Contacts of the strand formed by residues 229 - 233 (chain B) in PDB entry 3P3B
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 229 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B VAL* 4.3 9.9 - - + -
204B ILE* 3.2 22.4 - - + +
206B ILE* 4.4 17.3 - - + -
221B LEU* 4.0 25.4 - - + -
224B LEU* 3.8 34.3 - - + +
227B VAL* 2.8 31.5 + - + +
228B ASN* 1.3 71.5 - - - +
230B TYR* 1.3 62.1 + - - +
231B TRP 3.7 1.3 - - - +
255B GLN* 4.3 7.6 - - - +
256B ASN 3.4 19.9 - - - +
257B VAL* 3.6 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 230 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B LYS* 3.9 43.0 - - + -
204B ILE 2.7 15.1 + - - +
205B MET* 4.2 7.0 - - + -
228B ASN* 3.2 3.5 + - - +
229B LEU* 1.3 73.7 - - - +
231B TRP* 1.3 83.2 + + - +
256B ASN 4.6 0.9 - - - +
257B VAL* 3.9 1.5 - - - -
258B LEU* 3.1 39.8 + - + +
307B ARG* 3.8 9.6 + - - -
333B GLU* 2.4 35.0 + - - -
334B PHE* 3.2 26.8 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 231 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B TYR* 3.9 30.7 - + - -
168B LYS* 4.1 0.6 - - + +
204B ILE 4.3 0.7 - - - +
205B MET* 3.4 26.4 - - + +
206B ILE* 3.2 22.7 + - - +
229B LEU* 5.1 1.6 - - - +
230B TYR* 1.3 102.3 - + - +
232B LEU* 1.3 61.8 + - - +
233B GLU* 3.2 29.0 + - + +
257B VAL* 3.7 7.0 - - - -
258B LEU* 3.2 22.2 - - + +
260B ALA* 3.8 15.3 - - + -
281B VAL* 4.1 16.2 - - + -
283B GLN* 3.3 20.0 - - - -
309B ALA* 3.7 28.3 - - + -
333B GLU* 4.1 3.6 - - + -
334B PHE* 3.7 23.8 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 232 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171B VAL* 5.8 0.4 - - + -
206B ILE* 3.7 30.7 - - + +
208B ALA* 5.6 2.2 - - + -
212B TYR* 5.4 6.7 - - + -
217B THR* 3.4 31.9 - - + -
221B LEU* 4.1 12.6 - - + -
231B TRP* 1.3 74.1 - - - +
233B GLU* 1.3 59.8 + - - +
234B GLU 4.2 0.2 + - - -
235B ALA* 3.8 25.1 - - + +
243B TYR* 5.4 2.5 + - + -
246B LEU* 3.8 17.3 - - + -
257B VAL* 3.6 11.4 - - + +
258B LEU 2.8 13.1 + - - +
259B ILE* 3.7 12.2 - - + +
260B ALA 2.8 31.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B LYS* 2.8 23.4 + - - +
206B ILE 2.8 18.3 + - - +
207B ASP* 3.3 14.0 - - + +
208B ALA 3.1 18.4 + - - -
231B TRP* 3.2 18.0 + - + +
232B LEU* 1.3 74.3 - - - +
234B GLU* 1.3 77.1 + - + +
235B ALA* 3.1 3.0 + - - -
260B ALA 3.3 4.7 - - - +
263B GLU* 3.0 8.1 - - - +
283B GLN* 3.0 36.0 + - - +
311B HIS* 5.1 0.7 - - - +
336B GLU* 5.4 0.2 - - - +
393B MG 2.2 28.3 - - - -
395B TAR 3.0 5.7 - - - +
----------------------------------------------------------
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