Contacts of the helix formed by residues 232 - 255 (chain A) in PDB entry 5I9J
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 SER 232 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 1.3 77.5 - - - +
233A ALA* 1.3 59.8 + - - +
234A GLN* 3.5 9.7 + - - +
235A GLU* 2.9 37.1 + - - +
236A ARG* 2.9 28.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 1.3 73.9 - - - +
234A GLN* 1.3 58.4 + - - +
236A ARG* 3.4 31.3 + - - +
237A GLU* 3.0 27.5 + - - +
240A ARG* 5.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232A SER* 3.2 8.1 + - - +
233A ALA* 1.3 76.1 - - - +
235A GLU* 1.3 66.7 + - + +
237A GLU* 3.1 21.3 + - - +
238A TYR* 3.0 64.2 + - + +
321A GLN* 5.6 2.9 - - - +
368A SER* 4.8 4.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.2 26.2 - - + -
232A SER* 2.9 40.4 + - - +
234A GLN* 1.3 76.5 - - + +
236A ARG* 1.3 58.4 + - - +
238A TYR* 3.3 10.4 + - - +
239A ILE* 3.0 33.2 + - - +
321A GLN* 4.2 21.8 + - - +
322A ARG 5.0 3.8 - - - +
323A VAL* 3.9 21.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.0 41.7 + - + +
232A SER 2.9 18.3 + - - +
233A ALA* 3.5 35.6 - - - +
235A GLU* 1.3 76.9 - - - +
237A GLU* 1.3 56.8 + - - +
239A ILE* 3.3 9.0 + - + +
240A ARG* 2.9 46.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 237 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA 3.0 16.2 + - - +
234A GLN* 3.1 20.9 + - - +
236A ARG* 1.3 73.6 - - - +
238A TYR* 1.3 61.1 + - - +
240A ARG* 3.2 31.2 + - - +
241A GLN* 2.9 48.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLN* 3.0 53.2 + - + +
235A GLU* 3.6 11.2 - - - +
237A GLU* 1.3 75.3 - - - +
239A ILE* 1.3 62.9 + - - +
241A GLN* 3.2 9.1 + - - +
242A GLY 3.1 18.5 + - - -
321A GLN* 4.2 15.9 - - - -
323A VAL* 4.3 5.6 - - + -
327A THR* 3.9 6.9 - - + +
329A ILE* 3.5 36.8 - - + -
350A VAL* 3.5 18.5 - - + +
367A THR* 3.2 34.1 - - + -
368A SER 2.7 22.4 + - - -
369A HIS* 3.3 19.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.9 25.4 - - + -
235A GLU 3.0 20.2 + - - +
236A ARG* 3.7 8.5 - - + +
237A GLU 3.3 0.2 - - - -
238A TYR* 1.3 75.5 - - - +
240A ARG* 1.3 64.6 + - + +
242A GLY* 3.2 3.3 + - - -
243A LYS* 3.1 49.8 + - - +
323A VAL* 3.6 29.2 - - + -
324A GLU* 3.9 21.3 - - - +
327A THR* 4.1 15.4 + - - +
352A ARG* 4.4 7.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233A ALA 5.1 1.6 + - - -
236A ARG* 2.9 35.6 + - - +
237A GLU* 3.2 42.0 + - + +
239A ILE* 1.3 80.2 - - + +
241A GLN* 1.3 58.6 + - + +
243A LYS* 3.2 9.7 + - + +
244A GLU* 2.8 49.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A GLU* 2.9 36.3 + - + +
238A TYR* 3.2 20.1 + - - +
240A ARG* 1.3 75.8 - - + +
242A GLY* 1.3 57.8 + - - +
244A GLU* 3.4 16.1 + - - +
245A ALA* 3.0 29.5 + - - +
350A VAL* 3.6 11.5 - - + +
365A ILE* 3.9 14.8 - - + +
366A ALA 3.3 18.7 - - - +
367A THR* 2.7 32.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A TYR 3.1 12.9 + - - -
239A ILE* 3.7 3.1 - - - -
241A GLN* 1.3 77.4 - - - +
243A LYS* 1.3 55.2 + - - +
245A ALA* 3.4 6.9 + - - +
246A THR* 2.8 33.4 + - - -
327A THR* 5.6 1.6 - - - -
350A VAL* 4.4 11.1 - - - +
351A ARG 4.9 0.2 - - - -
352A ARG* 3.7 26.3 - - - +
363A SER 4.6 1.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A ILE* 3.1 32.9 + - + +
240A ARG* 3.7 10.5 - - + +
242A GLY* 1.3 73.4 - - - +
244A GLU* 1.3 60.5 + - + +
246A THR* 3.3 4.9 + - - -
247A ALA* 2.9 27.2 + - - +
324A GLU* 5.6 2.1 + - - -
352A ARG* 3.7 43.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ARG* 2.8 41.2 + - + +
241A GLN* 3.7 15.7 - - - +
243A LYS* 1.3 69.5 - - + +
245A ALA* 1.3 65.9 + - - +
247A ALA* 3.2 9.1 + - - +
248A VAL* 3.2 26.9 + - + +
365A ILE* 6.4 1.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLN 3.0 17.4 + - - +
242A GLY* 3.8 4.3 - - - +
244A GLU* 1.3 75.0 - - - +
246A THR* 1.3 62.4 + - - +
248A VAL* 3.2 4.0 + - - +
249A VAL* 3.0 25.5 + - - +
363A SER* 3.9 2.2 - - - -
364A GLY* 3.5 43.1 - - - +
365A ILE* 4.2 8.7 - - + +
385A PRO* 4.3 14.3 - - + +
386A GLY 4.8 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A GLY 2.8 21.8 + - - -
243A LYS* 3.5 8.5 - - - -
244A GLU 3.2 0.2 - - - -
245A ALA* 1.3 76.9 - - - +
247A ALA* 1.3 56.6 + - - +
249A VAL* 3.3 2.4 + - - +
250A ASP* 2.9 30.9 + - - +
352A ARG* 3.6 15.6 + - - +
354A GLU* 3.8 17.8 - - + +
356A ARG* 3.4 28.0 - - - +
361A LEU* 4.2 5.2 - - + -
363A SER* 3.5 23.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A LYS 2.9 12.3 + - - +
244A GLU* 3.2 12.1 + - - +
246A THR* 1.3 77.4 - - - +
248A VAL* 1.3 58.3 + - + +
250A ASP* 3.4 9.2 + - - +
251A GLN* 2.9 38.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLU* 3.2 14.8 + - + +
245A ALA 3.2 6.7 + - - +
247A ALA* 1.3 75.3 - - + +
249A VAL* 1.3 61.1 + - - +
251A GLN* 3.1 18.2 + - + +
252A ILE* 2.9 46.9 + - + +
276A VAL* 4.3 15.9 - - + -
385A PRO* 3.6 35.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ALA 3.0 16.0 + - - +
246A THR 3.6 7.2 - - - +
248A VAL* 1.3 73.7 - - + +
250A ASP* 1.3 65.2 + - - +
252A ILE* 3.2 4.1 + - - +
253A LEU* 2.9 31.9 + - + +
361A LEU* 3.7 23.3 - - + -
363A SER* 3.6 10.1 - - - +
385A PRO 5.0 0.7 - - - -
386A GLY* 3.4 39.7 - - - +
387A GLY* 4.2 2.5 - - - +
389A ILE* 3.8 25.6 - - + -
405A ILE* 4.1 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 250 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A THR* 2.9 22.2 + - - +
247A ALA* 3.6 8.6 - - - +
249A VAL* 1.3 77.2 - - - +
251A GLN* 1.3 61.6 + - + +
253A LEU* 3.3 11.2 + - - +
254A ALA* 3.0 24.8 + - - +
356A ARG* 2.9 44.3 + - - -
359A ARG* 5.4 1.4 + - - -
361A LEU* 3.7 9.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A ALA* 2.9 26.6 + - + +
248A VAL* 3.1 20.8 + - + +
250A ASP* 1.3 76.4 - - + +
252A ILE* 1.3 64.6 + - + +
254A ALA* 3.3 13.5 + - - +
255A GLN* 3.1 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 252 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A VAL* 2.9 39.2 + - + +
249A VAL* 3.2 4.7 + - - +
251A GLN* 1.3 78.4 - - + +
253A LEU* 1.3 62.6 + - - +
255A GLN* 3.0 17.5 + - - +
259A TRP* 3.0 24.1 + - + +
274A ILE* 4.2 9.0 - - + -
276A VAL* 4.0 26.7 - - + -
282A THR* 4.2 6.5 - - + -
284A ILE* 3.7 29.6 - - + -
385A PRO 5.1 2.0 - - - +
405A ILE* 3.8 36.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A VAL* 2.9 38.1 + - + +
250A ASP* 3.8 12.1 - - - +
252A ILE* 1.3 76.1 - - - +
254A ALA* 1.3 60.9 + - - +
255A GLN 3.3 0.7 + - - -
256A GLU* 3.6 18.0 + - - +
259A TRP* 4.3 14.5 - - + -
359A ARG* 3.9 28.3 - - - +
361A LEU* 5.0 1.1 - - + -
389A ILE* 4.0 21.8 - - + -
391A LEU* 5.2 4.7 - - + -
403A VAL* 4.3 22.7 - - + -
405A ILE* 4.3 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A ASP 3.0 17.1 + - - +
251A GLN* 3.7 8.3 - - - +
252A ILE 3.1 0.6 - - - -
253A LEU* 1.3 78.5 - - - +
255A GLN* 1.3 59.0 + - + +
256A GLU 3.5 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 255 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A GLN* 3.1 30.6 + - - +
252A ILE* 3.0 11.2 + - - +
254A ALA* 1.3 80.5 - - + +
256A GLU* 1.3 56.9 + - - +
257A GLU* 3.1 3.8 - - - -
258A ASN* 2.8 40.8 + - + +
259A TRP* 3.3 8.4 - - - -
274A ILE* 4.1 21.8 - - + +
275A GLU 5.8 1.0 + - - -
----------------------------------------------------------
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