Contacts of the helix formed by residues 225 - 236 (chain B) in PDB entry 6I53
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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B PHE* 2.8 24.5 + - + +
224B GLN* 1.3 94.5 - - + +
226B TYR* 1.3 69.3 + - - +
227B MET 3.7 0.7 - - - -
228B PRO* 3.5 4.7 - - - +
229B SER* 3.3 25.3 + - - -
264B ILE* 4.9 13.8 - - + +
268B LEU* 4.3 20.6 - - + -
281B ILE* 3.4 34.4 - - + +
284B TYR* 5.9 0.2 - - - -
285B LEU* 4.5 12.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B PRO* 3.5 25.8 - - + +
145B LEU* 4.5 5.5 - - + +
218B ILE* 5.8 3.6 - - + -
221B PHE* 3.0 40.0 + - + +
222B ILE* 3.8 21.8 - - + -
225B THR* 1.3 88.1 + - - +
227B MET* 1.3 61.0 + - - +
229B SER* 3.1 4.5 + - - -
230B ILE* 2.9 37.3 + - + +
281B ILE* 4.1 10.4 - - + +
284B TYR* 3.5 36.9 - + + -
442B TYR* 2.8 30.0 + + - -
443B TRP* 3.5 32.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE* 2.8 36.7 + - + +
223B LEU* 4.7 10.3 - - + -
226B TYR* 1.3 75.3 - - - +
228B PRO* 1.3 61.7 - - + +
230B ILE* 3.6 21.8 + - + +
231B LEU* 3.4 61.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ILE 3.7 9.9 - - - +
223B LEU 3.9 12.3 - - - +
224B GLN 3.3 21.8 - - - +
225B THR 3.5 7.2 - - - +
226B TYR 3.8 0.7 - - - -
227B MET* 1.3 89.8 - - + +
229B SER* 1.3 58.7 + - - +
231B LEU* 3.1 7.9 + - + +
232B ILE* 3.0 47.7 + - + +
264B ILE* 4.6 9.9 - - + -
277C THR* 5.2 5.8 - - + -
304C PHE* 4.9 22.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR 3.3 19.9 + - - -
226B TYR 3.1 4.9 + - - -
228B PRO* 1.3 77.9 - - - +
230B ILE* 1.3 57.2 + - - +
232B ILE 4.2 1.1 - - - +
233B THR* 2.6 30.5 + - - -
261B MET* 3.4 31.3 - - - +
264B ILE* 4.6 5.3 - - - +
284B TYR* 4.1 5.8 - - - -
285B LEU* 4.0 15.2 - - - +
288B CYS* 3.5 17.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B TYR* 2.9 28.0 + - + +
227B MET* 3.8 23.1 - - + +
228B PRO 3.2 0.4 - - - -
229B SER* 1.3 77.4 - - - +
231B LEU* 1.3 64.5 + - + +
233B THR* 3.3 5.6 + - - -
234B ILE* 3.0 49.9 + - + +
284B TYR* 3.3 21.8 - - - +
435B PHE* 4.6 15.9 - - + -
439B ASN* 5.1 7.2 - - - +
443B TRP* 5.9 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B MET* 3.4 45.7 + - + +
228B PRO* 3.1 6.7 + - + +
230B ILE* 1.3 78.1 - - + +
232B ILE* 1.3 60.5 + - + +
234B ILE* 3.4 14.9 + - + +
235B LEU* 3.0 34.2 + - + +
273C VAL* 6.5 0.4 - - + -
304C PHE* 4.5 29.4 - - + -
305C ILE* 6.2 2.9 - - + -
308C PHE* 3.9 34.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B PRO* 3.0 24.5 + - + +
229B SER* 4.7 0.2 - - - -
231B LEU* 1.3 75.9 - - + +
233B THR* 1.3 64.8 + - - +
235B LEU* 3.4 8.8 + - + +
236B SER 3.2 15.6 + - - -
257B THR* 3.4 26.5 - - + +
260B THR* 3.7 28.0 - - + +
261B MET* 4.4 14.4 - - + -
264B ILE* 3.9 18.2 - - + -
273C VAL* 4.3 19.7 - - + -
277C THR* 3.4 24.2 - - - +
304C PHE* 6.1 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B SER* 2.6 24.9 + - - -
230B ILE 3.3 5.5 + - - -
232B ILE* 1.3 77.3 - - - +
234B ILE* 1.3 61.2 + - - +
236B SER* 2.4 32.0 + - - +
237B TRP* 3.6 18.0 - - + -
261B MET* 4.5 2.9 - - - -
288B CYS* 3.8 17.0 + - - +
291B PHE* 4.0 27.1 - - + -
292B VAL* 4.1 11.7 - - + +
435B PHE* 4.1 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B ILE* 3.0 37.4 + - + +
231B LEU* 3.7 15.7 - - + +
232B ILE 3.3 0.2 - - - -
233B THR* 1.3 75.4 - - - +
235B LEU* 1.3 57.3 + - + +
237B TRP* 3.0 56.0 + - + +
238B VAL* 3.9 5.6 + - + +
435B PHE* 5.3 3.4 - - + -
308C PHE* 4.1 21.1 - - + -
312C VAL* 6.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.0 21.1 + - + +
232B ILE* 3.4 7.8 + - + +
233B THR 3.3 0.4 - - - -
234B ILE* 1.3 74.7 - - + +
236B SER* 1.3 61.0 + - - +
237B TRP 3.2 0.4 - - - -
238B VAL* 3.4 18.4 - - + +
253B LEU* 3.4 24.5 - - + +
257B THR* 4.9 4.0 - - + +
270C ILE* 6.2 4.0 - - + -
273C VAL* 3.7 42.4 - - + -
308C PHE* 3.6 37.2 - - + +
311C LEU* 3.8 25.8 - - + -
312C VAL* 4.2 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 236 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ILE 3.2 4.4 + - - -
233B THR* 2.4 29.2 + - - +
235B LEU* 1.3 76.1 - - - +
237B TRP* 1.3 64.0 + - - +
238B VAL 3.3 2.0 - - - -
239B SER* 3.2 22.7 + - - -
240B PHE* 4.2 0.2 - - - -
253B LEU* 5.2 5.9 - - - +
254B GLY* 5.7 4.1 + - - -
257B THR* 3.8 30.0 - - - +
292B VAL* 4.1 13.3 - - - +
295B ALA* 3.9 20.9 - - - +
----------------------------------------------------------
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