Contacts of the helix formed by residues 185 - 192 (chain B) in PDB entry 1TWF
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 THR 185 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU 4.1 5.8 - - - +
184B ALA* 1.3 78.3 - - - +
186B GLU* 1.3 65.8 + - - +
187B SER* 3.1 10.5 + - - -
188B ASP* 2.8 35.1 + - - +
189B LEU* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 186 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 1.3 75.7 - - - +
187B SER* 1.3 59.6 + - - +
189B LEU* 3.9 10.1 + - - +
190B TYR* 3.0 46.0 + - + -
196B PRO* 4.3 14.4 - - + +
62J ARG* 3.7 18.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 187 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B THR* 3.0 7.9 + - - -
186B GLU* 1.3 78.5 - - - +
188B ASP* 1.3 65.7 + - - +
189B LEU 3.1 1.8 - - - -
190B TYR* 3.0 15.0 + - - +
191B LYS* 3.1 38.1 + - - +
62J ARG* 4.1 21.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 188 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184B ALA* 3.8 11.7 - - + -
185B THR* 2.8 46.2 + - - +
187B SER* 1.3 76.5 - - - +
189B LEU* 1.3 63.8 + - - +
191B LYS* 3.3 18.1 + - - +
192B LEU* 3.1 30.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ARG* 5.4 10.8 - - - +
181B LEU* 4.0 33.7 - - + +
184B ALA* 3.6 26.5 - - + +
185B THR 3.0 22.9 + - - +
186B GLU* 4.0 5.6 - - - +
187B SER 3.1 0.2 - - - -
188B ASP* 1.3 76.2 - - - +
190B TYR* 1.3 62.5 + - - +
192B LEU* 3.1 14.2 + - - +
194B GLU* 3.1 36.9 + - + +
195B CYS 5.0 1.8 - - - +
196B PRO* 4.0 28.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B GLU* 3.0 28.3 + - + -
187B SER* 3.0 9.6 + - - +
189B LEU* 1.3 77.7 - - - +
191B LYS* 1.3 64.6 + - + +
193B LYS* 3.0 15.6 + - - +
194B GLU 4.0 2.7 + - - -
196B PRO* 3.4 33.2 - - + +
783B THR* 4.4 2.1 + - - +
59J LYS* 3.3 47.8 - - - +
62J ARG* 3.5 61.5 - - + +
63J TYR* 3.6 41.8 - + - -
64J ASN 5.1 1.8 + - - -
65J PRO* 5.7 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 191 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B SER* 3.1 33.2 + - - +
188B ASP* 3.6 16.8 + - - +
190B TYR* 1.3 76.2 - - + +
192B LEU* 1.3 60.2 + - + +
193B LYS* 2.9 13.7 + - - +
64J ASN* 5.8 9.7 - - - +
65J PRO* 5.8 0.7 - - - +
33L GLU* 6.1 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B TYR* 3.3 40.9 - - + +
114B PRO* 5.6 1.3 - - + +
115B GLN* 3.4 16.3 - - - +
180B TYR* 5.5 1.8 - - + -
181B LEU* 3.6 29.4 - - + +
184B ALA* 4.5 8.7 - - + -
188B ASP* 3.1 23.4 + - + +
189B LEU* 3.1 11.0 + - - +
191B LYS* 1.3 77.0 - - + +
193B LYS* 1.3 70.1 + - - +
194B GLU* 3.1 7.9 + - + +
----------------------------------------------------------
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