Contacts of the helix formed by residues 338 - 363 (chain E) in PDB entry 5KRA
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 SER 338 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E PHE* 1.3 76.3 - - - +
339E GLU* 1.3 77.1 + - - +
340E ALA* 3.8 6.4 + - - +
341E SER* 2.9 24.4 + - - -
342E MET* 3.3 17.2 - - - +
417E CYS* 4.6 5.5 - - - +
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Residues in contact with GLU 339 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E SER* 1.3 83.2 + - - +
340E ALA* 1.3 62.9 + - + +
341E SER 3.3 0.9 + - - -
342E MET* 3.8 2.1 - - - +
343E MET* 3.4 24.9 + - - +
417E CYS 5.2 2.7 - - - +
418E VAL* 4.0 27.6 - - + +
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Residues in contact with ALA 340 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338E SER* 3.8 3.5 + - - +
339E GLU* 1.3 79.7 - - + +
341E SER* 1.3 57.4 + - - +
342E MET 3.5 0.2 - - - -
343E MET* 4.5 5.1 - - - +
344E GLY* 2.9 25.2 + - - -
533E VAL* 4.4 23.8 - - + +
535E PRO* 5.4 6.8 - - + +
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Residues in contact with SER 341 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E PHE* 3.9 9.1 - - - -
338E SER* 2.9 38.5 + - - -
339E GLU 3.2 0.2 - - - -
340E ALA* 1.3 77.5 - - - +
342E MET* 1.3 67.5 + - - +
344E GLY* 3.8 1.0 - - - -
345E LEU* 3.1 32.9 + - - +
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Residues in contact with MET 342 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337E PHE* 3.9 40.8 - - + -
338E SER 3.3 16.9 + - - +
339E GLU* 3.4 3.6 + - - +
341E SER* 1.3 84.0 + - - +
343E MET* 1.3 80.6 + - + +
345E LEU* 3.3 7.8 + - - +
346E LEU* 3.2 37.7 + - - +
408E LEU* 6.0 1.8 - - - -
410E LEU* 3.8 25.4 - - + -
414E GLN* 3.6 35.0 - - + +
417E CYS* 4.3 7.2 - - + -
418E VAL 5.8 1.8 - - - +
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Residues in contact with MET 343 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339E GLU 3.4 16.1 + - - +
340E ALA* 4.5 4.7 - - - +
342E MET* 1.3 92.6 - - + +
344E GLY* 1.3 61.7 + - - +
346E LEU* 3.3 26.5 + - + -
347E THR* 2.9 37.4 + - - +
418E VAL* 4.5 12.3 - - + +
421E MET* 3.6 27.8 - - + +
524E HIS* 4.1 12.1 - - + -
528E MET* 3.6 42.2 - - + +
535E PRO* 6.1 4.0 - - + -
601E 6WS 6.1 2.0 - - - -
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Residues in contact with GLY 344 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330E GLU* 4.3 2.6 - - - +
340E ALA 2.9 21.5 + - - -
341E SER* 3.8 1.8 - - - -
342E MET 3.2 0.4 - - - -
343E MET* 1.3 76.9 - - - +
345E LEU* 1.3 61.2 + - - +
347E THR* 3.3 6.5 + - - -
348E ASN* 3.1 26.9 + - - +
535E PRO* 5.4 12.1 - - - +
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Residues in contact with LEU 345 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329E SER* 3.8 20.7 + - - +
330E GLU* 3.6 38.3 - - + +
331E TYR* 5.5 6.3 - - + -
337E PHE* 3.8 31.4 - - + -
341E SER* 3.1 21.9 + - - +
342E MET* 3.6 7.0 - - - +
344E GLY* 1.3 76.1 - - - +
346E LEU* 1.3 60.7 + - + +
348E ASN* 3.8 3.9 - - - +
349E LEU* 3.0 29.5 + - - +
352E ARG* 5.3 0.5 + - - -
408E LEU* 4.5 14.4 - - + -
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Residues in contact with LEU 346 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342E MET* 3.2 23.2 + - - +
343E MET* 3.3 32.9 + - + +
345E LEU* 1.3 75.0 - - - +
347E THR* 1.3 61.2 + - + +
349E LEU* 3.3 7.1 + - + +
350E ALA* 2.8 28.8 + - - +
404E PHE* 3.6 38.6 - - + -
408E LEU* 4.1 17.0 - - + -
410E LEU* 4.8 4.3 - - + -
421E MET* 5.0 0.4 - - - -
601E 6WS 3.6 41.3 - - + -
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Residues in contact with THR 347 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343E MET* 2.9 24.9 + - - +
344E GLY* 3.3 8.5 + - - -
346E LEU* 1.3 74.4 - - + +
348E ASN* 1.3 62.4 + - - +
350E ALA* 3.6 7.9 - - - +
351E ASP* 3.0 29.8 + - - +
525E LEU* 4.7 7.4 - - + -
528E MET* 3.8 18.2 - - + -
535E PRO* 3.5 17.6 + - + +
536E LEU* 3.6 31.2 - - + -
540E LEU* 4.1 9.6 - - + +
601E 6WS 5.3 4.5 - - + -
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Residues in contact with ASN 348 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330E GLU* 3.3 36.3 + - - +
344E GLY 3.1 16.9 + - - +
345E LEU 3.8 3.4 - - - +
347E THR* 1.3 81.6 + - - +
349E LEU* 1.3 61.2 + - - +
351E ASP* 3.6 5.9 + - - +
352E ARG* 3.1 56.5 + - - +
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Residues in contact with LEU 349 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327E LEU* 4.2 19.3 - - + +
328E TYR 4.1 12.6 - - - +
329E SER* 4.8 2.7 - - - +
345E LEU 3.0 17.3 + - - +
346E LEU* 3.5 6.1 - - + +
348E ASN* 1.3 77.0 + - - +
350E ALA* 1.3 63.9 + - - +
352E ARG* 3.4 23.6 + - - +
353E GLU* 3.0 41.1 + - + +
404E PHE* 3.3 41.7 - - + +
405E ALA* 4.4 5.4 - - + -
408E LEU* 4.8 7.9 - - + -
601E 6WS 4.5 11.7 - - + -
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Residues in contact with ALA 350 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346E LEU 2.8 17.2 + - - +
347E THR* 3.3 8.3 + - - +
349E LEU* 1.3 77.4 - - - +
351E ASP* 1.3 56.5 + - - +
353E GLU* 3.3 4.1 + - - +
354E LEU* 2.9 33.9 + - - +
387E LEU* 4.3 12.2 - - + +
540E LEU* 4.5 9.4 - - + -
601E 6WS 3.6 37.9 - - + -
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Residues in contact with ASP 351 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347E THR 3.0 16.8 + - - +
348E ASN* 3.9 6.9 - - - +
349E LEU 3.3 0.2 - - - -
350E ALA* 1.3 76.6 - - - +
352E ARG* 1.3 67.8 + - - +
354E LEU* 3.4 20.9 + - - +
355E VAL* 3.5 14.6 - - - +
537E SER* 2.6 38.6 + - - +
539E LEU* 4.0 18.4 - - - +
540E LEU* 4.5 4.1 + - + +
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Residues in contact with ARG 352 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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327E LEU* 3.8 30.6 - - + +
328E TYR 2.8 29.9 + - - +
329E SER* 3.9 9.5 - - - +
330E GLU* 4.2 6.0 - - - +
345E LEU 5.3 0.4 + - - -
348E ASN* 3.1 36.6 + - - +
349E LEU* 3.8 22.1 - - - +
350E ALA 3.3 0.4 - - - -
351E ASP* 1.3 83.6 - - - +
353E GLU* 1.3 60.8 + - - +
355E VAL* 3.4 14.9 + - - +
356E HIS* 3.3 20.7 + - + -
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Residues in contact with GLU 353 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325E PRO 5.7 2.9 - - - +
326E ILE* 6.0 0.2 - - - -
327E LEU* 3.8 27.5 + - + +
349E LEU* 3.0 31.7 + - + +
350E ALA* 3.3 2.2 + - - +
352E ARG* 1.3 74.9 - - - +
354E LEU* 1.3 59.2 + - - +
356E HIS* 3.3 6.3 + - - +
357E MET* 2.9 27.9 + - - +
387E LEU* 3.6 28.8 - - + +
394E ARG* 3.1 33.0 + - - -
404E PHE 4.3 0.7 - - - +
601E 6WS 3.5 16.6 - - - +
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Residues in contact with LEU 354 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350E ALA 2.9 17.2 + - - +
351E ASP* 3.5 8.5 - - - +
353E GLU* 1.3 77.0 - - - +
355E VAL* 1.3 61.1 + - - +
357E MET* 3.2 29.8 + - + +
358E ILE* 3.1 35.7 + - + +
383E TRP* 4.0 24.0 - - + -
387E LEU* 4.7 2.9 - - + +
539E LEU* 4.2 19.7 - - + -
540E LEU* 3.8 31.0 - - + +
543E MET* 3.9 27.8 - - + -
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Residues in contact with VAL 355 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351E ASP* 3.5 18.6 - - - +
352E ARG* 3.7 10.1 - - - +
353E GLU 3.3 0.6 - - - -
354E LEU* 1.3 76.8 - - - +
356E HIS* 1.3 62.1 + - + +
358E ILE* 3.5 9.7 + - - +
359E ASN* 2.7 42.7 + - - +
539E LEU* 4.3 15.0 - - + -
693G LEU* 4.7 15.3 - - + -
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Residues in contact with HIS 356 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E PRO* 4.2 18.8 - - + +
325E PRO* 3.7 28.8 - - + +
327E LEU* 3.6 30.0 - - + +
352E ARG* 3.3 23.3 + - + -
353E GLU* 3.3 8.2 + - - +
354E LEU 3.2 0.4 - - - -
355E VAL* 1.3 80.0 - - + +
357E MET* 1.3 60.1 + - - +
359E ASN* 3.4 6.1 + - - +
360E TRP* 2.8 28.7 + - - +
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Residues in contact with MET 357 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324E PRO* 5.1 2.9 - - - +
353E GLU 2.9 14.8 + - - +
354E LEU* 3.2 20.6 + - + +
356E HIS* 1.3 76.4 - - - +
358E ILE* 1.3 56.8 + - - +
360E TRP* 3.1 25.7 + - + -
361E ALA* 2.8 31.7 + - - +
379E LEU* 4.1 13.5 - - + -
383E TRP* 3.2 37.5 - - - +
386E ILE* 3.7 33.2 - - + -
387E LEU* 3.7 24.9 - - + -
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Residues in contact with ILE 358 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E LEU* 3.1 27.7 + - + +
355E VAL* 3.8 6.1 - - - +
356E HIS 3.3 0.2 - - - -
357E MET* 1.3 78.1 - - + +
359E ASN* 1.3 63.4 + - - +
361E ALA* 3.4 13.2 + - - +
362E LYS* 3.3 17.5 + - - +
379E LEU* 4.3 9.4 - - + -
539E LEU* 4.7 7.9 - - + -
543E MET* 6.0 0.9 - - + -
690G LEU* 3.6 27.4 - - + -
693G LEU* 3.6 52.0 - - + +
694G LEU* 3.7 25.8 - - + +
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Residues in contact with ASN 359 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355E VAL* 2.7 34.8 + - - +
356E HIS* 3.4 7.6 + - - +
357E MET 3.3 0.4 - - - -
358E ILE* 1.3 77.7 - - - +
360E TRP* 1.3 64.5 + - - +
361E ALA 3.3 0.2 - - - -
362E LYS* 3.6 34.5 + - + +
363E ARG* 3.4 22.7 + - - +
693G LEU* 4.6 3.5 + - - +
696G ASP 4.7 4.3 - - - +
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Residues in contact with TRP 360 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319E LEU* 5.0 3.6 + - - +
322E ALA* 3.1 39.0 - - + +
323E GLU* 4.1 4.2 + - - -
324E PRO* 3.7 21.8 - - + -
356E HIS 2.8 18.3 + - - +
357E MET* 3.3 34.1 - - + +
359E ASN* 1.3 76.6 - - - +
361E ALA* 1.3 71.1 + - + +
363E ARG* 3.0 14.3 + - - +
364E VAL* 3.3 29.8 + - + +
379E LEU* 5.3 0.2 - - + -
386E ILE* 3.7 28.3 - - + -
446E VAL* 5.4 0.6 - - - +
449E LYS* 3.7 50.5 - - + +
450E SER* 4.3 11.6 + - - -
453E LEU* 3.9 24.5 - - + -
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Residues in contact with ALA 361 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357E MET 2.8 16.3 + - - +
358E ILE 3.5 10.5 - - - +
359E ASN 3.3 0.2 - - - -
360E TRP* 1.3 81.8 - - + +
362E LYS* 1.3 61.6 + - - +
364E VAL* 3.1 16.0 + - - +
367E PHE* 3.1 43.8 - - + +
379E LEU* 4.0 15.5 - - + -
453E LEU* 4.0 13.2 - - + -
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Residues in contact with LYS 362 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.2 7.6 - - - +
358E ILE* 3.3 16.2 - - - +
359E ASN* 3.6 26.3 + - + +
360E TRP 3.2 0.6 - - - -
361E ALA* 1.3 77.7 - - - +
363E ARG* 1.3 60.8 + - + +
364E VAL 3.2 5.5 + - - +
367E PHE* 4.4 6.7 - - + -
368E VAL* 4.4 24.6 + - + +
375E GLN* 5.7 1.8 - - - +
693G LEU 2.7 30.1 + - - -
694G LEU* 3.3 31.3 + - + +
696G ASP 3.2 30.1 + - - -
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Residues in contact with ARG 363 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 3.7 49.4 - - + +
467B LYS* 5.1 6.5 - - - +
318E ALA* 4.2 7.4 + - - +
321E ASP* 3.5 23.2 + - - -
322E ALA* 3.5 47.3 - - + +
359E ASN 3.4 17.3 - - - +
360E TRP* 3.0 5.8 + - - +
362E LYS* 1.3 77.2 - - + +
364E VAL* 1.3 60.7 + - - +
365E PRO* 3.2 12.6 - - - +
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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