Contacts of the helix formed by residues 459 - 469 (chain F) in PDB entry 4YJL
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 459 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455F LYS 5.4 0.9 - - - +
456F LEU* 3.0 5.8 + - - +
458F PHE* 1.3 79.7 - - + +
460F GLU* 1.3 59.9 + - - +
461F GLU* 3.0 35.8 + - - +
462F HIS* 3.0 37.1 + - + +
463F ARG* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 460 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458F PHE 4.0 1.2 + - - -
459F ASP* 1.3 75.0 + - - +
461F GLU* 1.3 64.0 + - - +
463F ARG* 3.3 32.2 + - - +
464F HIS* 3.1 21.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 461 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F HIS* 5.3 0.9 + - - -
459F ASP* 3.0 25.7 + - - +
460F GLU* 1.3 79.8 - - - +
462F HIS* 1.3 69.3 + - + +
464F HIS* 3.4 9.6 + - - +
465F ALA* 3.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 462 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F HIS* 5.4 5.8 - + - -
406F MET* 3.4 26.1 - - + +
456F LEU* 3.2 41.2 + - + +
459F ASP* 3.0 34.8 + - + +
461F GLU* 1.3 79.8 + - + +
463F ARG* 1.3 56.0 + - - +
465F ALA* 3.2 2.4 + - - -
466F MET* 2.7 37.0 + - - +
802F EDO 3.8 24.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 463 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456F LEU 4.6 0.2 + - - -
457F SER* 2.9 40.0 + - - +
458F PHE 3.3 21.8 + - - -
459F ASP 2.9 9.8 + - - +
460F GLU* 3.3 37.6 + - + +
462F HIS* 1.3 75.4 - - - +
464F HIS* 1.3 54.3 + - - +
466F MET* 3.2 8.1 + - - +
467F ASN* 2.7 46.6 + - - +
507F ASN 3.3 27.1 + - - -
508F LEU* 4.0 15.9 - - + +
510F PHE* 4.7 13.3 + - - -
505L LEU* 3.7 25.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 464 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460F GLU* 3.1 12.8 + - + +
461F GLU* 3.4 12.8 - - - +
462F HIS 3.3 0.2 - - - -
463F ARG* 1.3 76.3 - - - +
465F ALA* 1.3 57.6 + - - +
467F ASN* 3.4 9.3 + - - +
468F GLU* 3.0 54.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 465 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F HIS* 3.3 44.4 - - + +
406F MET* 3.6 10.1 - - + -
461F GLU 3.1 12.5 + - - +
462F HIS* 3.2 7.8 + - - +
464F HIS* 1.3 75.1 - - - +
466F MET* 1.3 64.6 + - - +
468F GLU* 3.2 10.8 + - - +
469F LEU* 3.1 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 466 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406F MET* 3.3 21.0 - - + -
410F LEU* 4.6 3.4 - - + -
453F LEU* 3.6 32.5 - - + +
456F LEU* 3.7 15.3 - - + -
457F SER* 3.7 22.9 - - - +
462F HIS 2.7 27.6 + - - +
463F ARG* 3.4 7.0 - - - +
465F ALA* 1.3 73.1 - - - +
467F ASN* 1.3 57.4 + - - +
469F LEU* 3.0 14.6 + - - +
471F GLY* 2.9 39.4 + - - -
475F ILE* 4.3 12.1 - - - -
508F LEU* 4.0 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 467 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463F ARG* 2.7 32.4 + - - +
464F HIS* 3.7 7.8 - - - +
466F MET* 1.3 70.3 - - - +
468F GLU* 1.3 64.3 + - - +
469F LEU 3.2 0.7 + - - -
470F GLY* 3.3 8.5 + - - -
508F LEU* 3.7 12.2 + - - +
512F ASP* 3.6 12.9 + - - -
515F ASN* 2.8 33.2 + - - +
804F EDO 2.9 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 468 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464F HIS* 3.0 42.2 + - + +
465F ALA* 3.2 11.9 + - - +
467F ASN* 1.3 76.5 - - + +
469F LEU* 1.3 70.0 + - + +
470F GLY 3.6 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 469 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
403F HIS* 4.6 14.6 - - + -
406F MET* 4.1 27.1 - - + -
407F LEU* 4.4 24.7 - - + +
410F LEU* 3.5 18.3 - - + +
414F ARG* 3.3 25.2 + - - +
465F ALA* 3.1 18.4 + - + +
466F MET 3.0 2.9 + - - +
468F GLU* 1.3 88.8 - - + +
470F GLY* 1.3 60.0 + - - +
471F GLY 3.4 0.6 + - - -
----------------------------------------------------------
Back to top of page
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