Contacts of the helix formed by residues 428 - 452 (chain A) in PDB entry 5E2Q
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 GLU 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 1.3 75.5 - - - +
429A GLU* 1.3 64.4 + - + +
430A ASP* 4.3 14.1 - - + +
431A ASP* 2.9 38.9 + - - +
432A LYS* 3.3 10.7 + - - +
602A ARG* 4.1 28.0 + - - +
603A VAL 4.2 11.6 + - - +
604A ARG* 3.3 43.6 + - + +
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Residues in contact with GLU 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 2.4 41.6 + - - -
427A LEU 3.7 1.2 + - - +
428A GLU* 1.3 77.9 + - + +
430A ASP* 1.3 65.1 + - - +
431A ASP 3.1 1.3 + - - -
432A LYS* 2.5 44.6 + - - +
433A ASP* 4.6 3.1 + - - -
602A ARG* 5.4 5.4 + - - +
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Residues in contact with ASP 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 3.2 11.9 - - + +
429A GLU* 1.3 81.4 - - - +
431A ASP* 1.3 66.5 + - - +
433A ASP* 5.0 3.9 + - - +
434A LEU* 4.7 11.4 + - - +
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Residues in contact with ASP 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A LEU* 5.2 2.9 - - + -
428A GLU* 2.9 29.6 + - + +
430A ASP* 1.3 84.9 - - - +
432A LYS* 1.3 53.9 + - - +
433A ASP 3.3 2.5 - - - -
434A LEU* 3.2 9.5 + - - +
435A TYR* 2.7 36.1 + - - +
540A TYR* 2.7 40.4 + - - -
544A LEU* 3.8 25.3 - - + +
603A VAL 4.7 3.3 - - - +
604A ARG* 5.5 0.9 - - - -
605A LEU 5.3 2.6 + - - -
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Residues in contact with LYS 432 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A ARG* 3.5 35.8 + - + +
424A LEU* 4.0 36.3 + - + -
427A LEU* 3.6 27.8 + - + +
428A GLU 3.3 10.2 + - - +
429A GLU* 2.5 44.8 + - - +
431A ASP* 1.3 76.7 - - - +
433A ASP* 1.3 58.2 + - - +
435A TYR* 3.3 3.7 + - - +
436A ILE* 2.9 36.5 + - - +
602A ARG* 4.9 9.6 - - - +
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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
----------------------------------------------------------
421A ARG* 2.5 34.5 + - - -
429A GLU 4.6 3.9 + - - +
430A ASP 5.0 3.3 + - - +
431A ASP 3.3 0.4 - - - -
432A LYS* 1.3 77.3 - - - +
434A LEU* 1.3 62.5 + - - +
436A ILE* 3.9 9.6 - - - +
437A LEU* 3.2 25.1 + - - +
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Residues in contact with LEU 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ASP 4.7 12.2 + - - +
431A ASP* 3.2 12.4 + - - +
433A ASP* 1.3 75.9 - - - +
435A TYR* 1.3 65.3 + - - +
437A LEU* 3.5 4.4 + - + -
438A TRP* 3.3 54.5 + - + +
537A ASP* 3.9 18.8 - - + +
540A TYR* 4.3 15.0 - - + -
541A VAL* 3.5 13.4 - - + +
544A LEU* 6.1 0.2 - - + -
607A ARG* 3.7 22.7 - - - +
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Residues in contact with TYR 435 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419A THR* 4.7 0.7 - - + -
424A LEU* 3.8 18.2 - - + -
427A LEU* 3.7 23.6 - - + -
431A ASP 2.7 20.8 + - - +
432A LYS* 3.3 8.7 + - - +
434A LEU* 1.3 73.1 - - - +
436A ILE* 1.3 58.3 + - - +
439A LYS* 2.8 67.2 + - + +
541A VAL* 4.3 15.0 - - + +
544A LEU* 3.9 19.0 - - + +
545A ASN* 2.7 46.4 + - + -
548A ARG* 2.7 38.1 + - - -
7B PRO* 4.7 1.9 - - - +
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Residues in contact with ILE 436 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TYR 5.2 2.4 - - - +
419A THR* 4.1 41.6 + - + +
421A ARG* 3.6 41.3 - - + +
424A LEU* 3.9 14.4 - - + -
432A LYS 2.9 23.5 + - - +
433A ASP* 3.9 9.6 - - - +
435A TYR* 1.3 78.2 - - - +
437A LEU* 1.3 63.0 + - - +
438A TRP 3.3 0.9 + - - -
439A LYS* 3.9 4.5 + - - +
440A GLY 4.8 2.3 + - - -
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ASP 3.2 14.3 + - - +
434A LEU* 3.9 7.4 - - + +
435A TYR 3.3 0.4 - - - -
436A ILE* 1.3 82.2 - - - +
438A TRP* 1.3 93.8 + - + +
441A PRO* 4.0 9.8 - - - +
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Residues in contact with TRP 438 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434A LEU* 3.3 38.4 + - + +
436A ILE 3.2 0.2 - - - -
437A LEU* 1.3 110.3 - - + +
439A LYS* 1.3 67.7 + - - +
440A GLY 3.3 2.9 - - - -
441A PRO* 3.4 14.2 - - + +
442A SER* 2.9 24.9 + - - -
530A PHE* 3.9 24.2 - + - -
534A ASP* 3.6 40.8 - - + -
537A ASP* 3.6 25.2 + - + +
538A VAL* 3.7 19.3 - - + -
541A VAL* 3.6 22.7 - - + -
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Residues in contact with LYS 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A ALA* 2.7 33.6 + - - +
417A TYR 3.9 5.6 - - - -
418A ALA 3.4 6.3 + - - -
419A THR* 3.2 31.6 + - + +
435A TYR* 2.8 55.8 + - + +
436A ILE 3.9 1.7 + - - +
437A LEU 3.8 0.6 - - - -
438A TRP* 1.3 76.9 - - - +
440A GLY* 1.3 62.2 + - - +
442A SER* 2.6 22.4 + - - +
443A PHE* 3.1 30.1 - - + -
541A VAL* 4.0 4.9 - - - +
545A ASN* 4.6 6.7 - - - +
548A ARG* 5.4 0.7 - - - +
5B ILE* 6.1 1.3 - - + -
7B PRO* 5.2 9.2 + - + +
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Residues in contact with GLY 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TYR* 3.5 30.6 + - - -
436A ILE 4.8 2.0 + - - -
439A LYS* 1.3 83.6 - - - +
441A PRO* 1.3 69.1 - - - +
442A SER 3.1 0.3 + - - -
443A PHE* 3.2 40.1 - - - -
444A ASP* 3.4 1.9 + - - +
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Residues in contact with PRO 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417A TYR* 3.3 23.8 - - + +
437A LEU 4.0 7.9 - - - +
438A TRP* 3.4 32.8 - - + +
440A GLY* 1.3 89.2 - - - +
442A SER* 1.3 60.7 + - - +
444A ASP* 3.4 6.8 + - + +
445A VAL* 3.4 26.0 + - - +
530A PHE* 3.5 31.2 - - + -
538A VAL* 5.0 1.6 - - + -
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Residues in contact with SER 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A TRP 2.9 15.9 + - - -
439A LYS* 2.6 26.2 + - - +
440A GLY 3.1 0.2 - - - -
441A PRO* 1.3 78.2 - - - +
443A PHE* 1.3 57.7 + - - +
445A VAL* 3.3 6.6 + - - +
446A GLN* 3.0 23.8 + - - +
538A VAL* 4.1 25.9 - - - +
541A VAL* 4.1 15.6 - - - +
542A ASN* 4.3 18.6 + - - +
545A ASN* 5.3 5.5 - - - +
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Residues in contact with PHE 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A LEU* 3.9 30.1 - - + -
416A ALA 4.1 15.0 - - - -
417A TYR* 3.7 20.6 - + - -
439A LYS* 3.1 32.5 - - + -
440A GLY* 3.2 23.3 - - - -
442A SER* 1.3 80.5 + - - +
444A ASP* 1.3 62.7 + - - +
446A GLN* 3.5 11.2 - - + -
447A VAL* 2.7 36.9 + - + +
542A ASN* 5.5 0.4 - - - -
545A ASN* 5.9 5.2 - - - +
5B ILE* 3.4 47.3 - - + -
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Residues in contact with ASP 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A MET* 5.9 2.6 - - - +
342A LYS* 2.5 34.7 + - - -
343A PHE* 3.7 17.0 - - - -
408A SER* 4.4 0.7 + - - -
413A LEU* 3.7 22.4 - - + +
417A TYR* 4.7 9.5 + - + +
440A GLY 3.4 8.7 + - - +
441A PRO* 3.5 13.9 - - + +
442A SER 3.2 0.2 - - - -
443A PHE* 1.3 91.0 - - + +
445A VAL* 1.3 60.2 + - + +
447A VAL* 4.2 1.6 - - - +
448A GLY 3.6 13.0 + - - -
528A PHE* 3.7 14.2 - - - -
530A PHE* 6.4 0.2 - - + -
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Residues in contact with VAL 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441A PRO 3.4 15.5 - - - +
442A SER* 3.3 6.5 + - - +
443A PHE 3.2 0.2 - - - -
444A ASP* 1.3 77.2 - - + +
446A GLN* 1.3 65.2 + - - +
448A GLY* 3.2 2.6 + - - -
449A LEU* 3.1 30.6 + - + +
519A SER* 5.0 6.1 - - - -
524A VAL* 4.1 17.0 - - + -
525A LEU* 4.6 12.8 - - + -
528A PHE* 3.6 42.6 - - + -
530A PHE* 3.8 17.9 - - + -
538A VAL* 4.8 8.7 - - + -
542A ASN* 6.0 1.1 - - - +
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Residues in contact with GLN 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442A SER 3.0 15.8 + - - +
443A PHE* 3.2 12.8 + - + +
445A VAL* 1.3 77.8 - - - +
447A VAL* 1.3 57.0 + - + +
449A LEU* 3.4 3.2 + - - +
450A HIS* 2.8 34.3 + - + +
512A GLU* 3.1 50.2 + - - +
515A GLY* 3.4 19.5 - - - +
516A LEU* 3.9 2.0 - - - +
519A SER* 4.9 0.4 - - - -
542A ASN* 3.0 34.5 + - - +
546A MET* 4.0 9.2 - - + +
572A ARG* 5.9 2.9 - - - +
3B VAL* 6.0 1.8 - - + -
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Residues in contact with VAL 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 5.6 0.2 - - + -
373A PHE* 5.3 1.6 - - + -
388A ALA* 4.3 17.9 - - + +
389A GLY* 4.2 19.3 - - - -
407A VAL 5.0 0.9 - - - +
408A SER* 3.8 28.9 - - - +
413A LEU* 4.4 10.3 - - + -
443A PHE* 2.7 26.2 + - + +
444A ASP* 4.2 5.4 - - - +
446A GLN* 1.3 73.4 - - + +
448A GLY* 1.3 63.3 + - - +
450A HIS* 3.4 5.8 + - - +
451A ALA* 3.2 25.5 + - + +
3B VAL* 4.1 20.0 - - + +
5B ILE* 4.6 7.4 - - + -
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Residues in contact with GLY 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343A PHE* 4.4 6.5 - - - -
346A LEU* 4.0 12.6 - - - +
373A PHE* 3.5 22.4 - - - -
444A ASP 3.6 9.2 + - - -
445A VAL 3.2 7.2 + - - -
447A VAL* 1.3 80.9 - - - +
449A LEU* 1.3 59.3 + - - +
452A LEU* 3.2 29.3 + - - +
528A PHE* 4.5 1.6 - - - -
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 4.0 11.2 - - + -
445A VAL* 3.1 19.3 + - + +
446A GLN* 4.0 1.8 - - - +
448A GLY* 1.3 73.7 - - - +
450A HIS* 1.3 56.2 + - - +
453A LEU* 2.9 38.9 + - + +
454A GLY* 2.7 32.4 + - - -
514A VAL* 4.5 0.8 - - - +
515A GLY* 3.3 39.5 - - - +
518A LEU* 3.7 27.4 - - + +
519A SER* 3.7 7.2 - - - +
524A VAL* 3.8 27.4 - - + -
528A PHE* 5.2 0.2 - - + -
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Residues in contact with HIS 450 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446A GLN* 2.8 21.6 + - + +
447A VAL 3.4 4.9 + - - +
449A LEU* 1.3 76.0 - - - +
451A ALA* 1.3 57.0 + - - +
454A GLY* 3.3 2.8 - - - -
455A HIS* 3.0 40.8 + - - -
508A GLU* 3.0 27.1 + - - -
511A ALA* 3.4 23.7 - - + +
512A GLU* 3.3 47.6 + - + +
515A GLY* 4.8 1.2 - - - -
568A HIS* 4.4 5.4 - + - -
2B ARG 4.0 2.2 + - - -
3B VAL* 3.5 30.1 - - + +
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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
----------------------------------------------------------
373A PHE* 4.7 4.9 - - + -
390A ILE 4.2 17.3 - - - +
391A ASN* 2.7 27.8 + - + -
406A ASN* 3.2 17.7 - - + +
407A VAL 5.4 1.6 - - - +
447A VAL* 3.2 15.3 + - + +
448A GLY 4.5 0.7 - - - +
450A HIS* 1.3 79.6 - - - +
452A LEU* 1.3 57.9 + - - +
455A HIS* 3.4 10.8 - - - +
456A GLY 3.2 13.2 + - - -
3B VAL* 4.4 10.8 - - + -
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Residues in contact with LEU 452 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A LEU* 3.7 37.5 - - + +
347A VAL* 3.8 23.3 - - + -
350A ALA* 4.0 12.3 - - + -
354A LEU* 5.0 1.9 - - - +
368A PHE* 5.4 2.2 - - + -
371A PRO* 3.6 32.5 - - + -
373A PHE* 3.8 12.8 - - + -
404A PHE* 4.6 3.5 - - + -
406A ASN* 3.5 11.4 - - - +
448A GLY 3.2 14.7 + - - +
451A ALA* 1.3 78.7 - - - +
453A LEU* 1.3 74.6 + - + +
456A GLY* 3.3 24.3 - - - +
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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