Contacts of the helix formed by residues 238 - 253 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215B ARG* 3.6 26.6 - - - +
216B PHE* 3.5 25.4 - - - +
234B PHE* 3.9 8.0 - - + -
235B SER* 2.6 29.1 + - - +
237B ARG* 1.3 103.9 + - + +
239B GLU* 1.3 63.7 + - - +
240B ARG* 3.2 4.3 - - - +
241B SER* 3.1 32.4 + - - +
242B TRP 3.4 6.8 + - - -
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Residues in contact with GLU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A GLU* 3.8 14.8 - - + +
174A GLY* 3.4 30.5 + - - +
225A ARG* 5.6 2.9 + - - -
235B SER 3.8 0.4 + - - -
236B SER 3.3 14.3 + - - +
237B ARG 3.4 2.8 - - - +
238B GLU* 1.3 77.6 - - - +
240B ARG* 1.3 70.3 + - + +
242B TRP* 3.2 4.0 + - - +
243B PHE* 3.0 25.1 + - - +
274B THR* 6.0 1.0 - - - +
276B LEU* 3.5 28.2 - - + +
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Residues in contact with ARG 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A GLY* 4.0 21.7 + - - +
176A THR* 4.1 21.6 - - + +
237B ARG 5.4 5.7 + - - -
238B GLU* 3.1 2.2 + - - +
239B GLU* 1.3 86.3 + - - +
241B SER* 1.3 58.0 + - - +
243B PHE* 3.5 1.0 + - - +
244B ARG* 2.9 40.3 + - + +
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Residues in contact with SER 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B ARG* 6.0 1.6 - - - +
216B PHE* 4.9 5.8 - - - -
234B PHE* 3.7 16.5 - - - -
238B GLU* 3.1 31.3 + - - -
240B ARG* 1.3 76.3 - - - +
242B TRP* 1.3 65.9 + - - +
244B ARG* 3.7 4.8 - - - +
245B GLU* 3.0 28.2 + - - +
353B GLY* 4.5 14.7 - - - -
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Residues in contact with TRP 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A SER* 4.1 14.1 - - - -
173A GLU* 3.6 23.8 - - - -
234B PHE* 3.4 36.2 - + + -
238B GLU 3.4 1.4 + - - -
239B GLU 3.2 10.9 + - - +
241B SER* 1.3 80.0 - - - +
243B PHE* 1.3 85.4 + + + +
245B GLU* 3.6 1.4 + - - +
246B ALA* 3.1 24.5 + - + +
265B ALA* 4.6 7.4 - - + -
266B ASP* 3.8 25.4 - - - -
267B ASN* 4.4 13.0 - - - -
276B LEU* 3.6 46.9 - - + -
277B TRP 2.9 25.5 + - - +
278B LEU* 3.2 21.7 - - + +
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Residues in contact with PHE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A SER* 3.4 21.8 - - - -
173A GLU 3.5 17.0 - - - +
174A GLY 3.9 14.1 - - - -
175A THR* 3.0 32.5 - - + -
179A ASP* 3.7 30.5 - - + -
183A ASP* 5.8 0.7 - - - -
239B GLU 3.0 12.6 + - - +
240B ARG* 3.9 1.8 - - + +
242B TRP* 1.3 84.5 - + + +
244B ARG* 1.3 63.1 + - + +
246B ALA* 3.0 4.5 + - + +
247B GLU* 2.6 67.8 + - + +
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Residues in contact with ARG 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 3.5 25.2 + - - +
240B ARG* 2.9 26.6 + - + +
241B SER* 3.7 3.6 - - - +
243B PHE* 1.3 83.7 - - + +
245B GLU* 1.3 58.0 + - - +
247B GLU* 3.3 6.3 + - - +
248B ILE* 3.0 49.8 + - - +
353B GLY 3.6 23.6 - - - +
354B LEU 4.9 0.2 - - - -
355B ALA 3.1 22.5 + - - -
356B VAL* 4.6 0.8 - - - +
357B ARG* 4.1 8.1 - - - +
366B ASP* 3.1 48.7 + - - +
367B ILE 4.3 6.9 + - - -
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Residues in contact with GLU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B LYS* 2.8 28.3 + - - -
234B PHE* 4.1 4.3 - - - -
241B SER 3.0 17.8 + - - +
242B TRP 4.0 2.2 - - - +
244B ARG* 1.3 76.9 - - - +
246B ALA* 1.3 64.5 + - - +
248B ILE* 3.4 3.8 + - - +
249B TYR* 3.1 48.0 + - + -
260B LEU* 6.1 0.9 - - - +
278B LEU* 4.0 19.0 - - + +
351B ASP* 3.5 9.7 + - - -
352B LEU* 3.1 36.8 + - + +
353B GLY* 4.1 11.2 + - - +
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Residues in contact with ALA 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B TRP* 3.1 21.9 + - + +
243B PHE* 3.0 6.1 + - + +
245B GLU* 1.3 77.1 - - - +
247B GLU* 1.3 58.8 + - - +
249B TYR* 3.2 5.3 + - - +
250B GLN* 2.9 42.9 + - - +
262B PHE* 4.6 8.1 - - + -
265B ALA* 4.2 13.2 - - + -
278B LEU* 4.0 19.3 - - + +
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Residues in contact with GLU 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179A ASP* 4.3 8.6 - - - +
183A ASP* 3.0 29.2 - - - +
243B PHE* 2.6 53.2 + - + +
244B ARG* 3.3 9.2 - - - +
246B ALA* 1.3 73.1 - - - +
248B ILE* 1.3 63.2 + - - +
250B GLN* 5.2 1.8 - - - -
251B THR* 3.0 46.8 + - - +
357B ARG* 3.4 28.7 + - - +
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Residues in contact with ILE 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B ARG* 3.0 39.4 + - - +
245B GLU* 3.8 4.0 - - - +
246B ALA 3.3 0.2 - - - -
247B GLU* 1.3 75.6 - - - +
249B TYR* 1.3 59.0 + - - +
252B VAL* 3.0 36.3 - - + +
254B LEU* 4.5 2.7 - - + +
329B ILE* 4.2 21.8 - - + -
352B LEU* 3.6 35.2 - - + +
355B ALA* 3.4 33.2 - - + +
357B ARG* 4.2 25.8 - - + +
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Residues in contact with TYR 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B GLU* 3.1 48.7 + - + +
246B ALA 3.2 6.7 + - - +
248B ILE* 1.3 79.7 - - - +
250B GLN* 1.3 59.6 + - - +
253B MET* 3.0 25.5 + - - -
254B LEU* 3.6 25.5 + - + -
259B ILE* 4.0 16.7 - - + +
260B LEU* 2.6 46.4 + - + +
262B PHE* 3.4 46.9 - + + -
278B LEU* 6.2 0.2 - - + -
349B ILE 4.9 0.7 + - - -
350B ALA* 5.0 2.6 - - - -
351B ASP 5.2 0.2 + - - -
352B LEU* 3.8 23.6 - - + +
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Residues in contact with GLN 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191B SER* 5.6 2.3 - - - -
195B LEU* 5.0 8.6 - - - +
198B GLN* 2.8 44.1 + - - +
246B ALA* 2.9 28.6 + - - +
247B GLU* 4.5 1.5 - - - +
249B TYR* 1.3 72.1 - - - +
251B THR* 1.3 63.3 + - - +
253B MET* 3.1 20.1 + - - +
262B PHE* 3.8 22.9 - - + -
265B ALA* 4.8 5.9 - - - +
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Residues in contact with THR 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A TYR* 5.7 0.4 - - + -
183A ASP* 3.8 14.1 + - - +
247B GLU* 3.0 33.1 + - - +
250B GLN* 1.3 73.9 - - - +
252B VAL* 1.3 69.6 + - + +
253B MET* 3.9 10.9 - - - +
327B PRO* 6.1 0.2 - - + -
357B ARG* 3.0 32.3 - - - +
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B ILE* 3.0 24.8 + - - +
250B GLN 3.1 0.4 - - - -
251B THR* 1.3 89.5 - - + +
253B MET* 1.3 92.5 + - - +
254B LEU* 3.7 18.2 - - + -
326B LYS* 3.5 27.7 - - + +
327B PRO* 3.6 15.3 - - + -
329B ILE* 4.2 13.7 - - + -
357B ARG* 4.0 20.4 - - - -
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Residues in contact with MET 253 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189B SER 5.3 1.6 - - - +
190B GLY* 3.4 35.9 - - - +
191B SER* 4.4 14.4 - - - +
249B TYR 3.0 10.2 + - - -
250B GLN* 3.1 14.4 + - - +
251B THR 3.9 8.7 - - - +
252B VAL* 1.3 103.3 - - - +
254B LEU* 1.3 59.1 + - - +
255B ARG* 3.6 6.3 + - - +
315B HIS* 5.9 0.3 - - - -
325B GLY 2.9 32.8 - - - +
326B LYS* 5.0 4.4 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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