Contacts of the helix formed by residues 440 - 465 (chain C) in PDB entry 2X1L
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 ALA 440 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C SER* 3.2 12.0 + - - +
439C ASP* 1.3 78.3 - - - +
441C ALA* 1.3 65.8 + - - +
442C GLU* 4.1 20.0 - - + +
443C ASP* 3.3 11.9 + - - +
444C GLN* 3.1 24.1 + - - +
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Residues in contact with ALA 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C ASP 3.6 2.6 + - - -
440C ALA* 1.3 72.6 - - - +
442C GLU* 1.3 62.2 + - - +
444C GLN* 3.4 15.2 + - - +
445C GLN* 3.1 26.5 + - - +
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Residues in contact with GLU 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
440C ALA* 4.1 15.9 - - + +
441C ALA* 1.3 79.1 - - - +
443C ASP* 1.3 73.7 + - - +
445C GLN* 3.5 9.2 + - - +
446C ARG* 3.2 32.8 + - + +
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Residues in contact with ASP 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C LEU* 3.9 30.7 - - + +
438C SER* 2.7 38.8 + - - +
440C ALA* 3.3 9.4 + - - +
442C GLU* 1.3 90.4 - - - +
444C GLN* 1.3 60.2 + - - +
446C ARG* 3.4 4.6 + - - +
447C PHE* 2.9 30.0 + - - +
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Residues in contact with GLN 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C LEU 5.1 1.6 - - - +
438C SER 3.8 18.8 + - - +
439C ASP* 3.7 27.7 + - - +
440C ALA 3.1 14.3 + - - +
441C ALA* 3.7 12.7 - - - +
442C GLU 3.4 0.2 - - - -
443C ASP* 1.3 76.5 - - - +
445C GLN* 1.3 61.6 + - - +
447C PHE* 3.6 8.7 + - - +
448C ARG* 3.4 31.3 + - - +
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Residues in contact with GLN 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380C GLY* 3.8 12.8 + - - -
381C GLU* 3.3 29.6 + - - +
441C ALA 3.1 18.1 + - - +
442C GLU* 3.7 8.2 - - - +
444C GLN* 1.3 75.6 - - - +
446C ARG* 1.3 60.7 + - + +
448C ARG* 3.4 30.5 + - - +
449C THR* 2.8 32.3 + - - +
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381C GLU 3.8 5.1 + - - -
383C THR* 3.5 27.0 + - - +
386C ASP* 2.7 41.6 + - - -
430C GLN* 2.9 31.1 + - - +
435C LEU* 4.0 18.2 - - + -
442C GLU* 3.2 21.2 + - + +
443C ASP* 3.7 9.4 - - - +
444C GLN 3.4 0.2 - - - -
445C GLN* 1.3 76.7 - - - +
447C PHE* 1.3 59.5 + - - +
449C THR* 3.2 20.8 + - - +
450C VAL* 2.8 46.7 + - - +
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Residues in contact with PHE 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367C MET* 4.0 20.0 - - + -
371C ASN* 3.9 23.8 - - + -
372C LEU* 3.4 30.5 - - + -
432C PRO* 3.4 33.9 - - + -
435C LEU* 4.0 17.2 - - + +
436C ARG* 3.6 25.6 - - + -
443C ASP 2.9 16.8 + - - +
444C GLN* 3.8 9.2 - - - +
445C GLN 3.3 0.2 - - - -
446C ARG* 1.3 76.3 - - - +
448C ARG* 1.3 65.2 + - + +
450C VAL* 4.2 1.8 - - - +
451C LEU* 3.1 36.3 + - + +
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Residues in contact with ARG 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C LEU* 4.9 11.4 - - + -
377C PRO* 3.8 19.7 - - + +
378C ASP* 2.6 53.5 + - - +
379C PRO* 3.6 19.2 + - - +
380C GLY* 3.7 3.4 - - - +
444C GLN* 3.4 14.9 + - - +
445C GLN* 3.5 35.8 - - - +
446C ARG 3.3 0.2 - - - -
447C PHE* 1.3 85.1 - - + +
449C THR* 1.3 58.4 + - - +
451C LEU* 4.7 0.2 - - - -
452C TYR* 3.0 29.3 + - - +
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Residues in contact with THR 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C PRO* 4.2 7.0 - - + -
380C GLY* 2.9 23.3 + - - +
381C GLU 3.7 12.9 + - - +
382C PHE* 3.8 22.0 - - + -
386C ASP* 3.4 25.6 - - - +
426C TYR* 4.5 0.2 - - - -
445C GLN* 2.8 23.1 + - - +
446C ARG* 3.2 15.1 + - - +
448C ARG* 1.3 75.2 - - - +
450C VAL* 1.3 56.7 + - - +
452C TYR* 3.4 1.4 + - - +
453C THR* 2.7 37.5 + - - -
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Residues in contact with VAL 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C TYR* 3.4 22.5 - - + +
427C PHE* 4.9 3.4 - - + -
430C GLN* 3.4 45.5 - - + +
432C PRO* 4.1 25.8 - - + -
435C LEU* 4.6 5.6 - - + -
446C ARG* 2.8 39.0 + - - +
447C PHE* 4.2 3.1 - - - +
449C THR* 1.3 72.0 - - - +
451C LEU* 1.3 58.2 + - - +
453C THR 3.5 0.2 + - - -
454C THR* 2.7 36.6 + - - +
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Residues in contact with LEU 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER* 3.4 34.5 - - - +
367C MET* 3.8 30.5 - - + -
368C VAL* 3.9 23.1 - - + +
372C LEU* 3.8 28.7 - - + -
377C PRO* 4.1 10.1 - - + -
427C PHE* 4.9 4.5 - - + -
432C PRO* 5.6 1.1 - - + +
447C PHE* 3.1 26.1 + - + +
448C ARG* 4.0 3.1 - - - +
450C VAL* 1.3 75.4 - - - +
452C TYR* 1.3 64.7 + - - +
454C THR* 3.5 4.9 + - - -
455C LEU* 3.1 28.8 + - + +
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Residues in contact with TYR 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376C VAL* 4.1 8.5 - - + -
377C PRO* 3.4 27.3 - - + +
379C PRO* 3.7 31.6 - - + -
382C PHE* 4.0 22.2 - + - -
390C LEU* 5.8 1.3 - - + -
448C ARG 3.0 19.3 + - - +
449C THR 3.7 3.6 - - - +
451C LEU* 1.3 77.8 - - - +
453C THR* 1.3 64.5 + - - +
455C LEU* 3.2 6.5 + - - +
456C GLU* 3.0 24.8 + - + +
495C ARG* 3.4 32.3 - - - +
496C ILE* 2.7 44.1 + - + +
498C PRO* 4.1 9.9 - - + +
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Residues in contact with THR 453 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382C PHE* 3.6 21.0 - - - -
386C ASP* 4.0 11.8 - - - +
389C LEU* 4.0 20.4 - - + -
390C LEU* 3.8 25.3 - - + +
426C TYR* 3.6 21.2 + - + +
449C THR 2.7 22.3 + - - -
450C VAL 3.9 0.9 - - - -
452C TYR* 1.3 79.8 - - - +
454C THR* 1.3 62.8 + - - +
456C GLU* 3.4 6.0 + - - +
457C VAL* 3.2 23.0 + - - +
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Residues in contact with THR 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 3.8 24.9 - - + -
364C SER* 3.9 19.3 - - - +
389C LEU* 5.4 1.3 - - - -
423C ALA* 5.2 4.0 - - + +
426C TYR* 3.8 13.4 - - - -
427C PHE* 3.6 34.3 - - + -
450C VAL 2.7 22.3 + - - -
451C LEU 3.8 5.2 - - - -
453C THR* 1.3 77.2 - - - +
455C LEU* 1.3 62.0 + - - +
457C VAL* 3.4 8.6 + - - +
458C VAL* 3.1 22.1 + - - +
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Residues in contact with LEU 455 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364C SER* 3.9 26.5 - - - +
365C LEU* 3.8 29.2 - - + -
368C VAL* 3.7 23.3 - - + -
376C VAL* 4.6 13.9 - - + -
377C PRO* 3.8 19.5 - - + -
451C LEU* 3.1 23.2 + - + +
452C TYR* 3.6 7.2 - - - +
454C THR* 1.3 76.5 - - - +
456C GLU* 1.3 57.6 + - - +
458C VAL* 3.3 7.4 + - + +
459C ARG* 2.8 30.1 + - - +
480C LEU* 3.9 15.3 - - + +
496C ILE* 4.5 9.9 - - + -
502C LEU* 5.1 1.8 - - + -
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Residues in contact with GLU 456 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C LEU* 3.8 14.6 - - + -
452C TYR* 3.0 20.2 + - + +
453C THR 3.7 5.2 - - - +
454C THR 3.3 0.2 - - - -
455C LEU* 1.3 73.5 - - - +
457C VAL* 1.3 64.7 + - - +
459C ARG* 2.7 44.9 + - - +
460C ILE* 3.1 31.1 + - + +
492C ILE 4.3 0.3 - - - +
495C ARG* 3.0 47.9 + - - +
496C ILE* 3.0 21.8 + - + +
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Residues in contact with VAL 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360C LEU* 5.1 0.7 - - + -
389C LEU* 3.8 31.4 - - + +
390C LEU* 4.7 6.7 - - + -
393C ALA* 4.3 18.6 - - + +
419C VAL* 3.9 23.3 - - + +
420C LEU* 4.6 10.8 - - + -
423C ALA* 3.8 23.1 - - + -
453C THR 3.2 16.3 + - - +
454C THR* 3.6 8.1 - - - +
456C GLU* 1.3 76.1 - - - +
458C VAL* 1.3 61.9 + - - +
460C ILE* 3.4 2.9 + - - +
461C ALA* 3.0 23.4 + - + +
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Residues in contact with VAL 458 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 5.0 5.8 - - + +
360C LEU* 3.8 31.6 - - + -
361C ALA* 4.1 30.3 - - + -
364C SER* 4.6 5.6 - - - +
365C LEU* 6.0 0.9 - - + -
420C LEU* 5.1 3.1 - - + -
454C THR 3.1 15.2 + - - +
455C LEU* 3.6 9.4 - - + +
457C VAL* 1.3 75.0 - - - +
459C ARG* 1.3 55.2 + - - +
461C ALA* 3.5 5.8 + - - +
462C SER* 2.7 43.7 + - - +
476C LEU* 4.3 6.1 - - + -
480C LEU* 3.9 20.4 - - + -
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Residues in contact with ARG 459 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C LEU 2.8 17.6 + - - +
456C GLU* 2.7 44.9 + - - +
457C VAL 3.3 0.2 - - - -
458C VAL* 1.3 75.9 - - - +
460C ILE* 1.3 67.6 + - - +
462C SER* 3.4 2.4 + - - -
463C LEU* 3.1 45.6 + - + +
477C LEU* 4.1 7.5 - - + +
480C LEU* 3.7 21.3 - - + +
482C GLN* 3.4 28.1 + - - +
491C ALA 2.8 22.6 + - - -
492C ILE 3.0 18.8 + - - -
494C ASN 3.0 21.7 + - - -
496C ILE* 3.6 23.9 - - + +
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Residues in contact with ILE 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ALA* 3.6 36.1 - - + +
394C ASP* 3.6 22.7 - - - +
396C LEU* 4.4 5.6 - - + -
397C LEU 6.0 0.2 - - - +
456C GLU* 3.1 43.7 + - + +
457C VAL 3.8 3.8 - - - +
459C ARG* 1.3 85.5 - - - +
461C ALA* 1.3 63.4 + - - +
463C LEU* 3.4 9.1 + - - +
464C LEU* 3.1 39.0 + - + +
492C ILE* 4.1 21.5 - - + +
495C ARG* 4.1 2.5 - - - +
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Residues in contact with ALA 461 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 5.1 3.1 - - + -
396C LEU* 5.3 4.0 - - + -
416C ILE* 4.0 20.0 - - + -
419C VAL* 6.4 0.9 - - + -
420C LEU* 3.9 25.4 - - + -
457C VAL* 3.0 18.8 + - + +
458C VAL* 3.8 4.0 - - - +
460C ILE* 1.3 78.0 - - - +
462C SER* 1.3 57.6 + - - +
464C LEU* 3.2 5.9 + - - +
465C LEU* 2.9 40.6 + - + +
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Residues in contact with SER 462 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 5.3 1.1 - - - +
458C VAL* 2.7 26.5 + - - +
459C ARG 3.7 4.7 - - - -
460C ILE 3.3 0.2 - - - -
461C ALA* 1.3 75.1 - - - +
463C LEU* 1.3 61.3 + - - +
465C LEU* 3.5 5.9 + - - -
466C GLN* 3.5 3.8 - - - +
473C THR* 3.4 35.6 - - - +
476C LEU* 3.3 35.5 - - - +
477C LEU* 3.9 22.0 - - - -
480C LEU* 4.0 1.9 - - - +
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Residues in contact with LEU 463 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459C ARG* 3.1 54.0 + - + +
460C ILE* 3.7 4.9 - - - +
461C ALA 3.3 0.2 - - - -
462C SER* 1.3 75.8 - - - +
464C LEU* 1.3 59.9 + - - +
466C GLN* 2.9 40.3 + - - +
477C LEU* 3.9 17.9 - - + -
482C GLN* 4.7 2.2 - - + +
486C GLU 4.2 5.6 - - - +
487C ARG* 3.8 26.9 - - + +
488C ASP 4.2 4.7 - - - +
489C PHE* 3.2 15.0 - - + -
491C ALA* 4.3 3.1 - - + +
492C ILE* 3.8 28.0 - - + +
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Residues in contact with LEU 464 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PHE* 5.2 2.8 - - - -
396C LEU* 3.6 36.8 - - + -
397C LEU* 3.8 35.9 - - + +
400C VAL* 4.4 21.8 - - + +
404C PHE* 5.4 2.9 - - - -
416C ILE* 4.2 17.5 - - + +
460C ILE* 3.1 33.2 + - + +
461C ALA* 3.8 3.8 - - - +
463C LEU* 1.3 77.1 - - - +
465C LEU* 1.3 58.6 + - - +
466C GLN 3.3 1.6 - - - -
467C PRO* 3.3 16.3 - - - +
468C VAL* 5.5 2.1 - - - +
489C PHE* 3.9 12.2 - - + -
492C ILE* 3.8 13.9 - - + -
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Residues in contact with LEU 465 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357C LEU* 3.9 18.4 - - + -
413C LEU* 3.6 30.5 - - + -
416C ILE* 3.8 22.9 - - + -
417C TRP* 3.6 33.4 - - + -
420C LEU* 5.1 0.2 - - + -
461C ALA* 2.9 27.1 + - + +
462C SER* 3.5 2.4 + - - +
463C LEU 3.3 0.4 - - - -
464C LEU* 1.3 74.4 - - - +
466C GLN* 1.3 59.3 + - - +
467C PRO* 3.3 3.6 - - - -
468C VAL* 3.0 9.1 + - + +
469C MET* 2.8 39.5 + - + -
473C THR* 3.7 16.5 - - + +
----------------------------------------------------------
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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