Contacts of the helix formed by residues 225 - 233 (chain D) in PDB entry 1XVP
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 225 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216D ASN* 3.2 37.0 - - - +
223D ARG* 4.1 11.9 - - + +
224D TYR* 1.3 75.8 - - - +
226D ILE* 1.3 57.0 + - - +
227D GLU* 2.6 37.2 + - - +
228D ASP* 2.9 38.8 + - - +
229D GLY 3.6 0.7 + - - -
243D PHE* 4.2 1.8 - - - -
1003D CID 3.5 13.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215D GLN* 5.9 3.1 - - + +
216D ASN* 4.6 1.9 - - - +
225D THR* 1.3 74.6 - - - +
227D GLU* 1.3 87.9 + - + +
228D ASP 3.2 0.2 - - - -
229D GLY* 3.4 11.4 + - - +
230D ALA* 3.5 9.5 + - - +
239D LEU* 4.0 44.2 - - + +
240D GLU* 4.5 8.7 - - + +
243D PHE* 3.8 37.3 - - + -
1003D CID 5.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147D PRO* 5.5 11.9 - - + -
216D ASN* 4.9 1.0 + - - -
225D THR* 2.6 33.0 + - - +
226D ILE* 1.3 105.4 - - + +
228D ASP* 1.3 61.1 + - - +
230D ALA* 3.5 8.2 + - - +
231D ARG* 3.3 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 228 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D HIS* 3.2 30.1 + - - -
141D LEU* 4.3 8.3 - - + +
147D PRO* 5.9 1.6 - - - +
148D LEU* 5.3 1.4 + - - +
157D LEU* 4.3 10.6 - - + +
223D ARG 4.2 4.2 - - - +
224D TYR* 3.8 8.8 - - + -
225D THR* 2.9 37.8 + - - +
227D GLU* 1.3 78.8 - - - +
229D GLY* 1.3 63.8 + - - +
230D ALA 3.2 0.2 - - - -
231D ARG* 3.7 10.2 - - - +
232D VAL* 3.0 29.8 + - - +
1003D CID 3.4 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 229 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225D THR 3.6 2.6 + - - -
226D ILE 3.4 7.4 + - - -
227D GLU 3.3 0.4 - - - -
228D ASP* 1.3 79.8 - - - +
230D ALA* 1.3 63.7 + - - +
232D VAL* 3.5 1.0 + - - -
233D GLY 3.2 6.8 + - - -
234D PHE* 3.1 30.2 + - - -
239D LEU* 4.0 8.1 - - - -
1003D CID 3.3 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 230 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226D ILE 3.5 11.1 + - - +
227D GLU* 3.6 11.2 - - - +
228D ASP 3.2 0.2 - - - -
229D GLY* 1.3 77.3 - - - +
231D ARG* 1.3 63.5 + - + +
233D GLY* 3.4 12.0 + - - -
234D PHE 4.0 12.7 - - - +
239D LEU* 3.8 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D LEU* 3.7 28.8 + - + +
149D PRO 3.7 7.4 + - - -
150D THR* 3.1 38.1 + - - +
152D ALA 3.1 26.9 + - - -
154D VAL* 3.2 38.2 - - + +
157D LEU* 3.8 16.6 - - + -
227D GLU 3.3 15.9 + - - +
228D ASP* 3.7 12.1 - - - +
229D GLY 3.3 0.6 - - - -
230D ALA* 1.3 74.6 - - - +
232D VAL* 1.3 68.9 + - - +
233D GLY* 3.1 3.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154D VAL* 4.0 0.6 - - - +
157D LEU* 3.9 21.3 - - + -
158D VAL* 3.5 36.1 - - + +
161D PHE* 3.7 37.5 - - + -
228D ASP 3.0 17.2 + - - +
229D GLY 3.6 7.0 - - - +
231D ARG* 1.3 77.2 - - - +
233D GLY* 1.3 58.9 + - - +
234D PHE* 3.9 11.7 - - + -
333D ILE* 4.0 16.6 - - + +
336D LEU* 4.5 2.7 - - + -
1003D CID 4.4 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 233 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229D GLY 3.2 1.6 + - - -
230D ALA 3.7 8.5 - - - -
231D ARG 3.1 4.1 - - - -
232D VAL* 1.3 81.1 - - - +
234D PHE* 1.3 66.7 + - - +
235D GLN* 4.0 0.7 + - - +
332D HIS* 4.4 11.6 + - - -
333D ILE* 3.2 24.8 - - - +
----------------------------------------------------------
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