Contacts of the helix formed by residues 352 - 378 (chain A) in PDB entry 5WJ9
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 352 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 5.9 7.2 - - + -
49A PHE* 6.2 4.3 - - + -
320A LEU* 6.0 0.2 - - - +
350A PHE 3.6 5.0 + - - +
351A VAL* 1.3 79.4 - - - +
353A GLY* 1.3 72.3 + - - +
354A TRP* 3.4 34.5 - - - +
355A TYR* 3.4 35.2 + - + +
356A ILE* 3.5 6.3 + - - +
403A ARG* 3.4 27.6 - - - +
419A ARG* 5.3 0.5 + - - -
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Residues in contact with GLY 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A VAL 3.5 4.7 + - - -
352A ASN* 1.3 74.9 + - - +
354A TRP* 1.3 60.1 + - - +
356A ILE* 2.8 33.6 + - - +
357A LEU* 2.8 15.0 + - - +
419A ARG* 4.9 10.9 - - - +
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Residues in contact with TRP 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ASN* 3.4 35.8 - - - +
353A GLY* 1.3 74.5 - - - +
355A TYR* 1.3 52.1 + - - +
357A LEU* 3.5 19.2 + - + +
358A LEU* 2.8 36.3 + - - +
399A VAL 5.0 7.2 + - - -
400A GLY* 5.8 1.6 - - - -
402A ILE* 4.5 16.2 - - + +
403A ARG* 3.3 45.8 - - + +
412A ASN* 5.7 7.4 - - - -
415A ILE* 4.5 21.1 - - + +
416A ALA* 6.0 3.4 - - + -
419A ARG* 3.3 43.5 - - - -
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Residues in contact with TYR 355 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A PHE* 5.9 7.2 - + - -
55A LYS* 5.7 3.1 + - - -
65A LYS* 3.4 35.5 + - - +
315A LEU 5.3 0.7 - - - -
316A CYS* 3.7 22.3 - - + -
319A SER* 3.4 36.3 - - - +
320A LEU* 5.7 7.0 - - + -
351A VAL* 6.2 0.7 - - + -
352A ASN* 3.4 23.4 + - + +
353A GLY 3.2 0.4 - - - -
354A TRP* 1.3 75.5 - - - +
356A ILE* 1.3 54.4 - - - +
358A LEU* 3.2 11.7 + - + +
359A VAL* 2.8 38.7 + - - +
403A ARG* 3.3 35.4 + - - +
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Residues in contact with ILE 356 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LEU* 5.6 15.4 - - + +
351A VAL* 6.2 3.1 - - + -
352A ASN 3.5 5.8 + - - +
353A GLY* 2.8 28.5 + - - +
355A TYR* 1.3 75.6 - - - +
357A LEU* 1.3 52.5 + - + +
359A VAL* 3.5 11.4 + - + +
360A THR* 2.7 38.2 + - - +
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Residues in contact with LEU 357 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353A GLY 2.8 15.0 + - - +
354A TRP* 3.6 21.1 - - + +
356A ILE* 1.3 73.5 - - + +
358A LEU* 1.3 57.9 + - - +
360A THR* 3.3 7.9 + - - -
361A SER* 2.8 35.2 + - - +
396A LEU* 3.6 51.5 - - + +
399A VAL* 4.2 11.2 - - + -
400A GLY* 5.5 3.1 - - - +
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Residues in contact with LEU 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A LYS* 5.2 7.2 - - - +
69A GLN* 3.2 45.8 - - + +
72A LYS* 4.2 15.9 + - - +
312A SER* 4.8 7.0 - - - +
316A CYS* 5.5 2.2 - - + -
354A TRP 2.8 23.0 + - - +
355A TYR* 3.2 14.6 + - + +
357A LEU* 1.3 76.6 - - - +
359A VAL* 1.3 63.4 - - + +
361A SER* 2.6 21.0 + - - +
362A ASP* 2.8 15.7 + - + +
396A LEU 5.8 0.2 - - - -
397A VAL* 6.2 2.9 - - + -
400A GLY* 5.3 15.5 - - - +
403A ARG* 5.7 8.1 - - + -
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Residues in contact with VAL 359 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312A SER 4.9 0.4 - - - +
313A PHE* 3.7 34.3 - - + -
316A CYS* 3.1 41.5 - - + -
320A LEU* 4.7 12.6 - - + -
355A TYR 2.8 23.4 + - - +
356A ILE* 3.8 15.5 - - + +
357A LEU 3.3 0.2 - - - -
358A LEU* 1.3 75.9 - - + +
360A THR* 1.3 63.6 + - - +
362A ASP* 3.2 10.1 + - + +
363A VAL* 3.0 25.9 + - - +
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Residues in contact with THR 360 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ILE* 2.7 24.7 + - - +
357A LEU* 3.3 11.8 + - - -
359A VAL* 1.3 76.2 - - - +
361A SER* 1.3 61.5 + - - +
363A VAL* 3.4 7.3 + - - +
364A LEU* 3.3 32.1 + - + +
396A LEU* 5.0 9.9 - - + -
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Residues in contact with SER 361 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 5.5 0.2 + - - -
357A LEU 2.8 17.4 + - - -
358A LEU* 2.6 27.4 + - - +
360A THR* 1.3 71.1 - - - +
362A ASP* 1.3 55.4 + - - -
364A LEU* 3.5 7.4 + - - +
365A THR* 2.6 32.4 + - - -
393A SER* 3.6 12.1 + - - +
396A LEU* 3.5 38.2 + - - +
397A VAL* 4.2 11.2 - - - +
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Residues in contact with ASP 362 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.8 18.3 - - - +
309A CYS* 3.2 28.1 - - - +
310A SER* 4.3 1.0 + - - -
312A SER* 4.9 0.9 - - - +
313A PHE* 3.3 36.2 - - + +
358A LEU* 2.8 18.9 + - + +
359A VAL* 3.2 13.3 + - + +
361A SER* 1.3 72.4 - - - +
363A VAL* 1.3 64.3 + - - +
365A THR* 2.8 12.7 + - - -
366A ILE* 2.8 41.2 + - - +
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Residues in contact with VAL 363 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A PHE* 5.2 8.1 - - + -
359A VAL 3.0 16.8 + - - +
360A THR* 3.4 9.8 + - + +
362A ASP* 1.3 85.7 + - - +
364A LEU* 1.3 61.6 + - + +
366A ILE* 3.4 9.2 - - + +
367A SER* 2.8 42.6 + - - -
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Residues in contact with LEU 364 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A THR* 3.3 20.7 + - + +
361A SER 3.6 8.3 - - - +
362A ASP 3.2 0.6 - - - -
363A VAL* 1.3 85.0 - - + +
365A THR* 1.3 59.4 + - - +
367A SER* 4.4 4.3 - - - -
368A GLY* 2.8 25.6 + - - -
389A LEU* 3.7 38.5 - - + +
392A THR* 3.5 38.1 - - + -
393A SER* 3.8 7.6 - - - +
396A LEU* 4.2 12.3 - - + -
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Residues in contact with THR 365 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 4.6 0.2 + - - -
76A VAL* 3.5 21.8 - - + -
79A GLN* 6.1 0.4 - - + -
305A VAL* 3.8 9.9 - - + -
309A CYS* 3.4 27.8 - - - -
361A SER 2.6 20.3 + - - -
362A ASP* 2.8 13.2 + - - -
364A LEU* 1.3 70.1 - - - +
366A ILE* 1.3 53.6 + - - -
368A GLY* 3.2 1.7 + - - -
369A THR* 2.8 39.3 + - - +
390A LEU* 3.7 10.2 - - + +
393A SER* 2.6 27.0 + - - +
397A VAL* 4.5 5.7 - - - +
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Residues in contact with ILE 366 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 3.9 42.6 - - + +
309A CYS* 4.7 5.4 - - + -
310A SER* 4.6 12.6 - - - +
362A ASP* 2.8 31.1 + - - +
363A VAL* 3.4 17.5 - - + +
365A THR* 1.3 70.2 - - - +
367A SER* 1.3 65.4 + - - +
369A THR* 3.0 17.0 + - - -
370A ILE* 3.3 20.7 + - + +
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Residues in contact with SER 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A VAL* 2.8 29.8 + - - -
364A LEU* 4.1 5.2 - - - -
366A ILE* 1.3 71.0 - - - +
368A GLY* 1.3 65.1 + - - +
370A ILE* 3.1 27.3 - - - +
371A MET* 3.2 17.0 + - - +
389A LEU* 3.7 19.0 - - - +
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Residues in contact with GLY 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU 2.8 20.3 + - - -
365A THR 3.2 1.5 + - - -
367A SER* 1.3 75.5 - - - +
369A THR* 1.3 51.2 + - - +
371A MET* 2.8 9.5 + - - +
372A LYS* 2.8 32.3 + - - +
386A CYS* 3.8 2.7 - - - -
389A LEU* 4.2 13.8 - - - +
390A LEU* 3.6 22.2 - - - -
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Residues in contact with THR 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.5 26.2 - - + +
302A ASP* 4.2 10.5 - - - +
305A VAL* 3.5 30.1 - - + -
306A ILE* 3.2 28.5 - - - +
365A THR 2.8 20.1 + - - +
366A ILE* 3.0 17.5 + - - -
368A GLY* 1.3 70.1 - - - +
370A ILE* 1.3 56.2 + - - +
372A LYS* 3.2 8.3 + - - +
373A ILE* 2.8 30.7 + - - +
390A LEU* 3.8 3.7 - - + +
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A ILE* 4.5 15.0 - - + -
366A ILE* 3.4 17.0 - - + +
367A SER* 3.1 26.2 - - - +
369A THR* 1.3 78.2 + - - +
371A MET* 1.3 58.8 + - + +
373A ILE* 3.1 14.3 - - + +
374A GLY* 3.1 22.7 + - - -
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Residues in contact with MET 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367A SER* 3.2 24.2 + - - +
368A GLY* 2.8 12.4 + - - +
370A ILE* 1.3 78.0 - - + +
372A LYS* 1.3 52.9 + - - +
375A ILE* 2.8 37.6 + - - +
380A LEU* 3.6 26.8 - - + +
382A SER* 3.5 27.6 - - - +
385A VAL* 3.7 29.6 - - + -
386A CYS* 4.1 17.0 - - + +
389A LEU* 4.1 9.6 - - + -
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Residues in contact with LYS 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLN* 3.1 43.2 - - - +
82A LEU* 5.2 1.0 - - - +
83A PHE* 3.8 25.9 - - + +
298A ARG* 3.2 46.1 - - - +
302A ASP* 3.9 18.6 - - + +
368A GLY 2.8 11.5 + - - +
369A THR* 3.5 10.5 - - - +
371A MET* 1.3 74.3 - - - +
373A ILE* 1.3 61.4 + - - +
375A ILE* 3.4 8.0 - - + +
376A GLU* 2.8 48.2 + - + +
386A CYS* 4.0 8.7 - - - -
390A LEU* 4.7 2.5 - - + -
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Residues in contact with ILE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 4.3 26.2 - - + +
302A ASP* 3.2 36.7 + - - +
303A VAL* 5.7 2.2 - - + -
306A ILE* 6.3 2.5 - - + -
369A THR 2.8 15.1 + - - +
370A ILE* 3.1 27.6 - - + +
372A LYS* 1.3 72.0 - - - +
374A GLY* 1.3 58.8 + - - +
376A GLU* 4.8 5.6 - - - +
377A ALA* 2.8 47.6 + - + +
378A LYS* 4.4 0.6 - - - +
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Residues in contact with GLY 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ILE 3.1 9.3 + - - -
371A MET 3.7 3.4 - - - -
373A ILE* 1.3 86.0 - - - +
375A ILE* 1.3 56.6 + - - +
378A LYS* 2.8 48.4 + - - +
380A LEU* 3.6 14.6 - - - -
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Residues in contact with ILE 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A PHE* 4.3 15.9 - - + -
371A MET 2.8 23.9 + - - +
372A LYS* 3.4 13.7 - - + +
374A GLY* 1.3 72.9 - - - +
376A GLU* 1.3 68.1 + - + +
378A LYS 3.9 3.1 - - - +
380A LEU* 3.5 32.7 - - + +
381A ALA* 4.0 3.4 - - - -
382A SER 3.5 22.0 - - - +
383A TYR* 3.4 63.0 + - + +
386A CYS* 5.1 2.0 - - + -
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Residues in contact with GLU 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A SER* 6.1 1.1 - - - +
249A GLU* 3.0 54.9 - - + +
294A ASP* 5.2 5.1 - - - +
295A ASN* 5.1 10.7 - - - +
298A ARG* 4.0 45.6 + - - +
299A LEU* 5.3 2.8 + - - +
302A ASP* 5.7 0.7 - - - +
372A LYS* 2.8 32.7 + - + +
373A ILE* 4.2 6.9 - - - +
375A ILE* 1.3 79.5 - - + +
377A ALA* 1.3 72.2 + - - +
378A LYS 3.6 1.8 + - - +
383A TYR* 6.0 0.9 - - - -
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Residues in contact with ALA 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLU* 4.5 3.6 - - - -
283A GLU* 5.6 3.6 - - - -
295A ASN* 4.8 11.7 - - - +
299A LEU* 6.4 2.0 - - + -
373A ILE* 2.8 28.7 + - + +
376A GLU* 1.3 88.8 - - - +
378A LYS* 1.3 63.1 + - - +
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Residues in contact with LYS 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU* 5.4 8.2 + - - -
373A ILE 4.4 0.4 - - - +
374A GLY* 2.8 34.5 + - - +
375A ILE 3.9 4.9 - - - +
376A GLU 3.6 2.1 + - - +
377A ALA* 1.3 77.9 - - - +
379A ASN* 1.3 90.1 + - - +
380A LEU* 3.0 10.3 + - + +
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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