Contacts of the helix formed by residues 477 - 498 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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514A LYS* 5.8 9.6 - - + +
652A ARG* 5.0 7.0 - - - +
655A VAL 5.0 9.2 - - - +
656A LYS 5.3 2.1 - - - +
475B LYS 3.7 3.2 + - - -
476B PHE* 1.3 77.2 - - - +
478B LEU* 1.3 58.4 + - - +
479B SER* 3.5 10.2 + - - -
480B ARG* 3.1 38.4 + - - +
481B ALA* 2.9 22.3 + - - +
650B PRO* 5.3 1.7 - - - +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A ARG* 3.7 17.1 - - - +
654A LYS* 3.8 33.2 - - + +
476B PHE 3.6 2.1 + - - -
477B ASP* 1.3 74.4 - - - +
479B SER* 1.3 57.5 + - - +
481B ALA* 4.0 4.1 - - - +
482B THR* 2.6 46.7 + - - +
573B LEU* 3.8 21.5 - - + -
603B GLU* 3.8 34.1 - - + +
606B ALA* 4.4 6.1 - - + -
633B LEU* 4.3 15.9 - - + -
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Residues in contact with SER 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
655A VAL 4.3 3.9 + - - -
656A LYS* 3.7 40.7 + - - +
477B ASP* 3.3 8.4 + - - -
478B LEU* 1.3 81.0 - - - +
480B ARG* 1.3 58.3 + - - +
482B THR* 3.5 5.9 + - - -
483B PHE* 3.0 29.3 + - - +
650B PRO* 4.0 12.6 - - - +
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Residues in contact with ARG 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469B HIS* 3.6 15.8 + - - +
473B CYS* 3.8 15.2 - - - +
476B PHE* 3.4 42.9 - - + +
477B ASP* 3.1 32.4 + - - +
479B SER* 1.3 75.4 - - - +
481B ALA* 1.3 58.4 + - - +
483B PHE* 3.4 3.3 + - - +
484B TYR* 3.0 57.7 + - + +
650B PRO* 4.2 17.6 - - + +
651B PHE* 3.4 59.2 - - + +
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Residues in contact with ALA 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B PHE* 4.0 18.3 - - + +
477B ASP 2.9 19.3 + - - +
478B LEU 4.0 0.9 - - - +
480B ARG* 1.3 73.5 - - - +
482B THR* 1.3 58.0 + - - +
484B TYR* 3.4 3.4 + - - -
485B ALA* 2.9 30.8 + - - +
569B LEU* 4.8 2.0 - - + -
572B MET* 3.5 24.8 - - + +
573B LEU* 3.8 28.0 - - + -
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Residues in contact with THR 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B LEU* 2.6 28.7 + - - +
479B SER* 3.8 6.5 - - - -
481B ALA* 1.3 73.9 - - - +
483B PHE* 1.3 60.6 + - - +
485B ALA* 4.3 4.9 - - - -
486B ALA* 3.0 28.2 + - - +
569B LEU* 5.6 0.2 - - - -
573B LEU* 5.4 0.5 - - - +
633B LEU* 3.5 46.6 - - + +
634B PHE* 3.7 11.9 - - + -
637B ILE* 3.8 20.2 - - + -
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Residues in contact with PHE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B SER 3.0 18.8 + - - +
480B ARG 3.6 4.0 - - - +
482B THR* 1.3 73.6 - - - +
484B TYR* 1.3 78.9 + + - +
486B ALA* 3.3 5.7 + - - +
487B GLU* 3.1 57.0 + - - +
516B GLY 3.9 17.3 - - - -
517B HIS* 3.7 12.6 - + - -
637B ILE* 5.3 6.0 - - + +
642B LEU* 3.8 22.4 - - + -
647B ILE* 3.8 27.6 - - + -
649B PRO* 3.8 18.2 - - + -
650B PRO* 3.5 24.5 - - + -
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Residues in contact with TYR 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 3.6 30.1 - - + -
476B PHE* 3.8 21.8 - + - -
480B ARG* 3.0 61.1 + - + +
481B ALA 3.7 5.6 - - - +
482B THR 3.4 0.2 - - - -
483B PHE* 1.3 92.2 - + - +
485B ALA* 1.3 58.0 + - - +
487B GLU* 3.3 2.6 + - - +
488B ILE* 2.9 37.0 + - + +
512B LEU* 3.7 27.1 - - + +
516B GLY 4.0 7.9 + - - -
518B ILE* 3.6 22.4 - - + -
572B MET* 3.8 12.6 - - + -
649B PRO* 6.1 0.4 - - + -
650B PRO* 5.9 1.1 - - + -
651B PHE* 3.8 9.0 - - + +
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B ALA 2.9 18.6 + - - +
482B THR* 3.8 6.3 - - - +
483B PHE 3.3 0.2 - - - -
484B TYR* 1.3 75.5 - - - +
486B ALA* 1.3 56.2 + - - +
488B ILE* 4.5 0.7 - - - -
489B ILE* 3.0 34.9 + - - +
565B PHE* 3.5 25.3 - - + -
569B LEU* 4.0 20.0 - - + -
572B MET* 4.0 6.2 - - + +
633B LEU* 5.5 0.2 - - + -
634B PHE* 4.1 12.6 - - + -
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Residues in contact with ALA 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B THR 3.0 18.3 + - - +
483B PHE* 3.7 4.0 - - - +
484B TYR 3.3 0.2 - - - -
485B ALA* 1.3 74.5 - - - +
487B GLU* 1.3 64.3 + - - +
489B ILE* 3.4 1.2 + - - +
490B LEU* 3.2 18.9 + - - +
634B PHE* 3.9 8.2 - - + -
637B ILE* 4.1 14.4 - - + -
639B TRP* 3.3 34.3 - - + -
642B LEU* 3.5 20.9 - - + -
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Residues in contact with GLU 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B PHE* 3.2 36.9 - - + +
483B PHE* 3.1 36.7 + - + +
484B TYR 3.9 1.3 - - - +
486B ALA* 1.3 75.0 - - - +
488B ILE* 1.3 60.8 + - - +
490B LEU* 3.3 5.6 + - - +
491B GLY 3.2 17.8 + - - -
517B HIS* 2.7 29.6 + - - -
518B ILE* 2.9 45.3 + - + +
642B LEU* 3.8 23.4 - - + +
645B LYS* 5.4 0.2 - - - -
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Residues in contact with ILE 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B LEU* 4.7 3.6 - - + -
484B TYR* 2.9 33.3 + - + +
485B ALA* 3.8 5.2 - - - +
487B GLU* 1.3 72.2 - - - +
489B ILE* 1.3 64.1 + - - +
491B GLY* 3.3 1.6 + - - +
492B LEU* 2.9 34.8 + - + +
505B LEU* 4.3 15.9 - - + -
510B ILE* 4.0 22.7 - - + -
518B ILE* 3.7 22.4 - - + -
520B ILE* 4.2 5.1 - - + +
565B PHE* 3.7 23.3 - - + -
568B LEU* 3.6 24.0 - - + -
572B MET* 4.7 3.4 - - + -
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Residues in contact with ILE 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485B ALA 3.0 15.6 + - - +
486B ALA 3.6 7.0 - - - +
487B GLU 3.4 0.2 - - - -
488B ILE* 1.3 74.2 - - - +
490B LEU* 1.3 58.2 + - - +
492B LEU* 3.9 0.5 - - - +
493B GLN* 2.9 54.2 + - + +
562B TRP* 3.8 19.5 - - + -
565B PHE* 3.5 18.4 - - + -
628B ILE* 3.9 24.9 - - + -
629B ARG* 4.5 1.1 - - + -
634B PHE* 3.4 39.9 - - + -
639B TRP* 4.0 21.3 - - + -
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Residues in contact with LEU 490 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B HIS* 3.4 21.4 - - - +
440B PHE* 3.6 23.8 - - + -
486B ALA 3.2 13.2 + - - +
487B GLU 3.5 6.7 - - - +
488B ILE 3.3 0.4 - - - -
489B ILE* 1.3 76.4 - - - +
491B GLY* 1.3 58.7 + - - +
493B GLN* 4.0 3.5 - - - +
494B PHE* 3.1 22.5 + - - +
629B ARG* 3.3 37.3 + - - +
639B TRP* 3.7 17.3 - - + +
642B LEU* 3.6 24.0 - - + -
643B GLU* 3.6 34.0 - - + +
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Residues in contact with GLY 491 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438B HIS* 3.5 19.9 + - - -
440B PHE* 4.6 2.9 - - - -
441B LEU* 4.3 5.4 - - - +
487B GLU 3.2 10.4 + - - -
488B ILE 3.3 2.9 + - - -
490B LEU* 1.3 78.9 - - - +
492B LEU* 1.3 59.4 + - - +
494B PHE* 3.5 3.1 + - - +
495B LEU* 3.2 27.3 + - - +
520B ILE* 4.2 17.9 - - - -
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Residues in contact with LEU 492 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488B ILE* 2.9 29.3 + - + +
489B ILE 3.9 2.9 - - - +
491B GLY* 1.3 72.3 - - - +
493B GLN* 1.3 61.4 - - - +
495B LEU* 3.2 11.9 + - + +
496B HIS* 2.9 39.6 + - + +
502B TYR* 4.2 17.9 - - + -
505B LEU* 4.0 32.3 - - + -
520B ILE* 4.3 5.8 - - + +
561B ASP* 4.1 33.7 - - + +
562B TRP* 3.9 29.6 - - + -
565B PHE* 4.2 3.8 - - + -
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Residues in contact with GLN 493 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B ILE* 2.9 29.4 + - - +
490B LEU 4.0 3.1 - - - +
492B LEU* 1.3 71.9 - - - +
494B PHE* 1.3 59.9 + - - +
496B HIS* 3.9 7.7 - - - +
497B SER* 3.0 28.8 + - - -
562B TRP* 3.9 18.3 - - + -
623B GLY 5.8 1.4 + - - -
627B ASP* 5.0 3.6 + - - -
628B ILE* 3.7 23.4 - - - +
629B ARG* 2.7 49.2 + - - +
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Residues in contact with PHE 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B LEU* 3.9 22.9 - - + -
437B GLU* 3.6 35.2 - - + -
438B HIS* 3.6 29.8 - - + +
441B LEU* 3.6 31.6 - - + -
490B LEU 3.1 18.4 + - - +
491B GLY 3.6 3.8 - - - +
493B GLN* 1.3 73.9 - - - +
495B LEU* 1.3 69.8 + - - +
497B SER* 2.6 26.8 + - - -
498B LYS* 3.3 36.9 + - + +
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Residues in contact with LEU 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B VAL* 4.4 5.8 - - + -
434B LEU* 5.0 1.6 - - + -
441B LEU* 4.0 26.5 - - + -
491B GLY 3.2 17.2 + - - +
492B LEU* 3.3 17.3 - - + +
494B PHE* 1.3 82.1 - - + +
496B HIS* 1.3 65.2 + - + +
498B LYS* 3.1 13.8 + - - +
499B GLY 3.4 0.2 + - - -
500B ILE* 3.0 55.3 + - + +
502B TYR* 3.9 29.2 - - + -
520B ILE* 4.9 2.9 - - + -
523B PHE* 4.3 22.7 - - + -
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Residues in contact with HIS 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B LEU* 2.9 31.4 + - + +
493B GLN* 4.0 6.3 + - - +
494B PHE 3.3 0.2 - - - -
495B LEU* 1.3 78.2 - - + +
497B SER* 1.3 54.2 + - - +
499B GLY* 2.8 24.4 + - - -
500B ILE 3.0 28.3 - - - +
501B VAL* 4.4 0.2 - - - -
530B MET 5.2 1.4 - - - +
531B LEU* 4.0 5.4 - - - +
558B HIS* 3.7 33.3 + - + +
561B ASP* 2.8 37.6 + - + +
562B TRP* 3.6 35.3 + + - -
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Residues in contact with SER 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493B GLN 3.0 15.1 + - - -
494B PHE* 2.6 27.7 + - - -
496B HIS* 1.3 75.8 - - - +
498B LYS* 1.3 62.3 + - - +
499B GLY 3.3 0.7 - - - -
531B LEU* 3.6 17.7 - - - +
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Residues in contact with LYS 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B LEU* 4.0 17.2 - - + +
437B GLU* 3.2 35.2 + - - -
494B PHE* 3.4 43.5 - - + +
495B LEU 3.1 9.5 + - - +
496B HIS 3.0 0.6 - - - -
497B SER* 1.3 80.6 - - - +
499B GLY* 1.3 61.7 + - - +
500B ILE* 3.3 19.7 + - + +
529B ASN* 5.3 2.4 + - - -
531B LEU* 4.2 8.2 - - - +
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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) + - + + + + + -
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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