Contacts of the helix formed by residues 228 - 249 (chain A) in PDB entry 4M8J
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 THR 228 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A PRO* 3.2 21.7 + - + +
227A HIS* 1.3 82.2 + - - +
229A LEU* 1.3 58.9 + - - +
230A GLN* 3.7 12.1 + - - +
231A LEU* 3.0 33.8 + - - +
232A ASP* 2.9 22.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A THR* 1.3 73.9 - - - +
230A GLN* 1.3 63.3 + - - +
232A ASP* 3.4 13.4 + - + +
233A ALA* 3.2 21.6 + - + +
461A ILE* 4.8 18.0 - - + +
464A LEU* 4.3 8.5 - - + +
465A ALA* 3.6 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A THR* 3.1 11.1 + - - +
229A LEU* 1.3 83.5 - - - +
231A LEU* 1.3 59.5 + - - +
233A ALA* 3.5 8.8 + - + +
234A ILE* 3.2 28.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A THR* 4.2 22.7 - - + +
219A ILE* 4.8 10.5 - - + -
225A ILE* 3.7 34.3 - - + +
226A PRO 3.5 20.6 - - - +
227A HIS* 4.2 10.1 - - - -
228A THR* 3.0 22.7 + - - +
230A GLN* 1.3 75.7 - - - +
232A ASP* 1.3 63.9 + - - +
233A ALA 3.1 1.6 - - - -
234A ILE* 3.0 39.2 + - + +
235A ILE* 3.3 18.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 232 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 4.1 11.1 + - - +
213A PRO* 4.8 0.9 - - - +
216A THR* 3.5 12.1 - - - +
227A HIS* 2.9 34.3 + - - -
228A THR 2.9 15.3 - - - +
229A LEU* 3.4 14.4 + - + +
231A LEU* 1.3 75.9 - - - +
233A ALA* 1.3 61.8 + - - +
234A ILE 3.5 0.3 + - - -
235A ILE* 3.9 2.2 + - - +
236A ILE* 3.2 29.6 + - - +
461A ILE* 3.8 3.1 - - + -
464A LEU* 3.8 37.0 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
229A LEU* 3.2 15.1 + - + +
230A GLN* 3.6 13.0 - - + +
231A LEU 3.1 0.6 - - - -
232A ASP* 1.3 76.7 - - - +
234A ILE* 1.3 56.5 + - + +
236A ILE* 4.0 2.3 + - - +
237A SER* 2.5 33.3 + - - -
461A ILE* 3.5 23.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 234 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN* 3.2 25.6 - - + +
231A LEU* 3.0 26.4 + - + +
233A ALA* 1.3 74.4 - - - +
235A ILE* 1.3 61.5 + - + +
237A SER* 2.8 28.7 + - - -
238A CYS* 2.8 17.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 235 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A THR* 5.0 4.5 - - - -
215A VAL* 3.8 18.2 - - + -
216A THR* 3.8 20.2 - - + -
219A ILE* 3.5 31.0 - - + -
231A LEU* 3.3 16.8 + - + +
232A ASP 4.5 2.9 - - - +
233A ALA 3.7 0.2 - - - -
234A ILE* 1.3 80.2 - - + +
236A ILE* 1.3 51.9 + - - +
238A CYS* 3.1 10.4 + - + +
239A TRP* 2.8 73.4 + - + +
416A PHE* 4.9 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 3.9 22.0 - - + -
212A THR* 3.6 30.1 - - + -
232A ASP 3.2 15.4 + - - +
233A ALA 4.0 4.9 - - - +
234A ILE 3.2 0.4 - - - -
235A ILE* 1.3 75.6 - - - +
237A SER* 1.3 64.0 + - - +
239A TRP* 3.1 13.0 + - + +
240A ILE* 3.0 33.5 + - + +
457A GLY* 3.8 28.0 - - - +
460A GLY 4.4 1.3 - - - -
461A ILE* 3.6 34.1 - - + +
464A LEU* 4.4 3.4 - - + -
----------------------------------------------------------
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 ALA 2.5 21.9 + - - -
234A ILE* 2.8 12.4 + - - -
236A ILE* 1.3 74.9 - - - +
238A CYS* 1.3 58.6 + - - +
240A ILE* 3.1 15.8 + - - +
241A LEU* 3.0 38.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 238 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ILE* 2.8 16.8 + - + +
235A ILE* 3.5 13.2 - - + +
237A SER* 1.3 75.6 - - - +
239A TRP* 1.3 58.9 + - + +
241A LEU* 3.6 13.5 - - - +
242A LEU* 2.9 50.1 + - - +
416A PHE* 5.6 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 239 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A LEU* 3.9 20.6 - - + -
212A THR* 3.4 31.6 - - + -
215A VAL* 3.7 33.9 - - + -
235A ILE* 2.8 33.8 + - + +
236A ILE* 3.1 17.9 + - - +
238A CYS* 1.3 76.1 - - + +
240A ILE* 1.3 63.9 + - + +
242A LEU* 3.5 11.9 + - + +
243A ASN* 3.0 24.9 + - - +
416A PHE* 3.2 37.7 - + - -
419A THR* 3.0 32.3 + - + -
420A VAL* 4.0 13.5 - - + +
423A ILE* 4.9 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 240 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 3.0 26.4 + - + +
237A SER* 3.1 17.5 + - - +
239A TRP* 1.3 76.5 - - + +
241A LEU* 1.3 56.0 + - + +
243A ASN* 2.8 10.1 - - - +
244A ALA* 2.7 37.8 + - + +
423A ILE* 5.5 2.9 - - + -
450A ILE* 4.7 8.3 - - + -
453A SER* 3.7 40.2 - - - +
454A VAL* 3.8 31.9 - - + +
457A GLY* 5.3 1.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 241 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER* 3.0 24.6 + - - +
238A CYS* 3.6 16.6 - - - +
240A ILE* 1.3 82.5 - - + +
242A LEU* 1.3 57.7 + - - +
244A ALA* 3.1 6.8 + - + +
245A ILE* 2.9 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 242 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A CYS* 2.9 37.1 + - - +
239A TRP* 3.7 26.9 - - + +
241A LEU* 1.3 75.1 - - + +
243A ASN* 1.3 58.0 + - - +
245A ILE* 4.0 10.1 - - + +
246A CYS* 3.1 36.6 + - - -
416A PHE* 3.9 22.0 - - + -
420A VAL* 4.7 14.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 243 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239A TRP 3.0 15.3 + - - +
240A ILE* 2.8 20.8 - - - +
242A LEU* 1.3 73.7 - - - +
244A ALA* 1.3 65.1 + - - +
245A ILE 3.2 0.2 - - - -
246A CYS* 3.7 7.1 - - - +
247A VAL* 2.9 39.2 + - - +
420A VAL* 5.4 6.9 - - + +
423A ILE* 4.2 19.1 - - + +
424A ASN* 4.4 20.7 + - + +
427A SER* 3.7 25.5 + - - -
449A ARG* 5.1 2.6 + - - +
450A ILE* 4.8 3.2 - - - +
453A SER* 3.6 17.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 244 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240A ILE* 2.7 24.3 + - + +
241A LEU* 3.1 10.1 + - + +
243A ASN* 1.3 73.7 + - - +
245A ILE* 1.3 62.9 - - + +
247A VAL* 3.3 12.8 - - - +
248A ALA* 3.4 14.6 + - - +
450A ILE* 3.7 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 245 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A LEU* 2.9 30.3 + - + +
242A LEU* 4.0 10.1 - - + +
244A ALA* 1.3 76.4 - - + +
246A CYS* 1.3 66.5 + - - +
248A ALA* 3.4 2.8 + - - -
249A PHE* 3.2 52.3 + - + +
251A LEU* 3.8 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 246 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A LEU* 3.1 26.7 + - - +
243A ASN* 3.3 8.3 + - - +
245A ILE* 1.3 81.8 - - - +
247A VAL* 1.3 55.1 + - - +
250A GLY 2.7 29.5 + - - +
251A LEU* 3.2 30.0 - - + +
255A VAL* 4.3 25.6 - - + -
420A VAL* 5.8 7.0 - - - -
424A ASN* 5.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A ASN* 2.9 26.1 + - - +
244A ALA 3.3 9.4 - - - +
246A CYS* 1.3 74.3 - - - +
248A ALA* 1.3 69.8 + - - +
250A GLY* 3.2 14.9 + - - +
424A ASN* 5.3 1.0 - - - +
443A ASP* 4.1 16.0 - - - +
446A LEU* 3.5 19.2 - - + +
449A ARG* 3.2 46.4 - - - +
450A ILE* 3.7 22.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 248 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ALA 3.4 16.2 + - - +
245A ILE* 3.4 1.8 + - - +
247A VAL* 1.3 82.2 - - - +
249A PHE* 1.3 79.5 + - + +
250A GLY 3.3 2.9 + - - -
446A LEU* 3.6 30.5 - - + +
450A ILE* 6.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A ILE* 3.2 39.7 + - + +
246A CYS 4.2 0.9 - - - -
248A ALA* 1.3 94.1 - - + +
250A GLY* 1.3 57.0 + - - +
251A LEU* 2.8 22.9 + - + +
253A LYS* 6.1 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