Contacts of the strand formed by residues 252 - 259 (chain D) in PDB entry 1OFG
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 ARG 252 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C LEU 5.1 0.2 + - - -
180C GLY* 3.1 37.3 + - - -
181C MET* 3.9 9.9 - - + -
262C GLY* 2.5 36.7 + - - -
263C ALA* 3.4 3.8 - - - +
264C LEU* 3.5 23.4 - - + +
237D THR* 2.7 25.5 + - - -
238D TYR* 2.9 40.0 + - - +
239D SER* 5.0 0.6 - - - +
240D ASP* 5.0 2.8 - - - +
250D GLU* 4.6 0.7 - - - -
251D ASP* 1.3 105.2 + - - +
253D ILE* 1.3 57.1 + - - +
269D SER 3.3 3.8 - - - +
270D SER* 3.5 26.7 - - - -
272D SER* 3.3 14.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264C LEU* 5.7 0.4 - - - -
210D SER* 3.9 7.0 - - - +
211D LEU* 3.9 15.5 - - + -
235D ALA* 4.7 2.2 - - + -
236D TYR 3.3 12.8 - - - +
237D THR* 3.8 19.1 - - + +
250D GLU* 4.0 6.7 - - + -
252D ARG* 1.3 79.0 - - - +
254D ILE* 1.3 73.2 + - - +
255D TRP* 3.7 8.7 - - + -
268D ALA* 3.3 5.0 - - - +
269D SER* 3.1 48.9 + - - +
359D ILE* 4.2 15.3 - - + -
360D TYR* 4.1 29.4 - - + -
363D ALA* 4.4 9.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181C MET* 4.0 21.8 - - + -
254C ILE* 6.4 0.4 - - + -
256C GLN* 3.8 30.2 + - + +
257C MET 5.7 0.2 - - - +
264C LEU* 4.2 16.6 - - + -
265C SER 3.8 22.4 - - - +
266C HIS* 3.6 25.6 - - + +
235D ALA* 3.2 4.1 - - - +
236D TYR* 2.8 35.0 + - + +
253D ILE* 1.3 80.4 - - - +
255D TRP* 1.3 67.5 + - - +
256D GLN* 5.4 2.2 - - + -
266D HIS* 5.6 1.8 - - + -
267D GLY 3.3 11.0 - - - +
268D ALA* 3.7 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184D THR* 4.1 17.6 + - - -
186D ASN* 5.7 0.4 - - - -
211D LEU* 4.0 18.8 - - + -
215D GLY* 3.4 34.3 - - - -
218D GLY* 5.2 1.0 - - - -
219D LEU* 4.2 12.0 - - + +
222D THR* 5.6 0.6 + - - -
234D ARG 3.3 10.3 - - - +
235D ALA* 3.9 9.4 - - + -
253D ILE* 3.7 15.5 - - + -
254D ILE* 1.3 75.5 - - - +
256D GLN* 1.3 64.3 + - - +
257D MET* 4.0 30.3 - - + +
265D SER* 4.0 1.4 + - - +
266D HIS* 3.5 2.3 - - - +
267D GLY* 2.8 47.2 + - - +
268D ALA* 3.5 34.5 - - - -
269D SER* 3.6 11.9 - - - -
359D ILE* 3.9 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234C ARG* 5.6 0.3 - - - +
235C ALA* 4.6 3.8 + - - -
236C TYR* 3.2 39.2 + - + +
254C ILE* 3.8 35.1 - - + +
256C GLN* 2.9 35.4 - - - +
233D VAL* 3.4 3.3 - - - +
234D ARG* 2.7 56.5 + - + +
254D ILE* 5.4 1.6 - - + -
255D TRP* 1.3 77.2 - - - +
257D MET* 1.3 65.5 + - - +
265D SER 3.3 11.0 - - - +
266D HIS* 4.9 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C ILE* 5.7 0.3 - - - +
219D LEU* 3.7 33.4 - - + +
222D THR* 3.6 28.3 - - + +
223D ARG* 5.3 0.7 - - + -
230D PRO* 3.9 16.8 - - + -
232D GLU 3.3 9.2 - - - +
233D VAL* 3.5 20.9 - - + -
234D ARG* 6.3 0.4 - - - -
255D TRP* 4.0 22.2 - - + +
256D GLN* 1.3 77.2 - - - +
258D ARG* 1.3 60.5 + - - +
259D PHE* 3.8 13.6 - - + -
264D LEU* 3.4 8.2 - - - +
265D SER* 3.1 49.5 + - - +
355D LEU* 5.8 0.2 - - - -
359D ILE* 4.9 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C TYR* 3.3 28.5 + - + +
238C TYR* 3.7 36.1 + - - -
230D PRO* 3.3 3.1 - - - +
231D ILE* 2.8 52.5 + - + +
232D GLU* 3.0 50.7 + - + +
234D ARG* 5.4 1.8 - - - +
257D MET* 1.3 75.0 - - - +
259D PHE* 1.3 69.8 + - - +
262D GLY* 5.1 2.0 - - - +
263D ALA 3.6 2.9 - - - +
264D LEU* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222D THR* 3.5 23.3 - - + -
223D ARG* 4.8 2.9 - - + -
226D LEU* 3.5 27.4 - - + -
228D GLU* 3.5 43.1 - - + +
229D GLU 3.3 21.8 - - - -
230D PRO* 3.5 18.4 - - + -
231D ILE* 4.0 3.8 - - - +
257D MET* 3.8 20.9 - - + -
258D ARG* 1.3 85.2 + - - +
260D ARG* 1.4 54.5 + - - +
261D SER* 3.2 6.1 - - - +
262D GLY* 2.9 25.3 + - - -
263D ALA* 2.9 21.6 + - + +
264D LEU 4.7 0.4 - - - -
265D SER* 3.7 22.7 - - - -
----------------------------------------------------------
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