Contacts of the helix formed by residues 438 - 459 (chain A) in PDB entry 5E92
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 ASN 438 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435A ASN* 3.4 34.6 + - - +
436A LEU 5.3 0.2 - - - -
437A GLU* 1.4 75.1 + - - +
439A VAL* 1.4 62.9 + - - +
440A GLU* 3.3 7.8 - - + +
441A SER* 3.1 43.2 + - - +
442A PHE* 4.4 4.2 + - - -
444A GLN* 4.7 1.6 + - - -
526A GLU* 4.1 18.0 + - - -
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Residues in contact with VAL 439 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374A PRO* 6.2 2.0 - - + -
404A LEU* 3.5 38.2 - - + +
437A GLU 3.5 3.9 + - - -
438A ASN* 1.4 71.1 - - - +
440A GLU* 1.3 62.5 + - - +
441A SER 3.4 0.9 + - - -
442A PHE* 3.5 10.5 + - - +
443A LYS* 3.8 10.5 + - - +
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Residues in contact with GLU 440 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASN* 3.3 9.1 - - + +
439A VAL* 1.3 76.7 - - - +
441A SER* 1.4 53.1 + - - +
442A PHE 3.3 0.2 - - - -
443A LYS* 3.0 17.8 + - + +
444A GLN* 2.8 53.3 + - + +
526A GLU* 5.3 1.8 - - - +
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Residues in contact with SER 441 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A GLU* 4.6 1.2 - - - +
434A MET* 3.4 17.1 - - - +
435A ASN* 3.1 21.3 + - - -
438A ASN* 3.1 39.4 + - - +
439A VAL 3.2 1.0 - - - -
440A GLU* 1.4 77.6 - - - +
442A PHE* 1.4 65.0 + - - +
444A GLN* 3.4 22.3 + - - +
445A THR* 3.5 17.7 + - - +
525A PRO* 6.3 0.4 - - - -
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Residues in contact with PHE 442 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A VAL* 3.7 28.9 - - + +
378A ARG* 4.2 32.1 - - + -
402A LEU* 4.2 2.9 - - + -
404A LEU* 4.2 15.5 - - + -
413A LEU* 3.7 45.8 - - + -
434A MET* 3.6 31.0 - - + -
436A LEU* 5.7 7.9 - - + -
438A ASN 5.2 4.0 - - - -
439A VAL* 3.5 8.2 + - - +
440A GLU 3.3 0.4 - - - -
441A SER* 1.4 81.2 + - - +
443A LYS* 1.4 64.3 + - - +
445A THR* 2.7 27.9 + - - -
446A ASP* 3.5 4.5 + - - +
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Residues in contact with LYS 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A HIS* 2.9 65.7 + - + +
363A SER* 5.1 0.4 - - - +
364A ASP* 5.0 6.9 - - - +
374A PRO* 4.1 19.7 - - - +
376A VAL* 3.6 15.0 - - + +
404A LEU* 4.1 8.7 - - - -
439A VAL* 3.8 16.0 - - - +
440A GLU* 3.0 18.5 + - + +
442A PHE* 1.4 75.2 - - - +
444A GLN* 1.3 62.4 + - + +
446A ASP 3.3 2.6 + - - -
447A VAL* 3.2 21.5 + - + +
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Residues in contact with GLN 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438A ASN* 4.7 1.4 + - - -
440A GLU* 2.8 29.0 + - + +
441A SER* 3.4 21.1 + - - +
442A PHE 3.2 0.4 - - - -
443A LYS* 1.3 77.9 - - + +
445A THR* 1.4 59.6 + - - +
447A VAL* 3.4 7.6 + - + +
448A TYR 3.2 13.3 + - - -
525A PRO* 3.2 47.5 + - + +
526A GLU* 3.2 35.0 + - - +
528A ARG* 3.0 23.3 + - + +
529A LEU 6.1 0.7 - - - +
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Residues in contact with THR 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A ARG* 5.7 5.2 - - - +
426A ALA* 4.0 15.4 + - - +
428A GLU* 3.4 18.6 - - - +
429A VAL* 3.6 27.8 - - + +
434A MET* 3.8 14.1 - - + -
441A SER 3.5 12.8 - - - +
442A PHE* 2.7 24.6 + - - -
444A GLN* 1.4 73.9 - - - +
446A ASP* 1.3 66.4 + - - +
448A TYR* 3.4 4.2 + - - +
449A SER* 3.3 24.1 + - - -
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Residues in contact with ASP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A ILE* 4.6 1.8 - - + +
361A LEU* 5.4 0.5 - - - +
362A HIS* 2.8 28.1 + - + +
376A VAL* 3.5 8.4 - - - +
377A HIS* 2.8 26.5 + - - +
378A ARG* 3.0 27.7 + - - +
380A LEU* 3.4 31.9 + - + +
442A PHE 3.5 1.5 + - - -
443A LYS 3.3 11.6 + - - +
445A THR* 1.3 85.0 + - - +
447A VAL* 1.3 51.5 + - - +
449A SER* 3.3 3.6 + - - -
450A MET* 2.9 31.1 + - - +
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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
----------------------------------------------------------
358A ILE* 5.3 0.7 - - + -
362A HIS* 4.5 9.4 - - + +
443A LYS* 3.2 15.1 + - + +
444A GLN* 3.7 12.1 - - + +
445A THR 3.3 0.6 - - - -
446A ASP* 1.3 73.2 - - - +
448A TYR* 1.3 64.2 + - - +
450A MET* 3.3 12.2 + - + +
451A ALA* 3.0 22.2 + - - +
520A CYS* 3.7 28.9 - - + +
528A ARG* 4.1 6.7 - - + -
529A LEU 3.2 28.5 - - - +
530A THR* 4.3 2.0 - - - -
531A ALA* 3.9 24.0 - - + +
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Residues in contact with TYR 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A ARG 5.2 0.6 + - - -
424A TYR 3.7 5.6 - - - -
425A MET 3.5 17.0 + - - -
426A ALA* 3.4 17.7 - - + -
427A PRO* 3.6 24.0 - - + -
444A GLN 3.2 6.3 + - - -
445A THR 3.7 6.5 - - - +
446A ASP 3.3 0.4 - - - -
447A VAL* 1.3 75.3 - - - +
449A SER* 1.3 65.4 + - - +
451A ALA* 3.1 14.2 + - - +
452A LEU* 3.3 36.6 + - + +
474A PHE* 3.9 13.3 - - - -
491A VAL* 3.4 26.3 - - - +
497A ARG* 3.7 23.0 - - - -
520A CYS 3.4 11.6 + - - +
521A TRP* 3.7 25.7 - - + +
528A ARG* 3.9 21.3 - - - +
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Residues in contact with SER 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380A LEU* 3.5 31.1 + - - -
424A TYR* 2.6 29.2 + - - +
426A ALA 5.0 0.2 + - - -
445A THR 3.3 11.0 + - - -
446A ASP* 3.3 9.6 + - - -
448A TYR* 1.3 80.1 - - - +
450A MET* 1.3 62.6 + - - +
452A LEU* 3.1 18.4 + - - +
453A VAL* 3.2 18.1 + - - +
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Residues in contact with MET 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354A LEU* 4.0 13.9 - - + -
355A ALA* 4.2 21.5 - - - -
358A ILE* 3.6 32.8 - - + -
380A LEU* 4.6 3.1 - - - +
446A ASP 2.9 17.4 + - - +
447A VAL* 3.4 24.0 - - + +
449A SER* 1.3 76.3 - - - +
451A ALA* 1.4 55.8 + - - +
453A VAL* 3.1 10.0 + - - +
454A LEU* 2.9 37.6 + - + +
520A CYS* 4.3 4.0 - - - -
531A ALA* 4.4 14.4 - - - -
534A VAL* 3.7 35.4 - - + -
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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
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447A VAL 3.0 7.1 + - - +
448A TYR 3.1 10.3 + - - +
450A MET* 1.4 73.0 - - - +
452A LEU* 1.3 60.3 + - - +
454A LEU* 3.4 8.3 + - - +
455A TRP* 3.0 26.7 + - - +
517A LEU* 3.4 37.4 - - - +
520A CYS* 3.6 17.9 - - + -
521A TRP* 3.8 16.2 - - + -
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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
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423A ARG 3.8 9.0 - - - +
424A TYR* 3.7 34.8 - - + +
448A TYR* 3.3 41.2 + - + +
449A SER* 3.1 7.5 + - - +
451A ALA* 1.3 76.0 - - - +
453A VAL* 1.4 57.2 + - - +
455A TRP* 3.2 10.2 + - - +
456A GLU* 3.0 31.8 + - - +
473A PRO* 4.0 12.5 - - + +
474A PHE* 4.1 11.4 - - + -
497A ARG* 5.3 0.2 - - - -
498A PRO* 3.8 34.1 - - + -
521A TRP* 3.9 10.5 - - + -
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Residues in contact with VAL 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.6 29.2 - - + -
354A LEU* 3.6 15.5 - - + -
380A LEU* 4.6 1.3 - - + -
381A LYS* 3.8 15.5 - - - +
382A SER* 3.7 24.7 - - - +
385A ILE* 3.6 17.3 - - + -
424A TYR* 4.0 2.0 - - + -
449A SER 3.2 13.4 + - - +
450A MET* 3.1 10.1 + - - +
452A LEU* 1.4 76.8 - - - +
454A LEU* 1.3 55.7 + - - +
456A GLU* 3.1 14.4 + - - +
457A MET* 3.0 27.6 + - + +
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Residues in contact with LEU 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 4.7 1.6 - - + +
351A GLY* 3.7 33.0 - - - +
354A LEU* 4.4 8.5 - - + -
355A ALA* 6.2 0.7 - - + -
450A MET* 2.9 36.7 + - + +
451A ALA* 3.7 10.1 - - - +
452A LEU 3.4 0.2 - - - -
453A VAL* 1.3 71.4 - - - +
455A TRP* 1.4 61.3 + - - +
457A MET* 3.4 13.6 + - + +
458A THR* 2.8 33.7 + - - +
513A VAL* 5.2 4.0 - - + +
516A THR* 5.6 1.3 - - + -
517A LEU* 4.0 21.5 - - + +
520A CYS* 5.7 0.7 - - - -
534A VAL* 4.2 20.9 - - + -
538A PHE* 3.8 17.7 - - + -
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Residues in contact with TRP 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 ALA 3.0 14.0 + - - +
452A LEU* 3.2 8.9 + - - +
454A LEU* 1.4 75.1 - - - +
456A GLU* 1.4 84.6 + - + +
458A THR* 3.2 3.5 + - - -
459A SER* 2.8 48.3 + - - -
471A GLU* 3.7 28.0 - - + -
472A PRO 4.8 2.9 - - - -
473A PRO* 4.1 13.7 - - + -
474A PHE 5.8 0.2 - - - -
498A PRO* 3.3 31.2 - - + +
499A GLU* 3.0 27.8 + - + -
500A ILE* 4.0 17.0 - - + -
504A TRP* 3.6 19.6 - + - -
517A LEU* 3.9 11.6 - - + +
521A TRP* 3.7 14.6 - + + -
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Residues in contact with GLU 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A LEU* 3.5 19.5 - - + +
382A SER* 2.7 23.4 + - - -
424A TYR* 2.6 34.7 + - - -
452A LEU 3.0 13.1 + - - +
453A VAL* 3.1 17.4 + - - +
455A TRP* 1.4 87.0 - - + +
457A MET* 1.3 60.8 + - - +
459A SER* 2.8 20.6 + - - -
460A ARG* 3.6 5.5 + - - +
470A TYR* 2.5 34.2 + - + -
473A PRO* 3.6 18.5 - - + +
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Residues in contact with MET 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A LEU* 3.6 34.5 - - + -
337A LEU* 3.7 12.3 - - + +
342A ILE* 3.6 16.0 - - + +
347A LEU* 3.6 15.9 - - + -
350A LEU* 3.7 34.1 - - + +
351A GLY* 3.8 24.2 - - - -
354A LEU* 3.8 22.0 - - + -
393A CYS* 3.9 6.1 - - - -
453A VAL* 3.0 15.2 + - + +
454A LEU* 3.6 16.4 - - - +
455A TRP 3.3 0.2 - - - -
456A GLU* 1.3 75.9 - - - +
458A THR* 1.4 60.4 + - - +
460A ARG* 3.2 11.1 + - - +
461A CYS* 3.5 8.3 + - - +
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Residues in contact with THR 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347A LEU* 3.9 13.0 - - + +
454A LEU 2.8 18.7 + - - -
455A TRP* 3.2 6.7 + - - -
457A MET* 1.4 74.1 - - - +
459A SER* 1.4 57.6 + - - +
460A ARG 3.0 5.5 + - - -
461A CYS* 3.0 15.8 + - - +
464A VAL* 3.6 10.1 - - + +
504A TRP* 3.8 26.2 - - + -
510A ILE* 3.9 28.9 - - + -
513A VAL* 3.3 23.2 - - + +
514A CYS* 4.0 9.0 - - - -
517A LEU* 4.2 2.4 - - - +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455A TRP* 2.8 37.0 + - - -
456A GLU* 2.8 22.0 + - - -
458A THR* 1.4 70.4 - - - +
460A ARG* 1.3 66.1 + - - +
461A CYS 3.6 0.9 - - - -
464A VAL* 5.2 1.9 - - - +
467A VAL* 3.6 17.0 - - - +
468A LYS* 4.4 6.6 + - - +
470A TYR* 4.9 5.7 - - - -
471A GLU 5.2 1.2 + - - -
504A TRP* 3.5 29.5 - - - -
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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