Contacts of the helix formed by residues 235 - 247 (chain B) in PDB entry 5T4S
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 SER 235 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY* 1.3 73.6 - - - -
236B THR* 1.3 66.4 + - - +
237B SER* 3.5 9.8 + - - -
238B SER* 3.0 29.1 + - - -
239B ILE* 2.9 21.9 + - - +
303B MET 4.1 3.1 + - - -
304B ASP* 3.4 17.5 - - - +
311B PRO* 5.1 14.6 - - - -
312B THR 4.6 6.3 + - - -
313B TRP* 5.3 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY 3.8 1.0 + - - -
235B SER* 1.3 71.2 - - - +
237B SER* 1.3 57.7 + - - +
239B ILE* 3.4 1.7 + - - +
240B GLU* 2.8 54.5 + - + +
250B LYS* 6.2 2.0 - - - +
255B TYR* 5.0 1.0 + - - +
302B ALA* 3.9 22.5 - - + +
304B ASP* 2.6 31.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B SER* 3.2 10.2 + - - -
236B THR* 1.3 74.2 - - - +
238B SER* 1.3 71.3 + - - +
240B GLU* 3.2 13.7 + - - +
241B LYS* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 238 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B LEU* 3.4 21.2 - - - +
234B GLY 4.5 0.4 - - - -
235B SER* 3.0 27.7 + - - -
237B SER* 1.3 83.5 + - - +
239B ILE* 1.3 58.0 + - - +
241B LYS* 3.4 0.9 + - - -
242B LEU* 2.9 27.5 + - - +
313B TRP* 3.6 33.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B GLY* 3.5 24.0 - - - +
235B SER 2.9 21.1 + - - +
236B THR 4.0 2.5 - - - +
238B SER* 1.3 69.6 - - - +
240B GLU* 1.3 56.1 + - - +
242B LEU* 3.5 7.5 - - + +
243B MET* 2.8 58.2 + - + +
255B TYR* 3.7 24.9 - - + -
300B ILE* 3.7 21.8 - - + -
301B HIS 3.4 16.8 - - - +
302B ALA* 3.7 18.4 - - + +
313B TRP* 4.0 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B THR* 2.8 38.6 + - + +
237B SER* 3.2 12.8 + - - +
239B ILE* 1.3 75.5 - - - +
241B LYS* 1.3 55.9 + - - +
243B MET* 3.8 1.6 - - - +
244B GLU* 2.9 36.1 + - - +
255B TYR* 3.4 22.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.4 15.9 - - + +
216B LEU* 4.0 17.0 - - + -
237B SER 3.0 15.7 + - - +
238B SER 3.9 3.4 - - - +
240B GLU* 1.3 72.1 - - - +
242B LEU* 1.3 64.1 + - - +
244B GLU* 3.8 9.8 + - - +
245B ALA* 3.3 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208B VAL* 4.7 4.9 - - + -
210B VAL* 3.6 28.3 - - + -
215B LEU* 4.2 3.1 - - - -
216B LEU* 3.8 17.2 - - + +
238B SER 2.9 17.5 + - - +
239B ILE* 3.5 15.5 - - + +
241B LYS* 1.3 74.8 - - - +
243B MET* 1.3 64.0 + - + +
245B ALA* 3.2 5.7 + - - +
246B LEU* 3.0 34.3 + - + +
268B ILE* 4.1 21.3 - - + -
270B PHE* 6.4 0.4 - - + -
300B ILE* 3.8 41.3 - - + -
313B TRP* 4.8 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE* 2.8 32.4 + - + +
240B GLU 3.9 2.5 - - - +
242B LEU* 1.3 74.3 - - + +
244B GLU* 1.3 58.8 + - - +
246B LEU* 3.3 6.9 + - - -
247B GLY 3.0 7.6 + - - -
248B ALA* 2.9 45.8 + - - +
255B TYR* 3.4 48.0 - - + -
298B LEU* 3.6 33.7 - - + -
300B ILE* 3.5 39.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B GLU* 2.9 21.1 + - - +
241B LYS* 3.9 9.8 - - - +
243B MET* 1.3 77.8 - - - +
245B ALA* 1.3 60.6 + - - +
247B GLY* 3.3 12.4 + - - -
248B ALA 4.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL* 4.3 16.9 - - + +
215B LEU* 3.7 28.5 - - + -
241B LYS 3.3 11.7 + - - +
242B LEU 3.2 9.5 + - - +
244B GLU* 1.3 79.5 - - - +
246B LEU* 1.3 63.9 + - - +
247B GLY 3.6 0.2 + - - -
266B PRO* 5.3 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210B VAL* 3.9 27.4 - - + -
242B LEU* 3.0 26.3 + - + +
243B MET* 3.8 15.3 - - + +
244B GLU 3.3 0.4 - - - -
245B ALA* 1.3 77.7 - - - +
247B GLY* 1.3 58.4 + - - +
248B ALA* 3.3 7.4 + - + +
257B VAL* 4.8 0.2 - - - +
265B LEU* 3.3 32.4 - - + +
266B PRO* 4.3 9.1 - - + +
268B ILE* 3.8 28.0 - - + -
284B TYR* 4.0 21.1 - - + +
298B LEU* 3.8 25.6 - - + -
300B ILE* 4.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B MET 3.0 5.1 + - - -
244B GLU* 3.3 11.7 + - - -
245B ALA 3.3 0.8 + - - -
246B LEU* 1.3 77.9 - - - +
248B ALA* 1.3 61.6 + - - +
249B LYS* 4.1 13.4 + - - +
256B VAL 4.7 0.9 - - - +
257B VAL* 4.8 4.9 - - - +
----------------------------------------------------------
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