Contacts of the helix formed by residues 236 - 246 (chain D) in PDB entry 1XPM
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 PHE 236 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE* 3.6 29.8 - - + -
39D GLN* 3.2 16.6 - - + +
152D THR* 4.1 7.6 - - + -
202D LYS* 4.7 9.6 - - + -
234D VAL* 3.1 9.4 - - - +
235D PRO* 1.3 90.6 - - + +
237D THR* 1.3 64.8 + - - +
238D LYS* 3.5 20.2 - - + -
239D MET* 2.9 71.3 + - + +
240D GLY 3.6 2.6 + - - -
4402D CAA 3.4 55.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 237 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37D ILE 3.8 0.2 + - - -
38D GLY* 2.6 42.2 + - - +
39D GLN* 3.1 8.1 + - - +
234D VAL* 3.9 5.8 - - + +
236D PHE* 1.3 71.4 - - - +
238D LYS* 1.3 61.9 + - - +
239D MET 3.0 0.5 + - - -
241D LYS* 3.2 11.4 + - - +
263D TYR* 2.8 27.7 + - - -
267D VAL* 3.7 27.8 - - + +
271D ARG* 3.6 33.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 238 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35D ILE 4.8 2.0 - - - +
36D GLY 3.0 24.7 - - - +
37D ILE* 2.9 27.3 + - - +
38D GLY* 5.3 0.2 - - - -
236D PHE* 3.2 13.9 + - + -
237D THR* 1.3 72.8 + - - +
239D MET* 1.3 57.0 + - - +
241D LYS* 4.1 7.4 - - - +
242D LYS* 3.2 29.3 + - - +
4402D CAA 5.3 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 239 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LYS* 3.8 34.3 - - + +
205D TYR* 3.9 24.2 - - + -
206D ILE* 3.9 33.4 - - + -
235D PRO* 3.5 22.2 - - + -
236D PHE* 2.9 36.7 + - + +
238D LYS* 1.3 75.1 - - - +
240D GLY* 1.3 68.3 + - - +
241D LYS 3.0 2.1 + - - -
242D LYS* 3.2 7.6 + - + -
243D ALA* 3.1 13.3 + - - +
4402D CAA 4.2 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 240 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D TYR* 4.6 10.3 - - - -
232D PHE* 4.9 6.4 - - - -
233D HIS 5.0 6.3 + - - -
234D VAL* 6.0 0.6 - - - +
236D PHE 3.6 2.8 + - - -
237D THR 3.3 0.4 + - - -
239D MET* 1.3 79.6 - - - +
241D LYS* 1.3 56.3 + - - +
243D ALA* 4.0 6.5 - - - +
244D LEU* 3.0 28.4 + - - +
263D TYR* 2.9 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D THR 3.2 16.5 + - - +
238D LYS* 4.1 7.9 - - - +
239D MET 3.0 0.6 - - - -
240D GLY* 1.3 75.4 - - - +
242D LYS* 1.3 62.6 + - + +
244D LEU* 3.2 12.3 + - + +
245D GLU* 2.9 67.8 + - + +
260D ARG* 3.7 23.2 + - - +
263D TYR* 3.2 16.2 + - + -
264D GLU* 5.0 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 242 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202D LYS* 6.3 2.9 - - + -
206D ILE* 4.4 11.3 - - + +
238D LYS 3.2 17.0 - - - +
239D MET* 3.2 15.8 + - + +
241D LYS* 1.3 76.9 - - + +
243D ALA* 1.3 66.5 + - - +
245D GLU* 3.4 8.1 + - - +
246D SER* 3.2 21.3 + - - -
4402D CAA 5.1 10.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 243 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D TYR* 3.6 35.0 - - + -
206D ILE* 4.1 14.2 - - + +
209D PHE* 3.6 22.1 - - + -
232D PHE* 4.8 5.4 - - + -
239D MET 3.1 12.1 + - - +
240D GLY* 4.0 4.5 - - - +
242D LYS* 1.3 76.2 - - - +
244D LEU* 1.3 63.8 + - - +
246D SER* 2.5 27.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209D PHE* 4.9 1.6 - - - -
230D LEU* 4.2 9.9 - - + -
232D PHE* 3.9 31.1 - - + -
240D GLY 3.0 20.1 + - - +
241D LYS* 3.3 12.8 - - + +
243D ALA* 1.3 78.6 - - - +
245D GLU* 1.3 75.2 + - - +
246D SER 3.1 1.4 + - - -
247D ILE* 3.3 11.3 + - - +
248D ILE* 3.4 42.2 + - + +
259D LEU* 4.5 12.6 - - + +
260D ARG* 4.2 17.9 - - + -
263D TYR* 3.9 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241D LYS* 2.9 47.5 + - + +
242D LYS* 3.8 7.4 - - - +
243D ALA 3.4 0.2 - - - -
244D LEU* 1.3 79.0 - - - +
246D SER* 1.3 62.0 + - - +
247D ILE 3.2 1.1 + - - -
248D ILE* 3.0 23.9 + - - +
249D ASP* 4.2 10.2 + - - +
260D ARG* 2.8 44.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206D ILE* 3.8 15.6 - - - +
209D PHE* 4.3 1.0 - - - -
210D GLN* 3.4 30.7 + - - +
242D LYS 3.2 10.5 + - - -
243D ALA* 2.5 22.6 + - - -
244D LEU 3.1 0.2 - - - -
245D GLU* 1.3 77.4 - - - +
247D ILE* 1.3 65.2 + - - +
249D ASP* 5.1 3.8 - - - +
----------------------------------------------------------
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