Contacts of the strand formed by residues 186 - 193 (chain D) in PDB entry 2IBT
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 LYS 186 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185D GLY* 1.3 73.0 - - - -
187D THR* 1.3 63.1 + - - +
207D ARG* 3.9 7.4 + - - +
208D PHE* 3.4 4.1 - - - -
209D GLN* 2.9 59.8 + - + +
211D SER* 3.0 42.5 + - - +
212D GLY* 4.0 9.1 - - - +
213D LYS 3.7 20.4 - - - +
214D GLY 3.6 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 187 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D TRP* 4.4 4.7 - - + -
181D LEU* 3.8 9.5 + - + +
185D GLY 4.7 0.2 + - - -
186D LYS* 1.3 75.7 - - - +
188D SER* 1.3 65.0 + - - +
189D VAL* 4.0 14.4 - - + -
206D ILE* 4.0 22.7 - - + -
207D ARG 3.7 2.2 - - - -
208D PHE* 3.5 16.1 - - + +
214D GLY 2.9 8.8 + - - +
215D LEU* 3.3 19.0 - - + +
216D SER* 2.9 24.3 + - - -
238D TRP* 3.7 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 188 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187D THR* 1.3 73.9 + - - +
189D VAL* 1.3 64.7 + - - +
190D TYR* 3.7 28.0 + - - -
205D VAL 3.7 0.5 - - - +
206D ILE* 3.4 5.2 - - - +
207D ARG* 2.8 51.9 + - - -
216D SER* 3.3 18.2 + - - -
218D TRP* 3.7 10.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 189 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168D TRP* 3.7 29.8 - - + -
169D LEU* 4.2 11.4 - - + -
187D THR* 4.0 3.4 - - + -
188D SER* 1.3 75.7 - - - +
190D TYR* 1.3 61.6 + - - +
191D TYR* 4.8 0.4 - - + +
204D VAL* 3.8 35.0 - - + -
205D VAL 3.4 3.1 - - - +
206D ILE* 5.1 0.9 - - + -
215D LEU* 3.9 19.3 - - + -
216D SER 2.9 7.6 + - - +
217D LEU* 3.6 20.0 - - + +
218D TRP* 2.8 34.3 + - - +
243D ILE* 4.1 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 190 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30D PHE* 3.8 31.6 - + + -
34D LEU* 3.5 41.1 - - + +
188D SER* 3.7 29.0 + - - -
189D VAL* 1.3 73.6 - - - +
191D TYR* 1.3 64.1 + - - +
192D LEU* 3.4 2.4 + - - +
204D VAL* 3.2 5.4 - - - -
205D VAL* 2.8 50.5 + - + +
207D ARG* 3.9 17.3 - - + -
218D TRP* 3.4 49.6 + + + -
220D THR* 4.1 4.9 - - + -
229D PRO* 3.8 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 191 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D LEU* 6.4 0.4 - - + -
189D VAL* 4.1 1.6 - - + +
190D TYR* 1.3 71.4 - - - +
192D LEU* 1.3 58.0 + - - +
193D GLY* 3.4 20.7 - - - -
202D SER* 3.6 10.8 - - - -
203D ALA 4.3 3.8 - - - -
204D VAL* 4.1 12.5 - - + +
217D LEU* 5.7 0.9 - - + -
218D TRP 2.9 10.1 + - - +
219D ASP* 3.8 5.2 - - - +
220D THR* 2.6 32.8 + - - +
245D PHE* 3.6 22.7 - + + -
389D ARG* 3.0 37.9 - - - +
390D ASP* 2.6 37.8 + - - -
391D PHE* 3.8 28.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 192 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27D VAL* 4.2 20.9 - - + -
30D PHE* 4.0 24.9 - - + -
163D VAL* 4.3 8.5 - - + -
190D TYR 3.4 7.4 + - - +
191D TYR* 1.3 81.9 - - - +
193D GLY* 1.3 62.0 + - - +
194D GLU 4.1 0.3 + - - -
195D VAL* 3.7 36.7 - - + +
203D ALA* 3.0 12.3 + - + +
205D VAL* 3.7 24.5 - - + +
220D THR* 3.8 21.3 + - + +
227D PHE* 4.0 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 193 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191D TYR* 3.4 27.9 - - - -
192D LEU* 1.3 78.5 - - - +
194D GLU* 1.3 60.2 + - - -
195D VAL* 2.9 9.9 + - - +
201D VAL 3.9 0.2 - - - +
202D SER* 3.5 12.1 - - - -
203D ALA* 2.8 31.8 + - - +
----------------------------------------------------------
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