Contacts of the helix formed by residues 535 - 543 (chain W) in PDB entry 5IJO
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 ILE 535 (chain W).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
520W LEU 5.8 0.4 - - - +
523W LEU* 3.3 17.6 + - + +
524W LEU* 5.2 4.3 - - - +
525W VAL 4.7 1.4 - - - -
534W GLU* 1.3 71.3 - - - +
536W GLU* 1.3 63.8 + - - +
537W ARG 3.2 2.5 - - - -
538W PHE* 3.4 7.7 + - + +
539W PHE* 3.1 20.3 + - - +
547W ALA* 5.4 5.6 - - + +
573W PHE* 6.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 536 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534W GLU* 3.2 7.0 - - + +
535W ILE* 1.3 78.2 - - - +
537W ARG* 1.3 53.4 + - - +
539W PHE* 2.9 11.6 - - + +
540W LYS* 2.6 37.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 537 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
523W LEU* 5.6 2.9 - - + -
534W GLU* 4.2 10.0 + - + +
536W GLU* 1.3 79.3 - - - +
538W PHE* 1.3 61.6 + - - +
540W LYS* 3.4 8.0 + - - +
541W LEU* 3.2 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 538 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
519W GLN* 5.8 2.5 - - + +
520W LEU* 5.2 12.3 - - + -
523W LEU* 4.8 12.0 - - + +
534W GLU 5.0 0.2 + - - -
535W ILE* 3.4 17.5 + - + +
537W ARG* 1.3 77.6 - - - +
539W PHE* 1.3 55.7 + - - +
541W LEU* 5.1 2.0 - - - -
542W HIS* 2.8 44.0 + - + +
547W ALA* 5.2 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 539 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535W ILE 3.1 11.5 + - - +
536W GLU* 2.9 18.6 - - + +
538W PHE* 1.3 79.0 - - - +
540W LYS* 1.3 56.5 + - - +
543W GLN* 2.7 44.1 + - - +
544W GLU* 4.1 3.8 + - - +
547W ALA* 4.6 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 540 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536W GLU 2.6 17.7 + - - +
537W ARG* 3.6 9.4 - - - +
538W PHE 3.3 0.2 - - - -
539W PHE* 1.3 75.6 - - - +
541W LEU* 1.3 65.2 + - - +
543W GLN* 4.2 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 541 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W PHE* 4.8 7.2 - - + +
440W PRO* 4.3 25.1 - - + +
537W ARG 3.2 12.5 + - - +
538W PHE* 4.1 2.5 - - - +
540W LYS* 1.3 85.4 - - - +
542W HIS* 1.3 62.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 542 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439W PHE* 4.3 21.5 - - + +
538W PHE* 2.8 25.9 + - + +
541W LEU* 1.3 77.2 - - + +
543W GLN* 1.4 69.2 + - - +
546W GLN* 4.1 22.1 - - + +
547W ALA* 5.1 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 543 (chain W).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539W PHE* 2.7 26.6 + - - +
540W LYS 4.8 1.8 - - - -
541W LEU 3.6 0.6 - - - -
542W HIS* 1.4 77.4 - - - +
544W GLU* 1.3 66.3 + - - +
545W ASP* 3.4 8.1 - - + +
546W GLN* 3.6 4.2 + - + +
547W ALA* 3.2 21.7 + - - +
----------------------------------------------------------
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