Contacts of the helix formed by residues 193 - 201 (chain A) in PDB entry 1DM0
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 193 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 4.0 2.5 - - - -
127A GLY* 4.9 0.7 - - - +
190A TYR* 6.0 0.2 - - + -
191A VAL* 3.2 12.3 + - + +
192A MET* 1.3 78.2 - - - +
194A ALA* 1.3 64.9 + - - +
195A GLU* 3.2 14.5 + - - +
196A ASP* 2.9 36.4 + - - +
197A VAL* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A THR* 3.5 24.8 - - + +
193A THR* 1.3 75.5 - - - +
195A GLU* 1.3 76.5 + - - +
197A VAL* 2.9 15.1 + - - +
198A ASP* 3.0 18.6 + - - +
223A ARG* 5.9 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLN* 4.5 5.8 + - - +
193A THR* 3.1 14.4 - - - +
194A ALA* 1.3 88.4 + - - +
196A ASP* 1.4 61.7 + - - +
198A ASP* 3.7 11.8 - - - +
199A LEU* 3.6 18.4 + - - +
223A ARG* 5.5 1.7 + - - -
224A ILE* 5.5 1.7 - - - +
8E LYS* 3.1 42.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A GLN* 2.3 40.4 + - - +
174A ILE* 4.2 10.2 - - + +
190A TYR* 2.8 29.8 + - - +
192A MET* 3.9 19.1 - - + -
193A THR* 2.9 29.6 + - - +
195A GLU* 1.4 73.4 - - - +
197A VAL* 1.3 68.3 + - - +
199A LEU* 3.2 14.8 + - - +
200A THR* 3.3 13.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ARG* 3.3 30.5 - - + +
126A THR* 3.7 35.9 - - - +
192A MET* 4.1 15.3 - - + -
193A THR 3.1 13.9 + - - +
194A ALA* 2.9 7.9 + - - +
196A ASP* 1.3 79.2 - - - +
198A ASP* 1.3 63.7 + - - +
200A THR* 2.8 22.8 + - - -
201A LEU* 3.1 17.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194A ALA* 3.0 19.8 + - - +
195A GLU* 3.7 14.8 - - - +
196A ASP 3.5 0.2 - - - -
197A VAL* 1.3 73.6 - - - +
199A LEU* 1.3 59.8 + - - +
201A LEU* 3.3 14.0 - - - +
202A ASN* 2.4 39.3 + - - +
223A ARG* 3.1 54.4 + - - +
224A ILE* 4.3 9.1 - - + +
8E LYS* 4.6 6.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A PHE* 3.8 40.7 - - + -
173A GLN* 3.0 48.7 - - + +
174A ILE* 5.4 2.7 - - + -
195A GLU 3.6 6.9 + - - +
196A ASP* 3.2 10.9 + - - +
197A VAL 3.0 0.6 - - - -
198A ASP* 1.3 80.4 - - - +
200A THR* 1.3 55.3 + - - +
202A ASN* 2.6 28.1 + - - +
203A TRP 3.4 4.9 + - - -
206A LEU* 4.3 10.3 - - + -
224A ILE* 3.8 24.5 - - + -
226A PHE* 4.4 16.6 - - + -
235A SER* 4.3 3.4 - - - -
236A VAL* 4.6 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 5.3 0.9 - - - -
125A ARG* 2.9 28.4 + - - +
167A GLU* 3.3 43.0 - - + +
170A ARG* 5.6 1.7 + - - -
171A PHE* 3.8 9.1 - - + -
174A ILE* 3.8 20.4 - - + -
192A MET* 4.6 2.5 - - + -
196A ASP 3.3 10.7 + - - +
197A VAL 2.8 16.5 + - - -
199A LEU* 1.3 76.2 - - - +
201A LEU* 1.3 60.0 + - - +
202A ASN 3.2 1.2 + - - -
203A TRP* 3.5 15.6 + - - +
260A MET* 5.8 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A TYR* 5.9 2.7 - - + -
125A ARG* 4.0 15.0 - - - +
197A VAL* 3.1 27.6 - - + +
198A ASP* 3.3 18.2 - - - +
200A THR* 1.3 74.2 - - - +
202A ASN* 1.3 64.5 + - - +
203A TRP 3.5 0.7 - - - -
204A GLY 5.4 0.5 + - - -
205A ARG* 6.0 0.9 - - - +
----------------------------------------------------------
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