Contacts of the helix formed by residues 441 - 471 (chain A) in PDB entry 4H3T
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 LYS 441 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ARG 5.5 1.2 + - - -
421A TYR* 4.0 43.0 + - + +
422A LEU 5.7 1.0 + - - -
423A SER* 5.2 3.0 + - - -
437A VAL* 3.8 9.2 - - + -
438A PRO* 3.0 27.8 + - + +
440A GLY* 1.4 77.2 - - - +
442A ALA* 1.3 59.1 + - - +
443A ALA 3.4 2.5 - - - -
444A LEU* 3.3 14.1 + - + +
445A ALA* 2.9 29.5 + - - +
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Residues in contact with ALA 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437A VAL* 4.0 9.9 - - + +
438A PRO 3.2 7.3 + - - +
439A GLU* 3.1 20.9 + - - +
440A GLY 3.6 0.4 - - - -
441A LYS* 1.3 78.6 - - - +
443A ALA* 1.4 57.7 + - - +
445A ALA* 3.4 1.8 + - - +
446A LYS* 3.0 29.5 + - - +
449A ARG* 4.9 2.4 + - - -
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Residues in contact with ALA 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439A GLU 4.8 0.8 + - - -
440A GLY 5.4 1.0 + - - -
441A LYS 3.4 0.4 - - - -
442A ALA* 1.4 77.9 - - - +
444A LEU* 1.3 62.9 + - - +
446A LYS* 3.4 8.7 + - - +
447A ALA* 3.1 23.0 + - - +
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Residues in contact with LEU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TYR* 3.5 43.3 - - + +
441A LYS* 3.3 18.0 + - + +
442A ALA 3.3 0.4 - - - -
443A ALA* 1.3 75.6 - - - +
445A ALA* 1.3 60.0 + - - +
447A ALA* 3.2 8.9 + - + +
448A ALA* 2.9 27.8 + - + +
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Residues in contact with ALA 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A GLU* 4.2 5.0 - - + +
421A TYR* 3.8 24.6 - - + -
437A VAL* 3.8 24.7 - - + -
441A LYS 2.9 19.9 + - - +
442A ALA 3.9 2.2 - - - +
444A LEU* 1.3 72.5 - - - +
446A LYS* 1.3 57.0 + - - +
448A ALA* 3.2 2.6 + - - +
449A ARG* 2.9 49.2 + - - +
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Residues in contact with LYS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A ALA 3.0 18.8 + - - +
443A ALA* 3.6 8.5 - - - +
444A LEU 3.2 0.2 - - - -
445A ALA* 1.3 76.6 - - - +
447A ALA* 1.3 61.9 + - - +
449A ARG* 3.3 29.5 + - - +
450A SER* 3.1 22.5 + - - -
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Residues in contact with ALA 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A ALA 3.1 13.8 + - - +
444A LEU* 3.6 13.2 - - + +
446A LYS* 1.3 77.8 - - - +
448A ALA* 1.3 61.4 + - - +
450A SER* 3.3 8.3 + - - -
451A ALA* 3.0 22.7 + - - +
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Residues in contact with ALA 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A ALA* 3.6 20.7 - - - +
420A ARG* 4.2 14.6 + - - +
421A TYR* 3.9 22.9 - - + +
444A LEU* 2.9 15.6 + - + +
445A ALA 3.2 7.8 + - - +
447A ALA* 1.3 77.8 - - - +
449A ARG* 1.3 61.6 + - - +
451A ALA* 3.4 7.1 + - - +
452A LEU* 3.1 18.4 + - - +
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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
----------------------------------------------------------
410A ALA 5.0 2.9 - - - +
414A GLY* 3.4 40.5 - - - +
415A TYR* 6.3 0.2 - - - -
417A ALA* 3.8 9.6 - - + +
418A GLU* 2.8 31.5 + - + +
437A VAL* 4.8 2.6 - - - +
442A ALA 4.9 1.6 + - - -
445A ALA* 2.9 35.6 + - - +
446A LYS* 3.5 38.0 - - - +
448A ALA* 1.3 75.2 - - - +
450A SER* 1.3 58.9 + - - +
452A LEU* 3.3 3.3 + - - +
453A ALA* 3.0 28.1 + - - +
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Residues in contact with SER 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A LYS 3.1 13.6 + - - -
447A ALA* 3.3 11.4 + - - -
449A ARG* 1.3 75.0 - - - +
451A ALA* 1.4 57.0 + - - +
453A ALA* 3.3 7.7 + - - +
454A GLU* 2.9 39.9 + - - +
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Residues in contact with ALA 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447A ALA 3.0 17.1 + - - +
448A ALA* 3.8 8.3 - - - +
449A ARG 3.4 0.4 - - - -
450A SER* 1.4 74.5 - - - +
452A LEU* 1.3 56.2 + - - +
454A GLU* 3.3 8.1 + - - +
455A GLU* 3.0 27.4 + - - +
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 3.6 48.3 - - + +
416A VAL* 4.7 1.8 - - + -
417A ALA* 3.8 16.4 - - + +
420A ARG* 5.8 1.3 - - - +
448A ALA 3.1 16.4 + - - +
449A ARG 4.0 3.4 - - - +
451A ALA* 1.3 75.3 - - - +
453A ALA* 1.3 62.3 + - - +
455A GLU* 3.3 11.7 + - - +
456A ILE* 3.1 21.8 + - - +
495A LEU* 4.3 15.9 - - + +
498A ARG* 3.9 24.5 - - - +
499A GLU* 4.0 26.5 - - + +
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Residues in contact with ALA 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A ALA* 3.8 35.7 + - + +
449A ARG 3.0 13.4 + - - +
450A SER* 3.3 12.8 + - - +
452A LEU* 1.3 73.0 - - - +
454A GLU* 1.3 66.9 + - + +
456A ILE* 3.2 4.8 - - - +
457A TYR* 3.0 35.3 + - + -
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Residues in contact with GLU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A GLY 4.7 9.0 - - - +
322A GLN* 4.5 4.7 + - - +
325A ARG* 2.9 43.4 + - - -
450A SER* 2.9 32.2 + - - +
451A ALA* 3.3 7.4 + - - +
453A ALA* 1.3 74.9 - - - +
455A GLU* 1.3 61.5 + - - +
457A TYR* 3.3 4.6 + - - +
458A GLY* 3.0 19.8 + - - -
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Residues in contact with GLU 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ALA 3.0 14.1 + - - +
452A LEU* 3.5 17.0 - - + +
453A ALA 3.2 0.4 - - - -
454A GLU* 1.3 77.0 - - - +
456A ILE* 1.3 62.9 + - - +
458A GLY* 3.2 3.7 + - - +
459A ARG* 3.1 38.9 + - + +
495A LEU* 3.8 12.1 - - + -
498A ARG* 2.7 45.2 + - - -
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Residues in contact with ILE 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406A ALA 4.9 2.5 - - - +
409A ALA* 4.3 13.2 - - + -
410A ALA* 3.7 28.0 - - + +
413A LEU* 3.9 19.3 - - + -
452A LEU 3.1 11.4 + - - +
453A ALA 3.2 15.7 - - - +
455A GLU* 1.3 74.4 - - - +
457A TYR* 1.3 65.5 + - + +
459A ARG* 3.1 3.1 + - - -
460A LEU* 2.9 39.5 + - + +
488A VAL 4.5 2.5 - - - +
491A VAL* 3.8 17.3 - - + -
492A ALA* 3.9 25.6 - - + +
495A LEU* 3.6 17.1 - - + +
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Residues in contact with TYR 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 3.7 9.2 + - - +
324A TRP* 3.8 17.6 - + - -
325A ARG* 3.3 64.5 + - + +
403A VAL* 5.3 2.2 - - + +
406A ALA* 4.3 20.9 - - + -
407A ALA* 3.0 34.7 - - - +
410A ALA* 4.0 14.2 - - + +
453A ALA* 3.0 33.7 + - + -
454A GLU* 3.7 7.4 - - - +
456A ILE* 1.3 77.3 - - + +
458A GLY* 1.3 62.3 + - - +
460A LEU* 3.2 6.0 + - + +
461A ASP* 3.1 22.5 + - - +
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Residues in contact with GLY 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 3.8 14.9 - - - +
454A GLU 3.0 13.6 + - - -
455A GLU* 3.2 4.4 + - - -
457A TYR* 1.3 76.9 - - - +
459A ARG* 1.4 60.2 + - - +
461A ASP* 3.4 15.3 + - - +
462A ALA 4.8 1.0 + - - -
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Residues in contact with ARG 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A GLU* 3.1 35.8 + - + +
456A ILE 3.1 7.2 + - - +
458A GLY* 1.4 77.6 - - - +
460A LEU* 1.3 59.1 + - - +
461A ASP 3.3 0.2 - - - -
463A PRO* 3.3 20.4 - - - +
491A VAL* 3.9 27.1 + - + +
494A ASP* 3.2 26.5 + - - +
495A LEU* 3.6 27.3 - - - +
498A ARG* 3.6 12.9 - - - +
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Residues in contact with LEU 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TRP* 4.0 12.8 - - + -
406A ALA* 3.8 29.8 - - + +
456A ILE* 2.9 41.5 + - + +
457A TYR* 3.2 6.7 + - + +
459A ARG* 1.3 76.1 - - - +
461A ASP* 1.3 59.4 + - - +
463A PRO* 3.5 4.3 - - - -
464A TYR* 2.8 32.2 + - - +
484A TRP* 4.2 5.8 - - + -
487A LEU* 3.6 29.6 - - + -
488A VAL* 4.0 20.2 - - + -
491A VAL* 4.1 20.6 - - + -
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Residues in contact with ASP 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 3.6 16.4 - - + +
324A TRP* 2.7 32.5 + - - +
457A TYR 3.1 9.3 + - - +
458A GLY* 3.5 14.8 - - - +
459A ARG 3.3 2.4 - - - -
460A LEU* 1.3 81.7 - - - +
462A ALA* 1.3 66.2 + - - +
464A TYR* 3.8 1.7 - - - +
465A ARG* 3.0 54.1 + - - +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458A GLY 4.8 1.2 + - - -
459A ARG 4.7 0.4 + - - -
461A ASP* 1.3 77.5 + - - +
463A PRO* 1.4 72.6 - - + +
465A ARG* 3.3 10.1 + - - +
466A HIS* 3.1 23.4 + - - +
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Residues in contact with PRO 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ARG 3.3 24.9 - - - +
460A LEU* 3.5 6.3 - - - +
462A ALA* 1.4 94.7 - - + +
464A TYR* 1.4 55.9 + - - +
466A HIS* 3.4 7.5 + - + +
467A PHE* 3.0 28.6 + - - +
484A TRP* 3.6 6.8 - - + -
487A LEU* 3.8 39.1 - - + +
491A VAL* 5.8 1.8 - - + -
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Residues in contact with TYR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TRP* 3.4 52.0 - + + -
327A LEU* 3.5 17.1 - - + +
381A LEU* 5.3 0.2 - - + -
399A ALA* 2.9 26.2 + - - +
402A ALA* 3.9 8.3 - - + -
403A VAL* 3.5 20.8 - - + +
460A LEU 2.8 23.7 + - - +
461A ASP 3.8 3.6 - - - +
463A PRO* 1.4 71.0 - - - +
465A ARG* 1.3 61.6 + - + +
467A PHE* 3.2 24.7 + + - +
468A LEU* 2.8 45.0 + - + +
484A TRP* 3.5 28.2 - + + -
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Residues in contact with ARG 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A GLN* 5.0 1.6 - - - +
323A VAL* 4.1 6.9 - - - +
324A TRP* 4.3 10.6 - - + -
379A ASP* 3.2 29.5 + - - -
380A ARG 2.9 24.5 + - - -
381A LEU* 3.9 24.7 - - + +
382A ASP* 4.9 5.6 - - + +
461A ASP* 3.0 46.2 + - - +
462A ALA* 3.7 7.4 - - - +
464A TYR* 1.3 80.2 - - - +
466A HIS* 1.3 56.4 + - - +
468A LEU* 3.5 4.8 + - - +
469A THR* 3.0 33.8 + - - -
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Residues in contact with HIS 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462A ALA 3.1 13.2 + - - +
463A PRO* 3.7 10.5 - - + +
465A ARG* 1.3 72.7 - - - +
467A PHE* 1.3 66.9 + - - +
469A THR* 3.6 7.4 + - + -
470A GLY* 3.1 19.9 + - - -
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Residues in contact with PHE 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A VAL* 3.8 16.6 - - + -
399A ALA* 4.1 9.6 - - - -
402A ALA* 3.5 28.9 - - + -
463A PRO 3.0 17.4 + - - +
464A TYR* 3.2 27.6 + + - +
466A HIS* 1.3 78.3 + - - +
468A LEU* 1.3 75.3 - - - +
470A GLY* 3.2 11.4 + - - -
471A LEU* 3.4 33.6 + - + +
480A PRO* 3.8 36.2 - - + +
481A ARG* 5.1 0.2 - - - -
483A GLU* 6.2 0.2 - - + -
484A TRP* 4.0 30.7 - + + -
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Residues in contact with LEU 468 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 4.7 4.9 - - + -
381A LEU* 3.8 33.9 - - + -
382A ASP 3.4 22.0 - - - +
383A THR* 4.3 6.5 - - + +
384A PRO* 3.1 24.3 - - + +
387A VAL* 4.0 28.5 - - + -
399A ALA* 4.0 20.2 - - + -
464A TYR* 2.8 36.4 + - + +
465A ARG* 3.8 4.5 - - - +
467A PHE* 1.3 78.8 - - - +
469A THR* 1.3 61.8 + - - +
471A LEU* 3.1 13.7 + - + +
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Residues in contact with THR 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
356A LEU* 3.9 28.1 - - + +
382A ASP* 3.6 27.2 + - + +
384A PRO* 4.4 1.1 - - - -
465A ARG 3.0 19.2 + - - -
466A HIS* 3.9 9.4 - - + -
467A PHE 3.4 0.2 - - - -
468A LEU* 1.3 74.9 - - - +
470A GLY* 1.3 62.6 + - - +
471A LEU 3.2 1.4 + - - -
472A ALA* 3.3 21.3 + - - +
473A ASN* 5.4 0.9 - - - +
----------------------------------------------------------
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Residues in contact with GLY 470 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A HIS 3.1 14.9 + - - -
467A PHE 3.2 7.0 + - - -
469A THR* 1.3 76.8 - - - +
471A LEU* 1.3 60.3 + - - +
472A ALA 3.1 1.6 + - - -
473A ASN* 3.4 9.7 + - - +
474A ILE* 3.2 28.9 - - - +
----------------------------------------------------------
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A PRO* 4.3 7.2 - - + -
386A ALA* 4.3 8.9 - - - +
387A VAL* 4.0 15.7 - - + -
395A ALA* 3.7 14.8 - - + +
398A VAL* 3.6 30.3 - - + -
399A ALA* 4.0 11.4 - - + -
467A PHE* 3.4 26.9 + - + +
468A LEU* 3.1 12.6 + - + +
470A GLY* 1.3 76.2 - - - +
472A ALA* 1.3 62.5 + - - +
473A ASN 3.3 1.3 + - - -
474A ILE* 3.7 17.7 + - + +
477A LEU* 4.0 11.3 - - + +
480A PRO* 3.9 34.8 - - + -
----------------------------------------------------------
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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