Contacts of the helix formed by residues 448 - 471 (chain A) in PDB entry 6T2C
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 CYS 448 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA 3.5 17.0 - - - -
410A SER* 3.9 14.1 - - - -
411A GLU 3.5 9.0 - - - +
412A LEU* 4.2 3.6 - - - +
413A THR* 4.0 1.3 - - - -
417A TRP* 3.4 17.7 - - - -
445A VAL 3.8 13.2 - - - +
446A SER 3.1 2.8 + - - -
447A GLN* 1.3 82.7 - - - +
449A ARG* 1.3 80.9 + - - +
450A ALA* 3.1 22.8 + - - -
451A SER* 3.5 8.2 + - - +
633A ARG* 3.9 29.6 - - + -
636A LEU* 5.0 2.9 - - + -
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Residues in contact with ARG 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A LEU 4.6 2.8 + - - -
285A MET* 4.3 26.5 + - - +
287A ALA 5.9 1.0 + - - -
408A LYS* 3.6 43.1 + - - +
409A ALA* 4.3 7.2 - - - -
411A GLU* 3.4 14.6 + - - +
413A THR* 3.7 28.5 - - + +
448A CYS* 1.3 76.4 - - - +
450A ALA* 1.3 61.0 + - - +
452A GLU* 3.0 26.4 + - - +
453A TYR* 3.0 43.2 + - + -
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Residues in contact with ALA 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A ALA* 3.8 12.8 + - + +
448A CYS* 3.1 16.4 - - - -
449A ARG* 1.3 78.2 - - - +
451A SER* 1.3 56.7 + - - +
453A TYR* 3.3 14.3 + - + +
454A ILE* 2.9 32.4 + - - +
636A LEU* 3.8 17.7 - - + -
637A ALA* 4.1 12.1 - - - -
640A VAL* 3.9 16.7 - - + +
641A PHE* 6.4 0.2 - - + -
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Residues in contact with SER 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.8 13.2 - - - +
418A ILE* 4.7 13.2 - - - +
445A VAL 3.2 23.9 + - - -
446A SER* 3.3 19.7 + - - -
448A CYS 3.5 4.4 + - - -
449A ARG 3.2 0.4 - - - -
450A ALA* 1.3 76.2 - - - +
452A GLU* 1.3 59.6 + - - +
454A ILE* 3.3 13.8 + - - +
455A MET* 3.0 30.8 + - - +
580A LEU* 4.9 3.9 - - - +
636A LEU* 3.8 9.1 - - - +
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Residues in contact with GLU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LYS* 3.8 12.5 + - - -
413A THR* 5.7 1.0 - - - +
417A TRP* 3.4 49.8 - - + +
448A CYS 3.8 1.6 + - - -
449A ARG* 3.0 31.7 + - - +
451A SER* 1.3 79.3 - - - +
453A TYR* 1.3 69.5 + - + +
455A MET* 3.4 2.4 + - - +
456A LYS* 2.9 31.8 + - - +
482A THR* 4.6 2.1 - - + +
496A TYR* 2.4 38.2 + - + +
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Residues in contact with TYR 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 4.2 5.7 - + + -
284A LEU* 2.7 61.9 + - + +
285A MET* 3.7 7.8 + - - +
405A GLU* 5.0 1.6 + - - -
408A LYS 5.0 1.2 + - - -
409A ALA* 4.0 25.5 + - + +
449A ARG* 3.0 34.7 + - + +
450A ALA* 3.3 12.8 + - - +
452A GLU* 1.3 88.5 - - - +
454A ILE* 1.3 60.8 + - - +
456A LYS* 3.9 17.1 - - - +
457A ALA* 2.9 31.4 + - - +
576A MET* 4.4 2.6 - - - +
640A VAL* 4.2 14.1 - - + -
641A PHE* 4.2 15.3 - + - -
644A ILE* 4.6 7.2 - - + -
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Residues in contact with ILE 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A ILE* 6.1 1.8 - - + -
450A ALA 2.9 18.3 + - - +
451A SER* 3.5 14.4 - - - +
453A TYR* 1.3 76.8 - - - +
455A MET* 1.3 61.4 + - + +
457A ALA* 3.3 1.7 + - - +
458A VAL* 3.0 30.5 + - + +
576A MET* 4.1 26.2 - - + +
577A ARG* 4.2 33.9 - - + +
579A CYS* 4.2 5.6 - - + -
580A LEU* 3.9 31.0 - - + -
636A LEU* 4.4 6.1 - - + -
640A VAL* 3.7 22.7 - - + -
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Residues in contact with MET 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TRP* 3.4 37.0 - - + +
418A ILE* 4.9 11.9 - - + -
419A GLU 5.3 1.1 - - - +
451A SER 3.0 15.9 + - - +
452A GLU* 3.9 5.4 - - - +
453A TYR 3.4 0.2 - - - -
454A ILE* 1.3 79.2 - - + +
456A LYS* 1.3 62.9 + - - +
458A VAL* 3.4 4.8 + - + +
459A TYR* 3.0 47.7 + - + +
482A THR* 4.3 9.0 - - + -
483A LYS 3.6 28.3 - - - +
577A ARG* 4.9 11.9 - - - +
553B LYS* 6.3 1.6 - - - -
33V C 4.4 17.0 - - - +
34V U 4.0 14.4 - - - +
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Residues in contact with LYS 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.7 32.0 - - + +
283A LEU 3.4 24.0 + - - -
284A LEU 4.9 0.6 + - - -
287A ALA* 4.1 4.9 - - - +
452A GLU* 2.9 20.5 + - - +
453A TYR* 3.9 18.4 - - - +
455A MET* 1.3 77.4 - - - +
457A ALA* 1.3 56.4 + - - +
459A TYR* 3.4 3.4 + - - +
460A ILE* 3.0 36.9 + - + +
480A ILE* 3.9 22.4 - - + -
481A ILE 5.2 0.2 - - - -
482A THR* 3.8 16.3 - - + +
496A TYR* 3.8 41.4 - - + +
519A GLU* 5.1 1.4 + - - +
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Residues in contact with ALA 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A PHE* 3.7 23.1 - - + -
453A TYR 2.9 18.1 + - - +
454A ILE 3.8 0.9 - - - +
456A LYS* 1.3 73.8 - - - +
458A VAL* 1.3 64.7 + - - +
460A ILE* 4.6 0.9 - - - +
461A ASN* 2.4 42.1 + - - +
573A GLY 3.8 1.8 - - - +
576A MET* 3.7 32.8 - - + -
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Residues in contact with VAL 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454A ILE* 3.0 21.9 + - + +
455A MET* 3.7 5.6 - - - +
456A LYS 3.3 0.2 - - - -
457A ALA* 1.3 76.5 - - - +
459A TYR* 1.3 67.8 + - + +
461A ASN* 4.2 0.5 - - - +
462A THR* 3.0 36.1 + - - +
573A GLY 3.9 9.2 - - - +
574A MET* 3.6 20.9 - - - +
576A MET* 4.3 11.0 - - + +
577A ARG* 4.4 28.9 - - + +
33V C 3.9 33.0 - - + +
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Residues in contact with TYR 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A MET* 3.0 42.8 + - + +
456A LYS 3.9 2.7 - - - +
458A VAL* 1.3 85.8 - - + +
460A ILE* 1.3 62.3 + - + +
462A THR* 3.9 4.8 - - - +
463A ALA* 3.0 26.7 + - - +
480A ILE* 6.4 0.2 - - - -
481A ILE* 3.2 36.6 - - + +
482A THR* 4.8 1.1 - - - -
483A LYS* 4.3 24.0 - - + +
577A ARG* 5.3 0.4 - - - -
33V C 3.3 72.0 + + + +
34V U 3.9 9.9 - - - -
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Residues in contact with ILE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 5.4 6.5 - - + +
282A PHE* 3.6 33.7 - - + -
456A LYS* 3.0 21.2 + - + +
457A ALA* 4.0 4.5 - - - +
459A TYR* 1.3 78.2 - - + +
461A ASN* 1.3 66.4 + - - +
463A ALA* 3.8 4.1 - - - +
464A LEU* 2.9 36.5 + - + +
478A ILE* 5.3 3.0 - - + +
479A PRO 5.4 2.2 - - - +
480A ILE* 3.7 49.8 - - + -
499A ILE* 3.8 21.1 - - + -
515A PHE* 6.4 1.3 - - + -
519A GLU* 5.0 0.2 - - - +
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Residues in contact with ASN 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A LYS* 5.7 5.2 - - - +
282A PHE* 5.6 1.2 - - - -
457A ALA* 2.4 37.4 + - - +
460A ILE* 1.3 83.9 - - - +
462A THR* 1.3 57.5 + - - +
464A LEU* 3.8 8.6 - - - +
465A LEU* 3.0 31.2 + - - +
565A THR* 5.4 1.7 + - - -
569A LYS 4.5 1.4 - - - +
570A MET* 3.5 35.7 - - - +
573A GLY* 3.0 27.5 + - - -
574A MET* 3.8 9.7 - - - +
576A MET* 5.3 0.2 - - - +
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Residues in contact with THR 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A VAL 3.0 19.9 + - - -
459A TYR* 3.9 4.5 - - - +
461A ASN* 1.3 75.7 - - - +
463A ALA* 1.3 58.3 + - + +
465A LEU* 3.4 2.4 + - - +
466A ASN* 3.0 37.1 + - - +
574A MET* 3.5 19.2 - - + +
557B TYR* 3.3 26.2 - - - +
32V G 4.3 5.2 - - - +
33V C 2.9 35.8 + - + -
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Residues in contact with ALA 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A TYR 3.0 18.8 + - - +
460A ILE* 3.9 2.5 - - - +
462A THR* 1.3 78.2 - - - +
464A LEU* 1.3 57.6 + - - +
466A ASN* 3.4 7.0 + - - +
467A SER* 3.0 33.3 + - - -
478A ILE* 3.7 26.2 - - + +
479A PRO 5.2 2.9 - - - +
31V U 4.6 4.7 - - - +
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Residues in contact with LEU 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460A ILE* 2.9 28.8 + - + +
461A ASN* 3.8 7.0 - - - +
463A ALA* 1.3 78.7 - - - +
465A LEU* 1.3 56.3 + - - +
467A SER 3.6 0.5 + - - -
468A SER* 2.9 34.3 + - - +
478A ILE* 3.9 14.8 - - + +
499A ILE* 4.9 10.5 - - + -
501A LYS* 3.7 28.7 - - + -
513A VAL* 5.0 7.6 - - + -
515A PHE* 4.2 23.6 - - + -
565A THR* 4.1 23.8 - - + -
570A MET* 3.7 16.2 - - + -
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Residues in contact with LEU 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ASN 3.0 15.3 + - - +
462A THR 3.9 2.9 - - - +
464A LEU* 1.3 74.5 - - - +
466A ASN* 1.3 62.9 + - - +
468A SER* 4.3 3.1 - - - -
469A CYS* 2.9 50.1 + - - +
506A LEU* 5.9 1.6 - - + -
567A LYS* 4.9 8.3 - - + +
570A MET* 3.9 34.7 - - + -
571A LYS 4.5 3.8 - - - +
574A MET* 3.7 27.1 - - - -
45C LEU* 3.8 33.4 - - + -
49C TRP* 5.4 1.5 - - + +
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Residues in contact with ASN 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A THR* 3.0 23.2 + - - +
463A ALA* 3.9 5.7 - - - +
464A LEU 3.3 0.2 - - - -
465A LEU* 1.3 79.7 - - - +
467A SER* 1.3 58.2 + - - +
469A CYS* 5.2 2.0 - - - -
470A THR* 2.9 37.4 + - - +
557B TYR* 3.7 13.4 + - - -
560B ARG* 4.8 1.3 + - - +
48C LYS 4.5 8.0 - - - +
49C TRP* 4.8 6.3 - - - +
52C ALA* 4.4 13.2 - - - +
31V U 3.6 35.2 + - - +
32V G 3.5 23.8 + - - -
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Residues in contact with SER 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A ALA 3.0 16.8 + - - -
464A LEU 4.2 0.7 - - - -
466A ASN* 1.3 75.3 - - - +
468A SER* 1.3 56.5 + - - +
470A THR 4.6 0.2 - - - +
471A ALA* 2.9 17.5 + - - +
476A GLN* 3.0 30.3 + - - +
478A ILE* 3.9 15.3 - - - +
501A LYS* 2.5 39.5 + - - -
31V U 3.4 16.4 + - - +
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Residues in contact with SER 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 2.9 20.0 + - - +
465A LEU* 3.8 10.1 - - - -
466A ASN 3.2 0.2 - - - -
467A SER* 1.3 79.0 - - - +
469A CYS* 1.3 63.3 + - - +
470A THR 3.6 0.2 + - - -
472A MET* 3.4 21.1 - - - +
501A LYS* 3.8 10.0 - - - +
504A SER* 3.2 38.3 + - - +
506A LEU* 4.8 5.8 - - - +
513A VAL* 4.4 11.6 - - - +
570A MET* 4.6 9.1 - - - +
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Residues in contact with CYS 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A LEU* 2.9 37.8 + - - +
466A ASN 4.5 1.1 - - - +
468A SER* 1.3 78.4 - - - +
470A THR* 1.3 61.3 + - - +
472A MET* 5.1 11.2 - - - +
506A LEU* 6.4 1.3 - - - -
567A LYS* 5.7 8.1 - - - -
49C TRP* 3.7 61.3 - - + -
53C MET* 4.6 2.4 - - - +
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Residues in contact with THR 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ASN* 2.9 23.0 + - - -
469A CYS* 1.3 80.7 + - - +
471A ALA* 1.3 61.0 + - + +
472A MET* 3.8 5.4 + - - +
49C TRP* 5.3 5.0 + - - +
52C ALA* 5.0 8.3 - - - +
53C MET* 5.0 12.1 - - + +
30V C 4.0 47.2 + - + +
31V U 3.6 35.1 + - + +
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Residues in contact with ALA 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A ASN* 5.4 1.8 - - - +
467A SER 3.3 7.5 + - - +
470A THR* 1.3 78.6 - - + +
472A MET* 1.3 51.7 + - - +
473A GLU 3.3 8.3 + - - -
474A GLU* 3.7 18.9 + - - +
476A GLN* 3.7 25.9 + - - +
501A LYS* 2.5 30.0 + - - -
31V U 4.2 9.0 - - + +
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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