Contacts of the helix formed by residues 247 - 255 (chain D) in PDB entry 7UUT
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 ASP 247 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245D ASN* 3.7 26.5 + - - +
246D ALA* 1.3 79.4 - - - +
248D ILE* 1.3 76.7 + - - +
249D MET 3.1 0.4 - - - -
250D ALA* 3.1 20.2 + - + +
251D THR* 3.3 12.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 3.8 25.8 - - + -
197D VAL* 6.1 0.4 - - + -
223D ILE* 4.3 20.4 - - + -
241D ILE* 3.6 25.4 - - + -
243D GLY 3.7 19.3 - - - +
244D GLY* 4.5 4.9 - - - +
245D ASN 3.1 24.9 + - - +
247D ASP* 1.3 86.7 + - - +
249D MET* 1.3 60.8 + - + +
251D THR* 3.2 18.2 + - - +
252D ALA* 2.9 27.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C VAL* 6.3 3.8 - - + -
281C TRP* 4.1 32.1 - - + -
241D ILE* 3.8 27.4 - - + -
246D ALA* 3.1 13.2 + - - +
247D ASP 3.1 0.2 - - - -
248D ILE* 1.3 79.1 - - + +
250D ALA* 1.3 65.3 + - - +
252D ALA* 3.3 1.2 + - - +
253D VAL* 3.1 34.5 + - + +
262D ILE* 4.2 15.5 - - + -
264D ASN* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL* 6.3 3.4 - - + -
224D GLU* 5.6 0.2 - - - +
246D ALA 4.3 0.6 + - - -
247D ASP* 3.1 14.7 + - + +
249D MET* 1.3 79.0 - - - +
251D THR* 1.3 64.4 + - - +
253D VAL* 3.4 6.9 + - - +
254D LYS* 3.1 46.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 4.5 6.7 - - + -
223D ILE* 3.9 29.2 - - + +
224D GLU* 2.6 37.9 + - + +
247D ASP* 3.3 9.6 + - - +
248D ILE* 3.2 27.4 + - + +
250D ALA* 1.3 79.1 - - - +
252D ALA* 1.3 62.0 + - - +
254D LYS* 3.3 2.1 + - - +
255D ILE* 3.2 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D LEU* 3.8 20.4 - - + +
239D ALA* 4.2 4.7 - - + -
241D ILE* 3.8 7.0 - - + -
248D ILE 2.9 13.6 + - - +
249D MET 3.3 7.8 + - - +
251D THR* 1.3 76.8 - - - +
253D VAL* 1.3 61.3 - - - +
255D ILE* 3.3 6.4 + - - +
256D VAL* 3.1 28.8 + - - +
262D ILE* 3.8 31.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249D MET* 3.1 30.7 + - + +
250D ALA* 3.9 6.3 - - - +
251D THR 3.3 0.2 - - - -
252D ALA* 1.3 76.3 - - - +
254D LYS* 1.3 64.5 + - + +
255D ILE 3.4 0.3 + - - -
256D VAL* 3.5 15.8 + - - +
262D ILE* 4.1 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224D GLU* 3.7 35.5 + - + +
228D MET* 4.2 12.4 - - - +
250D ALA* 3.1 32.5 + - - +
251D THR 3.7 4.5 - - - +
252D ALA 3.2 0.2 - - - -
253D VAL* 1.3 81.1 - - + +
255D ILE* 1.3 59.8 + - - +
256D VAL 4.2 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171D ALA* 3.8 20.4 - - + -
173D LEU* 4.0 14.8 - - + -
224D GLU* 3.9 28.5 - - + +
227D ILE* 3.7 43.1 - - + -
228D MET* 4.3 7.2 - - - -
235D GLY* 3.3 7.0 - - - -
236D VAL* 2.9 30.4 + - + +
239D ALA* 4.1 9.6 - - + -
251D THR* 3.2 18.1 + - + +
252D ALA* 3.3 15.3 - - - +
254D LYS* 1.3 78.6 - - - +
256D VAL* 1.3 61.8 + - - +
----------------------------------------------------------
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