Contacts of the helix formed by residues 392 - 422 (chain A) in PDB entry 6R7Z
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 LEU 392 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLU* 4.6 19.7 - - + +
283A GLU 4.2 6.1 - - - +
284A PRO* 4.8 0.2 - - - -
285A ARG* 3.5 9.5 - - - +
390A HIS* 4.0 2.4 - - - +
391A ARG* 1.3 82.2 - - + +
393A GLU* 1.3 62.0 + - - +
394A SER* 4.0 11.0 - - - +
395A ALA* 4.3 15.0 - - + +
396A TYR* 3.4 21.1 + - - +
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Residues in contact with GLU 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLU 4.8 2.8 + - - +
285A ARG* 3.7 17.0 - - + +
286A PRO* 5.5 3.4 - - + -
392A LEU* 1.3 75.6 - - - +
394A SER* 1.3 56.9 + - - +
395A ALA 3.3 0.4 - - - -
396A TYR* 3.6 11.2 - - + +
397A GLN* 2.7 35.9 + - - +
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Residues in contact with SER 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A LEU* 3.5 6.3 - - - +
393A GLU* 1.3 78.8 - - - +
395A ALA* 1.3 57.3 + - - +
397A GLN* 3.4 6.0 + - - +
398A ASN* 2.8 30.1 + - - +
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Residues in contact with ALA 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A HIS* 5.0 6.3 - - + -
391A ARG 5.7 0.9 - - - +
392A LEU* 4.3 17.8 + - + +
393A GLU 3.3 0.4 - - - -
394A SER* 1.3 75.4 - - - +
396A TYR* 1.3 60.5 + - - +
398A ASN* 3.7 5.6 - - - +
399A HIS* 2.7 47.5 + - + +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ARG* 5.4 6.1 - - + -
382A GLU* 4.6 10.5 + - - +
385A THR* 3.7 42.9 - - - -
386A SER* 3.9 15.2 - - - -
390A HIS* 3.8 19.0 - - + +
392A LEU 3.4 19.3 + - - +
393A GLU* 3.4 13.7 + - + +
394A SER 3.3 0.4 - - - -
395A ALA* 1.3 79.7 - - - +
397A GLN* 1.3 66.3 + - + +
399A HIS* 3.6 4.6 + - - +
400A LEU* 3.1 28.6 + - + +
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Residues in contact with GLN 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A GLU 2.7 22.5 + - - +
394A SER* 3.7 6.7 - - - +
396A TYR* 1.3 79.9 - - + +
398A ASN* 1.3 51.0 + - - +
400A LEU* 3.4 6.0 + - - +
401A ILE* 2.7 36.8 + - - +
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Residues in contact with ASN 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A SER 2.8 21.1 + - - +
395A ALA* 3.3 8.2 + - - +
397A GLN* 1.3 71.8 - - - +
399A HIS* 1.3 64.9 + - + +
401A ILE* 3.3 7.2 + - - +
402A LEU* 2.8 29.6 + - - +
554A VAL* 5.7 10.5 - - + -
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Residues in contact with HIS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ILE* 5.9 7.6 - - + -
385A THR* 5.4 8.7 - - - -
395A ALA* 2.7 38.3 + - + +
396A TYR* 4.1 5.2 - - - +
398A ASN* 1.3 77.9 - - + +
400A LEU* 1.3 61.2 + - - +
402A LEU* 3.2 7.3 + - + +
403A LYS* 2.9 29.6 + - - +
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Residues in contact with LEU 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A ALA* 5.5 8.4 - - + +
382A GLU* 6.2 1.6 - - - -
385A THR* 4.7 15.8 - - - -
396A TYR* 3.1 24.6 + - + +
397A GLN* 3.7 6.1 - - - +
399A HIS* 1.3 76.8 - - - +
401A ILE* 1.3 57.5 + - - +
403A LYS* 3.9 5.4 - - - +
404A VAL* 3.0 31.7 + - - +
495A PHE* 4.7 5.3 - - + -
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Residues in contact with ILE 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLN 2.7 21.5 + - - +
398A ASN* 3.7 8.1 - - - +
399A HIS 3.3 0.2 - - - -
400A LEU* 1.3 72.9 - - - +
402A LEU* 1.3 57.1 + - - +
404A VAL* 4.2 0.3 - - - +
405A LEU* 2.9 34.5 + - - +
495A PHE* 4.4 20.5 - - + -
554A VAL* 6.0 5.6 - - + -
555A TRP* 5.2 11.4 - - + +
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Residues in contact with LEU 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ASN 2.8 17.7 + - - +
399A HIS* 3.2 8.7 + - - +
401A ILE* 1.3 76.8 - - - +
403A LYS* 1.3 62.7 + - - +
405A LEU* 4.0 4.0 - - - +
406A VAL* 3.1 25.6 + - - +
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Residues in contact with LYS 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A VAL* 6.0 6.5 - - + -
381A ALA* 4.5 19.1 - - + -
399A HIS 2.9 15.8 + - - +
400A LEU* 3.9 6.1 - - - +
402A LEU* 1.3 78.2 - - - +
404A VAL* 1.3 61.5 + - - +
406A VAL* 3.4 4.8 + - - +
407A PHE* 3.1 23.6 + - - +
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Residues in contact with VAL 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 6.4 2.7 - - + -
381A ALA* 5.5 5.4 - - + +
400A LEU 3.0 18.4 + - - +
401A ILE 4.2 1.3 - - - +
403A LYS* 1.3 73.8 - - - +
405A LEU* 1.3 60.1 + - - +
407A PHE* 4.0 5.9 - - - +
408A ASN* 2.9 32.2 + - - +
495A PHE* 3.6 28.0 - - + -
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Residues in contact with LEU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
401A ILE 2.9 19.9 + - - +
402A LEU* 4.0 4.3 - - - +
404A VAL* 1.3 74.7 - - - +
406A VAL* 1.3 61.8 + - - +
408A ASN* 4.1 3.7 - - - +
409A PHE* 2.9 32.7 + - - +
555A TRP* 6.3 4.5 - - + -
558A ALA* 6.1 5.6 - - + -
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A LEU 3.1 17.6 + - - +
403A LYS* 3.7 6.1 - - - +
404A VAL 3.3 0.2 - - - -
405A LEU* 1.3 78.9 - - - +
407A PHE* 1.3 61.0 + - - +
409A PHE* 3.9 4.6 - - - +
410A LEU* 3.1 25.6 + - - +
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Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A CYS* 4.2 22.4 - - + -
326A LEU* 5.2 3.8 - - + -
329A SER* 4.1 24.9 - - - -
373A MET* 3.4 42.0 - - + -
374A ASN* 3.6 17.7 - - + -
377A TYR* 3.6 21.5 - - + -
403A LYS 3.1 16.7 + - - +
404A VAL* 4.1 5.6 - - - +
406A VAL* 1.3 77.0 - - - +
408A ASN* 1.3 62.8 + - + +
410A LEU* 3.8 5.5 - - + +
411A ASN* 2.8 40.9 + - + +
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Residues in contact with ASN 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A ASN* 6.2 3.8 - - + -
404A VAL 2.9 19.7 + - - +
405A LEU* 4.1 4.5 - - - +
407A PHE* 1.3 80.3 - - + +
409A PHE* 1.3 60.7 + - - +
411A ASN* 4.2 4.2 - - - +
412A CYS* 3.0 32.7 + - - +
499A LEU* 6.1 5.6 - - + +
503A LEU* 6.3 3.1 - - + -
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Residues in contact with PHE 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405A LEU 2.9 19.8 + - - +
406A VAL* 3.9 4.9 - - - +
408A ASN* 1.3 77.2 - - - +
410A LEU* 1.3 58.0 + - - +
412A CYS* 4.0 2.0 - - - -
413A PHE* 2.9 36.3 + - + +
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Residues in contact with LEU 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 5.9 7.2 - - + -
329A SER* 5.9 6.7 - - - -
406A VAL 3.1 19.2 + - - +
407A PHE* 3.8 7.9 - - + +
409A PHE* 1.3 76.8 - - - +
411A ASN* 1.3 62.5 + - - +
414A ALA* 3.2 33.7 + - + +
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Residues in contact with ASN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A SER* 5.5 8.5 - - - -
370A ILE* 4.8 23.8 - - + +
373A MET* 6.2 0.9 - - + -
374A ASN* 6.2 1.6 - - + -
407A PHE* 2.8 41.6 + - + +
408A ASN* 4.2 4.0 - - - +
410A LEU* 1.3 73.4 - - - +
412A CYS* 1.3 60.9 + - - +
414A ALA* 4.8 2.3 + - - +
415A SER 5.7 0.9 + - - -
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Residues in contact with CYS 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ASN 3.0 18.9 + - - +
409A PHE* 4.1 2.2 - - - +
411A ASN* 1.3 81.3 - - - +
413A PHE* 1.3 61.0 + - + +
414A ALA 3.5 1.2 + - - -
415A SER* 4.7 5.8 + - - -
416A LEU* 4.9 5.0 + - - +
503A LEU* 5.7 9.2 - - + -
506A GLY* 6.6 0.2 - - - -
507A TYR* 4.8 29.4 + - + +
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Residues in contact with PHE 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A PHE* 2.9 17.9 + - + +
410A LEU* 5.5 0.2 - - - -
412A CYS* 1.3 75.6 - - + +
414A ALA* 1.3 60.3 + - - +
415A SER 3.4 2.0 - - - -
416A LEU* 3.9 10.7 - - + -
417A PHE* 3.0 29.3 + - - +
510A LEU* 5.5 11.0 - - + -
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Residues in contact with ALA 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A LEU* 6.3 1.3 - - - -
333A MET* 4.9 17.0 - - + -
337A PHE* 5.4 0.9 - - - -
410A LEU* 3.2 22.1 + - + +
411A ASN* 4.7 1.8 - - - +
412A CYS 3.5 1.6 - - - -
413A PHE* 1.3 76.9 - - - +
415A SER* 1.3 59.1 + - - +
417A PHE* 3.4 5.0 + - - +
418A TYR* 2.8 30.4 + - - +
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Residues in contact with SER 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A MET* 5.9 1.9 - - - +
336A TYR* 4.7 15.3 - - - -
337A PHE* 4.1 25.0 - - - -
411A ASN 5.7 0.4 + - - -
412A CYS 4.7 4.4 + - - -
413A PHE* 4.5 0.4 - - - +
414A ALA* 1.3 78.4 - - - +
416A LEU* 1.3 58.4 + - - +
418A TYR* 3.8 0.7 - - - +
419A ILE* 2.8 30.8 + - - +
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Residues in contact with LEU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412A CYS 4.9 2.6 + - - +
413A PHE* 3.5 16.3 + - + +
414A ALA 3.3 0.6 - - - -
415A SER* 1.3 77.4 - - - +
417A PHE* 1.3 59.4 + - - +
419A ILE* 4.0 5.0 - - - +
420A ALA* 3.0 31.9 + - - +
433A LEU* 6.3 2.7 - - + -
510A LEU* 5.7 7.9 - - + +
511A PHE* 5.5 11.2 - - + -
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Residues in contact with PHE 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A PHE 3.0 18.7 + - - +
414A ALA* 3.8 5.8 - - - +
416A LEU* 1.3 79.3 - - - +
418A TYR* 1.3 56.7 + - - +
420A ALA* 4.5 3.1 - - - +
421A PHE* 3.0 35.5 + - + +
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Residues in contact with TYR 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 3.6 30.5 - - + -
414A ALA 2.8 19.0 + - - +
415A SER 3.8 0.2 - - - +
417A PHE* 1.3 75.6 - - - +
419A ILE* 1.3 62.2 + - - +
422A VAL* 3.3 16.8 + - + +
423A LEU* 3.2 21.1 + - - +
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Residues in contact with ILE 419 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A PHE* 4.8 6.0 - - + -
415A SER 2.8 17.4 + - - +
416A LEU* 4.0 6.5 - - - +
418A TYR* 1.3 78.5 - - - +
420A ALA* 1.3 56.9 + - - +
423A LEU* 3.9 8.3 - - + +
424A LYS* 2.9 29.8 + - - -
425A ASP 3.8 6.7 + - - +
428A LEU* 5.8 0.9 - - + -
429A LEU* 4.5 24.4 - - + +
432A SER* 5.9 5.2 - - - -
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Residues in contact with ALA 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A LEU 3.0 19.3 + - - +
417A PHE* 4.2 3.1 - - - +
419A ILE* 1.3 80.2 - - - +
421A PHE* 1.3 59.7 + - + +
424A LYS* 3.9 15.7 - - - +
429A LEU* 5.8 3.6 - - + -
576A MET* 5.3 8.1 - - - +
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Residues in contact with PHE 421 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE* 3.0 16.7 + - + +
420A ALA* 1.3 79.9 - - + +
422A VAL* 1.3 60.1 + - - +
424A LYS* 4.9 2.7 - - - -
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Residues in contact with VAL 422 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A PHE 4.1 0.2 + - - -
418A TYR* 3.3 21.0 + - + +
421A PHE* 1.3 79.9 - - - +
423A LEU* 1.3 66.3 + - - +
424A LYS* 3.4 2.6 - - - +
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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