Contacts of the helix formed by residues 236 - 248 (chain G) in PDB entry 5LS6
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 236 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G THR* 5.6 4.7 - - + +
156G LYS* 3.6 18.8 - - - +
228G SER* 4.0 3.4 - - - -
235G GLY* 1.3 76.4 + - - -
237G ALA* 1.3 66.9 + - - +
238G GLU* 3.4 15.2 + - - +
239G GLU* 3.1 36.6 + - - +
240G LEU* 3.4 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 237 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G PHE* 3.5 45.0 - - + +
225G GLU* 3.8 22.9 - - + -
228G SER* 3.5 8.4 + - - +
236G THR* 1.3 76.1 - - - +
238G GLU* 1.3 60.3 + - - +
240G LEU* 3.3 3.6 + - - -
241G LYS* 3.2 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 238 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236G THR* 3.3 9.4 + - - +
237G ALA* 1.3 76.0 - - - +
239G GLU* 1.3 66.6 + - + +
241G LYS* 3.7 19.9 + - - +
242G GLU* 3.4 23.8 + - - +
245G LYS* 5.9 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G THR* 3.7 23.0 + - - +
234G LYS 4.1 8.0 - - - +
235G GLY 3.5 7.7 - - - +
236G THR* 3.1 42.6 + - - +
238G GLU* 1.3 78.5 - - + +
240G LEU* 1.3 58.8 + - - +
242G GLU* 3.6 7.1 + - - +
243G LYS* 3.1 29.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G PHE* 3.8 20.4 - - + -
224G PHE* 3.4 19.1 - - + -
227G ILE* 3.7 22.9 - - + +
228G SER* 3.7 30.5 - - - -
234G LYS* 3.4 47.6 - - + +
235G GLY 4.0 0.2 - - - +
236G THR 3.4 1.5 + - - +
237G ALA 3.3 7.0 + - - +
238G GLU 3.3 0.2 - - - -
239G GLU* 1.3 75.1 - - - +
241G LYS* 1.3 60.3 + - - +
242G GLU 3.2 1.3 - - - -
243G LYS* 3.5 24.8 - - + +
244G TYR* 2.9 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G ARG* 4.2 21.7 - - - +
220G SER 4.8 0.2 - - - +
221G ASP* 3.7 27.1 + - + +
224G PHE* 3.5 39.1 - - + -
237G ALA 3.2 13.8 + - - +
238G GLU* 4.1 20.3 + - - +
239G GLU 3.5 0.2 - - - -
240G LEU* 1.3 75.3 - - - +
242G GLU* 1.3 57.6 + - - +
244G TYR* 3.4 4.7 + - - +
245G LYS* 3.1 57.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 242 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G GLU* 3.4 15.4 + - - +
239G GLU* 3.7 9.4 - - - +
240G LEU 3.2 0.6 - - - -
241G LYS* 1.3 77.0 - - - +
243G LYS* 1.3 62.7 + - - +
245G LYS* 3.3 34.6 + - + +
246G GLU* 3.3 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ASP* 4.4 20.1 + - - -
171G PHE* 4.3 16.6 - - + -
234G LYS* 5.2 14.4 - - + +
239G GLU* 3.1 16.9 + - + +
240G LEU* 3.3 31.8 + - + +
242G GLU* 1.3 76.0 - - - +
244G TYR* 1.3 61.0 + - - +
246G GLU* 3.7 4.5 + - - +
247G LEU* 3.5 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 244 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171G PHE* 4.1 11.6 - + + -
172G VAL* 4.4 15.9 - - + -
175G VAL* 4.0 26.5 - - + +
176G ASN* 5.8 3.2 - - + +
216G ARG* 4.1 44.8 - - + +
224G PHE* 3.7 28.5 - + + -
240G LEU 2.9 16.7 + - - +
241G LYS 3.5 6.3 - - - +
242G GLU 3.3 0.2 - - - -
243G LYS* 1.3 77.1 - - - +
245G LYS* 1.3 54.4 + - - +
247G LEU* 4.4 1.7 - - - +
248G THR* 2.6 62.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 245 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216G ARG* 3.8 39.2 - - - +
238G GLU* 5.9 1.8 + - - -
241G LYS* 3.1 42.1 + - - +
242G GLU* 3.3 31.8 + - - +
244G TYR* 1.3 78.3 - - + +
246G GLU* 1.3 57.2 + - + +
248G THR* 2.8 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242G GLU* 3.3 33.4 + - - +
243G LYS* 3.7 5.1 + - - +
244G TYR 3.5 0.2 - - - -
245G LYS* 1.3 74.8 - - - +
247G LEU* 1.3 65.7 + - - +
248G THR 3.6 4.9 + - - +
249G GLN* 3.8 14.6 + - - +
604I SER* 6.0 7.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 247 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168G ASP* 3.5 42.2 - - + +
171G PHE* 4.4 12.6 - - + -
172G VAL* 3.2 33.4 - - + -
243G LYS 3.5 14.1 + - - +
244G TYR* 4.4 3.4 - - - +
245G LYS 3.5 0.4 - - - -
246G GLU* 1.3 80.7 - - - +
248G THR* 1.3 60.5 + - - +
249G GLN* 3.5 13.0 + - - +
348H SER* 5.5 4.7 - - - -
349H ASN* 5.1 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172G VAL* 3.9 20.6 - - + -
244G TYR* 2.6 52.7 + - + +
245G LYS* 2.8 28.1 + - - +
246G GLU 3.6 1.4 - - - +
247G LEU* 1.3 77.2 - - - +
249G GLN* 1.3 59.4 + - - +
----------------------------------------------------------
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