Contacts of the helix formed by residues 226 - 234 (chain C) in PDB entry 3JXI
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 226 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE 4.5 8.7 - - - -
214C ASN* 3.7 29.1 + - + +
215C SER 4.4 4.0 - - - +
216C PRO* 4.5 3.4 - - + -
217C PHE* 4.1 8.7 - - - -
224C GLY 3.7 9.4 - - - +
225C GLN* 1.3 82.2 - - - +
227C ALA* 1.3 66.1 + - - +
228C LEU* 3.5 17.9 + - - +
229C HIS* 2.9 29.6 + - - +
230C ILE* 3.3 11.8 + - - +
249C ASP 5.1 0.5 + - - -
252C ALA* 3.7 20.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 227 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C LEU* 3.5 39.3 - - + -
182C PRO* 4.6 8.6 - - + +
185C LEU* 3.8 12.2 - - + +
213C ILE* 3.7 13.0 + - + +
215C SER 5.0 1.2 + - - -
217C PHE* 4.5 3.4 - - - -
226C THR* 1.3 72.0 - - - +
228C LEU* 1.3 56.1 + - - +
230C ILE* 3.2 13.4 + - - +
231C ALA* 2.9 29.1 + - - +
243C LEU* 3.8 9.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213C ILE* 5.1 1.2 + - - +
214C ASN* 6.0 0.4 - - - +
226C THR* 3.1 12.1 + - - +
227C ALA* 1.3 78.2 - - - +
229C HIS* 1.3 62.4 + - - +
231C ALA* 3.4 1.4 + - - +
232C ILE* 3.1 34.8 + - + +
240C VAL* 4.2 28.3 - - + +
243C LEU* 4.0 9.5 - - + +
244C VAL* 4.2 18.6 - - + -
248C ALA* 4.3 21.3 - - + +
249C ASP 3.5 25.1 - - - +
250C VAL* 3.9 15.3 - - + -
274C PRO* 3.7 21.5 - - + -
290C LEU* 5.0 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 229 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224C GLY 4.0 4.3 - - - -
225C GLN* 3.7 8.4 - - + +
226C THR* 2.9 38.3 + - - +
228C LEU* 1.3 77.0 - - - +
230C ILE* 1.3 59.1 + - + +
232C ILE* 3.4 1.1 + - - -
233C GLU* 3.0 26.3 + - - +
252C ALA* 3.0 39.1 + - + -
254C ALA* 3.8 18.4 + - + -
270C PHE* 4.3 8.7 - + + -
272C GLU 3.0 17.8 + - - -
274C PRO* 3.7 18.3 - - + +
277C LEU* 3.3 28.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 230 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C PRO* 3.4 44.6 - - + +
185C LEU* 3.7 25.6 - - + +
186C LEU* 3.8 32.1 - - + -
217C PHE* 3.6 22.9 - - + -
225C GLN* 5.9 0.4 - - - +
226C THR 3.8 9.6 - - - +
227C ALA* 3.2 6.8 + - - +
229C HIS* 1.3 75.8 - - + +
231C ALA* 1.3 60.1 + - - +
233C GLU* 3.2 5.7 + - - +
234C ARG* 2.9 34.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 231 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU* 4.4 10.0 - - + +
188C LEU* 6.1 0.2 - - - -
227C ALA 2.9 16.2 + - - +
228C LEU 3.4 5.6 + - - +
230C ILE* 1.3 76.1 - - - +
232C ILE* 1.3 58.2 + - - +
234C ARG* 4.0 3.5 + - - -
235C ARG 3.6 0.9 + - - -
236C CYS* 2.9 35.4 + - - +
239C TYR* 4.2 9.2 - - + -
240C VAL* 3.7 25.2 - - + +
243C LEU* 3.8 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 232 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228C LEU* 3.1 25.5 + - + +
229C HIS 3.7 1.1 - - - +
231C ALA* 1.3 75.7 - - - +
233C GLU* 1.3 61.3 + - - +
235C ARG* 2.8 17.5 + - - -
240C VAL* 3.8 17.7 - - + -
274C PRO* 3.4 43.3 - - + +
277C LEU* 3.5 30.7 - - + -
278C ALA* 3.8 13.9 - - + +
283C GLN* 2.9 33.2 + - - +
286C ILE* 4.4 10.3 - - + -
290C LEU* 4.3 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C LEU* 5.3 2.3 - - - +
229C HIS 3.0 17.8 + - - +
230C ILE* 4.0 5.4 - - - +
232C ILE* 1.3 78.5 - - - +
234C ARG* 1.3 85.0 + - - +
235C ARG* 3.2 15.9 + - - +
268C PHE* 6.4 1.6 - - + -
277C LEU* 4.6 16.6 - - + -
281C THR* 5.5 7.5 - - + +
283C GLN* 4.8 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 234 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C LEU 3.6 15.1 + - - +
186C LEU* 2.8 54.6 + - - +
187C ASN* 4.0 2.0 - - - +
188C LEU* 4.0 35.0 + - + +
230C ILE* 2.9 24.2 + - + +
231C ALA* 4.4 4.0 - - - +
233C GLU* 1.3 91.1 + - - +
235C ARG* 1.3 71.5 + - - +
236C CYS* 3.3 4.5 + - - +
----------------------------------------------------------
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