Contacts of the helix formed by residues 518 - 529 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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474A PRO* 4.1 13.8 - - + +
475A ASP* 3.4 19.9 + - - -
478A LEU* 4.9 11.4 - - + -
479A LYS* 4.2 33.3 + - + +
482A MET* 3.6 40.2 - - + -
514A GLU 3.4 25.6 - - - -
515A LEU* 3.1 11.0 + - + +
517A PRO* 1.3 89.7 - - + +
519A LEU* 1.3 58.1 + - - +
520A ALA 3.1 3.1 - - - -
521A TYR* 3.0 15.4 + + + +
522A ILE* 2.8 29.7 + - + +
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Residues in contact with LEU 519 (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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515A LEU 3.0 6.9 + - - +
516A VAL* 3.2 20.0 + - + +
517A PRO 3.2 1.0 - - - -
518A TYR* 1.3 77.8 - - - +
520A ALA* 1.3 58.7 + - - +
522A ILE* 4.0 3.8 - - + -
523A LEU* 3.3 26.9 + - - +
548A LEU* 3.8 27.4 - - + -
552A VAL* 3.7 31.0 - - + -
555A HIS* 3.6 22.7 - - + +
556A LEU* 3.7 22.7 - - + +
561A TYR* 3.6 29.6 - - + +
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Residues in contact with ALA 520 (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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517A PRO 4.6 4.1 + - - +
518A TYR 3.1 0.8 - - - -
519A LEU* 1.3 76.2 - - - +
521A TYR* 1.3 64.5 + - - +
523A LEU* 4.3 2.3 - - - +
524A ASP* 3.4 23.0 + - - +
560A GLU* 6.1 0.7 - - + -
561A TYR* 3.7 27.1 + - + +
564A MET* 5.1 7.1 - - + +
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Residues in contact with TYR 521 (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 MET* 4.3 16.8 - - + -
483A THR* 3.7 38.1 + - + +
486A LEU* 3.9 13.2 - - + +
487A LYS* 3.8 11.3 + - - +
518A TYR* 3.0 18.0 + + + +
520A ALA* 1.3 78.9 - - - +
522A ILE* 1.3 64.4 + - - +
524A ASP* 3.7 9.8 + - + +
525A THR* 3.6 26.3 + - - -
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Residues in contact with ILE 522 (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 MET* 3.9 20.9 - - - -
486A LEU* 3.9 9.1 - - + +
504A PHE* 3.6 41.3 - - + -
508A GLU* 4.3 0.2 - - - +
515A LEU* 3.8 36.8 - - + +
518A TYR 2.8 20.4 + - - +
519A LEU* 4.2 5.8 - - - +
521A TYR* 1.3 76.7 - - - +
523A LEU* 1.3 63.3 + - - +
525A THR* 3.3 5.5 + - - -
526A LEU* 3.2 34.4 + - + +
548A LEU* 3.9 19.7 - - + -
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Residues in contact with LEU 523 (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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519A LEU 3.3 18.9 + - - +
520A ALA* 3.8 2.7 + - - +
521A TYR 3.4 0.2 - - - -
522A ILE* 1.3 77.4 - - - +
524A ASP* 1.3 61.0 + - - +
526A LEU* 4.4 7.0 - - + -
527A VAL* 2.8 38.2 + - + +
545A ILE* 5.9 1.1 - - + -
548A LEU* 3.9 24.0 - - + -
556A LEU* 3.8 11.7 - - + -
561A TYR* 3.7 46.4 - - + +
564A MET* 3.9 13.9 - - + -
565A LEU* 4.0 34.1 - - + -
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Residues in contact with ASP 524 (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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520A ALA 3.4 16.5 + - - +
521A TYR* 3.9 11.1 - - + +
522A ILE 3.3 0.8 - - - -
523A LEU* 1.3 77.5 - - - +
525A THR* 1.3 62.2 + - - +
527A VAL* 4.4 2.1 - - - +
528A PHE* 3.3 24.4 + - - +
564A MET* 4.3 11.7 - - + +
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Residues in contact with THR 525 (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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486A LEU* 3.4 49.5 + - + +
489A ILE* 4.2 9.6 - - + -
490A LEU* 3.6 30.1 - - + +
521A TYR* 3.6 16.9 + - - -
522A ILE 3.3 8.8 + - - -
523A LEU 3.2 0.2 - - - -
524A ASP* 1.3 77.7 - - - +
526A LEU* 1.3 58.8 + - - +
528A PHE* 3.4 1.6 + - - +
529A ALA* 3.0 26.3 + - - +
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Residues in contact with LEU 526 (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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486A LEU* 5.1 1.1 - - + -
489A ILE* 4.0 28.0 - - + -
501A CYS* 5.0 0.2 - - - -
504A PHE* 4.6 3.4 - - + -
508A GLU* 4.4 8.1 - - - +
522A ILE* 3.2 37.3 + - + +
523A LEU* 3.9 7.6 - - + +
525A THR* 1.3 80.2 - - - +
527A VAL* 1.3 63.8 + - + +
529A ALA* 3.2 17.8 + - - +
530A PHE* 3.6 6.6 + - - -
541A LEU* 3.8 28.1 - - + +
544A ALA* 4.5 15.3 - - + +
545A ILE* 4.2 25.4 - - + -
548A LEU* 4.1 14.6 - - + -
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Residues in contact with VAL 527 (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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523A LEU* 2.8 27.5 + - + +
524A ASP* 4.4 3.1 - - - +
526A LEU* 1.3 71.9 - - + +
528A PHE* 1.3 63.7 + - - +
530A PHE* 3.1 26.0 + - + +
531A SER* 4.5 3.1 + - - -
545A ILE* 5.8 0.9 - - + -
564A MET* 3.3 47.3 - - + +
565A LEU* 4.0 20.6 - - + -
568A PRO* 3.8 14.2 - - + +
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Residues in contact with PHE 528 (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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490A LEU* 3.6 37.2 - - + -
524A ASP* 3.3 21.6 + - - +
525A THR* 3.7 2.5 - - - +
527A VAL* 1.3 80.8 - - - +
529A ALA* 1.3 59.6 + - - +
530A PHE 3.0 1.4 + - - -
531A SER* 3.3 24.9 + - - -
532A LYS* 4.1 22.0 + - + +
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Residues in contact with ALA 529 (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* 4.3 4.7 - - + -
490A LEU* 3.7 18.6 - - + -
525A THR 3.0 13.8 + - - +
526A LEU* 3.4 14.1 - - - +
527A VAL 3.1 0.6 - - - -
528A PHE* 1.3 72.6 - - - +
530A PHE* 1.3 55.5 + - - +
531A SER 3.1 7.4 + - - -
532A LYS* 4.2 3.1 - - - -
533A TYR* 3.1 50.1 + - + +
541A LEU* 3.8 14.6 - - + +
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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
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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