Contacts of the helix formed by residues 178 - 184 (chain 2) in PDB entry 2WSC
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 178 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672 PHE* 5.5 7.4 - + + -
1742 VAL* 2.7 31.0 + - - +
1752 MET* 3.1 49.2 - - + +
1762 GLY 3.3 0.6 - - - -
1772 ALA* 1.3 76.9 - - - +
1792 PHE* 1.3 64.6 + - - +
1802 GLN 3.2 1.1 - - - -
1812 HIS* 3.1 41.7 + + + +
1822 ILE* 2.9 43.6 + - + +
2072 ALA* 6.3 3.8 - - - -
2082 PHE 5.8 1.8 - - - -
12142 CLA 3.2 66.6 - + + -
12192 CLA 6.3 1.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 179 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1752 MET 5.0 0.4 + - - -
1762 GLY* 3.3 25.4 + - - +
1782 TRP* 1.3 76.1 - - - +
1802 GLN* 1.3 74.0 + - - +
1822 ILE* 3.2 13.8 + - - +
1832 TYR* 2.8 61.3 - + - -
20102 CLA 5.1 19.5 - + + -
1044J CLA 5.6 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 180 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772 ALA* 3.9 20.9 + - - +
1782 TRP 3.2 0.4 - - - -
1792 PHE* 1.3 89.4 - - - +
1812 HIS* 1.3 64.2 + - - +
1832 TYR* 4.3 2.8 + - + -
1842 THR* 3.0 47.3 + - + +
12142 CLA 5.6 9.6 - - + -
30113 CLA 3.9 34.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 181 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1772 ALA 5.4 0.2 - - - +
1782 TRP* 3.1 42.8 + + + +
1802 GLN* 1.3 79.1 - - - +
1822 ILE* 1.3 55.9 + - - +
1832 TYR* 3.4 1.4 + - - -
1842 THR 4.6 0.3 - - - +
2032 THR* 4.0 15.4 - - + +
2042 ILE 2.8 28.2 + - - +
2052 PHE* 6.1 2.2 - - - -
2082 PHE 4.6 7.4 - - - -
12142 CLA 2.4 97.6 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 182 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662 GLU* 4.2 11.0 - - - +
672 PHE* 3.6 33.2 - - + -
1752 MET 5.7 0.9 - - - +
1782 TRP* 2.9 43.1 + - + +
1792 PHE* 3.6 9.9 - - - +
1802 GLN 3.2 0.2 + - - -
1812 HIS* 1.3 78.6 - - - +
1832 TYR* 1.3 63.6 + - + +
2042 ILE* 3.0 19.3 - - - +
2052 PHE* 3.1 41.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 183 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1792 PHE* 2.8 65.8 - + - -
1802 GLN* 4.2 2.1 + - - +
1812 HIS 4.6 0.4 - - - -
1822 ILE* 1.3 85.8 - - + +
1842 THR* 1.3 99.2 + - + +
1852 GLY 4.2 0.5 - - - -
1862 THR* 3.5 16.5 + - + -
1872 GLY 4.4 3.8 + - - -
2032 THR 4.5 6.2 - - - +
2042 ILE* 5.0 3.9 - - - +
20102 CLA 5.8 15.7 - + + -
1044J CLA 5.2 11.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 184 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1802 GLN* 3.0 28.1 + - + +
1812 HIS 4.6 0.2 - - - +
1832 TYR* 1.3 112.7 + - + +
1852 GLY* 1.3 63.3 - - - +
1862 THR* 4.0 7.6 - - + +
2032 THR* 4.0 18.9 - - - +
----------------------------------------------------------
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