Contacts of the helix formed by residues 225 - 246 (chain A) in PDB entry 1U54
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 LEU 225 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLY 3.5 4.6 + - - +
223A HIS 3.4 8.2 + - - +
224A PHE* 1.3 75.1 - - - +
226A LEU* 1.3 69.5 + - + +
227A GLY* 3.1 15.5 - - - +
228A THR* 2.9 31.1 + - - +
229A LEU 3.6 2.3 + - - -
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Residues in contact with LEU 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE 3.5 0.6 + - - -
225A LEU* 1.3 77.2 - - + +
227A GLY* 1.3 64.0 + - - +
228A THR 3.3 0.2 - - - -
229A LEU* 4.0 9.0 - - + +
230A SER* 3.0 26.8 + - - +
324A PHE* 3.7 31.2 - - + -
326A TYR* 3.7 23.3 - - + +
355A ASP* 4.1 22.9 - - + +
357A PRO* 4.1 22.7 - - + -
360A ILE* 5.3 2.2 - - + +
389A GLN 5.0 1.8 - - - +
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Residues in contact with GLY 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.1 16.5 + - - +
226A LEU* 1.3 76.3 - - - +
228A THR* 1.3 61.4 + - - +
230A SER* 3.2 5.5 + - - -
231A ARG* 3.1 37.6 + - - +
389A GLN 4.5 13.5 - - - -
390A PRO* 4.8 5.3 - - - +
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Residues in contact with THR 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223A HIS* 6.3 0.2 - - + -
224A PHE* 3.8 15.9 - - + -
225A LEU* 2.9 19.5 + - - +
227A GLY* 1.3 74.8 - - - +
229A LEU* 1.3 61.2 + - - +
231A ARG* 3.3 23.1 + - - +
232A TYR* 3.2 55.1 + - + +
263A ARG* 4.5 22.2 + - + +
264A ASP* 6.0 1.8 - - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217A LEU* 3.7 17.3 - - + -
224A PHE* 3.3 43.3 - - + +
225A LEU 3.6 2.6 + - - +
226A LEU* 3.7 10.3 + - + +
227A GLY 3.4 0.8 - - - -
228A THR* 1.3 78.3 - - - +
230A SER* 1.3 59.1 + - - +
232A TYR* 3.4 14.6 + - + +
233A ALA* 3.0 23.6 + - - +
323A MET* 3.4 29.7 - - + +
324A PHE* 3.6 41.0 - - + -
326A TYR* 4.1 15.7 - - + +
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Residues in contact with SER 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU 3.0 17.1 + - - -
227A GLY 3.2 5.8 + - - -
229A LEU* 1.3 75.9 - - - +
231A ARG* 1.3 60.7 + - - +
232A TYR 3.1 1.8 - - - -
233A ALA* 2.9 23.8 + - - +
234A VAL* 3.0 20.6 + - - +
324A PHE* 3.7 8.1 - - - -
360A ILE* 3.5 27.2 - - - +
385A LEU* 5.1 8.4 - - - +
388A ALA 4.6 8.2 + - - -
389A GLN 4.9 2.2 + - - -
390A PRO* 4.8 10.5 - - - -
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Residues in contact with ARG 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLY* 3.1 27.0 + - - +
228A THR* 3.3 22.2 + - + +
230A SER* 1.3 73.9 - - - +
232A TYR* 1.3 66.4 + - + +
234A VAL* 4.0 7.0 - - - +
235A GLN* 3.2 34.7 + - - +
264A ASP* 4.3 24.7 + - - +
390A PRO* 4.6 27.1 - - + +
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Residues in contact with TYR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LEU* 3.6 21.3 - - + -
224A PHE* 3.3 33.9 - + - -
228A THR* 3.2 32.2 + - + +
229A LEU* 3.5 16.8 - - + +
230A SER 3.1 0.8 - - - -
231A ARG* 1.3 78.9 - - + +
233A ALA* 1.3 67.4 + - - +
235A GLN* 3.0 5.2 + - - +
236A VAL* 2.7 28.0 + - + +
260A LEU* 3.8 19.5 - - + +
263A ARG* 2.7 33.8 + - - +
264A ASP* 4.5 7.2 - - - -
266A VAL* 4.0 27.8 - - + -
323A MET* 4.3 12.1 - - + -
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A LEU 3.0 12.4 + - - +
230A SER* 2.9 16.3 + - - +
232A TYR* 1.3 72.5 - - - +
234A VAL* 1.3 64.3 + - - +
236A VAL* 3.0 8.3 + - - +
237A ALA* 3.0 20.3 + - - +
316A PHE* 3.9 5.5 - - + -
320A LEU* 3.7 28.9 - - + -
323A MET* 4.5 6.3 - - - -
324A PHE* 5.3 0.2 - - + -
385A LEU* 3.4 22.9 - - + +
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Residues in contact with VAL 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A SER* 3.0 18.7 + - - +
231A ARG* 4.0 7.2 - - - +
233A ALA* 1.3 74.1 - - - +
235A GLN* 1.3 59.9 + - + +
237A ALA* 2.8 20.1 + - - +
238A GLU* 2.9 34.3 + - - +
382A ARG* 4.5 10.2 - - + +
385A LEU* 3.4 30.2 - - + +
386A LEU* 4.1 35.0 - - + +
390A PRO* 5.3 4.9 - - + -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188A ASN* 3.1 37.8 - - - +
231A ARG* 3.2 23.6 + - - +
232A TYR* 3.0 6.6 + - - +
234A VAL* 1.3 79.6 - - + +
236A VAL* 1.3 62.1 + - - +
238A GLU* 4.0 8.3 - - - +
239A GLY 3.0 18.2 + - - -
264A ASP 2.7 30.1 + - - +
265A LEU* 4.2 6.7 - - + +
266A VAL* 3.1 34.5 + - + +
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Residues in contact with VAL 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A TYR 2.7 20.4 + - - +
233A ALA* 3.4 8.1 - - - +
235A GLN* 1.3 74.1 - - - +
237A ALA* 1.3 57.8 + - - +
240A MET* 2.9 30.4 + - + +
253A LEU* 4.4 7.4 - - + -
258A LEU* 3.6 38.1 - - + -
266A VAL* 4.5 10.5 - - + -
267A LYS 6.4 0.2 - - - -
268A ILE* 3.5 18.9 - - + +
316A PHE* 3.5 26.5 - - + -
319A THR* 5.5 1.8 - - + -
323A MET* 4.1 9.9 - - + -
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Residues in contact with ALA 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA 3.0 10.6 + - - +
234A VAL* 2.8 10.7 + - - +
236A VAL* 1.3 75.8 - - - +
238A GLU* 1.3 52.9 + - - +
240A MET* 3.0 6.4 + - - +
241A GLY* 2.7 34.5 + - - -
316A PHE* 4.2 17.3 - - + -
378A PHE* 3.5 11.5 - - + +
381A LEU* 4.4 5.2 - - + -
382A ARG* 4.0 28.7 - - - +
385A LEU* 4.4 1.3 - - + -
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Residues in contact with GLU 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A HIS* 3.6 17.5 + - + +
188A ASN* 3.6 19.5 - - - +
234A VAL* 2.9 31.6 + - - +
235A GLN* 4.0 8.3 - - - +
237A ALA* 1.3 71.5 - - - +
239A GLY* 1.3 67.3 + - - +
241A GLY* 3.2 9.4 + - - -
242A TYR* 3.2 9.0 + - - +
382A ARG* 3.7 36.7 + - + +
386A LEU* 5.7 0.3 - - - +
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Residues in contact with GLY 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186A HIS* 4.1 4.9 - - - -
188A ASN* 3.8 17.2 - - - +
189A LEU* 3.8 19.9 - - - +
235A GLN 3.0 16.6 + - - -
236A VAL 3.6 5.4 - - - -
238A GLU* 1.3 77.4 - - - +
240A MET* 1.3 61.2 + - - +
241A GLY 3.4 0.2 + - - -
242A TYR* 3.5 14.0 - - - +
243A LEU* 3.5 11.4 + - - +
268A ILE* 4.0 2.7 - - - -
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Residues in contact with MET 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A VAL* 2.9 21.6 + - + +
237A ALA 3.0 1.5 + - - +
239A GLY* 1.3 75.3 - - - +
241A GLY* 1.3 59.1 + - - +
243A LEU* 3.6 29.3 + - + +
244A GLU 3.1 18.4 + - - -
250A HIS* 4.1 10.3 - - + -
253A LEU* 3.9 28.9 - - + -
268A ILE* 3.7 15.3 - - + -
312A ASP* 3.6 28.5 - - - +
378A PHE* 3.2 56.9 - - + -
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Residues in contact with GLY 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A ALA 2.7 18.1 + - - -
238A GLU* 3.2 2.4 + - - -
240A MET* 1.3 73.1 - - - +
242A TYR* 1.3 61.3 + - - +
244A GLU* 3.4 9.0 + - - +
245A SER* 3.0 26.3 + - - -
378A PHE* 3.7 13.9 - - - -
379A VAL* 5.2 6.9 - - - +
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Residues in contact with TYR 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER 4.4 0.5 + - - -
184A LEU* 3.8 22.3 - - + -
185A ASP* 3.1 41.0 + - - +
186A HIS* 3.4 25.4 - + + +
189A LEU* 3.5 23.6 - - + -
238A GLU 3.2 6.4 + - - +
239A GLY 3.5 9.2 - - - +
241A GLY* 1.3 73.7 - - - +
243A LEU* 1.3 67.0 + - + +
245A SER* 2.5 29.1 + - - -
246A LYS* 3.1 40.1 + - + +
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184A LEU* 3.4 36.1 - - + -
189A LEU* 3.5 22.4 - - + -
239A GLY 3.5 11.7 + - - +
240A MET* 3.7 32.3 - - + +
241A GLY 3.5 0.4 - - - -
242A TYR* 1.3 77.5 - - - +
244A GLU* 1.3 63.9 + - - +
246A LYS* 3.2 7.3 + - - -
247A ARG 3.1 18.4 + - - -
248A PHE* 3.2 26.7 + - + +
250A HIS* 4.0 29.4 - - + +
268A ILE* 5.6 0.2 - - + -
271A PHE* 4.5 4.0 - - + -
274A MET* 4.4 10.8 - - - -
312A ASP* 6.1 0.2 - - - +
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Residues in contact with GLU 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A MET 3.1 15.0 + - - +
241A GLY* 3.4 10.8 - - - +
242A TYR 3.1 0.4 - - - -
243A LEU* 1.3 77.1 - - - +
245A SER* 1.3 63.3 + - - +
247A ARG* 3.1 14.9 + - - +
309A HIS* 3.6 42.4 + - + +
377A THR* 3.2 41.0 + - - +
378A PHE* 3.4 20.0 + - + +
379A VAL* 4.2 8.0 + - - +
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Residues in contact with SER 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A GLY 3.0 12.2 + - - -
242A TYR* 2.5 28.5 + - - -
244A GLU* 1.3 77.7 - - - +
246A LYS* 1.3 65.2 + - - +
247A ARG* 3.1 11.6 + - - +
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Residues in contact with LYS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A SER* 4.3 16.8 + - - -
242A TYR* 3.1 55.1 + - + +
243A LEU* 3.5 5.2 - - - +
245A SER* 1.3 81.2 + - - +
247A ARG* 1.3 65.7 + - - +
248A PHE* 3.2 37.0 + - + -
276A ALA* 5.6 0.7 - - - +
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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