Contacts of the helix formed by residues 477 - 498 (chain A) in PDB entry 2JED
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 477 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475A LYS 4.0 1.2 + - - -
476A PHE* 1.3 73.5 - - - +
478A LEU* 1.3 64.9 + - - +
479A SER* 3.1 13.6 + - - -
480A ARG* 3.0 32.9 + - - +
481A ALA* 2.9 20.3 + - - -
650A PRO* 5.7 0.3 - - - +
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Residues in contact with LEU 478 (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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476A PHE 3.7 0.6 + - - -
477A ASP* 1.3 73.6 - - - +
479A SER* 1.3 54.4 + - - +
481A ALA* 3.6 1.0 + - - +
482A THR* 2.6 48.1 + - - +
573A LEU* 4.0 25.8 - - + +
602A LEU* 5.8 0.9 - - + -
603A GLU* 3.9 40.6 - - + +
606A ALA* 4.2 4.0 - - + -
633A LEU* 4.2 15.0 - - + -
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477A ASP* 3.1 13.3 + - - -
478A LEU* 1.3 76.8 - - - +
480A ARG* 1.3 60.1 + - - +
482A THR* 3.7 7.2 - - - +
483A PHE* 3.1 28.4 + - - +
650A PRO* 5.4 1.4 - - - +
600B ARG* 4.2 21.4 + - - -
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Residues in contact with ARG 480 (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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466A LEU* 5.2 0.2 - - - +
469A HIS* 4.3 10.9 + - - +
473A CYS* 4.4 9.1 - - - +
476A PHE* 3.6 40.1 - - + +
477A ASP* 3.0 30.2 + - - +
479A SER* 1.3 75.4 + - - +
481A ALA* 1.3 65.3 + - - +
483A PHE* 3.2 4.5 + - - +
484A TYR* 3.0 59.2 + - + -
512A LEU* 4.8 1.0 - - - +
650A PRO* 3.7 27.3 - - + +
651A PHE* 3.3 42.7 - - - +
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Residues in contact with ALA 481 (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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476A PHE* 4.1 10.7 - - + +
477A ASP 2.9 15.4 + - - +
478A LEU 3.9 0.4 - - - +
480A ARG* 1.3 72.6 - - - +
482A THR* 1.3 56.8 + - - +
484A TYR 3.5 0.2 + - - -
485A ALA* 2.9 31.8 + - - +
569A LEU* 4.5 2.5 - - + -
572A MET* 3.4 35.2 - - + +
573A LEU* 3.5 32.5 - - + -
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Residues in contact with THR 482 (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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478A LEU* 2.6 40.2 + - - +
479A SER* 3.7 8.1 - - - +
480A ARG 3.2 0.2 - - - -
481A ALA* 1.3 72.8 - - - +
483A PHE* 1.3 61.6 + - - +
485A ALA* 3.7 6.6 - - - +
486A ALA* 3.0 27.7 + - - +
569A LEU* 5.7 0.7 - - - -
573A LEU* 5.7 0.3 - - - +
633A LEU* 3.7 36.2 - - + +
634A PHE* 3.8 16.1 - - + -
637A ILE* 4.4 12.8 - - + -
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Residues in contact with PHE 483 (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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479A SER 3.1 17.7 + - - +
480A ARG 3.2 3.3 + - - +
482A THR* 1.3 76.4 - - - +
484A TYR* 1.3 78.6 + + - +
486A ALA* 3.3 6.3 + - - +
487A GLU* 3.1 64.3 + - - +
516A GLY 3.7 13.7 - - - -
517A HIS* 3.7 11.2 - - - -
637A ILE* 5.0 7.9 - - + -
642A LEU* 3.8 19.5 - - + -
647A ILE* 4.0 14.6 - - + -
649A PRO* 3.8 17.9 - - + -
650A PRO* 3.4 22.7 - - + -
600B ARG* 3.5 21.5 - - - +
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Residues in contact with TYR 484 (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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466A LEU* 3.6 33.7 - - + -
476A PHE* 3.9 18.2 - + - -
480A ARG* 3.0 61.0 + - + +
481A ALA 3.9 1.3 - - - +
483A PHE* 1.3 92.3 - + - +
485A ALA* 1.3 62.8 + - - +
486A ALA 3.3 0.2 + - - -
487A GLU* 3.4 2.1 + - - +
488A ILE* 3.0 31.8 + - + +
512A LEU* 3.9 26.4 - - + +
516A GLY 3.9 9.1 + - - -
518A ILE* 3.6 21.3 - - + +
572A MET* 3.8 16.4 - - - -
650A PRO* 4.4 3.6 - - + +
651A PHE* 4.1 8.5 + - - +
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Residues in contact with ALA 485 (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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481A ALA 2.9 19.4 + - - +
482A THR* 3.7 5.8 - - - +
483A PHE 3.3 0.2 - - - -
484A TYR* 1.3 75.7 - - - +
486A ALA* 1.3 57.5 + - - +
488A ILE* 4.5 0.9 - - - -
489A ILE* 2.9 33.9 + - - +
565A PHE* 3.4 26.9 - - + -
569A LEU* 4.1 19.7 - - + -
572A MET* 3.9 5.7 - - + +
633A LEU* 5.5 0.2 - - + -
634A PHE* 4.1 12.8 - - + -
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Residues in contact with ALA 486 (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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482A THR 3.0 19.0 + - - +
483A PHE* 3.7 3.4 - - - +
484A TYR 3.3 0.4 - - - -
485A ALA* 1.3 73.8 - - - +
487A GLU* 1.3 63.4 + - - +
489A ILE* 3.4 1.5 + - - -
490A LEU* 3.2 18.7 + - - +
634A PHE* 4.1 9.9 - - + -
637A ILE* 4.2 11.7 - - + -
639A TRP* 3.4 34.3 - - + -
642A LEU* 3.5 21.8 - - + -
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Residues in contact with GLU 487 (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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440A PHE* 3.2 35.9 - - + -
483A PHE* 3.1 43.2 + - + +
484A TYR 4.0 1.8 - - - +
486A ALA* 1.3 71.9 - - - +
488A ILE* 1.3 59.6 - - - +
490A LEU* 3.3 4.7 + - - +
491A GLY* 3.0 23.7 + - - -
517A HIS* 2.8 29.0 + - - +
518A ILE* 2.8 49.6 + - + +
642A LEU* 3.8 16.7 - - + +
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Residues in contact with ILE 488 (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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466A LEU* 4.8 1.8 - - + -
484A TYR* 3.0 32.9 + - + +
485A ALA* 3.7 5.2 - - - +
487A GLU* 1.3 71.4 - - - +
489A ILE* 1.3 57.9 + - - +
491A GLY* 3.1 2.0 + - - +
492A LEU* 2.8 46.6 + - + +
505A LEU* 4.2 14.4 - - + -
510A ILE* 4.1 26.7 - - + -
518A ILE* 3.7 22.4 - - + -
520A ILE* 4.3 4.6 - - + +
565A PHE* 3.6 22.9 - - + -
568A LEU* 3.7 28.5 - - + -
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Residues in contact with ILE 489 (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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485A ALA 2.9 19.3 + - - +
486A ALA 3.5 7.0 - - - +
488A ILE* 1.3 75.8 - - - +
490A LEU* 1.3 57.3 + - - +
492A LEU* 3.9 0.4 - - - +
493A GLN* 2.9 59.0 + - + +
562A TRP* 3.8 20.0 - - + -
565A PHE* 3.5 25.1 - - + -
628A ILE* 4.0 18.6 - - + -
629A ARG* 4.5 1.6 - - + -
634A PHE* 3.5 31.4 - - + -
639A TRP* 3.9 23.1 - - + -
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Residues in contact with LEU 490 (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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438A HIS* 3.4 6.0 - - - -
440A PHE* 3.5 29.4 - - + -
486A ALA 3.2 10.8 + - - +
487A GLU 3.3 6.5 + - - +
489A ILE* 1.3 75.5 - - - +
491A GLY* 1.3 61.1 + - - +
493A GLN* 4.2 3.4 - - - +
494A PHE* 3.1 24.3 + - - +
629A ARG* 3.4 28.8 + - - +
639A TRP* 3.7 22.9 - - + +
642A LEU* 3.6 25.4 - - + -
643A GLU* 3.8 41.0 - - - +
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Residues in contact with GLY 491 (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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438A HIS* 3.9 17.6 + - - -
440A PHE* 4.6 2.2 - - - -
441A LEU* 4.2 4.4 - - - +
487A GLU 3.0 13.5 + - - -
488A ILE 3.1 2.9 + - - -
490A LEU* 1.3 77.5 - - - +
492A LEU* 1.3 59.0 + - - +
494A PHE* 3.4 4.3 + - - +
495A LEU* 3.2 26.6 + - - +
520A ILE* 3.9 20.9 - - - -
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Residues in contact with LEU 492 (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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488A ILE* 2.8 33.6 + - + +
489A ILE 3.9 2.5 - - - +
491A GLY* 1.3 70.2 - - - +
493A GLN* 1.3 60.6 + - - +
495A LEU* 3.2 10.6 + - + +
496A HIS* 2.9 41.3 + - + +
502A TYR* 4.4 18.4 - - + -
505A LEU* 4.0 30.5 - - + -
520A ILE* 4.2 4.4 - - + +
561A ASP* 4.1 34.1 - - + +
562A TRP* 3.9 31.4 - - + -
565A PHE* 4.2 2.9 - - + -
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Residues in contact with GLN 493 (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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489A ILE* 2.9 28.4 + - - +
490A LEU 4.2 2.5 - - - +
492A LEU* 1.3 75.0 - - - +
494A PHE* 1.3 61.5 + - - +
496A HIS* 4.1 8.2 - - - +
497A SER* 3.1 23.2 + - - -
562A TRP* 3.8 19.2 - - + -
623A GLY 5.5 3.0 + - - -
627A ASP* 5.1 4.0 + - - -
628A ILE* 3.6 25.1 - - - +
629A ARG* 2.8 43.6 + - - +
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Residues in contact with PHE 494 (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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434A LEU* 4.0 13.2 - - + -
437A GLU* 3.7 35.7 - - + -
438A HIS* 3.5 35.0 - + + +
441A LEU* 3.8 24.9 - - + -
490A LEU 3.1 19.7 + - - +
491A GLY 3.5 4.5 - - - +
492A LEU 3.2 0.2 - - - -
493A GLN* 1.3 75.0 - - - +
495A LEU* 1.3 68.9 + - + +
497A SER* 2.6 25.4 + - - -
498A LYS* 3.4 43.8 - - + +
643A GLU* 5.3 0.7 - - - +
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Residues in contact with LEU 495 (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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431A VAL* 4.5 5.6 - - + -
434A LEU* 6.5 0.4 - - + -
441A LEU* 3.8 36.3 - - + -
491A GLY 3.2 14.8 + - - +
492A LEU* 3.2 16.0 + - + +
494A PHE* 1.3 83.1 - - + +
496A HIS* 1.3 62.1 + - + +
498A LYS* 3.2 10.6 + - - +
500A ILE* 2.9 58.7 + - + +
502A TYR* 4.1 24.7 - - + -
520A ILE* 5.0 3.6 - - + -
523A PHE* 4.1 19.1 - - + -
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Residues in contact with HIS 496 (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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492A LEU* 2.9 29.6 + - + +
493A GLN* 4.1 6.5 - - - +
495A LEU* 1.3 77.1 - - + +
497A SER* 1.3 59.1 + - - +
499A GLY* 3.0 17.8 + - - -
500A ILE 3.1 27.8 - - - +
501A VAL* 4.4 0.4 - - - -
530A MET 4.9 2.8 - - - +
531A LEU* 4.2 5.7 - - - +
558A HIS* 3.5 39.3 - - + +
561A ASP* 2.8 33.3 + - + -
562A TRP* 3.5 34.2 + + - -
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Residues in contact with SER 497 (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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493A GLN 3.1 14.2 + - - -
494A PHE* 2.6 29.1 + - - -
496A HIS* 1.3 75.4 - - - +
498A LYS* 1.3 64.0 + - - +
499A GLY 3.3 1.3 + - - -
531A LEU* 4.0 10.8 - - - +
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Residues in contact with LYS 498 (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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434A LEU* 4.1 23.9 - - + +
437A GLU* 3.2 27.4 + - - -
494A PHE* 3.4 51.1 - - + +
495A LEU 3.2 8.4 + - - +
496A HIS 3.2 0.8 - - - -
497A SER* 1.3 80.5 - - - +
499A GLY* 1.3 61.3 + - - +
500A ILE* 3.4 19.8 + - + +
528A GLU 4.4 4.3 - - - +
531A LEU* 4.3 8.1 - - - +
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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
------------------------------------------------------------
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