Contacts of the strand formed by residues 243 - 250 (chain D) in PDB entry 1INL
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 MET 243 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A MET* 5.2 0.4 - - - -
235A PHE* 3.6 46.7 - - + -
237A THR* 4.2 17.0 - - + -
207D ASP* 3.1 27.5 - - - +
208D PRO* 3.5 16.4 - - + +
209D PHE* 6.0 0.7 - - + -
233D LEU* 3.7 32.8 - - + -
241D SER* 3.1 9.8 - - - +
242D GLY* 1.3 76.2 - - - +
244D TRP* 1.3 60.5 + - - +
286D PRO* 4.2 3.8 - - + -
288D PHE* 3.7 35.4 - - + -
289D VAL* 3.8 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76D TYR* 3.7 30.2 - + - -
204D GLU* 3.2 18.0 + - - -
206D GLU* 3.5 37.0 - - - -
207D ASP* 3.3 38.8 - - + -
233D LEU* 3.4 7.8 - - - +
234D GLY 2.9 41.4 + - - +
236D MET* 4.0 12.3 - - + -
239D TYR* 3.6 40.8 - + + -
240D PRO* 3.7 21.5 - - + -
242D GLY 3.8 0.4 + - - -
243D MET* 1.3 75.7 - - - +
245D SER* 1.3 75.8 + - - +
246D TYR* 3.8 15.2 - + - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205D THR* 2.8 38.9 + - - -
206D GLU 2.6 27.0 + - - -
208D PRO* 4.1 3.8 - - - -
215D PHE* 3.2 23.7 - - - -
231D VAL* 4.2 1.6 - - - -
232D TYR 3.5 5.2 - - - -
233D LEU* 3.7 15.3 - - - -
243D MET 4.2 0.2 + - - -
244D TRP* 1.3 83.1 - - - +
246D TYR* 1.3 68.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75D MET 4.0 1.6 + - - -
76D TYR* 3.5 51.4 - + - +
79D MET* 3.8 17.3 - - + +
80D LEU* 4.0 33.0 - - + -
203D ALA 3.3 9.6 - - - +
204D GLU* 4.3 3.6 - - - -
205D THR* 3.6 0.9 - - - -
231D VAL* 3.4 5.0 - - - +
232D TYR* 2.8 74.0 + + + +
234D GLY* 3.9 13.6 - - - -
235D PHE 4.8 3.6 + - - -
236D MET* 4.7 2.4 - - - +
244D TRP* 3.8 30.5 - + - +
245D SER* 1.3 78.4 - - - +
247D THR* 1.3 63.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201D PHE* 4.1 3.6 - - - -
202D SER* 3.2 4.0 - - - -
203D ALA 2.8 32.7 + - - -
205D THR* 3.1 30.7 + - - +
219D TYR* 4.7 9.1 - - + +
222D ILE* 3.8 22.6 - - + +
229D THR* 3.5 32.1 - - + -
230D ARG 3.7 6.3 - - - +
231D VAL* 3.8 12.0 - - - +
232D TYR* 4.2 2.2 - - - -
246D TYR* 1.3 74.7 + - - +
248D PHE* 1.3 64.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83D VAL* 4.3 4.5 - - + -
84D PRO* 4.0 17.7 - - + -
87D LEU* 3.5 31.2 - - + -
200D VAL* 3.9 26.7 - - + -
201D PHE 3.4 12.1 - - - -
202D SER* 4.4 0.9 - - - +
228D ILE* 4.5 3.6 - - + -
229D THR* 3.3 3.5 - - - -
230D ARG* 2.8 38.8 + - + +
232D TYR* 3.8 18.2 - - + -
247D THR* 1.3 75.8 - - - +
249D ALA* 1.3 67.1 + - - +
250D SER* 3.9 17.7 - - - -
253D ILE* 3.5 18.6 - - + -
255D PRO* 3.2 32.3 - - + -
283D PHE* 4.3 5.6 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200D VAL* 3.7 0.5 - - - -
201D PHE* 2.8 52.2 + - + +
222D ILE* 3.9 10.1 - - + -
226D PHE* 3.5 27.1 - - + -
228D ILE 3.0 11.7 - - - +
229D THR* 4.2 0.4 - - - +
248D PHE* 1.3 83.8 - - - +
250D SER* 1.3 64.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199D GLY 3.9 15.5 - - - -
200D VAL* 4.3 2.0 - - - +
226D PHE* 3.6 8.9 - - - -
227D PRO* 3.3 22.3 - - - +
228D ILE* 3.0 19.0 + - - +
248D PHE* 3.9 9.9 - - - -
249D ALA* 1.3 76.7 - - - +
251D LYS* 1.3 63.0 + - - +
252D GLY 3.3 2.2 + - - -
253D ILE* 2.6 46.1 + - - -
----------------------------------------------------------
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