Contacts of the helix formed by residues 537 - 546 (chain E) in PDB entry 5KRA
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 SER 537 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ASP* 2.6 38.8 + - - +
535E PRO 4.3 0.6 + - - -
536E LEU* 1.3 77.0 - - - +
538E ASP* 1.3 60.2 + - - +
539E LEU* 4.1 2.9 - - - -
540E LEU* 3.1 19.9 + - - +
541E LEU* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 538 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536E LEU 3.9 0.9 + - - +
537E SER* 1.3 73.0 - - - +
539E LEU* 1.3 56.6 + - - +
541E LEU* 3.3 18.8 + - - +
542E GLU* 2.9 38.4 + - + +
689G ILE* 3.7 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 539 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351E ASP* 4.0 19.3 - - - +
354E LEU* 4.2 26.2 - - + -
355E VAL* 4.3 12.1 - - + -
358E ILE* 4.7 6.3 - - + -
537E SER* 3.2 1.9 - - - -
538E ASP* 1.3 79.0 - - - +
540E LEU* 1.3 61.3 + - - +
542E GLU* 3.2 5.3 + - + +
543E MET* 3.0 43.1 + - + +
689G ILE* 3.5 36.0 - - + +
690G LEU* 4.5 9.6 - - - +
693G LEU* 3.9 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 540 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347E THR* 4.1 27.1 - - + +
350E ALA* 4.5 11.2 - - + -
351E ASP* 4.8 3.8 - - + +
354E LEU* 3.8 18.2 - - + -
383E TRP* 3.6 37.5 - - + -
525E LEU* 5.1 5.8 - - + -
536E LEU* 3.8 32.5 - - + -
537E SER* 3.1 23.2 + - - +
539E LEU* 1.3 79.7 - - - +
541E LEU* 1.3 57.7 + - - +
543E MET* 3.5 2.0 + - - +
544E LEU* 3.1 27.9 + - + +
601E 6WS 4.9 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529E LYS* 4.2 29.8 - - + +
536E LEU* 3.7 42.2 - - + +
537E SER 2.8 19.1 + - - +
538E ASP* 3.6 21.1 - - - +
539E LEU 3.2 0.2 - - - -
540E LEU* 1.3 75.4 - - - +
542E GLU* 1.3 59.6 + - + +
544E LEU* 3.2 6.6 + - + +
545E ASP* 2.9 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 542 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E GLU* 4.8 4.0 - - - +
538E ASP* 2.9 20.6 + - + +
539E LEU* 3.2 6.7 + - + +
541E LEU* 1.3 74.3 - - + +
543E MET* 1.3 68.3 + - + +
545E ASP* 3.7 5.9 + - - +
546E ALA* 3.4 21.3 + - - +
687G HIS 4.3 5.4 - - - +
688G LYS* 3.6 21.6 - - + +
689G ILE* 2.8 52.0 + - - +
690G LEU* 4.2 3.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 543 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
354E LEU* 3.9 24.5 - - + -
357E MET* 6.1 0.2 - - - -
358E ILE* 6.0 0.9 - - + -
379E LEU* 3.3 35.9 - - + +
380E GLU* 3.8 8.5 - - - +
383E TRP* 3.3 48.3 + - + +
539E LEU* 3.0 25.1 + - + +
540E LEU* 3.8 6.3 - - - +
542E GLU* 1.3 79.4 - - - +
544E LEU* 1.3 60.6 + - - +
546E ALA* 3.7 8.7 - - - +
547E HIS* 3.6 12.6 - - - -
690G LEU* 4.0 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 544 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383E TRP* 4.7 2.2 - - + -
522E MET* 3.6 36.3 - - + +
525E LEU* 3.7 44.4 - - + +
526E TYR* 4.1 16.2 - - + +
529E LYS* 4.3 16.6 - - + -
536E LEU* 4.3 17.0 - - + -
540E LEU* 3.1 17.0 + - + +
541E LEU* 3.4 7.9 - - + +
542E GLU 3.2 0.4 - - - -
543E MET* 1.3 74.4 - - - +
545E ASP* 1.3 63.8 + - - +
546E ALA 3.1 4.7 - - - -
547E HIS* 3.1 18.0 + - - +
548E ARG* 4.0 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 545 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526E TYR* 5.5 4.2 - - - -
529E LYS* 2.9 32.3 + - - +
541E LEU* 2.9 25.0 + - - +
542E GLU* 3.7 6.5 + - - +
544E LEU* 1.3 77.1 - - - +
546E ALA* 1.3 61.4 + - - +
547E HIS 3.1 0.4 - - - -
548E ARG* 3.4 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 546 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
380E GLU* 3.6 41.7 - - + +
542E GLU 3.4 17.2 + - - +
543E MET 3.7 9.0 - - - +
544E LEU 3.1 1.2 - - - -
545E ASP* 1.3 77.3 - - - +
547E HIS* 1.3 60.9 + - - +
548E ARG 3.3 3.3 + - - +
----------------------------------------------------------
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