Contacts of the helix formed by residues 221 - 245 (chain A) in PDB entry 5I4V
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 THR 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A GLN 3.8 2.2 + - - -
220A LEU* 1.3 75.1 - - - +
222A ALA* 1.3 58.4 + - + +
223A ALA* 3.3 25.4 - - + +
224A GLN* 2.9 27.9 + - + -
225A GLU* 2.8 33.7 + - - +
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Residues in contact with ALA 222 (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 LEU 3.7 1.2 + - - -
221A THR* 1.3 74.6 - - + +
223A ALA* 1.3 64.1 + - - +
225A GLU* 3.0 10.9 + - - +
226A LEU* 2.9 36.4 + - + +
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Residues in contact with ALA 223 (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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221A THR* 3.3 15.6 - - + +
222A ALA* 1.3 78.6 - - - +
224A GLN* 1.3 58.1 + - + +
226A LEU* 3.2 9.1 + - - +
227A MET* 2.9 29.7 + - - +
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Residues in contact with GLN 224 (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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219A GLN 3.8 6.2 - - - +
220A LEU* 3.7 16.5 - - + +
221A THR* 2.9 39.5 + - - +
223A ALA* 1.3 76.9 - - + +
225A GLU* 1.3 65.4 + - - +
227A MET* 3.3 11.3 + - + +
228A ILE* 3.0 30.1 + - + +
398A PRO 4.9 1.0 + - - -
401A GLU* 4.0 13.5 + - - +
402A ALA* 3.7 36.1 - - + +
405A SER* 3.9 9.2 + - - -
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Residues in contact with GLU 225 (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 LEU* 4.2 24.2 - - + +
221A THR 2.8 16.2 + - - +
222A ALA* 3.0 12.6 + - - +
224A GLN* 1.3 72.6 - - - +
226A LEU* 1.3 60.4 + - + +
228A ILE* 3.3 4.1 + - - +
229A GLN* 2.9 45.0 + - + +
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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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222A ALA* 2.9 27.4 + - + +
223A ALA* 3.7 7.2 - - - +
225A GLU* 1.3 76.7 - - + +
227A MET* 1.3 61.1 + - - +
229A GLN* 3.6 22.4 - - + +
230A GLN* 2.9 28.6 + - - +
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Residues in contact with MET 227 (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 ALA 2.9 15.9 + - - +
224A GLN* 3.3 10.7 + - + +
226A LEU* 1.3 76.0 - - - +
228A ILE* 1.3 66.0 + - - +
230A GLN* 3.1 9.0 + - - +
231A LEU* 3.0 23.7 + - + +
290A PRO* 4.7 13.0 - - + -
372A LEU* 4.4 4.7 - - + -
398A PRO* 4.2 14.4 - - + +
399A TYR* 3.3 52.9 - - + +
402A ALA* 3.6 30.1 - - + -
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Residues in contact with ILE 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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220A LEU* 4.5 13.2 - - + -
224A GLN 3.0 18.7 + - - +
225A GLU* 3.7 3.8 - - - +
227A MET* 1.3 76.3 - - + +
229A GLN* 1.3 64.5 + - - +
231A LEU* 3.1 10.4 + - + +
232A VAL* 3.0 23.3 + - + +
368A ALA* 3.6 37.0 - - + +
371A ALA* 6.2 0.2 - - + -
372A LEU* 3.9 27.6 - - + -
402A ALA* 4.4 11.4 - - + +
406A TYR* 3.7 33.7 - - + -
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Residues in contact with GLN 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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225A GLU* 2.9 33.2 + - - +
226A LEU* 3.6 29.7 - - + +
228A ILE* 1.3 77.4 - - - +
230A GLN* 1.3 56.3 + - - +
232A VAL* 3.5 6.2 + - - +
233A ALA* 2.9 31.7 + - + +
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Residues in contact with GLN 230 (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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226A LEU 2.9 15.9 + - - +
227A MET* 3.1 11.6 + - - +
229A GLN* 1.3 76.7 - - - +
231A LEU* 1.3 57.8 + - - +
233A ALA* 3.4 7.0 + - - +
234A ALA* 2.9 26.0 + - - +
288A GLN* 3.5 44.6 + - - +
290A PRO* 4.4 17.9 - - + -
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Residues in contact with LEU 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 MET* 3.0 18.1 + - + +
228A ILE* 3.1 7.8 + - + +
230A GLN* 1.3 72.9 - - - +
232A VAL* 1.3 66.9 + - - +
234A ALA* 3.1 7.1 + - - +
235A GLN* 3.0 21.1 + - - +
285A PHE* 3.6 13.6 - - + -
288A GLN 4.9 1.8 - - - +
289A VAL* 4.1 25.4 - - + -
290A PRO* 4.0 26.2 - - + -
371A ALA* 3.9 27.8 - - + +
372A LEU* 3.9 31.2 - - + -
375A ALA* 4.2 2.7 - - + -
399A TYR* 4.1 15.9 - - + -
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Residues in contact with VAL 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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228A ILE* 3.0 20.9 + - + +
229A GLN* 3.8 6.7 - - - +
231A LEU* 1.3 76.3 - - - +
233A ALA* 1.3 64.2 + - - +
235A GLN* 3.3 12.0 + - - +
236A LEU* 3.3 28.0 + - + +
367A ASP* 4.1 18.6 - - + +
368A ALA* 3.6 38.4 - - + +
371A ALA* 4.4 6.3 - - + -
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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 GLN* 2.9 19.9 + - + +
230A GLN* 3.6 10.3 - - - +
232A VAL* 1.3 78.7 - - - +
234A ALA* 1.3 61.8 + - - +
236A LEU* 3.2 11.3 + - - +
237A GLN* 3.1 25.4 + - - +
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Residues in contact with ALA 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 GLN* 2.9 20.5 + - - +
231A LEU* 3.1 7.1 + - - +
233A ALA* 1.3 76.3 - - - +
235A GLN* 1.3 56.1 + - - +
237A GLN* 3.5 4.6 + - - +
238A CYS* 3.0 35.1 + - - -
285A PHE* 3.9 14.6 - - + -
288A GLN* 3.9 42.1 - - + +
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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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231A LEU 3.0 10.4 + - - +
232A VAL* 3.7 9.4 - - - +
234A ALA* 1.3 73.6 - - - +
236A LEU* 1.3 62.6 + - + +
238A CYS* 3.3 6.5 + - - +
239A ASN* 2.8 40.9 + - - +
281A GLU* 5.6 1.8 + - - -
285A PHE* 3.5 28.3 - - + -
315A GLU* 2.6 32.5 + - - -
318A ARG* 3.0 30.5 + - - +
367A ASP 4.1 0.3 - - - +
371A ALA* 3.5 21.9 - - + +
374A ILE* 3.6 13.0 - - - +
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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 VAL* 3.3 27.1 + - + +
233A ALA* 3.2 10.1 + - - +
235A GLN* 1.3 75.1 - - + +
237A GLN* 1.3 61.1 + - - +
239A ASN* 3.3 16.1 + - + +
240A LYS* 3.0 43.3 + - + +
367A ASP* 5.6 7.4 - - - +
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Residues in contact with GLN 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* 3.1 16.9 + - - +
234A ALA* 3.6 6.1 - - - +
236A LEU* 1.3 78.5 - - - +
238A CYS* 1.3 59.4 + - - +
240A LYS* 3.5 20.3 + - - +
241A ARG* 3.3 49.8 + - - +
288A GLN* 3.3 33.6 + - - +
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Residues in contact with CYS 238 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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234A ALA 3.0 24.7 + - - +
235A GLN* 3.6 7.2 - - - +
236A LEU 3.2 0.2 - - - -
237A GLN* 1.3 74.9 - - - +
239A ASN* 1.3 65.1 + - - +
241A ARG* 3.3 11.7 + - - +
242A SER* 3.1 23.9 + - - -
281A GLU* 3.9 21.0 - - + +
284A ASP* 3.7 17.0 - - + -
285A PHE* 3.5 37.7 - - + -
288A GLN* 4.1 8.7 - - - -
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Residues in contact with ASN 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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235A GLN* 2.8 32.9 + - - +
236A LEU* 3.6 18.7 - - + +
238A CYS* 1.3 71.6 - - - +
240A LYS* 1.3 65.5 + - + +
242A SER* 3.1 8.5 + - - -
243A PHE* 3.0 22.2 + - - +
281A GLU* 3.0 25.5 + - - -
315A GLU* 5.0 2.2 + - - -
318A ARG* 6.0 1.7 - - - -
319A ARG* 3.3 22.9 + - - +
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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236A LEU* 3.0 30.2 + - - +
237A GLN* 3.7 20.5 - - - +
238A CYS 3.3 0.2 - - - -
239A ASN* 1.3 76.5 - - + +
241A ARG* 1.3 62.1 + - - +
243A PHE* 3.2 10.3 + - - +
244A SER* 3.1 21.7 + - - -
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Residues in contact with ARG 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 GLN* 3.3 53.4 + - - +
238A CYS* 3.3 15.5 + - - +
239A ASN 3.3 0.8 - - - -
240A LYS* 1.3 77.8 - - - +
242A SER* 1.3 61.4 + - - +
244A SER* 3.2 24.9 - - - +
245A ASP* 3.5 12.2 - - - +
284A ASP* 3.5 26.7 + - - +
288A GLN* 4.7 4.2 + - - -
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Residues in contact with SER 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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238A CYS 3.1 10.4 + - - -
239A ASN* 3.1 10.0 + - - -
241A ARG* 1.3 77.1 - - - +
243A PHE* 1.3 61.8 + - - +
245A ASP* 3.0 20.1 + - - +
246A GLN 3.7 1.2 + - - -
277A ILE* 3.8 21.2 - - - +
281A GLU* 2.6 39.2 + - - +
330A LEU* 3.6 20.5 - - - +
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Residues in contact with PHE 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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239A ASN 3.0 12.7 + - - +
240A LYS* 3.2 10.3 + - - +
242A SER* 1.3 75.4 - - - +
244A SER* 1.3 63.7 + - - +
246A GLN* 3.1 48.5 + - + +
247A PRO* 4.2 1.6 - - - +
330A LEU* 4.4 6.9 - - + +
331A LYS* 3.3 53.2 - - + +
332A ASP* 5.2 0.9 - - - -
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Residues in contact with SER 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 LYS 3.1 16.3 + - - -
241A ARG* 3.2 15.9 + - - +
243A PHE* 1.3 77.5 - - - +
245A ASP* 1.3 61.8 + - - +
246A GLN 3.2 0.2 - - - -
247A PRO* 3.2 18.4 - - - +
248A LYS* 5.5 0.3 - - - +
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Residues in contact with ASP 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 ARG 3.5 14.1 - - - +
242A SER* 3.0 14.6 + - - +
244A SER* 1.3 80.8 - - - +
246A GLN* 1.3 63.9 + - - +
247A PRO* 3.3 2.2 - - - -
248A LYS* 2.9 45.7 + - + +
249A VAL* 3.6 7.6 - - - +
277A ILE* 3.8 22.9 - - + +
280A GLN* 3.8 17.7 - - - +
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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