Contacts of the helix formed by residues 230 - 250 (chain A) in PDB entry 5H1Y
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 GLY 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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205A THR* 4.0 4.5 - - - +
207A ILE* 3.7 2.9 - - - -
208A GLN* 2.8 39.8 + - - +
228A GLY 3.3 2.6 + - - -
229A SER* 1.3 72.3 - - - +
231A LYS* 1.3 61.5 + - - +
232A THR 3.2 4.2 + - - -
233A LEU* 3.5 6.3 + - - -
234A VAL* 3.6 0.2 - - - +
501A SO4 2.5 24.3 + - - -
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Residues in contact with LYS 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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207A ILE* 3.9 2.9 - - + -
225A ALA* 4.3 18.6 + - + +
226A PHE 4.2 6.5 - - - +
227A THR* 4.3 10.8 + - - +
229A SER* 3.4 14.3 - - - +
230A GLY* 1.3 78.4 - - - +
232A THR* 1.3 68.3 + - - +
234A VAL* 3.0 28.1 + - - +
235A PHE* 3.2 12.6 - - + -
269A LEU* 6.4 0.2 - - - -
344A ASP* 2.9 30.7 + - - +
345A GLU* 3.7 10.7 - - - +
374A PHE* 3.8 30.1 + - + +
375A SER* 5.7 0.4 - - - +
376A ALA* 6.0 1.6 - - - +
501A SO4 3.3 16.3 + - - +
502A MG 2.7 28.4 - - - -
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Residues in contact with THR 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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231A LYS* 1.3 81.1 - - - +
233A LEU* 1.3 54.6 + - + +
235A PHE* 3.4 24.2 + - + -
236A THR* 2.5 53.1 + - + +
269A LEU* 5.9 1.7 - - - +
272A GLN* 5.2 5.1 + - - +
273A THR* 4.0 13.6 + - + +
276A ILE* 3.8 30.0 - - + +
344A ASP* 5.0 1.2 + - - -
501A SO4 2.6 30.7 + - - -
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Residues in contact with LEU 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A PHE* 4.7 2.9 - - + -
196A LEU* 3.8 24.2 - - + -
201A ILE* 4.1 20.9 - - + -
208A GLN* 3.7 32.3 - - + +
212A ILE* 4.2 4.5 - - + +
230A GLY* 3.5 1.9 + - - -
231A LYS 3.3 0.6 - - - -
232A THR* 1.3 76.8 - - - +
234A VAL* 1.3 64.6 + - - +
236A THR* 3.3 9.6 - - - +
237A LEU* 3.1 43.5 + - + +
238A PRO* 3.5 0.9 - - - +
276A ILE* 4.5 8.1 - - + -
280A TYR* 3.7 30.5 - - + +
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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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207A ILE* 3.8 17.7 - - + +
208A GLN* 3.8 15.9 - - + -
211A GLY* 3.6 35.9 - - - +
212A ILE* 3.8 7.4 - - - +
215A ILE* 3.8 10.1 - - + +
221A MET* 4.2 2.7 - - + -
230A GLY 3.6 13.9 - - - +
231A LYS* 3.0 20.3 + - - +
233A LEU* 1.3 78.7 - - - +
235A PHE* 1.3 57.6 + - - +
238A PRO* 3.0 25.6 - - - +
374A PHE* 4.0 19.1 - - + -
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Residues in contact with PHE 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 LYS* 3.2 23.8 + - + -
232A THR* 3.4 28.9 + - + -
234A VAL* 1.3 79.7 - - - +
236A THR* 1.3 63.7 + - + +
238A PRO* 4.2 0.4 - - - -
239A VAL* 3.6 4.9 - - - +
262A ILE* 3.9 21.7 - - + +
273A THR* 3.9 26.0 - - + -
340A TYR* 2.6 37.2 + - - +
342A ALA* 4.1 12.8 - - + -
344A ASP* 3.3 37.5 - - + -
372A LEU* 3.9 5.6 - - + -
374A PHE* 3.9 32.8 - + + -
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Residues in contact with THR 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 THR* 2.5 40.1 + - + +
233A LEU* 3.3 16.5 - - - +
235A PHE* 1.3 89.8 - - + +
237A LEU* 1.3 70.9 + - - +
238A PRO 3.4 0.4 - - - -
239A VAL* 3.3 4.8 - - - +
240A ILE* 3.1 31.5 + - - +
262A ILE* 4.3 2.0 - - + -
273A THR* 4.0 10.8 - - + -
276A ILE* 4.2 10.9 - - + +
277A LEU* 3.7 27.6 - - + -
280A TYR* 5.9 0.2 - - - -
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Residues in contact with LEU 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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183A PHE* 5.0 1.3 - - + -
188A PHE* 3.5 32.0 - - + -
192A ILE* 4.1 15.3 - - + -
196A LEU* 4.5 17.7 - - + -
212A ILE* 4.5 5.6 - - + -
233A LEU* 3.1 43.4 + - + +
236A THR* 1.3 82.0 + - - +
238A PRO* 1.3 66.0 - - + +
240A ILE* 3.4 8.2 + - + +
241A MET* 3.2 23.7 + - - +
280A TYR* 3.9 40.4 - - + -
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Residues in contact with PRO 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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188A PHE* 5.3 0.9 - - + -
212A ILE* 4.4 19.1 - - + -
215A ILE* 3.6 31.6 - - + -
216A LEU* 4.0 22.2 - - + -
233A LEU 3.5 2.2 - - - +
234A VAL* 3.0 29.8 - - - +
235A PHE 4.2 0.7 - - - -
236A THR 3.7 2.9 - - - +
237A LEU* 1.3 93.4 - - + +
239A VAL* 1.3 58.4 + - - +
241A MET* 3.0 7.8 + - + +
242A PHE* 2.9 33.3 + - + -
340A TYR* 4.7 0.2 - - - +
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Residues in contact with VAL 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 PHE 3.6 13.7 - - - +
236A THR* 3.3 13.2 + - - +
238A PRO* 1.3 77.3 - - - +
240A ILE* 1.3 59.1 + - - +
242A PHE* 3.4 8.4 - - + +
243A CYS* 2.8 43.8 + - - -
259A TYR* 4.5 4.9 - - + -
260A GLY* 4.0 15.3 - - - -
262A ILE* 5.0 5.4 - - + -
277A LEU* 4.7 3.1 - - + -
316A MET* 3.9 16.8 - - + -
340A TYR* 3.5 47.2 + - + -
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Residues in contact with ILE 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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192A ILE* 5.1 4.7 - - + -
236A THR* 3.1 20.3 + - - +
237A LEU* 3.5 12.8 - - + +
239A VAL* 1.3 77.6 - - - +
241A MET* 1.3 61.3 + - - +
243A CYS* 3.4 1.5 + - - -
244A LEU* 2.9 27.4 + - - +
277A LEU* 3.8 24.5 - - + +
280A TYR* 3.6 30.7 - - + -
281A CYS* 4.2 3.8 - - - -
284A LEU* 3.5 30.5 - - + -
292A LEU* 3.5 9.1 - - + +
316A MET* 3.7 26.2 - - + -
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Residues in contact with MET 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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187A LYS 5.1 5.6 - - - +
188A PHE* 4.3 18.4 - - + -
189A PRO* 3.4 41.5 - - + -
192A ILE* 5.1 4.0 - - - -
216A LEU* 5.0 8.7 - - + -
237A LEU 3.2 12.9 + - - +
238A PRO* 3.0 12.2 + - + +
240A ILE* 1.3 85.5 - - - +
242A PHE* 1.3 68.0 + - + +
244A LEU* 3.1 30.5 + - + +
245A GLU* 3.2 29.1 + - + +
284A LEU* 5.3 1.3 - - - -
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Residues in contact with PHE 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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215A ILE 3.7 20.4 - - - -
216A LEU* 4.0 32.1 - - + -
218A GLY* 5.3 1.1 - - - -
238A PRO* 2.9 23.8 + - + -
239A VAL* 3.1 15.2 + - + +
241A MET* 1.3 78.9 - - + +
243A CYS* 1.3 62.2 + - - +
245A GLU* 3.3 6.3 + - - +
246A GLN* 3.1 24.9 + - - +
259A TYR* 3.7 27.3 + + + +
340A TYR* 4.0 20.0 - + + -
370A GLN* 3.6 22.0 - - - -
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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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239A VAL* 2.8 22.9 + - - +
240A ILE 3.6 5.6 - - - +
242A PHE* 1.3 73.4 - - - +
244A LEU* 1.3 57.6 + - - +
246A GLN* 3.4 7.0 + - - +
247A GLU* 2.9 31.9 + - - +
252A PHE* 6.1 0.2 - - - -
259A TYR* 3.7 24.9 - - - -
292A LEU* 3.7 15.0 - - + +
315A HIS* 3.8 25.8 - - + -
316A MET* 3.7 27.8 - - + -
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Residues in contact with LEU 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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189A PRO* 4.8 3.8 - - + -
240A ILE 2.9 16.0 + - - +
241A MET* 3.1 29.6 + - + +
243A CYS* 1.3 75.9 - - - +
245A GLU* 1.3 69.5 + - - +
247A GLU* 4.0 1.2 - - - +
248A LYS* 3.1 42.2 + - + +
284A LEU* 4.3 24.2 - - + -
289A SER* 3.7 31.0 - - - +
290A PRO* 4.1 17.9 - - + +
292A LEU* 3.7 17.5 - - + +
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Residues in contact with GLU 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 MET* 3.2 20.1 + - + +
242A PHE* 3.8 7.6 - - + +
244A LEU* 1.3 87.5 - - - +
246A GLN* 1.3 62.0 + - + +
248A LYS* 3.2 16.4 + - - +
249A ARG* 2.9 30.4 + - - +
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Residues in contact with GLN 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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242A PHE 3.1 14.6 + - - +
243A CYS* 3.8 6.7 - - - +
245A GLU* 1.3 78.1 - - - +
247A GLU* 1.3 57.1 + - - +
249A ARG* 3.1 11.8 + - - +
250A LEU* 2.8 32.2 + - - +
252A PHE* 4.0 18.4 - - + -
259A TYR* 3.3 45.1 + - + -
339A ARG* 4.3 16.4 + - - +
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Residues in contact with GLU 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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243A CYS 2.9 17.9 + - - +
244A LEU 4.0 2.7 - - - +
246A GLN* 1.3 75.6 - - - +
248A LYS* 1.3 63.3 + - - +
250A LEU 3.9 3.1 - - - -
251A PRO* 3.1 43.3 - - + +
252A PHE* 2.7 33.1 + - - +
290A PRO* 3.6 30.8 - - + +
291A LEU 4.6 3.5 - - - +
292A LEU* 3.9 8.7 - - + -
315A HIS* 2.7 35.1 + - - +
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Residues in contact with LYS 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 LEU* 3.1 36.6 + - + +
245A GLU* 3.6 19.5 - - - +
247A GLU* 1.3 74.3 - - - +
249A ARG* 1.3 64.4 + - - +
250A LEU* 4.6 0.3 - - - -
251A PRO* 4.6 3.8 - - - +
288A SER 5.1 1.0 + - - -
289A SER* 3.5 25.7 + - - +
290A PRO* 3.6 27.9 - - + +
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Residues in contact with ARG 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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245A GLU 2.9 16.8 + - - +
246A GLN* 3.5 12.1 - - - +
248A LYS* 1.3 80.0 - - - +
250A LEU* 1.3 64.6 + - + +
251A PRO* 4.4 2.2 - - - +
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Residues in contact with LEU 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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246A GLN 2.8 15.6 + - - +
247A GLU 3.4 2.9 - - - -
249A ARG* 1.3 86.3 - - + +
251A PRO* 1.4 86.7 - - + +
252A PHE* 3.3 11.6 + - - -
253A SER* 6.0 1.1 - - - +
256A GLU* 5.3 12.1 - - - +
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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