Contacts of the strand formed by residues 258 - 266 (chain B) in PDB entry 5DK3
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 258 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B PRO 3.9 2.4 - - - +
245B PRO* 3.3 23.8 - - - +
246B LYS 4.8 0.5 + - - +
256B THR* 3.4 30.4 + - - +
257B PRO* 1.3 80.5 - - - +
259B VAL* 1.3 66.4 + - - +
260B THR* 3.9 7.6 + - - +
305B VAL* 3.4 36.3 - - + +
306B LEU 3.3 5.2 - - - +
307B THR* 3.8 19.6 + - - +
308B VAL* 4.3 1.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 3.9 6.7 - - + -
243B PHE 3.6 13.2 - - - +
245B PRO* 4.3 11.0 - - + -
258B GLU* 1.3 75.7 - - - +
260B THR* 1.3 60.5 + - - +
277B TRP* 3.7 26.1 - - + -
305B VAL* 3.6 1.7 - - - -
306B LEU 2.7 37.1 + - - +
308B VAL* 4.1 12.1 - - + -
313B TRP* 4.3 7.2 - - + -
319B TYR* 3.8 42.0 - - + -
336B ILE* 3.8 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 260 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241B PHE 3.7 1.6 - - - +
242B LEU* 3.4 4.9 - - - +
243B PHE* 2.7 52.2 + - + +
244B PRO 5.5 0.9 + - - -
258B GLU* 3.9 8.9 + - - +
259B VAL* 1.3 74.1 - - - +
261B CYS* 1.3 59.8 + - - +
262B VAL* 3.8 22.4 - - + -
303B VAL* 3.8 18.2 - - + -
304B SER 3.5 3.8 - - - +
305B VAL* 3.7 16.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 261 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B VAL* 3.6 24.9 - - - -
241B PHE 3.7 2.5 - - - -
242B LEU* 3.9 5.8 - - + -
260B THR* 1.3 70.9 - - - +
262B VAL* 1.3 61.0 + - - +
275B PHE* 3.9 13.2 - - + -
277B TRP* 3.5 18.5 - - + -
302B VAL 4.1 0.9 - - - +
303B VAL* 3.5 2.9 - - - +
304B SER* 2.7 36.3 + - - +
321B CYS* 2.0 49.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 262 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B SER 3.9 0.5 - - - +
240B VAL* 3.5 1.4 - - - +
241B PHE* 2.7 50.0 + - + +
243B PHE* 3.9 20.9 - - + -
260B THR* 3.8 20.6 - - + -
261B CYS* 1.3 78.8 - - - +
263B VAL* 1.3 67.6 + - - +
264B VAL* 4.3 5.2 - - + -
301B ARG* 3.4 42.2 - - + +
302B VAL 3.7 2.2 - - - -
303B VAL* 3.8 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PRO* 4.1 10.1 - - + -
239B SER 3.3 10.5 - - - +
240B VAL* 4.0 12.8 - - + -
262B VAL* 1.3 79.8 - - - +
264B VAL* 1.3 68.8 + - - +
266B VAL* 3.7 23.1 - - + +
273B VAL* 5.4 1.1 - - + -
275B PHE* 3.5 31.9 - - + -
300B TYR 3.9 0.9 - - - +
301B ARG* 3.5 6.9 - - - +
302B VAL* 3.1 32.1 + - + +
323B VAL* 3.5 27.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 264 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PRO* 3.3 5.7 - - - +
239B SER* 2.8 46.6 + - - +
241B PHE* 4.0 24.0 - - + -
262B VAL* 4.6 7.2 - - + -
263B VAL* 1.3 77.8 - - - +
265B ASP* 1.4 70.9 + - - +
266B VAL* 3.3 2.5 - - - -
299B THR* 5.3 1.8 - - - +
300B TYR 3.8 6.1 - - - +
301B ARG* 4.0 25.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B LEU* 4.0 32.7 - - + +
237B GLY 4.1 8.3 - - - +
238B PRO* 3.3 25.8 - - + +
239B SER* 4.2 13.9 + - - +
264B VAL* 1.4 82.9 - - - +
266B VAL* 1.4 58.3 + - - +
267B SER* 3.9 2.1 + - - -
299B THR* 3.8 26.2 + - - +
300B TYR 3.9 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 266 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B PRO* 3.8 15.0 - - + -
263B VAL* 3.7 33.2 - - + +
264B VAL 4.0 3.1 - - - +
265B ASP* 1.4 75.5 - - - +
267B SER* 1.3 63.6 + - - +
270B ASP 3.5 21.1 - - - +
271B PRO 3.8 7.4 - - - +
273B VAL* 3.8 28.5 - - + -
299B THR* 3.4 5.2 - - - -
300B TYR* 2.8 47.2 + - + +
302B VAL* 5.0 3.8 - - + -
325B ASN* 4.1 3.4 - - - +
----------------------------------------------------------
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