Contacts of the helix formed by residues 542 - 546 (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 THR 542 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A ARG 5.1 0.2 + - - -
504A ASP* 3.3 21.8 + - - +
505A LEU 5.7 0.2 - - - -
506A LYS* 3.6 25.8 + - + +
541A GLY* 1.3 73.9 + - - -
543A PRO* 1.4 76.8 - - + +
544A ASP* 4.5 3.6 - - + +
545A TYR* 2.9 44.5 + - + +
546A ILE* 3.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 543 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541A GLY 4.2 3.8 - - - +
542A THR* 1.4 91.1 - - + -
544A ASP* 1.3 63.8 + - - +
545A TYR 3.2 0.5 + - - -
546A ILE* 3.3 9.0 - - + +
584A GLU* 3.7 26.5 - - + +
587A LEU* 3.7 19.6 - - + +
588A PHE* 4.2 14.2 - - + -
591A ILE* 3.1 22.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 544 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A THR* 3.2 4.2 + - + +
543A PRO* 1.3 79.9 - - - +
545A TYR* 1.3 74.6 + - + +
546A ILE 3.6 0.6 + - - +
563A TRP* 5.2 0.2 + - - -
567A VAL* 3.6 18.1 - - + +
571A GLU* 4.6 1.6 - - - +
577A SER* 3.5 34.9 + - - +
578A PRO* 5.3 0.5 - - - +
579A PHE* 3.9 11.3 + - - +
587A LEU* 3.8 26.7 - - - +
591A ILE* 4.2 9.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 545 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A MET* 3.9 11.3 - - + +
505A LEU 3.3 20.9 - - - +
506A LYS* 3.5 28.3 - - + -
507A LEU 3.3 14.9 + - - -
508A ASP* 5.2 2.2 - - - -
542A THR* 2.9 32.0 + - + +
544A ASP* 1.3 84.8 - - + +
546A ILE* 1.3 63.1 + - - +
547A ALA 3.6 0.9 + - - -
563A TRP* 3.7 5.9 - - - -
564A SER* 2.8 44.5 + - - +
567A VAL* 3.5 20.6 - - + -
568A LEU* 3.9 13.5 - - + -
571A GLU* 2.4 40.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 546 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A PHE* 3.9 27.4 - - + -
540A CYS 3.3 27.6 - - - +
541A GLY* 4.5 4.0 - - - -
542A THR 3.1 12.6 + - - +
543A PRO* 3.3 20.2 - - + +
544A ASP 3.6 0.6 - - - -
545A TYR* 1.3 77.1 - - - +
547A ALA* 1.3 67.9 + - - +
550A ILE* 3.5 29.2 - - + -
551A LEU* 3.8 19.1 - - + -
563A TRP* 3.6 3.8 + - - -
564A SER* 5.0 0.7 - - - -
588A PHE* 3.9 9.0 - - + -
591A ILE* 3.4 26.0 - - + +
----------------------------------------------------------
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