Contacts of the helix formed by residues 351 - 377 (chain A) in PDB entry 4FE1
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 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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347A VAL* 3.1 17.1 + - - +
348A LEU 4.8 0.5 - - - +
349A THR 3.8 0.4 - - - -
350A THR* 1.3 81.6 - - - +
352A TRP* 1.3 61.5 + - - +
354A ALA* 3.3 16.7 + - - +
355A GLN* 3.5 16.6 + - - +
415A PHE* 3.1 24.3 - - - -
419A ASP* 2.6 37.2 + - - -
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Residues in contact with TRP 352 (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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65A LEU* 3.9 21.8 - - + +
68A ILE* 4.3 5.2 - - + -
69A SER* 3.0 41.2 + - - +
72A ILE* 3.4 48.5 - - + +
73A PHE* 5.6 0.4 - - - -
76A HIS* 4.8 8.3 - + - -
190A PHE* 4.3 21.8 - + + -
350A THR 5.4 1.3 - - - -
351A SER* 1.3 70.2 + - - +
353A HIS* 1.3 64.7 + - + +
355A GLN* 3.2 16.1 + - + +
356A LEU* 2.9 28.4 + - - +
419A ASP* 4.2 2.0 + - - -
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Residues in contact with HIS 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ASP* 5.7 1.1 - - - -
59A ASP* 2.9 34.6 + - - -
351A SER* 3.3 0.8 + - - -
352A TRP* 1.3 83.5 - - + +
354A ALA* 1.3 56.6 + - - +
356A LEU* 3.4 7.8 + - + +
357A ALA* 2.9 24.6 + - - +
411A HIS* 3.2 51.6 + + - +
414A ILE* 3.4 32.3 - - + +
415A PHE* 3.9 8.1 - - - +
418A ARG* 4.3 6.3 + - - -
419A ASP* 3.8 22.0 - - - +
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Residues in contact with ALA 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A VAL* 4.2 9.0 - - + +
348A LEU* 3.6 20.0 - - + -
351A SER* 3.3 25.2 + - - +
352A TRP 3.2 0.2 - - - -
353A HIS* 1.3 73.4 - - - +
355A GLN* 1.3 66.4 + - - +
357A ALA* 3.2 8.5 + - - +
358A ILE* 3.1 26.5 + - - +
415A PHE* 3.8 21.2 - - + +
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Residues in contact with GLN 355 (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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193A VAL* 5.0 9.3 - - - +
348A LEU* 2.7 49.5 + - + +
351A SER 3.5 9.4 + - - +
352A TRP* 3.2 20.3 + - + +
354A ALA* 1.3 78.8 - - - +
356A LEU* 1.3 58.2 + - - +
358A ILE* 3.3 5.0 + - - +
359A ASN* 2.9 55.9 + - - +
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Residues in contact with LEU 356 (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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352A TRP 2.9 16.5 + - - +
353A HIS* 3.7 7.4 - - + +
355A GLN* 1.3 77.7 - - - +
357A ALA* 1.3 61.3 + - - +
359A ASN* 4.6 6.7 - - + +
360A LEU* 2.9 56.0 + - + +
411A HIS* 3.2 41.7 - - + +
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Residues in contact with ALA 357 (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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353A HIS 2.9 14.0 + - - +
354A ALA* 3.2 12.1 + - - +
356A LEU* 1.3 76.6 - - - +
358A ILE* 1.3 65.3 + - + +
361A ALA* 3.0 22.4 + - - +
408A GLY* 3.2 32.8 - - - +
411A HIS* 4.2 2.0 - - - +
412A GLY* 3.5 20.4 - - - +
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Residues in contact with ILE 358 (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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348A LEU* 3.6 42.2 - - + -
354A ALA 3.1 6.6 + - - +
355A GLN* 3.7 8.7 - - - +
357A ALA* 1.3 81.8 - - + +
359A ASN* 1.3 73.3 + - - +
361A ALA* 3.1 8.5 + - - +
362A MET* 3.0 33.0 + - + +
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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
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355A GLN* 2.9 41.3 + - - +
356A LEU* 4.3 7.6 - - + +
358A ILE* 1.3 83.6 - - - +
360A LEU* 1.3 57.5 + - - +
362A MET* 3.6 4.2 + - - +
363A MET* 2.9 38.6 + - + +
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Residues in contact with LEU 360 (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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356A LEU* 2.9 46.7 + - + +
359A ASN* 1.3 74.7 - - - +
361A ALA* 1.3 66.9 + - - +
363A MET* 4.4 3.8 - - + -
364A GLY 3.0 19.9 + - - -
404A LEU* 3.3 59.0 - - + +
407A GLY* 3.7 23.1 - - - +
408A GLY* 3.5 6.5 - - - +
411A HIS* 4.1 6.7 - - + -
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Residues in contact with ALA 361 (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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357A ALA 3.0 18.7 + - - +
358A ILE* 3.5 6.5 - - - +
360A LEU* 1.3 76.4 - - - +
362A MET* 1.3 64.4 + - + +
364A GLY* 3.9 0.7 - - - -
365A SER* 3.0 33.3 + - - -
405A VAL* 4.1 19.6 - - + +
408A GLY* 4.0 6.9 - - - -
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Residues in contact with MET 362 (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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358A ILE* 3.0 29.1 + - + +
359A ASN* 4.1 4.7 - - - +
361A ALA* 1.3 81.5 - - + +
363A MET* 1.3 59.4 + - - +
365A SER* 3.8 9.8 - - - -
366A LEU* 2.9 32.0 + - - +
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Residues in contact with MET 363 (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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359A ASN* 2.9 29.9 + - + +
360A LEU* 3.8 5.8 - - + +
362A MET* 1.3 75.8 - - - +
364A GLY* 1.3 58.1 + - - +
366A LEU* 3.3 18.5 + - + +
367A SER* 2.9 27.6 + - - -
404A LEU* 3.8 22.9 - - + -
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Residues in contact with GLY 364 (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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360A LEU 3.0 12.5 + - - -
361A ALA 3.9 0.9 - - - -
363A MET* 1.3 74.1 - - - +
365A SER* 1.3 64.2 + - - +
367A SER 3.1 2.3 + - - -
368A ILE* 3.0 30.1 + - - +
401A GLY* 3.2 18.2 - - - -
404A LEU* 3.5 23.6 - - - +
405A VAL* 3.9 3.4 - - - -
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Residues in contact with SER 365 (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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361A ALA 3.0 18.7 + - - -
362A MET* 3.8 13.8 - - - -
363A MET 3.4 0.2 - - - -
364A GLY* 1.3 75.5 - - - +
366A LEU* 1.3 57.8 + - - +
368A ILE* 3.2 12.0 + - - +
369A ILE* 3.0 40.0 + - - +
405A VAL* 3.9 8.7 - - - +
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Residues in contact with LEU 366 (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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362A MET 2.9 18.5 + - - +
363A MET* 3.4 21.3 - - + +
365A SER* 1.3 77.5 - - - +
367A SER* 1.3 57.2 + - - +
369A ILE* 3.0 22.3 + - + +
370A VAL* 2.9 43.9 + - + +
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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
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363A MET* 2.9 14.4 + - - -
364A GLY* 3.1 9.1 + - - -
366A LEU* 1.3 76.0 - - - +
368A ILE* 1.3 57.7 + - - +
370A VAL* 3.3 10.3 + - - +
371A ALA 3.0 21.5 + - - -
397A HIS* 2.5 46.4 + - - +
400A ILE* 3.8 12.2 - - - +
401A GLY* 3.5 12.0 + - - -
404A LEU* 5.5 0.7 - - - -
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Residues in contact with ILE 368 (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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364A GLY 3.0 28.2 + - - +
365A SER* 3.5 11.0 - - - +
366A LEU 3.1 0.2 - - - -
367A SER* 1.3 73.6 - - - +
369A ILE* 1.3 70.7 + - + +
371A ALA* 3.0 5.5 + - - +
372A GLN* 3.0 25.9 + - + +
397A HIS 4.4 0.7 - - - -
398A MET* 3.7 38.1 - - + +
401A GLY* 3.6 26.2 - - - +
402A GLY* 4.0 3.4 - - - +
405A VAL* 4.2 7.9 - - + -
606A ILE* 5.2 4.5 - - + -
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Residues in contact with ILE 369 (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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365A SER* 3.0 28.0 + - - +
366A LEU* 3.4 22.2 - - + +
368A ILE* 1.3 79.8 - - + +
370A VAL* 1.3 58.2 + - + +
372A GLN* 3.3 6.1 + - - +
373A HIS* 2.9 59.3 + - + +
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Residues in contact with VAL 370 (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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366A LEU* 2.9 32.9 + - + +
367A SER* 3.4 11.2 - - - +
369A ILE* 1.3 73.4 - - + +
371A ALA* 1.3 60.1 + - - +
373A HIS* 4.6 4.3 - - - -
374A MET* 2.9 49.5 + - + +
397A HIS* 3.5 28.3 - - + +
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Residues in contact with ALA 371 (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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367A SER 3.0 7.4 + - - +
368A ILE 3.0 8.9 + - - +
370A VAL* 1.3 80.2 - - - +
372A GLN* 1.3 60.8 + - - +
374A MET* 4.5 3.6 - - - +
375A TYR* 3.6 11.3 + - - -
393A LEU 5.1 0.2 - - - -
394A PHE* 3.0 50.5 - - + +
397A HIS* 3.7 17.9 - - + -
398A MET* 3.7 18.6 - - + +
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Residues in contact with GLN 372 (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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368A ILE* 3.0 21.6 + - + +
369A ILE* 3.8 9.9 - - - +
370A VAL 3.3 0.2 - - - -
371A ALA* 1.3 78.8 - - - +
373A HIS* 1.3 67.9 + - + +
375A TYR* 2.9 47.5 + - - -
376A ALA* 4.2 3.8 + - - +
394A PHE* 4.3 9.1 - - - -
398A MET* 3.7 20.2 - - + +
609A VAL* 5.0 5.7 - - - +
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Residues in contact with HIS 373 (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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369A ILE* 2.9 42.3 + - + +
370A VAL* 4.1 4.3 - - - +
372A GLN* 1.3 86.6 - - + +
374A MET* 1.3 65.7 + - + +
375A TYR 3.4 0.7 + - - -
376A ALA* 3.7 0.7 + - - -
377A MET* 3.5 46.8 + - + +
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Residues in contact with MET 374 (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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370A VAL* 2.9 40.1 + - + +
371A ALA* 4.5 2.9 - - - +
372A GLN 3.5 0.2 - - - -
373A HIS* 1.3 78.2 - - + +
375A TYR* 1.3 59.8 + - - +
378A PRO* 3.7 20.1 - - - +
379A PRO* 3.9 16.5 - - + +
380A TYR* 4.3 23.1 - - + -
383A LEU* 4.4 10.5 - - + +
390A GLN* 3.8 12.3 - - - +
393A LEU* 3.6 37.0 - - + -
397A HIS* 4.5 13.0 - - - -
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Residues in contact with TYR 375 (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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371A ALA 3.6 11.2 + - - +
372A GLN* 2.9 56.0 + - - -
373A HIS 3.3 0.4 - - - -
374A MET* 1.3 79.4 - - - +
376A ALA* 1.3 76.3 + - + +
378A PRO* 4.1 1.0 - - - +
390A GLN* 3.4 25.9 + - - +
394A PHE* 4.0 12.6 - + + -
512A ALA* 5.7 0.2 - - - +
526A MET* 3.1 18.9 - - - +
529A ILE* 4.0 23.7 - - + +
613A PHE* 3.5 36.1 - + + -
617A MET* 4.0 16.2 - - + +
622A TRP* 6.3 0.2 - - + -
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Residues in contact with ALA 376 (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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285A LEU* 5.6 0.9 - - - +
372A GLN 4.6 3.4 - - - +
373A HIS* 3.7 2.3 + - - +
375A TYR* 1.3 106.4 - - + +
377A MET* 1.3 63.1 + - + +
378A PRO* 3.7 5.4 - - - +
510A SER* 3.0 26.7 + - - +
511A VAL 4.4 2.3 + - - -
512A ALA* 3.9 13.0 - - + -
526A MET* 3.7 18.8 - - + +
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Residues in contact with MET 377 (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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285A LEU* 4.7 2.0 - - - -
292A LEU* 3.4 28.3 - - + +
373A HIS* 3.5 45.4 + - + +
374A MET 3.9 2.6 - - - +
375A TYR 3.4 0.2 - - - -
376A ALA* 1.3 87.3 - - + +
378A PRO* 1.3 71.0 - - - +
379A PRO* 2.9 12.0 - - - +
509A ALA* 3.2 33.2 - - - +
510A SER* 3.8 10.3 - - - -
513A PHE* 6.0 0.7 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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