Contacts of the helix formed by residues 422 - 451 (chain A) in PDB entry 2PFV
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 ASP 422 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419A ASN* 2.9 31.4 + - + +
420A TRP 4.1 0.2 - - - +
421A GLU* 1.3 78.3 - - - +
423A HIS* 1.3 82.6 + - - +
424A ASN* 2.8 31.3 + - - +
425A VAL* 3.5 19.6 - - + +
426A LEU* 3.1 26.3 + - - +
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Residues in contact with HIS 423 (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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390A LEU* 3.2 45.2 + - + +
391A GLY* 4.6 3.2 - - - -
393A MET* 3.2 15.7 + - - +
394A ASP* 3.5 37.0 - - + +
421A GLU 3.7 7.4 + - - -
422A ASP* 1.3 75.8 + - - +
424A ASN* 1.3 61.0 + - - +
426A LEU* 3.2 5.2 + - + +
427A LEU* 2.9 26.0 + - - +
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Residues in contact with ASN 424 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A LEU* 3.2 32.2 - - - +
422A ASP* 2.8 27.8 + - - +
423A HIS* 1.3 74.1 - - - +
425A VAL* 1.3 59.2 + - + +
427A LEU* 4.0 1.3 - - - +
428A SER* 3.0 30.1 + - - -
495A MET 4.6 2.8 - - - +
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Residues in contact with VAL 425 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A LEU* 4.1 36.1 - - + -
419A ASN* 3.5 26.5 - - + +
420A TRP* 4.5 4.0 - - - -
422A ASP* 3.4 25.8 + - + +
423A HIS 3.2 0.4 - - - -
424A ASN* 1.3 74.3 - - + +
426A LEU* 1.3 61.9 + - - +
428A SER* 3.5 6.1 + - - -
429A CYS* 3.0 29.1 + - + +
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Residues in contact with LEU 426 (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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393A MET* 3.5 38.8 - - + +
396A ILE 3.8 17.7 - - - +
397A THR* 4.7 7.6 - - + -
398A ARG* 5.0 2.9 - - + +
401A TRP* 3.3 25.3 - - + -
420A TRP* 3.5 27.1 - - + +
421A GLU* 4.9 3.8 - - - +
422A ASP 3.1 18.0 + - - +
423A HIS* 3.2 10.5 + - + +
425A VAL* 1.3 74.9 - - + +
427A LEU* 1.3 65.1 + - - +
429A CYS* 3.4 5.6 + - + +
430A PHE 3.1 15.9 + - - -
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Residues in contact with LEU 427 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345A PHE* 4.2 16.2 - - + -
382A PHE* 6.2 0.9 - - + -
386A LYS* 4.4 6.5 - - + +
389A CYS* 3.8 30.7 - - + -
390A LEU* 3.6 24.5 - - + +
393A MET* 3.7 11.2 - - + -
423A HIS 2.9 17.0 + - - +
424A ASN* 4.0 2.7 - - - +
426A LEU* 1.3 74.7 - - - +
428A SER* 1.3 67.6 + - - +
430A PHE* 2.7 31.9 + - + +
431A ILE* 3.1 9.2 + - + +
495A MET* 3.4 37.2 - - + -
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Residues in contact with SER 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A ASN 3.0 20.2 + - - -
425A VAL* 3.6 7.9 - - - -
427A LEU* 1.3 77.0 - - - +
429A CYS* 1.3 63.9 + - - +
431A ILE* 3.2 7.3 + - - +
432A SER* 3.0 23.3 + - - -
495A MET 3.5 23.3 + - - -
496A LEU* 3.9 4.7 + - - +
497A ALA 5.1 1.8 + - - -
499A GLU* 4.9 3.8 + - - +
500A GLY* 3.9 24.4 + - - -
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Residues in contact with CYS 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A ARG* 3.8 20.4 - - - -
401A TRP* 4.2 5.6 - - + -
413A LEU* 4.6 8.7 - - - -
418A LEU* 6.6 0.4 - - + -
425A VAL* 3.0 15.0 + - + +
426A LEU* 3.4 14.4 - - + +
427A LEU 3.1 0.2 - - - -
428A SER* 1.3 75.5 - - - +
430A PHE* 1.3 53.6 + - - +
432A SER* 3.0 3.5 + - - -
433A ASP* 2.7 61.5 + - - +
499A GLU* 5.7 3.4 - - - +
503A ARG* 3.7 22.9 - - - +
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Residues in contact with PHE 430 (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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345A PHE* 3.5 54.7 - + + -
348A ALA* 3.7 17.0 - - + -
349A ILE* 3.5 14.6 - - + -
379A LEU* 5.3 4.5 - - + -
382A PHE* 4.2 21.5 - + + -
393A MET* 5.2 0.4 - - - -
401A TRP* 3.7 37.9 - + + -
426A LEU 3.1 9.7 + - - +
427A LEU* 2.7 24.5 + - + +
429A CYS* 1.3 74.0 - - - +
431A ILE* 1.3 73.6 + - + -
433A ASP* 3.3 2.4 + - - +
434A CYS* 3.0 41.0 + - - -
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Residues in contact with ILE 431 (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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379A LEU* 4.4 13.5 - - + -
382A PHE* 6.5 1.6 - - + -
427A LEU* 3.1 14.3 + - + +
428A SER* 3.7 4.7 - - - +
430A PHE* 1.3 89.1 - - + +
432A SER* 1.3 63.7 + - - +
434A CYS* 3.0 9.5 + - - +
435A ILE* 3.0 34.3 + - + +
487A VAL* 5.9 0.9 - - + -
492A LEU* 3.6 25.4 - - + -
495A MET* 3.5 45.5 - - + +
496A LEU* 3.9 28.3 - - + -
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Residues in contact with SER 432 (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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428A SER* 3.0 12.8 + - - -
429A CYS* 3.0 9.7 + - - -
431A ILE* 1.3 77.0 - - - +
433A ASP* 1.3 57.3 + - - +
435A ILE* 3.2 10.7 + - - +
436A ASP* 2.9 36.8 + - - +
496A LEU* 3.5 15.1 - - - +
500A GLY* 3.7 15.8 + - - -
503A ARG* 3.5 32.8 - - - -
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Residues in contact with ASP 433 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A ILE* 5.4 3.4 - - + -
398A ARG* 2.7 41.6 + - - -
401A TRP* 3.0 29.9 + - + +
402A LEU* 4.2 11.2 - - + -
411A TYR* 4.0 2.9 - - + -
429A CYS* 2.7 31.4 + - - +
430A PHE 3.7 4.3 - - - +
432A SER* 1.3 73.0 - - - +
434A CYS* 1.3 54.2 + - - +
436A ASP* 3.6 4.3 - - - +
437A THR* 2.7 39.7 + - - +
503A ARG* 2.9 17.2 + - - +
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Residues in contact with CYS 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A ALA* 4.4 2.7 - - - -
349A ILE* 3.5 14.8 - - - -
352A ILE* 3.5 29.5 - - + +
375A THR* 4.8 0.4 - - - +
379A LEU* 4.1 22.0 - - + -
430A PHE* 3.0 54.9 + - - -
431A ILE* 3.2 9.4 - - - +
433A ASP* 1.3 78.3 - - - +
435A ILE* 1.3 61.3 + - - +
437A THR* 3.4 3.1 + - - -
438A LEU* 3.1 20.1 + - - +
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Residues in contact with ILE 435 (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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376A MET* 4.8 2.5 - - + -
379A LEU* 4.4 13.9 - - + -
431A ILE* 3.0 30.6 + - + +
432A SER* 3.2 9.8 + - - +
434A CYS* 1.3 74.3 - - - +
436A ASP* 1.3 65.7 + - - +
438A LEU* 3.3 7.8 + - + +
439A ALA* 3.1 21.7 + - - +
480A LEU* 4.1 8.4 - - + +
483A VAL* 4.0 34.8 - - + -
487A VAL* 4.7 5.2 - - + -
496A LEU* 4.5 14.4 - - + -
504A LEU* 4.7 15.3 - - + -
507A LEU* 3.7 20.6 - - + -
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Residues in contact with ASP 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU 3.9 13.9 - - - +
411A TYR* 3.6 8.1 - - + +
412A THR* 3.0 38.7 + - - +
432A SER* 2.9 15.3 + - - +
433A ASP 3.6 4.7 - - - +
435A ILE* 1.3 75.8 - - - +
437A THR* 1.3 58.9 + - - +
439A ALA* 3.3 1.7 + - - +
440A VAL* 2.9 37.4 + - + +
503A ARG* 2.5 33.4 + - - +
507A LEU* 3.6 19.6 - - + +
510A ARG* 6.2 0.2 - - - +
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Residues in contact with THR 437 (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 ILE* 4.4 15.4 - - + +
352A ILE* 4.0 13.7 - - + -
353A ILE* 3.7 25.6 - - + -
402A LEU* 5.4 0.7 - - - +
403A PRO* 5.8 0.6 - - + +
410A GLU 5.6 0.2 - - - -
411A TYR* 3.9 18.9 + - - +
433A ASP* 2.7 23.6 + - - +
434A CYS* 3.7 7.6 - - - -
436A ASP* 1.3 75.1 - - - +
438A LEU* 1.3 63.3 + - - +
440A VAL* 4.8 2.7 - - - +
441A ASN* 2.7 46.1 + - - +
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Residues in contact with LEU 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE* 3.5 16.8 - - + -
356A ALA* 5.0 1.8 - - + -
371A ALA* 4.3 9.2 - - + -
372A THR* 3.8 38.6 - - - +
375A THR* 4.2 15.5 - - + +
376A MET* 4.1 14.1 - - + -
434A CYS 3.1 13.9 + - - +
435A ILE* 3.6 10.3 - - + +
437A THR* 1.3 78.2 - - - +
439A ALA* 1.3 63.4 + - - +
441A ASN* 4.0 1.3 - - - +
442A LEU* 3.0 40.1 + - + +
479A ASN* 5.7 1.6 - - + -
480A LEU* 5.9 1.6 - - + -
483A VAL* 4.0 25.1 - - + -
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Residues in contact with ALA 439 (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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435A ILE 3.1 13.2 + - - +
436A ASP 3.3 3.8 + - - +
438A LEU* 1.3 81.2 - - - +
440A VAL* 1.3 58.0 + - - +
442A LEU* 3.2 7.3 + - - +
443A GLU* 2.9 29.1 + - - +
476A ILE* 3.7 25.1 - - + +
480A LEU* 4.8 5.8 - - + -
507A LEU* 4.0 26.5 - - + -
511A TYR* 4.3 5.4 - - + -
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Residues in contact with VAL 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A GLU* 3.3 45.1 - - + +
436A ASP* 2.9 18.2 + - + +
437A THR* 4.5 3.1 - - - +
439A ALA* 1.3 75.7 - - + +
441A ASN* 1.3 60.4 + - - +
443A GLU* 3.3 7.0 + - - +
444A ARG* 2.9 28.9 + - - +
458A VAL* 3.5 33.3 - - + +
459A ALA* 5.1 1.1 - - + -
510A ARG* 3.5 24.9 - - - +
511A TYR* 4.2 2.7 - - - +
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Residues in contact with ASN 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A ILE 5.0 0.2 - - - +
353A ILE* 3.6 25.1 - - - +
356A ALA* 3.7 20.3 - - + +
357A ASN* 3.4 27.6 + - - +
410A GLU* 5.4 2.3 - - - +
437A THR* 2.7 42.6 + - - +
440A VAL* 1.3 76.2 - - - +
442A LEU* 1.3 59.8 + - - +
444A ARG* 3.6 17.8 - - - +
445A LYS* 3.0 27.7 + - - +
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Residues in contact with LEU 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA* 3.8 30.7 - - + +
369A THR* 3.9 13.2 - - - +
371A ALA* 4.3 5.6 - - + -
372A THR* 3.7 22.7 - - - +
438A LEU* 3.0 26.1 + - + +
439A ALA* 3.5 5.4 - - - +
441A ASN* 1.3 76.3 - - - +
443A GLU* 1.3 58.4 + - - +
445A LYS* 3.4 14.7 + - - +
446A ALA* 2.9 28.2 + - - +
475A PHE* 3.8 20.0 - - + -
476A ILE* 3.7 12.8 - - + -
479A ASN* 3.7 24.2 - - + +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A ALA 2.9 13.7 + - - +
440A VAL* 3.4 8.9 - - - +
442A LEU* 1.3 74.7 - - - +
444A ARG* 1.3 59.5 + - - +
446A ALA* 3.1 6.5 + - - +
447A GLN* 2.6 56.7 + - - +
458A VAL* 3.2 11.6 - - - +
459A ALA 3.1 15.2 + - - -
472A ILE* 3.6 21.1 - - + -
476A ILE* 3.6 9.3 - - + +
510A ARG* 4.8 0.2 + - - -
511A TYR* 2.6 33.0 + - + +
514A TYR* 2.7 23.5 + - - -
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Residues in contact with ARG 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 4.6 11.2 - - - +
410A GLU* 3.4 27.5 + - - -
440A VAL* 2.9 18.8 + - - +
441A ASN* 3.6 19.2 - - - +
442A LEU 3.3 0.2 - - - -
443A GLU* 1.3 75.1 - - - +
445A LYS* 1.3 58.4 + - - +
447A GLN* 3.3 2.9 + - - +
448A ILE* 2.9 51.5 + - + +
456A PRO* 3.4 35.4 + - + +
458A VAL* 3.9 23.6 - - + +
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Residues in contact with LYS 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A ALA 3.4 23.1 + - - +
357A ASN* 3.8 13.9 - - + +
359A ILE* 3.1 33.8 + - - +
360A SER* 3.8 16.9 - - - +
361A THR 3.9 12.0 + - - +
362A ILE* 4.5 6.9 - - + +
363A PRO* 5.6 0.4 - - - +
369A THR* 5.2 5.5 - - - +
441A ASN 3.0 17.3 + - - +
442A LEU* 3.6 18.1 - - - +
444A ARG* 1.3 77.9 - - - +
446A ALA* 1.3 61.3 + - - +
448A ILE* 3.4 8.7 + - - +
449A ALA* 2.9 25.5 + - - +
475A PHE* 4.2 20.4 - - - -
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Residues in contact with ALA 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.7 24.2 - - + -
442A LEU 2.9 15.3 + - - +
443A GLU* 3.1 11.0 + - - +
445A LYS* 1.3 78.9 - - - +
447A GLN* 1.3 56.6 + - - +
449A ALA* 3.3 0.9 + - - +
450A LEU* 2.9 35.5 + - - +
472A ILE* 4.2 17.9 - - + -
475A PHE* 4.0 18.8 - - + -
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Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU* 2.6 49.9 + - - +
444A ARG 3.7 4.7 - - - +
446A ALA* 1.3 73.7 - - - +
448A ILE* 1.3 54.1 + - - +
450A LEU* 4.5 0.7 - - - +
451A MET* 2.7 55.3 + - + +
454A GLN 5.9 0.4 - - - -
455A GLU 4.7 0.7 - - - +
456A PRO* 3.6 13.4 - - + +
457A ASP* 3.1 41.8 + - - +
458A VAL* 3.9 3.0 - - - +
466A ASN* 3.5 18.3 + - - +
472A ILE* 3.7 21.8 - - + -
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Residues in contact with ILE 448 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357A ASN* 5.6 2.2 - - - +
444A ARG* 2.9 41.0 + - + +
445A LYS* 3.7 8.5 - - - +
447A GLN* 1.3 77.4 - - - +
449A ALA* 1.3 63.2 + - - +
451A MET 4.2 5.4 - - - -
452A PRO* 3.1 31.1 - - + +
454A GLN 5.2 2.7 - - - +
456A PRO* 3.6 20.0 - - + -
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360A SER 3.5 22.2 - - - +
361A THR* 5.1 0.9 - - - -
362A ILE* 3.9 21.3 - - + +
445A LYS 2.9 18.2 + - - +
446A ALA 3.6 4.5 - - - +
448A ILE* 1.3 81.4 - - - +
450A LEU* 1.3 62.7 + - + +
452A PRO* 3.9 9.7 - - - +
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Residues in contact with LEU 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A ILE* 3.8 17.7 - - + -
446A ALA 2.9 19.3 + - - +
447A GLN* 4.3 2.5 - - - +
449A ALA* 1.3 78.6 - - + +
451A MET* 1.3 63.3 + - + +
452A PRO* 3.4 8.7 - - - +
468A HIS* 3.6 53.1 + - + +
471A ARG* 3.5 37.0 - - - +
472A ILE* 3.9 16.2 - - + -
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Residues in contact with MET 451 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A GLN* 2.7 45.8 + - + +
448A ILE* 3.9 2.1 - - - +
450A LEU* 1.3 80.0 - - + +
452A PRO* 1.3 66.1 - - - +
453A ASN 3.2 2.9 - - - -
454A GLN* 3.0 42.3 + - + +
465A LYS 3.5 22.0 - - - +
466A ASN* 3.4 33.4 - - - +
467A LYS* 3.7 13.0 - - + -
468A HIS* 3.6 18.6 - - + +
472A ILE* 4.9 1.1 - - + -
----------------------------------------------------------
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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