Contacts of the strand formed by residues 229 - 236 (chain A) in PDB entry 1UOU
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 ALA 229 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 3.6 0.6 + - - -
113A VAL* 3.3 25.3 - - + +
114A ASP 3.4 3.3 + - - -
227A LEU* 3.5 6.7 - - - +
228A SER* 1.3 84.8 + - - +
230A LEU* 1.3 62.1 + - - +
264A LEU* 4.8 0.4 - - - -
265A ARG* 3.5 9.0 - - + +
313A LEU* 4.2 7.0 - - + -
316A LEU* 3.9 21.1 - - + +
317A SER* 4.0 31.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP* 3.4 23.1 - - + +
116A HIS* 4.3 7.0 - - + +
218A ILE* 5.2 4.7 - - + -
219A LEU* 4.5 9.2 - - + -
222A LYS* 3.5 45.3 - - + -
227A LEU* 4.1 9.0 - - + -
229A ALA* 1.3 74.7 - - - +
231A VAL* 1.3 73.9 + - - +
232A VAL* 4.9 7.4 - - + -
264A LEU* 4.2 7.9 - - + -
265A ARG 3.1 9.6 + - - +
266A VAL* 3.4 32.9 - - + -
267A ALA 3.1 23.2 + - - -
313A LEU* 4.6 0.2 - - - -
316A LEU* 3.5 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A ASP 3.1 7.5 + - - +
115A LYS* 3.2 18.6 - - + +
116A HIS 3.0 23.0 + - - +
230A LEU* 1.3 80.5 - - - +
232A VAL* 1.3 69.1 - - - +
267A ALA* 3.2 14.8 - - + +
268A ALA 5.3 0.4 - - - -
269A ALA* 4.9 4.9 - - + +
309A LEU* 4.4 23.1 - - + +
312A ALA* 4.4 9.4 - - + +
313A LEU* 3.9 39.7 - - + +
316A LEU* 4.0 11.7 - - + -
476A LEU* 5.5 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A HIS* 3.1 20.0 - - + +
118A THR* 4.1 16.2 - - + -
218A ILE* 4.6 14.1 - - + -
230A LEU* 4.9 7.0 - - + -
231A VAL* 1.3 76.5 - - - +
233A ASP* 1.3 60.1 + - - +
234A VAL* 3.4 2.0 + - + +
255A LEU* 3.9 33.9 - - + -
266A VAL* 4.0 14.8 - - + -
267A ALA 2.9 15.3 + - - +
268A ALA* 3.2 14.0 - - + +
269A ALA 3.0 22.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 4.4 3.3 - - + +
116A HIS 2.8 13.3 + - - +
117A SER* 3.4 10.0 + - - +
118A THR* 2.9 27.2 + - - +
123A ASP* 3.9 3.3 - - - +
231A VAL* 4.1 2.0 + - - +
232A VAL* 1.3 68.2 - - - +
234A VAL* 1.3 61.1 + - - +
235A LYS* 3.1 31.0 + - - +
269A ALA* 3.7 7.4 - - - +
271A THR* 2.9 30.9 + - - +
305A LEU* 3.8 8.7 - - - +
309A LEU* 3.5 31.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.6 13.0 - - + +
232A VAL 4.0 8.5 - - - +
233A ASP* 1.3 73.9 + - - +
235A LYS* 1.3 64.5 + - - +
248A ALA* 3.5 33.4 - - + +
251A LEU* 4.5 8.7 - - + -
252A ALA* 4.1 17.5 - - + +
255A LEU* 3.9 26.7 - - + -
268A ALA* 4.4 1.8 - - + -
269A ALA 2.7 14.5 + - - +
270A LEU* 3.2 17.3 - - + +
271A THR 2.9 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A SER* 3.5 7.6 - - - +
118A THR* 3.5 9.5 + - - -
119A GLY 3.3 32.1 - - - +
120A GLY* 3.5 6.5 - - - -
123A ASP* 2.7 36.3 + - - -
233A ASP* 3.1 22.9 + - - +
234A VAL* 1.3 81.6 - - - +
236A PHE* 1.3 64.2 + - - +
240A ALA* 3.1 17.1 - - + +
241A VAL 4.7 0.7 + - - -
242A PHE* 4.3 6.6 + - - +
248A ALA* 4.3 2.4 - - - +
271A THR* 3.1 18.0 + - - +
273A MET* 3.0 41.2 - - + +
277A LEU* 5.2 0.2 - - - +
305A LEU* 3.8 6.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A LYS* 1.3 77.5 - - - +
237A GLY* 1.3 63.2 + - - +
240A ALA* 3.5 9.2 - - - -
242A PHE 3.6 15.9 - - - +
243A PRO 4.1 3.1 - - - +
244A ASN 4.4 2.0 - - - +
245A GLN* 3.7 44.0 - - + -
248A ALA* 3.8 20.9 - - + -
249A ARG* 6.3 0.4 - - - -
270A LEU* 4.0 18.2 - - + -
271A THR 3.2 18.1 + - - -
272A ALA* 3.3 40.7 - - + +
273A MET 2.9 24.3 + - - -
473A PHE* 4.1 15.7 - + - -
----------------------------------------------------------
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