Contacts of the strand formed by residues 225 - 232 (chain G) in PDB entry 3IXS
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 GLU 225 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G SER* 1.3 76.1 - - - +
226G ILE* 1.3 63.3 + - - +
227G GLU* 4.3 3.1 + - + +
249G LYS* 3.9 35.7 + - + +
250G THR* 3.4 8.7 - - - +
251G SER* 3.8 19.4 + - - -
145H ARG* 3.0 23.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 226 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224G SER* 3.2 15.7 - - - +
225G GLU* 1.3 80.6 - - - +
227G GLU* 1.3 76.1 + - - +
228G LEU* 4.3 7.0 + - + +
248G ILE* 4.0 1.2 - - - +
249G LYS* 3.5 1.3 - - - -
250G THR* 2.8 38.6 + - - +
251G SER 5.1 0.7 - - - -
252G GLY* 3.0 37.0 - - - +
311G LEU* 4.9 9.0 - - + +
312G GLU* 5.1 7.4 - - + +
315G SER* 5.8 3.4 - - - -
325G MET* 4.4 25.4 - - + +
145H ARG* 3.3 28.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 227 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225G GLU* 5.4 2.9 - - + +
226G ILE* 1.3 83.8 - - - +
228G LEU* 1.3 64.8 + - - +
248G ILE 3.1 7.9 - - - +
249G LYS* 3.4 25.7 - - + +
324G PRO* 3.7 8.1 - - + +
325G MET 3.5 13.5 + - - -
145H ARG* 5.7 0.6 - - - +
146H PRO 4.0 14.4 + - - +
147H ARG* 3.2 19.5 + - + -
148H LEU* 2.6 47.0 + - + +
153H ARG* 2.8 36.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 228 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226G ILE* 4.9 3.8 - - + +
227G GLU* 1.3 76.5 - - - +
229G VAL* 1.3 78.4 + - - +
230G PHE* 4.0 20.2 - - + +
247G TYR* 3.7 2.6 - - - -
248G ILE* 2.9 54.8 + - + +
250G THR* 5.6 0.2 - - + -
259G LEU* 3.9 4.9 - - + -
311G LEU* 3.8 26.5 - - + -
324G PRO* 4.4 2.0 - - - -
325G MET* 3.1 31.2 - - + +
327G LEU* 3.8 25.4 - - + -
148H LEU* 3.9 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 229 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 1.3 75.8 - - - +
230G PHE* 1.3 61.2 + - - +
231G ARG* 3.8 31.0 - - + +
245G THR* 3.8 10.1 - - + -
246G ARG 3.6 2.0 - - - -
247G TYR* 3.6 25.6 - - + -
324G PRO* 4.4 8.3 - - + -
325G MET 2.7 13.7 + - - +
326G GLU* 3.4 16.5 - - + +
327G LEU 2.9 27.5 + - - +
148H LEU* 3.5 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 230 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228G LEU* 4.0 14.6 - - + +
229G VAL* 1.3 72.4 - - - +
231G ARG* 1.3 60.2 + - - +
244G GLN 3.9 2.3 - - - +
245G THR* 3.3 5.1 - - - +
246G ARG* 2.8 50.5 + - + +
248G ILE* 4.4 11.2 - - + -
259G LEU* 3.7 33.2 - - + -
262G TYR* 4.5 3.4 - + - -
263G LEU* 3.4 38.1 - - + -
293G ILE* 3.5 27.4 - - + -
327G LEU* 3.4 23.6 - - + -
328G TYR 3.9 7.2 - - - -
329G TYR* 3.8 24.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 231 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229G VAL* 3.8 32.8 - - + +
230G PHE* 1.3 76.7 - - - +
232G PRO* 1.3 70.4 - - + +
245G THR* 4.0 17.5 + - + +
247G TYR* 5.0 3.2 + - - -
326G GLU* 4.0 31.2 + - + +
327G LEU 2.8 11.2 + - - +
328G TYR* 3.0 39.5 + - + -
329G TYR* 3.0 28.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 232 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G ARG* 1.3 91.7 - - + +
233G HIS* 1.3 69.3 + - - +
234G PRO* 3.2 4.2 - - - +
237G MET* 3.9 17.9 - - + -
243G ALA* 3.5 33.9 - - + +
244G GLN 3.8 5.4 - - - +
245G THR* 3.8 14.1 - - - +
328G TYR* 3.6 8.6 - - - -
329G TYR* 3.6 21.2 - - + +
----------------------------------------------------------
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