Contacts of the helix formed by residues 235 - 249 (chain X) in PDB entry 5A31
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 TRP 235 (chain X).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203X LEU* 5.1 1.1 - - + -
232X ASN 3.6 17.6 + - - -
233X LEU* 3.5 24.8 - - + +
234X ASP* 1.3 78.0 - - + +
236X LEU* 1.3 83.6 + - + +
237X SER* 3.2 3.8 - - - -
238X VAL* 3.0 22.3 + - - +
239X TRP* 3.3 31.0 + + + -
261X LEU* 4.7 5.5 - - + +
264X LYS* 6.0 4.5 - - + -
266X LEU* 5.3 9.9 - - + -
267X LEU* 4.4 23.1 - - + -
56Y LEU* 4.9 8.7 - - + -
59Y LEU* 3.2 52.3 - - + -
60Y LEU* 5.1 1.3 - - + -
63Y LEU* 3.4 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 236 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201X LEU* 5.0 8.5 - - + -
203X LEU* 4.9 8.7 - - + -
206X ILE* 5.1 7.6 - - + -
222X MET* 4.3 15.5 - - + -
226X VAL* 3.5 31.6 - - + -
229X THR* 5.3 1.6 - - - +
233X LEU* 4.1 34.1 + - + +
234X ASP 3.4 1.8 - - - -
235X TRP* 1.3 105.0 - - + +
237X SER* 1.3 60.9 + - - +
239X TRP* 3.4 10.6 + - + +
240X ILE* 3.2 35.2 + - + +
56Y LEU* 6.3 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219X VAL* 5.2 2.8 - - - +
223X THR* 5.0 16.8 - - - -
226X VAL* 4.9 10.2 - - - +
234X ASP 4.1 12.5 + - - -
236X LEU* 1.3 78.7 - - - +
238X VAL* 1.3 69.4 + - - +
240X ILE* 3.4 12.8 + - - +
241X LYS* 3.1 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 238 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234X ASP 5.7 0.4 - - - +
235X TRP* 3.0 11.9 + - - +
237X SER* 1.3 81.7 - - - +
239X TRP* 1.3 61.0 + - - +
241X LYS* 3.3 12.0 + - + +
242X ALA* 2.9 28.8 + - - +
257X THR* 3.6 22.2 - - - +
260X SER* 5.3 6.5 - - - +
261X LEU* 3.5 28.0 - - + -
264X LYS* 6.3 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 239 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203X LEU* 3.2 54.3 - - + -
206X ILE* 5.0 8.1 - - + -
207X LEU* 4.2 20.4 - - + -
210X LEU* 5.0 0.7 - - + -
235X TRP* 3.3 26.2 + + + -
236X LEU* 3.4 13.0 - - + +
238X VAL* 1.3 77.5 - - - +
240X ILE* 1.3 73.8 + - + +
242X ALA* 3.4 1.1 + - - +
243X TYR* 3.1 76.1 + + + -
261X LEU* 4.3 22.2 - - + +
267X LEU* 5.1 3.1 - - + -
270X ASN* 5.7 0.6 - - - +
272X ASP* 5.8 1.1 - - - -
273X LEU* 4.4 8.6 - - + +
55Y LEU* 4.7 6.5 - - + -
59Y LEU* 3.8 23.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206X ILE* 4.3 15.3 - - + -
210X LEU* 3.5 21.8 - - + +
219X VAL* 3.3 39.9 - - + +
222X MET* 3.4 37.5 - - + -
223X THR* 5.3 1.1 - - + +
226X VAL* 5.4 1.1 - - + -
236X LEU* 3.2 32.0 + - + +
237X SER* 3.6 10.3 - - - +
238X VAL 3.2 0.2 - - - -
239X TRP* 1.3 82.1 - - + +
241X LYS* 1.3 55.3 + - - +
243X TYR 3.3 1.2 + - - -
244X ALA* 2.8 33.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 241 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219X VAL* 5.1 13.7 - - + -
237X SER* 3.1 16.7 + - - +
238X VAL* 3.3 16.8 + - + +
240X ILE* 1.3 79.1 - - - +
242X ALA* 1.3 63.4 + - - +
244X ALA* 3.2 8.0 + - - +
245X PHE* 3.0 48.6 + - + -
257X THR* 5.1 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238X VAL 2.9 18.1 + - - +
239X TRP 3.5 5.8 - - - +
241X LYS* 1.3 78.4 - - - +
243X TYR* 1.3 59.5 + - + +
245X PHE* 3.3 3.8 + - - +
246X VAL* 2.9 31.2 + - - +
254X ALA* 4.1 2.6 - - - +
257X THR* 3.7 24.9 - - + +
258X ILE* 3.7 27.6 - - + +
261X LEU* 4.5 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 243 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X LEU* 3.6 30.1 - - + -
210X LEU* 3.4 22.2 - - + -
239X TRP* 3.1 67.0 + + + +
242X ALA* 1.3 77.5 - - + +
244X ALA* 1.3 65.9 + - - +
246X VAL* 3.0 38.2 + - + +
247X HIS* 3.1 14.8 + - + -
258X ILE* 4.8 5.4 - - + -
272X ASP* 3.5 11.9 + - - -
273X LEU* 3.6 16.2 - - + +
276X SER* 2.7 34.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210X LEU* 3.7 9.1 - - + +
215X LYS* 3.3 34.7 - - + +
219X VAL* 5.1 4.5 - - + -
240X ILE 2.8 15.1 + - - +
241X LYS* 3.2 14.1 + - - +
243X TYR* 1.3 74.9 - - - +
245X PHE* 1.3 59.3 + - + +
247X HIS* 3.1 7.6 + - - +
248X THR* 2.9 30.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241X LYS* 3.0 47.7 + - + -
242X ALA 3.6 6.3 - - - +
244X ALA* 1.3 75.1 - - + +
246X VAL* 1.3 65.6 + - - +
248X THR* 2.4 40.2 + - + +
249X GLY 3.5 2.8 + - - -
250X ASP 3.8 7.1 + - - +
253X ARG* 3.3 42.6 - - + -
254X ALA* 3.7 19.7 - - - +
257X THR* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 246 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242X ALA 2.9 22.9 + - - +
243X TYR* 3.0 35.6 + - + +
245X PHE* 1.3 77.3 - - - +
247X HIS* 1.3 73.3 + - + +
249X GLY* 3.6 11.3 + - - -
254X ALA* 3.8 11.4 - - + +
258X ILE* 5.2 5.8 - - + -
276X SER* 6.0 2.2 - - - -
280X LEU* 4.1 24.6 - - + +
283X ARG* 3.9 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 247 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207X LEU* 3.9 20.7 - - + +
210X LEU* 3.5 26.2 - - + +
211X SER* 3.4 40.2 + - - +
243X TYR* 3.1 23.9 + - - -
244X ALA 3.1 5.4 + - - +
246X VAL* 1.3 88.6 + - + +
248X THR* 1.3 63.2 + - - +
249X GLY 3.2 1.5 + - - -
283X ARG* 5.7 1.9 + - - -
405X CYS* 4.5 17.3 - - - -
406X ARG* 6.1 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 248 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244X ALA* 2.9 22.7 + - + +
245X PHE* 2.4 46.6 + - + +
247X HIS* 1.3 76.9 - - - +
249X GLY* 1.3 58.8 + - - +
250X ASP* 3.4 20.8 + - - +
405X CYS* 5.7 2.5 - - - +
436X THR* 4.4 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 249 (chain X).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245X PHE 3.5 3.0 + - - -
246X VAL 3.6 9.9 + - - -
247X HIS 3.2 4.0 - - - -
248X THR* 1.3 78.2 + - - +
250X ASP* 1.3 62.9 + - - +
251X ASN* 3.4 17.1 + - - -
405X CYS* 5.0 19.1 - - - +
407X LEU* 5.6 1.7 - - - +
436X THR 5.8 0.9 - - - -
437X LEU* 4.8 16.5 - - - +
----------------------------------------------------------
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