Contacts of the helix formed by residues 518 - 533 (chain B) in PDB entry 5J3V
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 TYR 518 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474B PRO* 3.7 24.3 + - + +
475B ASP* 4.3 6.6 + - - -
478B LEU* 5.3 4.9 - - + -
479B LYS* 3.3 44.2 + - + +
482B MET* 4.1 34.1 - - + -
483B THR* 6.1 0.9 - - - -
514B GLU 3.8 23.3 - - - -
515B LEU* 2.9 10.5 + - - +
517B PRO* 1.3 95.9 - - + +
519B LEU* 1.3 64.8 + - - +
520B ALA 3.4 2.7 - - - -
521B TYR* 3.2 16.7 + + + +
522B ILE* 3.0 25.3 + - + +
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Residues in contact with LEU 519 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
515B LEU 3.0 11.7 + - - +
516B VAL* 3.2 21.2 + - + +
517B PRO 3.4 0.8 - - - -
518B TYR* 1.3 77.7 - - - +
520B ALA* 1.3 57.4 + - - +
522B ILE* 3.3 3.3 + - + -
523B LEU* 2.8 37.2 + - + +
548B LEU* 3.9 32.3 - - + -
552B VAL* 4.0 18.8 - - + -
555B HIS* 3.9 34.3 - - + +
556B LEU* 4.2 17.9 - - + -
561B TYR* 3.8 22.0 - - + +
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Residues in contact with ALA 520 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B PRO 5.3 1.2 + - - +
518B TYR 3.4 0.8 - - - -
519B LEU* 1.3 79.1 - - - +
521B TYR* 1.3 60.4 + - - +
523B LEU* 4.5 1.2 - - - +
524B ASP* 3.3 24.6 + - - +
561B TYR* 3.5 31.8 + - + +
564B MET* 5.2 5.7 - - + +
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B MET* 4.4 9.2 - - + -
483B THR* 3.8 39.8 + - + +
486B LEU* 3.5 29.7 - - + +
487B LYS* 4.5 11.1 - - - +
518B TYR* 3.2 18.3 + + + +
519B LEU 3.2 0.6 - - - -
520B ALA* 1.3 78.5 - - - +
522B ILE* 1.3 63.4 + - - +
524B ASP* 3.7 8.5 + - - +
525B THR* 3.1 29.8 + - - -
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Residues in contact with ILE 522 (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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482B MET* 3.6 27.1 - - + -
486B LEU* 3.8 11.0 - - + -
504B PHE* 3.6 37.7 - - + -
508B GLU* 4.3 3.6 - - - +
515B LEU* 4.2 30.3 - - + +
518B TYR* 3.0 23.7 + - + +
519B LEU* 3.9 4.3 - - - +
521B TYR* 1.3 74.8 - - - +
523B LEU* 1.3 65.2 + - - +
525B THR* 3.0 5.7 + - - -
526B LEU* 3.0 37.7 + - + +
548B LEU* 4.4 11.7 - - + -
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Residues in contact with LEU 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519B LEU* 2.8 19.4 + - + +
520B ALA* 4.5 2.2 - - - +
522B ILE* 1.3 78.1 - - - +
524B ASP* 1.3 62.5 + - - +
526B LEU* 4.5 7.6 - - + +
527B VAL* 3.1 39.2 + - + +
545B ILE* 5.7 1.3 - - + -
548B LEU* 4.2 20.8 - - + +
556B LEU* 4.1 11.2 - - + -
561B TYR* 3.6 51.1 - - + +
564B MET* 4.2 9.4 - - - -
565B LEU* 4.1 33.9 - - + -
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Residues in contact with ASP 524 (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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520B ALA 3.3 19.7 + - - +
521B TYR* 3.8 10.9 - - - +
522B ILE 3.2 0.6 - - - -
523B LEU* 1.3 78.5 - - - +
525B THR* 1.3 62.5 + - - +
527B VAL* 4.4 1.8 - - - +
528B PHE* 3.3 24.7 + - - +
564B MET* 4.3 16.1 - - + +
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Residues in contact with THR 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 3.3 50.9 - - + +
489B ILE* 4.6 7.0 - - + -
490B LEU* 3.8 22.6 - - + +
521B TYR* 3.1 20.3 + - - -
522B ILE 3.0 9.2 + - - -
524B ASP* 1.3 78.1 + - - +
526B LEU* 1.3 61.2 + - - +
528B PHE* 3.4 5.1 + - - +
529B ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486B LEU* 4.9 3.1 - - + -
489B ILE* 4.0 28.5 - - + -
504B PHE* 5.0 2.0 - - + -
508B GLU* 4.4 4.0 - - - +
522B ILE* 3.0 35.7 + - + +
523B LEU* 4.1 6.1 - - + +
525B THR* 1.3 76.6 - - - +
527B VAL* 1.3 64.6 + - + +
529B ALA* 3.1 15.8 + - - +
530B PHE* 3.3 9.2 + - - +
541B LEU* 3.8 31.0 - - + +
544B ALA* 4.2 23.3 - - + +
545B ILE* 4.4 18.7 - - + +
548B LEU* 4.0 20.2 - - + -
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Residues in contact with VAL 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523B LEU* 3.1 28.6 + - + +
524B ASP* 4.4 2.7 - - - +
526B LEU* 1.3 76.3 - - + +
528B PHE* 1.3 62.3 + - - +
530B PHE* 3.1 22.8 + - - +
531B SER* 4.3 3.8 + - - -
545B ILE* 5.7 2.7 - - + -
564B MET* 3.3 38.4 - - + +
565B LEU* 4.0 26.0 - - + -
568B PRO* 4.0 17.3 - - + +
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Residues in contact with PHE 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490B LEU* 3.6 33.2 - - + -
524B ASP* 3.3 21.1 + - - +
525B THR* 3.7 4.5 - - - +
526B LEU 3.2 0.4 - - - -
527B VAL* 1.3 74.8 - - - +
529B ALA* 1.3 61.2 + - - +
530B PHE 3.0 5.8 + - - -
531B SER* 3.4 19.5 + - - -
532B LYS* 3.9 17.9 + - + +
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Residues in contact with ALA 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 4.2 17.5 - - + -
490B LEU* 3.7 20.2 - - + -
525B THR 3.0 13.6 + - - +
526B LEU* 3.1 11.4 + - - +
528B PHE* 1.3 72.6 - - - +
530B PHE* 1.3 58.0 + - - +
531B SER 3.1 7.1 + - - -
532B LYS* 3.9 5.6 - - - +
533B TYR* 3.3 38.1 + - + -
541B LEU* 3.4 10.8 - - + +
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Residues in contact with PHE 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526B LEU 3.3 5.6 + - - +
527B VAL* 3.1 18.6 + - - +
528B PHE 3.0 1.0 - - - -
529B ALA* 1.3 77.7 - - - +
531B SER* 1.3 58.7 + - - +
533B TYR 4.7 3.1 + - - +
538B LEU* 3.9 23.5 - - + +
541B LEU* 3.6 20.0 - - + -
542B TYR* 3.5 45.8 - + - -
545B ILE* 4.3 15.5 - - + -
568B PRO* 3.6 32.8 - - + -
569B LEU* 4.1 8.5 - - + -
572B LYS* 3.5 24.7 - - + -
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Residues in contact with SER 531 (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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527B VAL 4.4 5.0 + - - -
528B PHE* 3.4 15.2 + - - -
529B ALA 3.1 0.2 - - - -
530B PHE* 1.3 82.9 + - - +
532B LYS* 1.3 61.3 + - - +
533B TYR 3.4 7.2 - - - +
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Residues in contact with LYS 532 (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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490B LEU* 3.2 38.2 + - + +
491B ASP 4.1 5.2 + - - -
492B SER* 4.7 7.0 - - - +
497B GLN* 4.1 21.5 - - - +
528B PHE* 3.9 18.9 + - + +
529B ALA* 3.6 9.5 + - - +
531B SER* 1.3 79.9 - - - +
533B TYR* 1.3 67.6 + - + +
534B GLN* 4.0 13.9 + - - +
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Residues in contact with TYR 533 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B ILE* 3.0 33.9 + - - +
490B LEU* 5.9 0.2 - - + -
497B GLN* 3.2 50.4 + - + +
501B CYS* 3.9 5.7 - - + +
529B ALA* 3.3 18.3 + - + +
530B PHE 5.4 1.0 - - - +
531B SER 3.4 7.2 - - - +
532B LYS* 1.3 87.3 - - + +
534B GLN* 1.3 63.0 + - - +
535B HIS* 3.8 3.4 + - - -
537B ASN* 3.4 37.7 - - + -
538B LEU* 3.8 21.8 - - + +
541B LEU* 3.5 40.2 - - + -
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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