Contacts of the helix formed by residues 227 - 253 (chain A) in PDB entry 4PHZ
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 227 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 3.2 0.8 + - - -
226A ASP* 1.3 70.4 + - - +
228A ASP* 1.3 67.9 + - - +
229A ARG 3.2 0.4 - - - -
230A ARG* 3.4 32.0 - - + +
231A ILE* 3.3 28.1 + - - +
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Residues in contact with ASP 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202A TRP* 3.8 15.6 - - + -
206A LYS* 2.9 31.6 + - - -
223A VAL 3.5 1.0 - - - +
224A ILE* 3.4 23.4 - - + -
225A GLY 2.6 39.5 + - - +
227A ASP* 1.3 75.9 - - - +
229A ARG* 1.3 56.7 - - - +
231A ILE* 3.1 14.0 + - - +
232A GLY 3.0 22.9 + - - -
141B LEU* 3.7 9.1 - - + +
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Residues in contact with ARG 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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221A ASP* 5.3 3.6 + - - -
224A ILE* 3.5 23.8 + - + +
225A GLY* 3.1 11.7 - - - -
226A ASP* 3.0 47.9 + - + +
228A ASP* 1.3 76.6 - - - +
230A ARG* 1.3 57.8 + - - +
232A GLY 3.5 0.2 + - - -
233A ALA* 3.0 24.4 + - - +
85B TRP* 5.6 1.4 - - - -
141B LEU* 3.7 27.8 + - + +
142B LEU* 3.2 41.5 + - + +
144B GLY* 6.1 1.4 - - - -
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Residues in contact with ARG 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A ASP* 5.1 11.7 + - + -
227A ASP* 3.3 32.2 + - + +
228A ASP 3.2 0.8 - - - -
229A ARG* 1.3 75.8 - - - +
231A ILE* 1.3 67.1 + - + +
233A ALA* 3.4 5.6 + - - +
234A ILE* 3.0 37.6 + - + +
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Residues in contact with ILE 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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198A TRP* 5.1 1.1 - - + -
201A PHE* 3.8 40.4 - - + -
202A TRP* 4.5 5.8 - - + -
205A ARG* 4.7 9.0 - - - +
227A ASP* 3.4 19.1 - - + +
228A ASP* 3.1 19.8 + - - +
230A ARG* 1.3 76.0 - - + +
232A GLY* 1.3 57.2 + - - +
234A ILE* 3.3 7.5 + - + +
235A VAL* 2.9 41.4 + - + +
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Residues in contact with GLY 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TRP* 4.2 14.4 - - - -
202A TRP* 4.9 0.2 - - - -
228A ASP 3.0 10.1 + - - -
229A ARG 3.5 1.1 + - - -
231A ILE* 1.3 77.2 - - - +
233A ALA* 1.3 55.9 + - - +
235A VAL* 3.1 3.3 + - - +
236A LEU* 2.8 31.5 + - - +
138B VAL* 3.8 12.2 - - - +
141B LEU* 3.7 24.0 - - - +
142B LEU* 5.0 0.2 - - - -
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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 ARG 3.0 19.6 + - - +
230A ARG* 3.7 7.4 - - - +
232A GLY* 1.3 74.1 - - - +
234A ILE* 1.3 66.2 + - + +
236A LEU* 4.0 5.1 - - - +
237A ALA* 3.2 23.4 + - - +
142B LEU* 4.0 22.8 - - + +
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Residues in contact with ILE 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 ARG* 3.0 34.0 + - + +
231A ILE* 3.8 6.7 - - + +
233A ALA* 1.3 82.5 - - + +
235A VAL* 1.3 71.8 + - + +
237A ALA* 3.0 7.3 + - + +
238A LEU* 2.8 42.4 + - + +
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Residues in contact with VAL 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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194A VAL* 5.8 6.1 - - + -
198A TRP* 3.8 37.5 - - + -
231A ILE* 2.9 32.7 + - + +
232A GLY 3.7 2.9 - - - +
234A ILE* 1.3 77.7 - - + +
236A LEU* 1.3 51.6 + - - +
238A LEU* 3.1 11.6 + - + +
239A THR* 2.8 48.6 + - - +
134B ILE* 4.6 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 GLY 2.8 14.8 + - - +
233A ALA* 4.0 4.7 - - - +
235A VAL* 1.3 77.9 - - - +
237A ALA* 1.3 61.4 + - - +
239A THR* 3.7 6.2 - - + -
240A ILE* 3.0 35.5 + - + +
134B ILE* 4.4 9.2 - - + -
135B TRP* 3.8 56.3 - - + +
138B VAL* 3.7 27.0 - - + +
139B ILE* 5.1 8.1 - - + -
142B LEU* 4.6 10.8 - - + -
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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 3.2 14.9 + - - +
234A ILE* 3.0 9.6 + - + +
236A LEU* 1.3 78.8 - - - +
238A LEU* 1.3 64.0 + - + +
240A ILE* 3.9 7.6 + - - +
241A LEU* 3.1 23.9 + - - +
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Residues in contact with LEU 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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234A ILE* 2.8 33.8 + - + +
235A VAL* 3.4 14.1 - - + +
237A ALA* 1.3 76.2 - - + +
239A THR* 1.3 58.4 + - - +
241A LEU* 3.4 14.4 + - + +
242A ALA* 2.9 30.7 + - - +
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Residues in contact with THR 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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191A TRP* 3.5 31.8 - - + -
194A VAL* 5.6 1.0 - - - +
235A VAL* 2.8 34.3 + - - +
236A LEU* 3.7 7.2 - - + -
238A LEU* 1.3 71.2 - - - +
240A ILE* 1.3 65.6 + - + +
242A ALA* 3.4 2.6 + - - +
243A THR* 3.0 26.3 + - - -
131B VAL* 3.9 23.1 - - + -
134B ILE* 3.7 32.2 - - + +
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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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236A LEU* 3.0 34.0 + - + +
237A ALA* 4.2 6.3 - - - +
239A THR* 1.3 76.3 - - + +
241A LEU* 1.3 58.1 + - - +
243A THR* 3.2 8.5 + - + +
244A ILE* 2.8 48.1 + - + +
131B VAL* 5.8 1.6 - - + -
135B TRP* 3.8 33.0 - - + -
160B LEU* 5.1 15.5 - - + -
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Residues in contact with LEU 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 3.1 21.2 + - - +
238A LEU* 3.5 15.3 - - + +
239A THR 3.2 0.2 - - - -
240A ILE* 1.3 77.8 - - - +
242A ALA* 1.3 54.5 + - - +
244A ILE* 3.1 13.4 + - + +
245A VAL* 2.8 46.3 + - + +
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Residues in contact with ALA 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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187A TRP* 3.8 9.9 - - + -
191A TRP* 3.9 21.1 - - + -
238A LEU 2.9 17.0 + - - +
239A THR 3.7 5.2 - - - +
241A LEU* 1.3 77.6 - - - +
243A THR* 1.3 56.5 + - - +
245A VAL* 3.8 7.9 - - - +
246A GLY* 2.9 26.9 + - - -
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Residues in contact with THR 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 TRP* 4.6 8.4 - - - -
191A TRP* 4.1 2.4 - - - -
239A THR 3.0 19.3 + - - -
240A ILE* 3.5 7.9 - - + +
242A ALA* 1.3 75.6 - - - +
244A ILE* 1.3 66.6 + - + +
246A GLY* 4.3 0.2 - - - -
247A TYR* 3.2 22.9 + - - +
131B VAL* 3.3 31.3 - - + +
160B LEU* 4.3 22.7 - - + -
163B PRO* 4.4 20.4 - - + +
164B ASN* 4.6 10.1 - - - +
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Residues in contact with ILE 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 ILE* 2.8 37.0 + - + +
241A LEU* 3.6 13.2 - - + +
243A THR* 1.3 70.1 - - + +
245A VAL* 1.3 70.8 + - + +
247A TYR* 3.4 6.8 + - - +
248A ALA* 3.0 26.8 + - + +
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Residues in contact with VAL 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 LEU* 2.8 37.2 + - + +
242A ALA* 3.8 8.7 - - - +
244A ILE* 1.3 74.5 - - + +
246A GLY* 1.3 68.0 + - - +
247A TYR 3.0 0.9 + - - -
248A ALA* 3.0 6.7 + - - +
249A VAL* 2.9 37.2 + - + +
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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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187A TRP* 4.0 20.2 - - - -
242A ALA 2.9 21.0 + - - -
245A VAL* 1.3 76.5 - - - +
247A TYR* 1.3 59.5 + - - +
249A VAL* 3.7 5.3 + - - +
250A THR* 2.8 33.8 + - - +
167B PRO* 3.9 6.5 - - - -
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Residues in contact with TYR 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 THR 3.2 20.5 + - - +
244A ILE* 3.5 7.0 - - - +
245A VAL 3.0 1.0 + - - -
246A GLY* 1.3 75.0 - - - +
248A ALA* 1.3 61.9 + - + +
250A THR* 2.9 8.9 + - - -
251A ASN* 2.9 48.7 + - - +
162B TYR* 5.7 4.0 - + - -
163B PRO* 4.1 27.1 - - + +
166B TRP* 3.4 44.2 + + + -
167B PRO* 4.2 5.2 - - - +
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Residues in contact with ALA 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 ILE* 3.0 16.0 + - + +
245A VAL* 3.0 6.1 + - - +
247A TYR* 1.3 82.6 - - + +
249A VAL* 1.3 64.7 + - + +
251A ASN* 3.2 19.5 - - - +
252A SER* 3.2 12.5 + - - -
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Residues in contact with VAL 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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183A ARG* 5.3 3.6 - - - +
245A VAL* 2.9 36.4 + - + +
246A GLY* 3.9 6.7 - - - +
248A ALA* 1.3 68.0 - - + +
250A THR* 1.3 60.5 + - + +
251A ASN 2.9 4.3 - - - -
252A SER* 2.6 30.4 + - - -
253A THR* 3.1 18.6 + - - +
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Residues in contact with THR 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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183A ARG* 3.5 25.4 - - + +
246A GLY* 2.8 21.4 + - - +
247A TYR* 2.9 10.2 + - - -
249A VAL* 1.3 81.5 - - + +
251A ASN* 1.3 51.5 + - - +
253A THR* 2.6 28.3 - - - +
254A PHE* 3.5 14.7 - - - +
166B TRP* 3.7 13.1 + - - -
167B PRO* 3.4 40.3 - - + +
170B ALA* 4.4 9.3 - - - +
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Residues in contact with ASN 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 TYR* 2.9 32.9 + - - +
248A ALA* 3.2 18.2 - - - +
249A VAL 2.9 0.2 - - - -
250A THR* 1.3 74.2 + - - +
252A SER* 1.3 53.7 + - - +
253A THR 2.9 10.5 - - - +
254A PHE 4.3 4.2 - - - +
255A PRO* 3.3 24.5 - - - +
166B TRP* 3.6 19.4 + - - +
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A ALA 3.2 9.9 + - - -
249A VAL* 2.6 19.0 + - - -
251A ASN* 1.3 67.3 - - - +
253A THR* 1.3 65.6 + - - -
255A PRO* 3.4 19.7 - - - +
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Residues in contact with THR 253 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183A ARG* 3.7 29.0 + - - +
249A VAL* 3.1 16.3 + - - +
250A THR* 2.6 21.2 - - - +
251A ASN 2.9 1.7 - - - -
252A SER* 1.3 83.5 - - - +
254A PHE* 1.3 87.4 + - + +
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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
------------------------------------------------------------
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