Contacts of the helix formed by residues 1556 - 1559 (chain B) in PDB entry 2IUK
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 PRO1556 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1553B LEU 3.5 13.2 - - - +
1554B LEU 3.3 5.8 - - - -
1555B TYR* 1.4 103.6 - - + +
1557B HIS* 1.3 61.2 + - + +
1558B TYR 3.3 7.5 + - - -
1559B ARG* 3.6 19.1 - - + +
1793B ARG* 3.2 36.8 - - + +
1794B GLU 5.9 2.2 - - - +
1860B ASN* 3.3 36.8 + - - +
1861B SER* 3.8 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS1557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1533B MET* 4.5 0.5 - - - +
1553B LEU 3.6 24.2 + - - -
1554B LEU* 3.4 12.2 + - - +
1556B PRO* 1.3 80.4 - - + +
1558B TYR* 1.3 66.5 + - + +
1561B THR* 3.9 3.1 + - - -
1650B TRP* 5.2 9.4 + - - -
1708B ILE* 4.9 5.2 - - + +
1709B VAL* 3.5 45.6 - - + +
1712B ALA* 3.5 22.7 - - + +
1713B SER* 4.8 2.5 - - - -
1790B LEU* 4.5 6.5 + - - +
1793B ARG* 5.2 4.3 - - - -
1811B PHE* 5.9 1.2 - - - -
1860B ASN* 3.4 39.5 + - + -
1861B SER* 3.2 19.8 - - - -
1862B ILE* 4.0 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1267B GLU* 4.2 12.2 - - - +
1533B MET* 3.4 34.5 - - + -
1536B PHE* 3.9 11.9 - - + +
1537B ALA* 3.8 34.1 - - + -
1540B THR* 3.1 39.7 + - + -
1541B ASN* 5.2 3.6 - - - -
1554B LEU* 3.3 45.3 - - + +
1555B TYR* 3.9 12.9 + - - +
1556B PRO 3.3 0.6 - - - -
1557B HIS* 1.3 80.2 - - + +
1559B ARG* 1.4 55.6 + - - +
1560B ASP 3.1 1.4 + - - -
1561B THR* 2.8 35.7 + - - +
1674B TRP* 4.8 0.9 - - - -
1708B ILE* 3.8 14.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1269B PHE* 3.6 44.2 - - + +
1271B HIS* 4.2 13.7 + - - -
1555B TYR 4.4 3.8 + - - +
1556B PRO* 3.6 18.9 + - + +
1558B TYR* 1.4 72.1 - - - +
1560B ASP* 1.3 71.0 + - + +
1561B THR 3.3 1.0 + - - -
1786B ASP* 3.6 35.8 + - - +
1787B GLU* 4.8 11.0 + - - +
1788B ILE* 3.9 29.0 - - - +
1794B GLU* 3.2 27.3 + - - -
1860B ASN* 5.9 0.7 - - + -
1861B SER* 2.6 29.0 + - - +
1862B ILE 3.4 2.8 - - - +
1863B SER* 3.7 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