Contacts of the helix formed by residues 238 - 253 (chain E) in PDB entry 1IAS
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 GLU 238 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ARG* 3.6 25.6 - - - +
216E PHE* 3.6 24.3 - - - +
234E PHE* 3.9 7.6 - - + -
235E SER* 2.6 29.1 + - - +
237E ARG* 1.3 103.9 + - + +
239E GLU* 1.3 62.7 + - - +
240E ARG* 3.1 4.3 - - - +
241E SER* 3.1 33.4 + - - +
242E TRP 3.4 6.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 239 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173C GLU* 4.0 13.6 - - + +
174C GLY* 3.5 29.6 + - - +
225C ARG* 5.6 2.9 + - - -
235E SER 3.8 0.4 + - - -
236E SER 3.3 13.7 + - - +
237E ARG 3.5 2.8 + - - +
238E GLU* 1.3 77.8 - - - +
240E ARG* 1.3 72.2 + - + +
242E TRP* 3.2 4.3 + - - +
243E PHE* 3.0 25.1 + - - +
274E THR* 6.0 0.7 - - - +
276E LEU* 3.5 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 240 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C GLY* 4.2 20.0 - - - +
176C THR* 4.3 19.5 - - + +
237E ARG 5.4 5.1 + - - -
238E GLU* 3.1 2.5 + - - +
239E GLU* 1.3 87.7 + - + +
241E SER* 1.3 57.4 + - - +
243E PHE* 3.9 0.9 - - - +
244E ARG* 2.9 40.4 + - + +
368E ALA* 5.6 10.3 - - + +
369E PRO* 5.8 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 241 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215E ARG* 6.0 1.5 - - - +
216E PHE* 4.9 5.6 - - - -
234E PHE* 3.7 16.4 - - - -
238E GLU* 3.1 31.7 + - - -
240E ARG* 1.3 75.6 - - - +
242E TRP* 1.3 66.9 + - - +
244E ARG* 3.8 5.0 - - - +
245E GLU* 3.0 27.5 + - - +
353E GLY* 4.2 15.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 242 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C SER* 4.0 15.5 - - - -
173C GLU* 3.4 27.1 - - + -
234E PHE* 3.4 36.1 - + + -
238E GLU 3.4 1.4 + - - +
239E GLU 3.2 10.7 + - - +
241E SER* 1.3 80.4 - - - +
243E PHE* 1.3 84.0 + + + +
245E GLU* 4.0 1.7 - - - +
246E ALA* 3.1 25.7 + - + +
265E ALA* 4.6 6.7 - - + -
266E ASP* 3.8 24.7 - - - -
267E ASN* 4.3 13.7 - - - -
276E LEU* 3.6 44.9 - - + -
277E TRP 2.9 24.9 + - - +
278E LEU* 3.2 23.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 243 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172C SER* 3.5 13.7 - - - -
173C GLU 3.5 22.9 - - - +
174C GLY 3.8 14.8 - - - -
175C THR* 2.8 36.1 - - + -
179C ASP* 3.6 31.6 - - + -
183C ASP* 5.8 0.4 - - - -
239E GLU 3.0 9.6 + - - +
240E ARG 3.9 1.6 - - - +
242E TRP* 1.3 88.8 - + + +
244E ARG* 1.3 60.1 + - + +
246E ALA* 3.1 5.4 + - + +
247E GLU* 2.6 66.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 244 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP* 3.5 23.7 + - - +
240E ARG* 2.9 25.6 + - + +
241E SER 3.8 3.6 - - - +
243E PHE* 1.3 83.4 - - + +
245E GLU* 1.3 57.9 + - - +
247E GLU* 3.3 6.5 + - - +
248E ILE* 3.0 48.5 + - - +
353E GLY 3.4 24.0 - - - +
355E ALA 3.0 24.0 + - - -
356E VAL* 4.6 0.4 - - - +
357E ARG* 4.4 5.7 - - - +
366E ASP* 2.9 46.5 + - - -
367E ILE 4.0 0.4 - - - -
368E ALA* 3.3 30.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 245 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232E LYS* 2.8 27.7 + - - -
234E PHE* 4.1 4.3 - - - -
241E SER 3.0 16.8 + - - +
242E TRP 4.0 2.2 - - - +
244E ARG* 1.3 72.9 - - - +
246E ALA* 1.3 67.3 + - - +
248E ILE* 3.4 3.7 + - - +
249E TYR* 3.1 47.8 + - + -
260E LEU* 6.1 1.4 - - - +
278E LEU* 3.9 18.7 - - + +
351E ASP* 3.5 10.4 + - - +
352E LEU* 3.1 36.8 + - + +
353E GLY* 4.0 12.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 246 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E TRP* 3.1 22.6 + - + +
243E PHE* 3.6 5.6 - - + +
245E GLU* 1.3 77.0 - - - +
247E GLU* 1.3 56.7 - - - +
249E TYR* 3.2 6.2 + - - +
250E GLN* 2.9 42.3 + - - +
262E PHE* 4.5 8.7 - - + -
265E ALA* 4.1 14.6 - - + -
278E LEU* 4.0 18.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 247 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C ASP* 4.1 10.4 - - - +
183C ASP* 2.9 28.6 - - - +
243E PHE* 2.6 52.6 + - + +
244E ARG* 3.4 9.6 - - - +
246E ALA* 1.3 72.0 - - - +
248E ILE* 1.3 62.9 + - - +
250E GLN* 5.2 2.2 - - - -
251E THR* 3.0 50.0 + - - +
357E ARG* 3.5 27.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 248 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244E ARG* 3.0 39.8 + - - +
245E GLU* 3.8 4.0 - - - +
247E GLU* 1.3 76.7 - - - +
249E TYR* 1.3 61.4 + - - +
252E VAL* 2.8 32.2 - - + +
254E LEU* 4.5 1.6 - - + -
329E ILE* 4.3 21.1 - - + -
352E LEU* 3.5 35.4 - - + +
355E ALA* 3.4 34.1 - - + +
357E ARG* 4.3 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 249 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E SER* 4.1 2.2 + - - -
245E GLU* 3.1 47.6 + - + -
246E ALA 3.6 6.5 - - - +
248E ILE* 1.3 81.5 - - - +
250E GLN* 1.3 65.7 + - - +
252E VAL* 3.4 8.2 + - - +
253E MET* 3.4 9.9 + - - -
254E LEU* 3.9 27.5 + - + +
259E ILE* 3.9 13.8 - - + +
260E LEU* 2.6 44.2 + - + +
262E PHE* 3.4 49.4 - + + -
349E ILE 4.9 0.5 + - - -
350E ALA* 5.1 2.4 - - - -
351E ASP 5.3 0.2 + - - -
352E LEU* 3.9 25.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 250 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E SER* 3.0 31.4 + - - +
195E LEU* 5.1 9.9 - - - +
198E GLN* 2.8 44.1 + - - +
246E ALA* 2.9 28.3 + - - +
247E GLU* 4.5 1.7 - - - +
249E TYR* 1.3 70.7 - - - +
251E THR* 1.3 54.1 + - - +
252E VAL 2.7 12.8 + - - -
262E PHE* 3.9 23.4 - - + -
265E ALA* 4.9 4.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 251 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C TYR* 5.6 1.1 - - + -
183C ASP* 4.0 13.9 + - - +
186C THR* 5.8 3.8 - - + -
247E GLU* 3.0 43.0 + - - -
248E ILE 4.7 0.4 - - - -
250E GLN* 1.3 72.0 - - - +
252E VAL* 1.3 66.3 + - + +
357E ARG* 3.4 25.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 252 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248E ILE* 2.8 27.1 - - + +
249E TYR 3.7 0.7 - - - +
250E GLN 2.7 6.1 + - - -
251E THR* 1.3 90.2 - - + +
253E MET* 1.3 68.0 + - - +
254E LEU* 2.9 29.6 + - + +
325E GLY 4.0 14.8 - - - +
326E LYS* 4.4 9.2 - - + +
327E PRO* 3.4 33.7 - - + -
329E ILE* 5.0 6.5 - - + -
357E ARG* 5.0 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 253 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189E SER 5.7 1.8 - - - +
191E SER* 3.0 37.0 - - - +
249E TYR 3.4 3.5 + - - -
252E VAL* 1.3 81.4 - - - +
254E LEU* 1.3 68.0 + - - +
255E ARG* 2.7 44.1 + - - +
324E GLN* 3.4 39.3 - - + +
325E GLY 5.1 0.9 - - - +
326E LYS* 6.4 2.0 - - - -
----------------------------------------------------------
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