Contacts of the helix formed by residues 236 - 249 (chain A) in PDB entry 3OLJ
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 PHE 236 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133A PHE* 4.0 8.1 - + - -
134A PHE* 3.8 24.2 - + + -
137A SER* 3.5 32.5 - - - -
138A ASP* 4.2 16.8 - - - -
141A VAL* 4.5 14.1 - - + -
231A VAL* 3.4 15.6 + - + -
232A GLU* 3.6 27.1 - - + +
234A ILE 3.1 1.2 - - - +
235A PHE* 1.3 86.6 - - + +
237A SER* 1.3 65.0 + - - +
238A GLY 3.4 1.8 - - - -
239A SER* 3.2 6.3 + - - -
240A PHE* 3.0 42.2 + + + -
262A ILE* 6.3 0.2 - - + -
266A GLU* 3.3 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A GLY 3.4 20.9 + - - -
234A ILE* 2.8 20.9 + - - -
236A PHE* 1.3 78.3 - - - +
238A GLY* 1.3 62.3 + - - +
240A PHE* 3.4 9.9 + - - +
241A ALA* 3.0 29.1 + - - +
323A TYR* 3.7 10.0 + - - -
324A ILE* 3.5 15.9 - - - +
327A VAL* 3.9 24.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER* 1.3 81.1 + - - +
239A SER* 1.3 58.6 + - - +
241A ALA* 3.4 3.2 + - - +
242A SER* 2.9 29.5 + - - -
300A GLU* 3.0 16.7 + - - -
304A LEU* 3.6 22.4 - - - -
320A MET* 3.7 11.6 - - - +
324A ILE* 3.9 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A VAL* 3.7 15.5 - - - +
133A PHE* 3.8 21.2 - - - -
134A PHE* 3.2 31.6 - - - -
206A LYS* 4.9 0.2 + - - -
235A PHE 4.8 0.9 + - - -
236A PHE 3.2 5.1 + - - -
238A GLY* 1.3 72.9 - - - +
240A PHE* 1.3 67.0 + - - +
242A SER* 3.1 11.1 + - - -
243A ILE* 3.0 25.7 + - - +
300A GLU* 4.1 1.8 + - - -
303A PHE* 3.9 15.4 - - - -
304A LEU* 4.3 1.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A PHE* 3.7 16.8 - + - -
176A TYR* 3.8 13.2 - - - -
232A GLU 4.5 2.5 - - - -
236A PHE* 3.0 44.5 + + + -
237A SER* 3.7 9.0 - - - +
239A SER* 1.3 77.4 - - - +
241A ALA* 1.3 56.3 + - - +
243A ILE 3.2 2.1 + - - -
244A PHE* 2.9 36.3 + - + -
259A ASN* 3.2 23.8 + - - +
262A ILE* 4.0 3.6 - - + -
263A SER* 3.7 46.0 - - - -
266A GLU* 3.7 27.8 - - + -
350A MET* 4.9 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER 3.0 17.8 + - - +
238A GLY 3.7 4.9 - - - +
239A SER 3.3 0.4 - - - -
240A PHE* 1.3 76.9 - - - +
242A SER* 1.3 56.8 + - - +
244A PHE 3.3 0.5 + - - -
245A TRP* 2.8 29.5 + - - +
315A MET* 4.4 2.7 - - - -
320A MET* 4.0 13.9 - - + -
323A TYR* 3.8 21.3 - - + -
347A PHE* 4.5 5.8 - - + -
349A PHE* 3.6 6.8 - - + -
350A MET* 3.9 22.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 3.2 39.6 - - - -
130A VAL* 5.1 0.2 - - - -
238A GLY 2.9 17.1 + - - -
239A SER* 3.1 14.2 + - - -
241A ALA* 1.3 75.3 - - - +
243A ILE* 1.3 65.5 + - - +
245A TRP* 3.2 5.7 - - - +
246A LEU* 3.2 18.5 + - - +
304A LEU* 4.7 0.2 - - - +
310A VAL* 3.7 11.8 - - - +
313A ILE* 3.6 9.3 - - - +
315A MET* 3.8 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A PHE* 5.4 1.3 - - + -
127A ILE* 5.2 7.0 - - + -
130A VAL* 4.2 23.8 - - + -
131A LEU* 5.9 1.8 - - + -
134A PHE* 4.9 3.4 - - + -
239A SER 3.0 15.7 + - - +
240A PHE 3.8 0.4 - - - +
242A SER* 1.3 79.7 - - - +
244A PHE* 1.3 66.8 + - - +
246A LEU* 3.1 27.8 + - + +
247A LYS 3.1 9.0 + - - -
255A LEU* 3.8 35.0 - - + -
256A THR* 3.7 14.0 - - + +
259A ASN* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A PHE* 2.9 25.5 + - + +
241A ALA 3.7 1.6 - - - +
243A ILE* 1.3 77.7 - - - +
245A TRP* 1.3 59.1 + - - +
247A LYS* 3.2 22.1 + - + +
248A LYS* 3.1 20.6 + - - +
256A THR* 5.3 1.3 - - - -
259A ASN* 3.4 17.3 - - - -
260A GLU* 3.7 36.1 - - + -
263A SER* 3.6 23.6 - - - -
349A PHE* 3.8 20.7 - - + +
350A MET* 3.6 38.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A ALA 2.8 13.8 + - - +
242A SER 3.2 9.0 - - - +
244A PHE* 1.3 76.6 - - - +
246A LEU* 1.3 61.5 + - + +
248A LYS* 3.1 27.2 + - + +
249A ARG* 3.1 45.3 + - + +
313A ILE* 2.9 36.1 + - + -
314A GLY* 3.6 19.4 + - - -
315A MET* 3.4 31.8 - - + +
347A PHE* 6.3 0.9 - + - -
349A PHE* 3.8 30.2 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 5.3 3.8 - - + -
123A GLU* 6.2 0.2 - - + -
126A PHE* 6.1 0.2 - - + -
127A ILE* 3.6 38.1 - - + -
242A SER 3.2 8.0 + - - +
243A ILE* 3.1 23.2 + - + +
245A TRP* 1.3 78.4 - - - +
247A LYS* 1.3 59.2 + - - +
249A ARG* 3.3 33.0 + - - +
250A GLY 3.3 0.2 + - - -
251A LEU* 2.9 48.6 + - + +
252A MET* 5.4 2.7 - - + -
255A LEU* 3.9 19.7 - - + -
256A THR* 4.4 6.3 - - + -
313A ILE* 4.5 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ILE 3.1 8.0 + - - +
244A PHE* 3.4 28.3 - - + +
245A TRP 3.2 0.2 - - - -
246A LEU* 1.3 74.7 - - - +
248A LYS* 1.3 56.9 + - - +
250A GLY* 2.8 25.1 + - - +
251A LEU 4.5 2.2 - - - +
256A THR* 3.7 29.3 - - + +
260A GLU* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE 3.1 11.5 + - - +
245A TRP* 3.1 30.3 + - + +
247A LYS* 1.3 75.7 - - - +
249A ARG* 1.3 60.9 + - + +
250A GLY 3.1 0.9 + - - -
348A ASP* 2.7 34.6 + - - -
349A PHE* 4.0 28.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU* 4.6 2.2 - - - +
123A GLU* 2.9 33.1 + - - -
245A TRP* 3.1 41.3 + - + +
246A LEU* 3.6 24.4 - - - +
247A LYS 3.1 1.0 - - - -
248A LYS* 1.3 77.4 - - + +
250A GLY* 1.3 61.8 + - - +
251A LEU* 3.6 33.8 + - + +
313A ILE* 3.1 21.6 + - - +
314A GLY* 5.3 0.2 - - - -
----------------------------------------------------------
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