Contacts of the helix formed by residues 249 - 257 (chain D) in PDB entry 4XH9
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 ILE 249 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179D ILE* 3.7 36.3 - - + -
182D MET* 3.6 28.5 - - + -
236D ILE* 4.2 16.8 - - + -
246D VAL* 4.5 4.5 - - + -
248D GLN* 1.3 74.4 - - - +
250D GLY* 1.3 68.6 + - - +
251D HIS* 3.4 3.1 - - - -
252D ILE* 3.3 19.8 + - + +
253D LEU* 3.1 37.4 + - + +
325D ILE* 4.3 16.2 - - + -
335D ASP* 2.8 12.9 + - - +
339D LEU* 4.1 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248D GLN 3.8 0.2 - - - -
249D ILE* 1.3 80.8 - - - +
251D HIS* 1.3 56.5 + - - +
253D LEU* 3.3 3.0 + - - +
254D VAL* 2.9 34.1 + - - +
335D ASP* 2.8 19.2 + - - -
338D LEU* 3.7 20.1 - - - +
339D LEU* 4.2 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ALA* 5.3 4.5 - - + +
248D GLN* 3.5 47.6 + - + +
250D GLY* 1.3 77.5 + - - +
252D ILE* 1.3 90.7 + - + +
254D VAL* 3.6 6.9 + - - +
255D SER* 3.3 26.2 + - - -
338D LEU* 3.9 20.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D LEU* 3.8 26.0 - - + -
235D ARG* 3.7 39.4 - - + +
236D ILE* 4.3 7.6 - - + +
239D ALA* 3.6 30.7 - - + -
246D VAL* 5.8 0.2 - - + -
248D GLN 4.3 5.2 - - - +
249D ILE* 3.3 15.9 + - + +
250D GLY 3.2 0.4 - - - -
251D HIS* 1.3 101.9 - - + +
253D LEU* 1.3 59.0 + - - +
255D SER* 3.3 5.7 + - - -
256D TRP* 2.9 28.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182D MET* 3.8 29.6 - - + -
232D LEU* 4.3 16.8 - - + -
249D ILE* 3.1 33.2 + - + +
250D GLY 3.8 3.6 - - - +
252D ILE* 1.3 76.6 - - + +
254D VAL* 1.3 60.9 + - - +
256D TRP* 4.4 13.9 - - + +
257D LEU* 2.9 50.7 + - + +
318D TYR* 6.0 0.2 - - + -
322D LEU* 3.9 20.0 - - + -
325D ILE* 4.8 2.0 - - + -
339D LEU* 3.8 24.7 - - + -
342D ALA* 4.2 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250D GLY 2.9 21.9 + - - +
251D HIS* 3.8 7.4 - - - +
253D LEU* 1.3 75.1 - - - +
255D SER* 1.3 61.1 + - - +
258D PRO* 3.2 21.8 - - - +
338D LEU* 3.3 32.8 - - + +
341D ASP* 4.2 10.5 - - + -
342D ALA* 3.9 13.5 - - + +
345D ILE* 3.4 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251D HIS 3.3 15.3 + - - -
252D ILE* 3.9 4.0 - - - -
253D LEU 3.2 0.4 - - - -
254D VAL* 1.3 82.2 - - - +
256D TRP* 1.3 62.7 + - - +
258D PRO* 3.7 8.3 - - - +
259D ARG* 4.0 12.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186D GLU* 3.9 1.1 - - - -
228D LEU* 2.8 43.1 + - + +
229D HIS* 3.8 17.7 - + - -
231D ASP* 4.3 5.2 - - - -
232D LEU* 3.6 48.9 - - + +
235D ARG* 5.6 4.5 - - - +
252D ILE* 2.9 19.5 + - + +
253D LEU* 4.1 5.8 - - + +
255D SER* 1.3 78.1 - - - +
257D LEU* 1.3 83.3 + - + +
258D PRO 3.3 0.4 - - - -
259D ARG* 2.9 43.9 + - - +
260D LEU* 3.7 32.0 + - + -
318D TYR* 3.4 36.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253D LEU* 2.9 31.4 + - + +
256D TRP* 1.3 104.1 - - + +
258D PRO* 1.4 66.3 - - + +
260D LEU* 3.0 35.4 + - + +
318D TYR* 4.4 12.6 - - + -
322D LEU* 3.6 20.6 - - + -
342D ALA* 3.3 35.7 - - + +
345D ILE* 3.8 10.5 - - + -
346D ILE* 4.1 17.5 - - + -
349D VAL* 3.8 7.2 - - - +
----------------------------------------------------------
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