Contacts of the helix formed by residues 243 - 263 (chain D) in PDB entry 4IA4
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 TRP 243 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161D LYS* 3.6 32.8 - - + +
165D LEU* 4.0 33.0 - - + -
239D TRP 4.7 0.6 + - - -
240D ASP 3.2 23.9 + - - -
241D ASP 2.8 9.7 + - - -
242D GLN* 1.3 73.3 - - - +
244D ILE* 1.3 79.2 + - + +
245D PHE 3.2 0.2 - - - -
246D TRP* 3.2 8.1 + - - +
247D VAL* 2.9 52.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 244 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155D VAL* 3.5 31.6 - - + -
161D LYS* 4.3 13.9 - - + +
164D ALA* 3.8 11.0 - - + +
165D LEU* 3.3 40.2 - - + +
168D GLU* 4.3 7.0 - - + +
241D ASP* 2.9 24.4 + - + +
243D TRP* 1.3 106.0 - - + +
245D PHE* 1.3 64.7 + - + +
246D TRP 3.0 0.4 + - - -
248D GLY* 2.8 27.7 + - - -
249D PRO* 3.4 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 245 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153D ASN* 3.4 35.9 - - + -
154D SER* 3.5 25.4 - - - -
155D VAL 4.3 1.6 - - - -
168D GLU* 3.8 25.1 - - + -
217D THR* 3.4 29.2 - - + -
220D GLY* 5.2 0.9 - - - -
222D ASN 5.9 0.4 - - - +
223D PRO* 3.3 25.1 - - - +
226D SER* 3.2 26.7 - - - +
241D ASP* 3.9 17.3 - - + -
242D GLN* 3.4 25.8 + - - +
243D TRP 3.2 1.2 - - - -
244D ILE* 1.3 83.6 - - + +
246D TRP* 1.3 59.1 + - - +
249D PRO* 3.4 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 246 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 5.3 4.7 - - + -
123D MET* 6.0 4.0 - - + -
127D CYS* 4.2 16.2 - - - -
223D PRO* 3.8 21.4 + - + -
224D ALA* 5.2 0.7 - - - -
227D PHE* 3.6 38.6 - + + +
242D GLN* 2.9 46.0 + - + +
243D TRP* 3.2 8.9 + - - +
244D ILE 3.0 0.4 - - - -
245D PHE* 1.3 82.9 - - - +
247D VAL* 1.3 67.1 + - + +
248D GLY 3.4 1.1 - - - -
249D PRO* 3.9 1.1 - - - -
250D PHE* 2.7 62.1 + + + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 247 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 4.2 11.7 - - + -
243D TRP* 2.9 43.2 + - + +
246D TRP* 1.3 77.7 - - + +
248D GLY* 1.3 59.8 + - - +
250D PHE* 4.1 2.4 - - - +
251D ILE* 2.9 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 248 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 3.7 7.5 - - - +
168D GLU* 4.4 1.6 - - - -
169D ILE* 3.6 37.6 - - - -
244D ILE 2.8 14.3 + - - -
247D VAL* 1.3 75.5 - - - +
249D PRO* 1.3 70.5 - - - +
251D ILE* 3.1 2.4 + - - +
252D GLY* 2.8 20.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 249 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ALA* 3.7 7.6 - - + +
168D GLU* 3.9 11.2 - - - +
172D THR* 3.2 23.9 - - - +
221D ILE* 3.7 20.4 - - - +
222D ASN 3.9 3.8 - - - +
223D PRO* 3.5 25.8 - - + -
244D ILE 3.4 12.1 - - - +
245D PHE* 3.4 22.9 - - + +
246D TRP 3.8 1.3 - - - +
248D GLY* 1.3 87.3 - - - +
250D PHE* 1.3 56.7 + - - +
253D ALA* 2.9 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 250 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D PRO* 4.2 11.0 - - + -
103D ALA* 4.9 1.8 - - - -
106D PHE* 3.2 68.9 - + + -
123D MET* 4.1 23.1 - - + -
223D PRO* 3.4 25.8 - - + -
246D TRP* 2.7 49.3 + + - +
247D VAL* 4.1 3.4 - - - +
248D GLY 3.2 0.6 - - - -
249D PRO* 1.3 77.5 - - - +
251D ILE* 1.3 60.4 + - + +
253D ALA* 3.5 1.0 + - - -
254D ALA* 3.0 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 251 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D LEU* 5.6 2.0 - - + -
169D ILE* 4.2 30.1 - - + -
247D VAL* 2.9 48.1 + - + +
248D GLY 3.7 2.2 - - - +
250D PHE* 1.3 72.6 - - + +
252D GLY* 1.3 65.2 + - - +
254D ALA* 3.3 7.6 - - + +
255D VAL* 2.9 37.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 252 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ILE* 3.7 31.4 - - - +
172D THR* 4.6 0.2 - - - -
173D PHE* 4.2 10.9 - - - -
248D GLY 2.8 11.8 + - - -
249D PRO 3.9 1.1 - - - -
251D ILE* 1.3 74.3 - - - +
253D ALA* 1.3 65.9 + - - +
254D ALA 2.9 1.8 + - - -
255D VAL* 3.0 7.6 + - - +
256D ALA* 2.8 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 253 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103D ALA* 3.2 29.2 - - + +
106D PHE* 4.0 11.0 - - + -
107D GLY* 4.0 7.0 - - - +
172D THR* 4.0 2.4 - - - +
176D VAL* 3.6 24.3 - - + +
249D PRO 2.9 18.1 + - - +
250D PHE 3.8 4.7 - - - +
252D GLY* 1.3 73.5 - - - +
254D ALA* 1.3 60.7 + - - +
256D ALA* 3.5 1.7 - - - +
257D ALA* 3.1 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 254 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106D PHE* 4.2 3.3 - - + -
110D LEU* 3.8 24.1 - - + +
250D PHE 3.0 14.8 + - - +
251D ILE* 3.3 13.5 - - + +
252D GLY 3.0 0.6 - - - -
253D ALA* 1.3 72.9 - - - +
255D VAL* 1.3 68.2 + - + +
257D ALA* 3.1 6.2 + - - +
258D ALA* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 255 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ILE* 5.2 5.6 - - + -
173D PHE* 4.3 16.8 - - + -
251D ILE* 2.9 28.0 - - + +
252D GLY* 3.0 7.4 + - - +
254D ALA* 1.3 75.4 - - + +
256D ALA* 1.3 53.6 + - - +
258D ALA* 3.0 11.1 + - + +
259D TYR* 2.7 35.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 256 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173D PHE* 3.2 27.0 - - + +
176D VAL* 3.2 34.8 - - + -
177D TYR* 4.0 8.1 - - - +
180D PHE* 4.3 3.1 - - - -
252D GLY 2.8 15.1 + - - +
253D ALA 3.5 0.9 - - - +
255D VAL* 1.3 76.3 - - - +
257D ALA* 1.3 64.5 + - - +
259D TYR* 3.1 4.0 + - - +
260D HIS* 2.8 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 257 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107D GLY 3.8 15.3 - - - +
110D LEU* 4.6 13.2 - - + -
111D ALA* 5.1 5.4 - - + +
180D PHE* 3.2 28.4 - - + -
253D ALA 3.1 10.2 + - - +
254D ALA* 3.1 8.5 + - - +
256D ALA* 1.3 78.4 - - - +
258D ALA* 1.3 64.1 + - - +
260D HIS* 3.3 0.9 + - - +
261D GLN* 2.8 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 258 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254D ALA 3.0 12.1 + - - +
255D VAL* 3.0 15.3 - - + +
257D ALA* 1.3 75.7 - - - +
259D TYR* 1.3 61.3 + - - +
261D GLN* 5.3 0.2 - - - -
262D TYR* 2.7 47.1 + - + +
263D VAL* 4.8 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 259 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE* 4.2 11.4 - - + -
43A ALA* 3.4 21.1 + - - +
46A ILE* 3.3 42.2 - - + +
173D PHE* 3.6 26.9 - + + -
177D TYR* 3.4 44.2 + + - -
255D VAL* 2.7 18.7 + - + +
256D ALA 3.5 6.3 - - - +
258D ALA* 1.3 72.0 - - - +
260D HIS* 1.3 64.0 + - - +
263D VAL* 2.6 52.1 + - + +
264D LEU* 3.6 16.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 260 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LYS* 5.5 7.2 - - - -
177D TYR* 4.7 13.9 - + + -
180D PHE* 3.4 55.8 + + + +
181D SER* 4.3 13.6 + - - -
183D THR* 5.6 0.7 - - - -
256D ALA 2.8 19.8 + - - +
257D ALA 3.8 2.5 - - - +
259D TYR* 1.3 77.6 - - - +
261D GLN* 1.3 73.2 + - + +
264D LEU* 3.5 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 261 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D LEU 4.8 0.5 - - - +
111D ALA* 3.4 45.4 - - - +
113D LYS* 4.5 13.5 - - - +
180D PHE* 4.5 7.9 - - - -
257D ALA* 2.8 19.5 + - - +
258D ALA* 5.3 0.2 - - - -
260D HIS* 1.3 90.1 + - + +
262D TYR* 1.3 66.9 + - + +
263D VAL 3.2 2.7 + - - -
264D LEU 3.8 11.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 262 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG* 5.5 0.2 - - - -
258D ALA* 2.7 29.6 + - + +
261D GLN* 1.3 77.9 - - + +
263D VAL* 1.3 58.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 263 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TRP* 5.8 7.4 - - + -
39A ARG* 3.2 17.3 + - - +
42A ILE* 4.4 25.5 - - + +
258D ALA 4.3 0.4 - - - +
259D TYR* 2.6 55.4 + - + +
261D GLN 3.2 0.2 - - - -
262D TYR* 1.3 81.4 - - + +
264D LEU* 1.3 70.7 + - - +
----------------------------------------------------------
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