Contacts of the helix formed by residues 248 - 260 (chain A) in PDB entry 1TDH
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 SER 248 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY* 3.4 7.5 - - - -
246A SER* 2.9 20.9 + - - -
247A GLU* 1.3 76.5 - - - +
249A GLY* 1.3 57.8 + - - +
250A GLU* 3.3 2.9 - - - -
251A GLU* 3.3 20.9 + - - -
252A ASP* 2.8 54.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A GLY 5.4 1.0 + - - -
246A SER 4.6 3.1 + - - -
247A GLU* 3.2 6.7 + - - +
248A SER* 1.3 77.1 - - - +
250A GLU* 1.3 61.6 + - - +
252A ASP* 3.4 6.4 + - - +
253A PHE* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU 4.8 3.9 + - - +
248A SER 3.3 0.6 - - - -
249A GLY* 1.3 74.6 - - - +
251A GLU* 1.3 63.0 + - - +
253A PHE* 3.4 5.4 + - - +
254A ALA* 3.1 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A SER* 3.3 21.2 + - - +
250A GLU* 1.3 79.8 - - - +
252A ASP* 1.3 69.6 + - - +
254A ALA* 3.3 8.5 + - - +
255A ALA* 3.1 22.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 5.1 5.7 - - - +
240A GLY* 4.5 11.8 - - - +
243A GLY* 3.5 22.9 - - - +
248A SER* 2.8 43.3 + - - +
249A GLY* 3.9 5.4 + - - +
251A GLU* 1.3 85.8 - - - +
253A PHE* 1.3 62.3 + - - +
255A ALA* 3.2 8.3 + - - +
256A PHE* 3.0 21.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A GLY 3.0 17.1 + - - +
250A GLU* 4.0 5.8 - - - +
252A ASP* 1.3 76.3 - - - +
254A ALA* 1.3 58.3 + - - +
256A PHE* 3.6 28.1 - + + +
257A ARG* 2.8 66.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLU 3.1 13.9 + - - +
251A GLU* 3.6 11.7 - - - +
252A ASP 3.2 0.2 - - - -
253A PHE* 1.3 80.1 - - - +
255A ALA* 1.3 62.4 + - - +
257A ARG* 3.5 11.3 + - - +
258A ALA* 3.2 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A LEU* 3.6 30.5 - - + +
251A GLU* 3.1 14.3 + - + +
252A ASP* 3.6 9.9 - - - +
253A PHE 3.2 0.2 - - - -
254A ALA* 1.3 75.6 - - - +
256A PHE* 1.3 63.8 + - - +
258A ALA* 3.3 7.3 + - - +
259A TRP* 3.0 23.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 256 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 3.7 52.3 - + + -
236A VAL* 4.3 14.8 - - + -
239A LEU* 4.0 11.0 - - + +
252A ASP 3.0 14.1 + - - +
253A PHE* 3.2 31.4 + + + +
255A ALA* 1.3 75.5 - - - +
257A ARG* 1.3 68.0 + - - +
259A TRP* 3.0 28.2 + + - +
260A LEU* 3.3 41.5 + - + +
263A TYR* 6.3 0.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 257 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PHE* 2.8 50.1 + - + +
254A ALA* 3.6 10.6 - - - +
256A PHE* 1.3 80.7 - - - +
258A ALA* 1.3 60.6 - - - +
259A TRP 3.3 0.2 + - - -
260A LEU* 3.4 28.0 + - + +
265A MET* 5.2 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254A ALA 3.2 13.6 + - - +
255A ALA* 3.7 7.2 - - - +
256A PHE 3.2 0.2 - - - -
257A ARG* 1.3 80.9 - - - +
259A TRP* 1.3 61.3 + - - +
260A LEU 3.7 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 259 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 4.0 12.8 - + - -
178A LEU* 4.5 0.2 - - + -
181A GLU* 4.0 15.3 - - + +
185A ARG* 3.8 20.6 + - - +
232A VAL* 3.7 28.9 - - + -
235A GLU* 2.9 29.5 + - + +
236A VAL* 3.4 32.5 - - + -
239A LEU* 3.8 20.6 - - + -
255A ALA 3.0 13.2 + - - +
256A PHE* 3.0 17.7 + + - +
258A ALA* 1.3 77.9 - - - +
260A LEU* 1.3 91.1 + - + +
261A ARG* 3.6 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 260 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A TYR* 4.4 4.5 - - + -
181A GLU* 3.7 21.5 - - + +
256A PHE* 3.3 39.9 + - + +
257A ARG* 3.7 16.9 - - + +
258A ALA 3.4 7.2 - - - +
259A TRP* 1.3 103.2 - - + +
261A ARG* 1.3 60.8 + - - +
263A TYR* 4.0 35.9 - - + +
265A MET* 3.9 20.2 - - - +
----------------------------------------------------------
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