact with GLU 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ARG* 2.8 38.2 + - - -
346A GLN 3.3 6.5 + - - +
347A GLU* 3.2 10.8 + - - +
349A GLU* 1.3 83.5 - - - +
351A ARG* 1.3 65.6 + - + +
353A THR* 3.9 5.1 - - - -
354A LYS* 3.2 24.1 + - - +
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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
----------------------------------------------------------
90A THR* 5.3 7.4 - - - +
93A ARG* 3.0 41.5 - - - +
319A ILE* 3.7 28.2 - - + +
320A GLY 2.8 28.1 + - - -
321A CYS* 3.5 9.9 - - - -
347A GLU* 3.0 37.1 + - + +
348A LEU 3.6 7.4 - - - +
350A GLU* 1.3 82.1 - - + +
352A LEU* 1.3 56.6 + - - +
354A LYS* 3.5 5.4 + - - +
355A ASP* 3.0 28.5 + - - +
6T T 3.3 16.2 + - - -
7T C 3.3 17.6 + - - -
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Residues in contact with LEU 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 4.0 21.1 - - + -
348A LEU* 2.7 45.5 + - + +
349A GLU* 3.8 3.8 - - - +
350A GLU 3.3 0.2 - - - -
351A ARG* 1.3 71.3 - - - +
353A THR* 1.3 60.2 + - - +
355A ASP* 3.2 3.6 + - + +
356A ARG 2.8 26.0 + - - -
363A ALA* 4.2 0.9 - - + -
387A LEU* 4.2 8.3 - - + -
390A TYR* 3.2 51.8 - - + +
395A MET* 4.3 6.5 - - - -
426A ALA* 3.6 28.0 - - + -
429A PHE* 4.2 9.4 - - + -
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Residues in contact with THR 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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349A GLU* 3.0 28.4 + - - +
350A GLU* 3.9 6.0 - - - -
352A LEU* 1.3 75.0 - - - +
354A LYS* 1.3 64.0 + - - +
356A ARG* 3.5 18.8 + - - +
357A ASN* 3.1 40.2 + - - +
390A TYR* 3.8 17.9 + - - +
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Residues in contact with LYS 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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90A THR* 6.5 1.3 - - + -
94A GLU* 4.7 20.4 + - - +
350A GLU 3.2 16.3 + - - +
351A ARG* 3.8 6.1 - - - +
353A THR* 1.3 79.6 - - - +
355A ASP* 1.3 58.0 + - - +
357A ASN* 3.2 7.0 + - - +
358A ASP* 2.2 67.4 + - - +
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Residues in contact with ASP 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ILE* 3.8 18.0 - - + +
351A ARG 3.0 18.3 + - - +
352A LEU* 3.4 5.8 - - + +
354A LYS* 1.3 74.9 - - - +
356A ARG* 1.3 59.2 + - - +
358A ASP* 4.6 0.7 - - - -
359A ASN* 2.8 57.5 + - - +
360A ASP 3.9 0.3 + - - -
361A ARG* 2.7 49.2 + - - +
390A TYR* 4.9 0.9 + - - -
429A PHE* 3.3 15.1 - - - -
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Residues in contact with ARG 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A LEU 2.8 19.8 + - - +
353A THR* 3.8 24.3 + - - +
355A ASP* 1.3 73.5 + - - +
357A ASN* 1.3 61.9 + - - +
360A ASP* 3.1 26.9 + - - +
361A ARG 3.3 23.6 - - - +
362A VAL* 3.3 23.7 - - + +
390A TYR* 3.5 37.1 - - + +
432A SER* 4.7 6.1 - - - +
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Residues in contact with ASN 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A THR* 3.1 33.5 + - - +
354A LYS* 3.8 6.7 - - - +
356A ARG* 1.3 81.0 + - - +
358A ASP* 1.3 71.8 + - - +
360A ASP* 4.6 7.2 - - - +
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Residues in contact with ASP 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LYS* 2.2 60.0 + - - +
355A ASP* 4.6 0.2 - - - -
357A ASN* 1.3 83.9 - - - +
359A ASN* 1.3 79.4 + - - +
360A ASP* 3.6 6.1 + - - +
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Residues in contact with ASN 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A LEU* 3.7 43.9 - - + +
355A ASP* 2.8 37.1 + - - +
358A ASP* 1.3 93.8 - - - +
360A ASP* 1.3 73.4 + - - +
361A ARG* 3.2 12.3 + - + +
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Residues in contact with ASP 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ARG* 3.1 15.2 + - - +
357A ASN 4.6 5.7 - - - +
358A ASP 4.4 6.7 - - - +
359A ASN* 1.3 80.7 - - - +
361A ARG* 1.3 59.1 + - - +
431A ALA* 3.7 6.4 - - - +
432A SER 3.1 35.4 + - - +
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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