Contacts of the helix formed by residues 436 - 461 (chain A) in PDB entry 2JDQ
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 436 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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394A PHE* 3.1 41.2 - - + -
398A LYS* 4.0 5.4 - - - -
434A VAL* 2.9 5.0 + - + -
435A MET* 1.3 78.1 - - - +
437A SER* 1.3 66.5 + - - +
438A LYS* 3.2 19.2 + - - +
439A ILE* 3.3 38.5 + - + +
440A VAL* 3.3 9.3 - - - +
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Residues in contact with SER 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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436A ASP* 1.3 74.6 + - - +
438A LYS* 1.3 67.6 + - - +
440A VAL* 4.0 7.4 - - - +
441A GLN* 3.1 33.5 + - - +
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Residues in contact with LYS 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 4.0 23.6 - - - +
436A ASP* 3.2 15.6 - - - +
437A SER* 1.3 89.1 + - - +
439A ILE* 1.3 60.9 + - - +
441A GLN* 3.4 8.2 + - - +
442A VAL* 3.2 26.7 + - - +
721E LYS* 3.7 27.3 - - - +
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Residues in contact with ILE 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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394A PHE* 4.1 13.0 - - + -
397A ARG* 4.2 3.1 - - + -
398A LYS* 3.4 47.5 - - + +
401A ALA* 4.4 5.6 - - + -
431A LEU* 3.3 37.1 - - + +
434A VAL* 3.7 27.4 - - + -
436A ASP* 3.3 25.2 + - + +
438A LYS* 1.3 75.7 - - - +
440A VAL* 1.3 65.5 + - + +
442A VAL* 3.2 6.4 + - + +
443A ALA* 2.8 28.9 + - - +
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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
----------------------------------------------------------
431A LEU 3.5 15.0 - - - +
432A LEU* 4.0 29.8 - - + +
434A VAL 3.5 19.5 - - - +
436A ASP 3.3 18.8 + - - +
437A SER* 4.0 7.2 - - - +
439A ILE* 1.3 75.1 - - + +
441A GLN* 1.3 54.7 + - - +
443A ALA* 4.2 4.9 - - - -
444A LEU* 2.7 46.3 + - + +
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Residues in contact with GLN 441 (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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437A SER* 3.1 20.8 + - - +
438A LYS* 3.5 13.0 - - - +
440A VAL* 1.3 75.3 - - - +
442A VAL* 1.3 59.9 + - + +
444A LEU* 3.7 11.6 - - - +
445A ASN* 2.9 29.8 + - - +
695E LEU* 4.7 7.3 - - + +
696E ILE 4.3 5.0 - - - +
697E LEU* 2.7 57.1 + - + +
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Residues in contact with VAL 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398A LYS* 4.9 0.7 - - + +
401A ALA* 3.7 22.7 - - + +
402A TRP* 3.4 58.6 - - + +
405A THR* 2.8 42.5 + - + +
438A LYS 3.2 14.6 + - - +
439A ILE* 3.2 10.7 + - + +
440A VAL 3.2 0.6 - - - -
441A GLN* 1.3 76.9 - - + +
443A ALA* 1.3 58.8 + - - +
445A ASN* 3.3 5.5 + - - -
446A GLY 3.1 9.5 + - - -
695E LEU* 4.3 6.5 - - + -
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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
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405A THR* 4.5 3.4 - - - -
428A LEU* 3.5 34.3 - - - +
431A LEU* 3.8 19.9 - - + +
432A LEU* 3.9 10.1 - - + -
439A ILE 2.8 17.7 + - - +
440A VAL* 3.2 4.7 + - - +
442A VAL* 1.3 74.7 - - - +
444A LEU* 1.3 64.0 + - - +
446A GLY* 3.3 1.7 + - - -
447A LEU* 3.2 27.2 + - - +
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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
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432A LEU* 3.9 22.8 - - + +
440A VAL* 2.7 32.9 + - + +
441A GLN* 3.7 12.3 - - - +
443A ALA* 1.3 72.4 - - - +
445A ASN* 1.3 63.3 + - - +
447A LEU* 3.5 8.5 + - + +
448A GLU* 2.9 25.0 + - - +
484A LEU* 6.5 1.1 - - + -
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Residues in contact with ASN 445 (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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405A THR* 3.3 5.0 - - + +
441A GLN 2.9 14.6 + - - +
442A VAL* 3.3 6.3 + - - +
444A LEU* 1.3 77.6 - - - +
446A GLY* 1.3 56.3 + - - +
448A GLU* 3.4 19.5 + - - +
449A ASN* 3.1 47.4 + - - -
695E LEU* 3.0 34.6 - - + +
696E ILE* 4.9 5.1 + - - +
737E ARG* 2.8 35.1 + - - +
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Residues in contact with GLY 446 (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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405A THR* 3.5 17.2 + - - -
408A THR* 3.4 19.5 + - - -
428A LEU* 4.4 5.8 - - - -
442A VAL 3.1 10.9 + - - -
443A ALA 3.3 1.7 + - - -
444A LEU 3.3 0.4 - - - -
445A ASN* 1.3 74.3 - - - +
447A LEU* 1.3 59.6 + - - +
449A ASN 3.4 0.7 + - - -
450A ILE* 3.0 38.8 + - - +
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Residues in contact with LEU 447 (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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425A ILE* 4.3 8.5 - - + -
428A LEU* 4.1 22.0 - - + +
429A CYS* 3.9 27.1 - - - -
432A LEU* 3.5 35.4 - - + -
443A ALA 3.2 18.7 + - - +
444A LEU* 3.8 9.6 - - + +
446A GLY* 1.3 73.5 - - - +
448A GLU* 1.3 64.1 + - - +
450A ILE* 3.4 10.0 + - + +
451A LEU* 3.0 32.2 + - + +
472A ILE* 4.0 26.4 - - + +
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Residues in contact with GLU 448 (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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444A LEU 2.9 18.5 + - - +
445A ASN* 3.5 21.4 + - - +
447A LEU* 1.3 77.4 - - - +
449A ASN* 1.3 65.8 + - - +
451A LEU* 3.5 10.1 + - - +
452A ARG* 3.2 24.5 + - + +
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Residues in contact with ASN 449 (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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405A THR 3.7 1.6 + - - -
408A THR* 3.0 39.4 + - - +
409A SER* 3.3 24.5 - - - +
445A ASN* 3.1 38.9 + - - +
446A GLY 3.7 0.4 - - - +
447A LEU 3.3 0.2 - - - -
448A GLU* 1.3 76.0 - - - +
450A ILE* 1.3 65.6 + - - +
452A ARG* 3.2 27.3 + - - +
453A LEU* 3.3 27.6 + - - +
737E ARG* 4.9 1.2 + - - -
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Residues in contact with ILE 450 (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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408A THR* 3.9 23.8 - - + -
416A ILE* 4.2 17.5 - - + -
420A VAL* 4.2 9.9 - - + -
424A CYS* 4.1 18.2 - - - -
425A ILE* 4.4 13.0 - - + -
428A LEU* 4.0 19.3 - - + -
446A GLY 3.0 24.0 + - - +
447A LEU* 3.7 8.3 - - + +
449A ASN* 1.3 74.8 - - - +
451A LEU* 1.3 57.0 + - - +
453A LEU* 3.3 4.5 + - - +
454A GLY 3.0 22.9 + - - -
468A TYR* 3.2 44.0 - - + -
472A ILE* 5.3 3.1 - - + -
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Residues in contact with LEU 451 (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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447A LEU* 3.0 24.0 + - + +
448A GLU* 3.7 8.3 - - - +
449A ASN 3.3 0.2 - - - -
450A ILE* 1.3 77.3 - - - +
452A ARG* 1.3 62.3 + - - +
454A GLY 3.1 5.9 + - - +
455A GLU* 3.2 5.2 + - - +
466A ASN* 2.8 45.3 + - - +
468A TYR* 4.3 1.8 - - + -
469A CYS* 4.0 24.9 - - - +
472A ILE* 3.6 28.9 - - + -
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Residues in contact with ARG 452 (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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408A THR 4.1 10.3 + - - -
409A SER 4.1 12.1 + - - -
411A GLY 4.9 2.6 + - - -
448A GLU* 3.2 14.0 + - + +
449A ASN* 3.2 37.2 + - - +
451A LEU* 1.3 78.1 - - - +
453A LEU* 1.3 91.1 + - - +
455A GLU* 3.2 24.4 + - + +
456A GLN* 3.6 10.1 + - - +
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Residues in contact with LEU 453 (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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370A ARG* 5.6 3.6 - - - +
408A THR 4.3 3.1 - - - +
411A GLY 4.0 11.4 - - - +
412A SER* 4.3 1.6 - - - +
413A ALA* 4.2 21.5 - - + +
416A ILE* 3.5 42.4 - - + -
449A ASN 3.3 13.4 + - - +
450A ILE 3.3 7.2 + - - +
451A LEU 3.3 0.2 - - - -
452A ARG* 1.3 95.6 - - - +
454A GLY* 1.3 60.3 + - - +
455A GLU 3.1 0.4 - - - -
456A GLN* 3.0 51.7 + - - +
457A GLU* 3.2 17.3 + - - +
468A TYR* 4.5 1.8 - - + -
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Residues in contact with GLY 454 (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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450A ILE 3.0 10.5 + - - -
451A LEU 3.1 2.8 + - - -
453A LEU* 1.3 77.0 - - - +
455A GLU* 1.3 54.8 + - - +
457A GLU* 3.6 2.9 + - - -
458A ALA* 3.1 25.5 + - - +
466A ASN* 3.3 24.7 - - - -
467A PRO* 3.4 14.1 - - - +
468A TYR* 3.7 16.5 - - - -
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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
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451A LEU 3.2 11.8 + - - +
452A ARG* 3.2 13.9 + - - +
453A LEU 3.1 0.6 - - - -
454A GLY* 1.3 75.2 - - - +
456A GLN* 1.3 64.5 + - - +
457A GLU 3.2 0.2 - - - -
458A ALA* 3.2 16.6 + - - +
459A LYS* 3.4 42.8 + - - +
466A ASN* 3.0 26.0 + - - +
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Residues in contact with GLN 456 (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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370A ARG* 5.8 3.4 - - - +
413A ALA* 4.1 7.0 + - + +
452A ARG* 3.6 11.1 + - - +
453A LEU* 3.0 35.7 + - - +
455A GLU* 1.3 78.4 - - - +
457A GLU* 1.3 57.0 + - + +
459A LYS* 3.4 7.2 + - - +
460A ARG* 3.1 59.2 + - - +
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Residues in contact with GLU 457 (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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413A ALA* 3.2 36.9 - - + +
414A GLU* 5.2 0.5 - - - +
417A LYS* 4.2 24.2 + - - -
453A LEU* 3.2 17.6 + - + +
454A GLY* 3.9 9.2 - - - +
455A GLU 3.2 0.4 - - - -
456A GLN* 1.3 74.4 - - - +
458A ALA* 1.3 56.8 + - - +
459A LYS 3.2 3.1 - - - -
460A ARG* 3.9 22.1 + - - +
461A ASN* 3.2 42.1 + - - +
467A PRO* 4.3 15.7 - - + -
468A TYR* 4.3 13.2 + - - +
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Residues in contact with ALA 458 (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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454A GLY 3.1 15.6 + - - +
455A GLU* 3.2 16.2 + - - +
457A GLU* 1.3 75.8 - - - +
459A LYS* 1.3 62.6 + - + +
461A ASN* 5.2 0.2 - - - -
462A GLY* 3.5 10.6 + - - -
463A THR* 4.7 2.7 - - - -
464A GLY* 3.3 26.0 + - - +
465A ILE 3.3 36.3 - - - +
466A ASN* 4.0 2.0 - - + +
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Residues in contact with LYS 459 (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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455A GLU* 3.4 43.7 + - - +
456A GLN* 4.1 5.2 - - - +
457A GLU 3.2 0.2 - - - -
458A ALA* 1.3 83.6 - - - +
460A ARG* 1.3 64.2 + - - +
461A ASN 3.2 1.1 + - - -
462A GLY* 3.6 11.1 + - - +
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Residues in contact with ARG 460 (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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413A ALA* 3.6 21.3 - - - +
414A GLU* 2.9 28.8 + - - -
456A GLN* 3.1 46.9 + - - +
457A GLU* 3.9 25.0 + - - +
459A LYS* 1.3 77.3 - - - +
461A ASN* 1.3 63.5 + - - +
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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
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457A GLU* 3.2 32.7 + - - +
460A ARG* 1.3 83.9 - - - +
462A GLY* 1.3 58.1 + - - +
463A THR* 3.1 28.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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