Contacts of the strand formed by residues 225 - 234 (chain B) in PDB entry 5IZL
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 LEU 225 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PRO* 4.4 1.1 - - + +
224B PHE* 1.3 77.7 - - - +
226B MET* 1.3 63.9 + - - +
245B ILE* 3.4 6.2 - - - +
246B LEU* 3.0 45.8 + - + -
247B SER* 2.9 27.6 + - - +
302B LEU* 3.4 29.4 - - + -
303B VAL 3.4 11.0 - - - +
304B CYS* 3.9 4.9 - - + -
309B LEU* 3.6 26.0 - - + -
423B PRO* 4.4 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 226 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PHE* 3.5 20.4 - - + -
225B LEU* 1.3 78.4 - - - +
227B SER* 1.3 66.5 + - - +
228B VAL* 3.6 23.6 + - + -
241B MET* 3.7 21.5 - - + +
243B GLY* 3.3 35.4 - - - +
244B THR 3.5 10.8 - - - +
245B ILE* 4.4 5.6 - - - -
246B LEU* 4.3 1.1 - - - +
286B LEU* 4.5 8.1 - - + -
288B ILE* 3.9 26.9 - - + -
302B LEU* 3.6 10.8 - - - +
303B VAL* 2.8 38.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 227 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ILE* 4.1 13.3 - - - +
226B MET* 1.3 72.9 - - - +
228B VAL* 1.3 64.1 + - - +
229B ASP* 3.8 1.1 + - - +
243B GLY* 3.0 5.9 - - - -
244B THR* 2.8 39.8 + - - -
246B LEU* 4.0 14.4 - - - +
301B GLY 3.8 3.8 - - - -
302B LEU* 4.5 1.3 - - - -
341B HIS* 2.8 39.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 228 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B MET* 3.6 31.0 - - + +
227B SER* 1.3 76.1 + - - +
229B ASP* 1.3 59.5 + - - +
230B HIS 3.7 24.5 - - - +
231B CYS* 4.6 7.9 - - + -
241B MET* 4.1 16.2 - - + -
242B THR 3.7 3.8 - - - +
298B LEU* 5.1 8.5 - - + -
299B GLU 4.8 0.7 - - - +
300B ARG* 3.3 26.8 - - - +
301B GLY 2.9 24.3 + - - +
303B VAL* 4.2 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 229 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 5.3 7.2 - - - +
51B LEU* 5.9 2.5 - - + -
53B PHE* 3.0 34.7 - - + -
227B SER* 3.8 2.5 + - - +
228B VAL* 1.3 73.1 - - - +
230B HIS* 1.3 90.9 + - + +
242B THR* 2.5 42.6 + - - +
243B GLY* 4.4 4.0 - - - -
285B ARG* 2.7 27.3 + - - -
299B GLU 3.8 10.8 - - - +
300B ARG* 5.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ASP* 5.7 2.5 + - - -
51B LEU 4.9 5.9 + - - -
53B PHE* 4.3 14.4 - + + -
228B VAL* 3.6 5.5 - - - +
229B ASP* 1.3 121.2 + - + +
231B CYS* 1.3 63.4 + - - +
232B PHE* 4.4 17.7 - + + -
240B VAL 3.7 0.6 - - - +
241B MET* 3.3 4.7 - - - -
242B THR* 3.0 38.2 + - - +
285B ARG* 4.4 4.2 + - - -
299B GLU 4.4 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B VAL* 4.6 5.4 - - + -
230B HIS* 1.3 75.8 - - - +
232B PHE* 1.3 64.0 + - - +
239B THR* 3.6 9.0 - - - -
240B VAL 3.2 3.6 - - - -
241B MET* 3.8 14.4 - - + -
293B PHE* 3.1 43.1 - - - -
295B PRO* 3.5 16.8 - - + +
298B LEU* 3.4 26.6 - - - +
299B GLU* 4.6 5.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230B HIS* 4.4 18.8 - + + -
231B CYS* 1.3 81.2 - - - +
233B SER* 1.3 65.7 + - - +
234B ILE* 4.7 9.0 - - + -
239B THR* 3.3 6.9 - - - +
240B VAL* 2.6 70.3 + - + -
242B THR* 4.6 11.0 - - + -
295B PRO* 4.1 7.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B PHE* 1.3 80.9 - - - +
234B ILE* 1.3 64.8 + - - +
235B LYS 4.3 0.7 + - - -
238B GLY 3.1 11.2 - - - -
239B THR* 4.0 6.1 - - - +
292B GLN* 3.9 24.3 + - - -
295B PRO* 3.8 17.2 - - - +
----------------------------------------------------------
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
----------------------------------------------------------
232B PHE* 4.2 10.7 + - + -
233B SER* 1.3 77.5 - - - +
235B LYS* 1.3 75.6 + - + +
236B GLY 3.3 1.8 + - - +
237B GLN* 3.1 49.8 - - + +
238B GLY* 2.6 24.2 + - - +
240B VAL* 3.5 28.0 - - + -
292B GLN* 4.4 4.7 - - - +
----------------------------------------------------------
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