Contacts of the helix formed by residues 231 - 255 (chain A) in PDB entry 5LXG
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 SER 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A PHE* 2.7 28.3 + - - +
230A CYS* 1.3 80.7 - - - +
232A PRO* 1.4 66.3 - - - +
234A PRO* 3.1 34.5 - - - +
235A ARG* 3.6 5.4 - - - +
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Residues in contact with PRO 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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229A TYR 5.1 1.8 - - - +
230A CYS 3.3 11.4 - - - +
231A SER* 1.4 80.9 - - - +
233A GLN* 1.3 66.4 + - + +
235A ARG* 3.3 32.3 + - - +
236A LEU* 3.1 24.7 + - - +
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Residues in contact with GLN 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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232A PRO* 1.3 80.1 - - - +
234A PRO* 1.4 69.5 - - + +
236A LEU* 3.6 4.5 + - - +
237A ILE* 3.3 42.7 + - + +
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Residues in contact with PRO 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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228A PHE* 3.4 26.2 - - + -
231A SER* 3.1 43.1 - - - +
232A PRO* 5.1 0.2 - - + -
233A GLN* 1.4 93.8 - - + +
235A ARG* 1.3 55.0 + - - +
237A ILE* 2.7 34.7 - - + +
238A TYR* 2.8 16.3 - - + -
284A HIS* 4.2 14.4 - - + +
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Residues in contact with ARG 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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224A LEU* 4.0 11.4 - - - +
225A TYR* 3.4 62.5 + - - +
228A PHE* 3.6 17.2 + - + -
229A TYR* 3.6 21.0 + - - +
231A SER 3.6 12.1 - - - +
232A PRO* 3.6 35.6 + - - +
233A GLN 3.3 0.4 - - - -
234A PRO* 1.3 77.9 - - - +
236A LEU* 1.3 65.6 + - - +
238A TYR* 3.4 5.8 + - - +
239A LEU* 3.2 38.9 + - + +
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Residues in contact with LEU 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 PRO 3.1 16.2 + - - +
233A GLN* 4.1 4.9 - - - +
234A PRO 3.5 0.2 - - - -
235A ARG* 1.3 79.0 - - - +
237A ILE* 1.3 73.3 + - + +
239A LEU* 3.5 9.9 + - - +
240A SER* 3.0 38.1 + - - +
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Residues in contact with ILE 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 GLN* 3.3 28.4 + - + +
234A PRO* 2.7 36.8 - - + +
236A LEU* 1.3 86.4 - - + +
238A TYR* 1.3 80.7 + - + +
240A SER* 3.5 11.1 + - - -
241A ILE* 3.3 24.2 + - + +
284A HIS* 6.1 0.9 - - + +
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Residues in contact with TYR 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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224A LEU* 3.8 22.2 - - + -
228A PHE* 4.5 7.6 - + - -
234A PRO* 2.8 32.3 + - + +
235A ARG* 3.4 5.4 + - - +
237A ILE* 1.3 92.6 - - + +
239A LEU* 1.3 62.2 + - - +
241A ILE* 3.5 17.3 + - + +
242A VAL* 3.3 25.9 + - + +
277A SER* 4.8 2.8 + - - -
280A VAL* 3.3 21.7 - - + +
281A PRO* 2.6 55.6 - - + -
284A HIS* 3.0 40.4 - + + +
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Residues in contact with LEU 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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220A PHE* 4.8 1.3 - - + -
221A VAL* 3.9 44.0 - - + +
224A LEU* 3.8 22.4 - - + -
225A TYR* 5.8 2.7 - - + +
235A ARG* 3.2 35.6 + - + +
236A LEU* 3.6 8.7 - - - +
238A TYR* 1.3 76.6 - - - +
240A SER* 1.3 64.1 + - - +
242A VAL* 3.4 5.9 + - + +
243A CYS* 3.0 35.3 + - - -
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Residues in contact with SER 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 LEU* 3.0 26.1 + - - +
237A ILE* 3.8 8.5 - - - -
238A TYR 3.4 0.2 - - - -
239A LEU* 1.3 77.1 - - - +
241A ILE* 1.4 52.9 + - - +
243A CYS* 3.4 5.5 + - - +
244A VAL* 2.8 44.3 + - - +
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Residues in contact with ILE 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 ILE* 3.3 21.1 - - + +
238A TYR* 3.7 19.3 - - + +
239A LEU 3.3 0.4 - - - -
240A SER* 1.4 75.4 - - - +
242A VAL* 1.3 51.8 + - - +
244A VAL* 3.3 5.7 + - - +
245A LEU* 2.8 62.8 + - + +
277A SER* 3.8 15.0 - - - +
280A VAL* 6.5 1.6 - - + -
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Residues in contact with VAL 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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216A ILE* 5.1 1.8 - - + -
217A MET* 4.1 25.3 - - + +
220A PHE* 3.3 48.0 - - + -
224A LEU* 4.6 5.8 - - + -
238A TYR* 3.3 16.4 + - + +
239A LEU* 3.4 8.7 + - + +
241A ILE* 1.3 75.7 - - - +
243A CYS* 1.3 53.9 + - - +
245A LEU* 3.3 5.8 + - - +
246A GLY* 2.5 33.6 + - - -
274A LEU* 4.7 5.7 - - + +
277A SER* 3.8 17.5 - - - +
281A PRO* 6.5 1.3 - - + -
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Residues in contact with CYS 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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175A MET* 6.1 4.9 - - - -
217A MET* 4.0 19.5 - - - -
221A VAL* 6.0 5.2 - - - -
239A LEU* 3.0 29.0 + - - +
240A SER* 3.9 5.4 - - - +
242A VAL* 1.3 74.7 - - - +
244A VAL* 1.3 57.2 + - + +
247A ILE* 2.7 49.3 + - + +
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Residues in contact with VAL 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 SER* 2.8 28.3 + - - +
241A ILE* 3.8 5.6 - - - +
243A CYS* 1.3 70.9 - - + +
245A LEU* 1.3 64.1 + - + +
247A ILE* 3.9 5.1 - - - +
248A SER* 2.9 32.3 + - - -
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Residues in contact with LEU 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 ILE* 2.8 44.0 + - + +
242A VAL* 3.7 3.1 - - - +
244A VAL* 1.3 78.7 - - + +
246A GLY* 1.3 52.5 + - - +
248A SER* 3.3 7.2 - - - +
249A ALA* 2.8 28.4 + - - +
270A VAL* 3.2 18.8 - - + +
273A GLY* 3.2 40.2 - - - +
274A LEU* 3.5 15.7 - - + +
277A SER* 3.9 7.9 - - - -
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Residues in contact with GLY 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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213A ALA* 4.4 0.4 - - - +
217A MET* 3.5 27.7 - - - +
242A VAL 2.5 21.6 + - - -
243A CYS 3.4 1.3 - - - -
245A LEU* 1.3 71.5 - - - +
247A ILE* 1.4 58.5 + - - +
249A ALA* 3.1 4.9 + - - +
250A ILE* 3.0 32.7 + - - +
274A LEU* 3.8 9.4 - - - +
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Residues in contact with ILE 247 (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 MET* 3.6 22.7 - - + -
243A CYS* 2.7 42.1 + - + +
244A VAL* 4.0 4.7 - - - +
246A GLY* 1.4 66.4 - - - -
248A SER* 1.3 67.2 + - - +
250A ILE* 3.3 10.0 + - + +
251A ILE* 2.9 44.5 + - + +
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Residues in contact with SER 248 (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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244A VAL* 2.9 21.8 + - - -
245A LEU* 3.3 11.2 - - - -
247A ILE* 1.3 77.8 - - - +
249A ALA* 1.4 51.8 + - - +
251A ILE* 3.8 4.8 - - - +
252A VAL* 2.8 42.8 + - - +
270A VAL* 2.5 37.1 - - - +
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Residues in contact with ALA 249 (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 ALA* 3.7 20.6 - - + -
245A LEU 2.8 12.8 + - - +
246A GLY* 3.1 11.1 + - - +
248A SER* 1.4 69.6 - - - +
250A ILE* 1.3 61.1 + - - +
252A VAL* 3.8 2.9 - - - +
253A ALA* 2.9 31.5 + - - +
267A ARG* 5.5 1.4 - - - +
270A VAL* 3.0 21.9 - - + +
271A PHE* 5.3 2.5 - - - +
274A LEU* 4.2 11.2 - - + -
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Residues in contact with ILE 250 (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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210A SER* 3.6 31.1 + - - +
213A ALA* 4.0 14.6 - - + -
214A LEU* 3.4 32.5 - - + -
217A MET* 4.2 8.7 - - + -
246A GLY 3.0 16.2 + - - +
247A ILE* 3.9 9.0 - - + +
249A ALA* 1.3 72.7 - - - +
251A ILE* 1.4 60.0 + - + +
253A ALA* 3.2 3.0 + - - +
254A GLN* 2.8 47.1 + - - +
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Residues in contact with ILE 251 (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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247A ILE* 2.9 37.7 + - + +
248A SER* 3.9 4.5 - - - +
250A ILE* 1.4 76.9 - - + +
252A VAL* 1.3 62.9 + - + +
254A GLN* 5.1 4.7 - - + +
255A TRP* 2.8 32.3 + - - +
256A ASP* 5.2 6.5 - - - +
257A ARG* 3.8 39.7 - - + +
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Residues in contact with VAL 252 (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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248A SER* 2.8 33.3 + - - +
249A ALA* 3.8 5.2 - - - +
251A ILE* 1.3 76.9 - - + +
253A ALA* 1.3 60.3 + - - +
255A TRP* 3.2 20.4 - - - +
260A THR* 4.7 5.6 - - + +
264A ARG* 5.9 4.9 - - - +
266A THR* 4.5 7.0 - - + -
267A ARG* 3.0 46.4 - - + +
270A VAL* 3.8 21.1 - - + -
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Residues in contact with ALA 253 (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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206A LYS* 3.9 10.6 - - - +
209A TYR* 3.8 32.9 - - + +
210A SER* 4.3 8.1 - - - +
249A ALA 2.9 17.9 + - - +
250A ILE 3.7 2.9 - - - +
252A VAL* 1.3 76.6 - - - +
254A GLN* 1.3 58.1 + - - +
255A TRP* 2.9 21.7 + - - -
267A ARG* 4.6 22.6 + - + +
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Residues in contact with GLN 254 (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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206A LYS* 3.3 35.7 - - + +
207A LEU* 3.7 23.0 - - - +
210A SER* 3.4 24.0 + - - +
250A ILE* 2.8 27.1 + - - +
251A ILE* 4.6 4.8 - - + +
253A ALA* 1.3 68.2 - - - +
255A TRP* 1.3 82.7 + - - +
256A ASP* 2.9 30.4 + - + +
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Residues in contact with TRP 255 (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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202A ARG* 5.6 7.0 - - - -
206A LYS* 2.7 38.8 - - - +
251A ILE* 2.8 23.2 + - - +
252A VAL* 3.2 16.6 - - - +
253A ALA* 2.9 26.8 + - - -
254A GLN* 1.3 73.7 - - - +
256A ASP* 1.3 67.7 + - - +
257A ARG 3.3 2.9 + - - -
258A PHE* 3.5 27.1 + - - +
259A ALA* 3.5 7.6 - - + +
260A THR* 2.7 46.7 + - + +
261A PRO* 5.2 8.1 - - + -
264A ARG* 5.9 0.2 - - - +
267A ARG* 5.7 2.8 - - - +
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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