Contacts of the helix formed by residues 539 - 543 (chain B) in PDB entry 6WCZ
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 TRP 539 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ARG* 3.5 29.5 - - - +
536B THR* 3.7 39.2 + - + +
537B ALA 3.8 0.6 - - - -
538B GLY* 1.3 73.5 - - - +
540B ASP* 1.3 59.8 + - + +
541B THR* 5.1 0.2 - - - +
542B ARG* 2.8 33.7 + - - +
543B ILE* 3.3 29.5 - - + +
601B ARG* 4.2 10.5 - - - -
612B ASN* 3.7 24.0 - - + +
615B THR* 4.4 12.6 - - + -
616B ASN* 3.5 38.1 - - + -
619B VAL* 4.8 7.6 - - + -
665B ASP* 3.5 31.6 - - + +
688B LYS* 4.4 20.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 540 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ARG* 4.1 13.4 - - - +
476B TRP* 3.7 19.3 - - + -
539B TRP* 1.3 87.5 - - + +
541B THR* 1.3 64.0 + - + +
542B ARG 3.4 0.3 + - - -
543B ILE* 3.9 11.2 + - - +
600B GLN* 3.5 17.8 - - - +
601B ARG* 2.8 47.3 + - - +
602B GLY 2.9 23.3 - - - +
603B SER* 5.3 3.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 541 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359B LYS* 3.6 30.7 - - + +
360B VAL* 5.4 0.9 - - + -
362B THR* 5.0 8.0 - - - +
364B VAL* 4.5 7.6 - - - +
470B LYS* 3.8 14.4 - - + +
476B TRP* 6.4 0.9 - - + -
538B GLY* 2.7 36.8 + - - -
540B ASP* 1.3 81.2 - - + +
542B ARG* 1.3 70.2 + - - +
543B ILE 3.6 2.3 + - - +
600B GLN* 2.9 31.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 542 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B THR* 4.9 13.6 - - - +
364B VAL* 3.3 34.4 - - - +
365B PRO* 4.6 11.7 + - - +
536B THR* 6.3 1.1 - - + -
537B ALA 4.5 6.3 - - - +
538B GLY 3.3 18.4 - - - +
539B TRP* 2.8 10.6 + - - +
541B THR* 1.3 90.2 + - - +
543B ILE* 1.3 57.3 + - - +
686B MET 4.6 3.3 + - - +
687B GLY* 3.5 38.8 + - - +
688B LYS* 3.3 31.3 + - + +
689B VAL* 4.7 20.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 543 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B VAL* 5.7 2.1 - - - +
539B TRP* 3.3 45.5 - - + +
540B ASP* 3.9 12.9 + - - +
541B THR 3.6 3.5 + - - +
542B ARG* 1.3 82.8 - - - +
544B SER* 1.3 62.9 + - - +
547B ASP* 3.5 27.8 - - + +
548B LEU* 5.1 6.5 - - + -
599B ASP* 3.0 13.9 - - - +
600B GLN* 4.1 13.7 - - - +
601B ARG* 4.6 16.4 - - + +
611B LEU* 4.0 27.6 - - + -
615B THR* 5.1 4.7 - - + -
688B LYS* 4.8 5.4 - - - -
----------------------------------------------------------
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