Contacts of the strand formed by residues 241 - 247 (chain B) in PDB entry 1DY7
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 GLU 241 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 5.6 8.2 + - + +
71B VAL* 6.1 0.9 - - + -
216B ARG* 3.2 23.5 + - - +
217B ASP* 5.6 0.2 - - - -
239B GLY 3.6 0.6 - - - -
240B SER* 1.3 81.9 - - - +
242B ALA* 1.3 61.9 + - - +
243B ARG* 2.8 35.0 + - - +
262B ALA* 3.5 2.3 - - - +
263B TYR* 2.8 44.6 + - + -
264B TRP* 3.2 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 242 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B HIS* 5.0 0.2 - - - +
214B ILE* 3.7 21.5 - - + -
215B GLY 3.6 2.7 - - - +
216B ARG* 2.9 22.2 + - - -
218B GLY* 3.8 16.6 - - - +
238B ILE* 3.9 8.1 - - + -
241B GLU* 1.3 78.2 - - - +
243B ARG* 1.3 81.1 + - - +
261B GLY 3.4 17.9 - - - +
262B ALA* 4.1 1.6 - - - +
263B TYR* 4.1 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 243 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B HIS* 3.5 38.3 - - - +
201B ILE* 3.2 19.2 - - - +
214B ILE* 4.1 6.7 - - - -
216B ARG* 3.1 33.0 + - - +
241B GLU* 2.8 36.3 + - - +
242B ALA* 1.3 93.2 + - - +
244B SER* 1.3 61.3 + - - +
261B GLY 3.7 3.0 + - - -
263B TYR* 3.5 41.6 - - + -
300B VAL 5.2 0.9 + - - +
602B DHE 2.9 59.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 244 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B ILE* 3.7 9.9 - - - +
243B ARG* 1.3 80.2 - - - +
245B ILE* 1.3 61.8 + - - +
260B ALA* 3.3 3.8 - - - -
261B GLY* 2.9 34.7 + - - -
300B VAL* 4.0 2.4 + - - +
301B ALA 2.9 27.9 + - - -
303B ILE* 3.4 22.6 - - - +
602B DHE 3.6 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201B ILE* 3.8 9.9 - - + -
203B ARG* 3.2 27.1 + - + +
212B PHE* 3.9 33.4 - - + +
213B VAL 4.4 3.4 - - - +
214B ILE* 3.7 21.5 - - + +
220B VAL* 3.5 41.1 - - + -
244B SER* 1.3 76.8 - - - +
246B GLU* 1.3 71.1 + - - +
258B ALA* 5.0 1.1 - - + -
259B ILE 3.1 16.2 - - - +
260B ALA* 4.6 0.9 - - + -
271B MET* 4.5 8.7 - - + -
303B ILE* 4.4 3.1 - - - +
602B DHE 3.7 9.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 246 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ARG* 3.6 27.2 + - - +
245B ILE* 1.3 77.1 - - - +
247B THR* 1.3 94.2 + - - +
249B LYS* 3.0 34.8 + - - +
258B ALA* 3.3 5.5 - - - +
259B ILE* 2.8 36.7 + - + +
303B ILE* 3.6 26.8 - - + +
304B LEU* 3.8 27.8 - - - +
305B ALA* 3.8 9.0 + - + +
312B PHE* 4.8 0.7 - - + -
565B ASP* 4.4 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 247 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203B ARG* 4.7 2.2 - - + -
204B LEU 2.7 33.9 + - - +
205B SER* 3.7 12.3 - - - +
212B PHE* 3.6 36.6 - - + -
246B GLU* 1.3 92.0 + - - +
248B SER* 1.3 64.6 + - - +
249B LYS* 3.4 12.0 + - - +
255B ASP* 6.5 0.4 - - - -
257B TYR 3.6 8.5 - - - +
258B ALA* 4.8 0.7 - - + -
305B ALA* 3.1 22.2 - - - +
312B PHE* 3.5 4.0 - - - -
----------------------------------------------------------
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