Contacts of the helix formed by residues 229 - 250 (chain A) in PDB entry 4U1D
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 ASP 229 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASP* 3.0 27.6 + - + +
228A SER* 1.3 79.1 - - - +
230A ALA* 1.3 65.9 + - - +
231A ASP* 2.9 18.5 + - - +
232A THR* 2.6 38.0 + - - +
233A LEU* 3.2 25.1 + - - +
235A ARG* 4.5 0.7 + - - -
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Residues in contact with ALA 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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228A SER 3.5 4.4 + - - +
229A ASP* 1.3 73.9 + - - +
231A ASP* 1.3 64.2 + - - +
233A LEU* 3.3 9.3 + - - +
234A GLN* 3.0 25.1 + - - +
270A SER* 5.6 0.3 + - - -
271A LYS* 6.6 0.2 - - + -
272A ARG* 3.4 36.0 + - + +
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Residues in contact with ASP 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229A ASP* 2.9 15.1 + - - +
230A ALA* 1.3 78.4 - - - +
232A THR* 1.3 63.4 + - - +
234A GLN* 3.4 5.4 + - - +
235A ARG* 3.2 47.7 + - - +
272A ARG* 2.8 30.7 + - - +
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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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176A GLU* 2.7 27.9 + - - +
225A VAL* 3.9 15.0 - - + -
226A ASP* 3.6 19.8 + - - +
227A LEU* 4.2 4.9 - - + -
229A ASP* 2.6 24.9 + - - +
231A ASP* 1.3 74.6 - - - +
233A LEU* 1.3 62.2 + - - +
235A ARG* 3.5 12.1 + - - +
236A TYR* 3.2 49.8 + - + -
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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
----------------------------------------------------------
227A LEU* 3.2 44.9 - - + +
228A SER 4.9 4.3 - - - +
229A ASP 3.2 13.1 + - - +
230A ALA* 3.7 10.3 - - - +
231A ASP 3.2 0.4 - - - -
232A THR* 1.3 75.4 - - - +
234A GLN* 1.3 60.2 + - - +
236A TYR* 3.3 7.9 + - + +
237A LEU* 2.8 32.6 + - - +
266A LEU* 4.5 10.3 - - + +
269A ILE* 3.5 44.0 - - + +
270A SER* 3.8 22.4 - - - +
271A LYS* 5.1 0.7 - - + +
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Residues in contact with GLN 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 ALA 3.0 16.1 + - - +
231A ASP* 3.8 6.0 - - - +
233A LEU* 1.3 76.0 - - - +
235A ARG* 1.3 63.2 + - + +
237A LEU* 3.5 9.7 + - + +
238A ASP* 3.1 22.0 + - - +
270A SER* 5.1 3.3 + - - +
272A ARG* 3.2 47.7 + - + +
273A ALA 4.0 18.9 + - - +
274A PRO* 5.5 3.2 - - + +
275A LYS* 5.8 9.7 - - - +
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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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176A GLU* 2.9 39.4 + - - +
177A ILE* 3.7 36.1 - - - +
180A SER* 4.0 28.9 + - - +
229A ASP* 4.5 0.4 + - - -
231A ASP* 3.2 29.8 + - - +
232A THR* 3.6 19.2 + - - +
233A LEU 3.2 0.4 - - - -
234A GLN* 1.3 77.0 - - + +
236A TYR* 1.3 68.3 + - + +
238A ASP* 3.2 13.9 + - - +
239A GLN* 3.2 23.4 + - - +
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Residues in contact with TYR 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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171A ASN* 4.9 7.1 + - - -
176A GLU* 4.8 9.3 + - + +
179A TYR* 4.3 25.9 - + - -
209A HIS 6.6 0.2 - - - -
210A LEU* 3.6 24.6 - - + +
213A ALA* 5.4 1.0 - - - +
225A VAL* 3.8 23.1 - - + +
227A LEU* 3.6 18.8 - - + -
232A THR* 3.2 38.0 + - + +
233A LEU* 3.7 6.7 - - + +
235A ARG* 1.3 80.1 - - + +
237A LEU* 1.3 63.9 + - - +
239A GLN* 3.1 29.7 + - - -
240A ARG* 3.1 32.5 + - - +
266A LEU* 3.5 17.0 - - + -
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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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233A LEU 2.8 18.1 + - - +
234A GLN* 3.7 10.5 - - + +
236A TYR* 1.3 76.4 - - - +
238A ASP* 1.3 63.6 + - - +
240A ARG* 3.4 1.3 + - + +
241A PHE* 3.0 57.2 + - + -
263A VAL* 3.7 31.2 - - + +
266A LEU* 3.4 19.5 - - + +
267A MET* 3.9 22.2 - - + +
270A SER* 4.6 15.5 - - - +
272A ARG 5.3 2.2 - - - +
274A PRO* 4.6 13.5 - - + -
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Residues in contact with ASP 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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184A LYS* 3.4 30.0 + - - +
234A GLN 3.1 15.0 + - - +
235A ARG* 3.4 11.4 - - - +
237A LEU* 1.3 76.5 - - - +
239A GLN* 1.3 63.2 + - - +
241A PHE* 3.4 11.6 + - - +
242A GLN* 3.1 21.5 + - - +
275A LYS* 6.0 0.2 + - - -
278A THR* 5.7 5.4 - - - +
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Residues in contact with GLN 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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179A TYR* 4.3 8.1 - - - -
180A SER* 3.0 43.0 + - - +
183A VAL* 4.0 34.1 - - + +
184A LYS* 4.1 8.5 - - + +
187A MET* 3.6 7.0 - - + +
206A LEU* 4.8 1.4 - - - +
235A ARG* 3.2 15.3 + - - +
236A TYR* 3.1 20.3 + - - +
238A ASP* 1.3 77.0 - - - +
240A ARG* 1.3 79.0 + - - +
242A GLN* 3.0 10.0 + - - +
243A GLN* 2.7 34.1 + - - +
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Residues in contact with ARG 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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179A TYR* 5.7 1.8 + - - -
206A LEU* 3.5 38.9 + - - +
207A ARG* 5.3 3.4 - - - +
209A HIS* 5.7 0.6 - - - +
210A LEU* 4.1 27.1 - - - +
236A TYR* 3.1 30.0 + - - +
237A LEU* 4.0 3.6 - - - +
239A GLN* 1.3 114.8 + - - +
241A PHE* 1.3 57.0 + - - +
243A GLN* 3.0 27.8 + - + +
244A VAL* 2.9 27.2 + - - +
259A SER 4.6 1.0 - - - +
262A ASP* 4.6 14.2 + - + +
263A VAL* 3.5 30.5 - - + +
266A LEU* 3.9 19.6 - - + +
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Residues in contact with PHE 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 LEU* 3.0 52.2 + - + +
238A ASP* 3.5 12.3 - - - +
239A GLN 3.2 0.2 - - - -
240A ARG* 1.3 76.2 - - - +
242A GLN* 1.3 59.9 + - - +
244A VAL* 3.5 5.8 + - - +
245A ASP* 3.3 19.1 + - - +
263A VAL* 3.7 18.5 - - + +
267A MET* 4.1 8.3 - - - -
274A PRO* 4.1 12.8 - - + -
278A THR* 4.3 20.2 - - - -
279A LEU* 3.5 22.9 - - + -
281A ASN* 5.5 1.2 - - - +
282A TYR* 3.3 49.0 - + + -
285A ASN* 5.1 0.7 + - - -
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Residues in contact with GLN 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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184A LYS* 3.2 49.2 + - - +
187A MET* 3.5 32.8 - - - +
188A HIS* 4.2 8.9 - - - +
238A ASP* 3.1 12.1 + - - +
239A GLN* 3.0 9.5 + - - +
241A PHE* 1.3 74.8 - - - +
243A GLN* 1.3 60.8 + - - +
244A VAL 3.2 0.2 - - - -
245A ASP* 3.0 8.9 + - + +
246A VAL* 2.8 42.8 + - + +
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Residues in contact with GLN 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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187A MET* 3.6 16.5 - - + +
199A PHE* 3.4 17.0 - - + -
203A ALA* 3.8 18.6 + - + +
206A LEU* 3.6 24.9 - - - +
207A ARG* 3.3 21.5 - - - +
239A GLN 2.7 16.9 + - - +
240A ARG* 3.2 27.3 + - - +
242A GLN* 1.3 72.3 - - - +
244A VAL* 1.3 60.4 + - - +
247A SER* 2.9 28.8 + - - -
259A SER* 2.7 29.1 + - - +
262A ASP* 3.6 10.1 + - - +
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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 ARG 2.9 12.6 + - - +
241A PHE 3.6 9.2 - - - +
243A GLN* 1.3 77.0 - - - +
245A ASP* 1.3 64.0 + - - +
247A SER* 3.3 4.6 + - - -
248A VAL* 3.1 27.9 + - + +
256A ALA* 4.3 1.6 - - + +
259A SER* 3.4 41.3 - - - +
260A ILE* 3.7 21.1 - - + +
263A VAL* 3.9 8.7 - - + -
282A TYR* 4.3 14.1 - - + -
285A ASN* 3.9 24.9 - - + +
286A LEU* 4.9 0.9 - - + -
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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 PHE 3.3 9.8 + - - +
242A GLN* 3.0 15.2 + - + +
244A VAL* 1.3 80.6 - - - +
246A VAL* 1.3 62.7 + - + +
248A VAL* 3.3 2.3 + - - +
249A LYS* 3.1 53.3 + - - +
281A ASN* 3.7 20.8 + - - +
285A ASN* 2.8 32.3 + - - +
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Residues in contact with VAL 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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187A MET* 4.0 28.7 - - + +
188A HIS* 5.6 0.7 - - - -
191A LEU* 4.1 27.4 - - + +
199A PHE* 3.6 26.9 - - + -
242A GLN* 2.8 31.8 + - + +
245A ASP* 1.3 73.4 - - + +
247A SER* 1.3 56.5 + - - +
249A LYS* 3.1 7.7 + - + +
250A LEU* 2.9 48.7 + - + +
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Residues in contact with SER 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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199A PHE* 3.2 23.3 - - - -
243A GLN 2.9 21.1 + - - -
244A VAL 3.4 6.3 - - - -
246A VAL* 1.3 78.2 - - - +
248A VAL* 1.3 58.8 + - - +
250A LEU* 3.4 1.4 + - - -
251A GLU 3.2 3.3 + - - -
252A LEU* 2.9 36.6 + - - +
255A GLU* 3.7 12.0 - - - +
256A ALA* 3.5 26.5 - - - -
259A SER* 3.8 6.1 + - - -
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Residues in contact with VAL 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* 3.1 18.4 + - + +
245A ASP* 3.7 4.9 - - - +
246A VAL 3.2 0.2 - - - -
247A SER* 1.3 76.8 - - - +
249A LYS* 1.3 63.4 - - + +
251A GLU* 3.2 15.2 + - - +
253A TRP* 3.5 31.8 - - + -
256A ALA* 4.2 2.9 - - + -
285A ASN* 4.0 24.5 - - + +
288A LYS* 4.0 26.2 - - + +
289A VAL* 3.6 28.3 - - + -
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Residues in contact with LYS 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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191A LEU* 3.6 40.4 - - + +
194A GLN* 5.2 2.9 + - - +
245A ASP* 3.1 47.0 + - - +
246A VAL* 3.7 1.1 - - + +
248A VAL* 1.3 79.7 - - + +
250A LEU* 1.3 63.6 + - - +
251A GLU* 3.2 6.9 + - - +
285A ASN* 6.0 0.2 - - - +
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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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190A CYS 4.0 13.2 - - - +
191A LEU* 3.6 17.0 - - + -
194A GLN* 3.4 44.4 - - - +
196A LYS* 3.1 35.6 + - + +
199A PHE* 4.3 13.5 - - + -
246A VAL* 2.9 34.1 + - + +
247A SER 4.0 0.4 - - - +
249A LYS* 1.3 76.3 - - - +
251A GLU* 1.3 66.9 + - - +
252A LEU* 3.0 33.4 + - + +
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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
------------------------------------------------------------
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