Contacts of the helix formed by residues 244 - 267 (chain A) in PDB entry 5FQU
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 244 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243A SER* 1.3 90.2 + - - +
245A VAL* 1.3 66.2 + - - +
246A LEU* 3.7 9.5 + - - +
247A ASP* 2.8 39.9 + - - +
248A VAL* 3.2 17.0 + - - +
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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
----------------------------------------------------------
244A THR* 1.3 72.7 - - - +
246A LEU* 1.3 66.2 + - - +
248A VAL* 3.1 16.8 + - + +
249A MSE 3.3 27.4 + - + +
130B GLY* 6.5 0.9 - - - -
192B PRO* 5.3 1.1 - - + -
193B ALA* 3.9 40.6 - - + +
246B LEU* 5.3 1.8 - - + -
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Residues in contact with LEU 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A ALA* 4.1 23.8 - - + +
244A THR* 3.7 9.5 + - - +
245A VAL* 1.3 78.3 - - - +
247A ASP* 1.3 67.4 + - - +
249A MSE 3.2 8.7 + - - +
250A ASN* 3.0 55.4 + - - +
245B VAL* 5.8 1.6 - - + -
249B MSE 4.5 14.9 - - + +
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Residues in contact with ASP 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A ARG* 3.0 35.8 + - - +
241A ASP 3.0 14.9 - - - +
242A LEU* 3.6 20.1 - - + +
243A SER* 4.1 1.8 - - - -
244A THR* 2.8 39.6 + - - +
246A LEU* 1.3 83.3 - - - +
248A VAL* 1.3 61.2 + - - +
250A ASN* 3.7 7.5 + - - +
251A GLN* 3.2 22.3 + - - +
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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
----------------------------------------------------------
242A LEU* 4.5 15.7 - - + +
243A SER 5.8 0.4 - - - +
244A THR 3.7 12.8 - - - +
245A VAL* 3.1 11.9 + - + +
247A ASP* 1.3 77.3 - - - +
249A MSE 1.3 59.2 + - + +
251A GLN* 3.2 9.2 - - - +
252A SER* 3.1 21.6 + - - -
168B ILE* 3.7 31.5 - - + +
192B PRO* 4.3 27.8 - - + -
197B PRO* 4.5 18.8 - - + -
204B LEU* 5.5 2.0 - - + -
206B VAL* 4.4 7.2 - - + -
210B MSE 5.8 0.7 - - + -
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Residues in contact with MSE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A VAL* 3.3 31.2 - - + +
246A LEU* 3.2 6.3 + - - +
248A VAL* 1.3 77.0 - - + +
250A ASN* 1.3 61.0 + - - +
251A GLN 3.2 0.2 - - - -
252A SER* 3.1 11.1 + - - -
253A ILE* 3.0 32.1 + - - +
192B PRO* 4.4 19.3 - - + -
193B ALA* 4.2 3.6 - - + -
246B LEU* 3.5 32.1 - - + +
249B MSE 4.3 39.7 - - + +
250B ASN* 4.7 9.2 - - - +
253B ILE* 3.7 26.1 - - + +
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Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ILE* 5.7 2.6 - - - +
192A PRO 4.5 12.0 - - - +
193A ALA* 5.1 2.4 - - - +
237A ARG* 5.7 6.5 - - - -
246A LEU* 3.0 51.2 + - - +
247A ASP* 3.9 6.9 - - - +
249A MSE 1.3 73.4 - - - +
251A GLN* 1.3 55.0 + - - +
253A ILE* 3.2 17.3 + - - +
254A THR* 2.8 38.8 + - - +
249B MSE 4.7 6.1 - - - +
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Residues in contact with GLN 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A LEU* 3.1 43.8 - - - +
237A ARG* 3.0 40.6 + - + +
242A LEU* 3.8 8.0 - - + +
247A ASP 3.2 11.8 + - - +
248A VAL 3.2 11.4 - - - +
249A MSE 3.2 0.2 - - - -
250A ASN* 1.3 75.8 - - - +
252A SER* 1.3 60.3 + - - +
254A THR* 3.2 8.9 + - - -
255A LEU* 2.8 35.1 + - + +
168B ILE* 3.1 37.2 + - + +
169B ALA 4.2 0.4 + - - -
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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
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248A VAL* 3.1 9.6 + - - -
249A MSE 3.1 14.3 + - - -
251A GLN* 1.3 77.7 - - - +
253A ILE* 1.3 58.7 + - - +
255A LEU* 2.8 29.7 + - - +
256A MSE 3.2 9.4 + - - -
168B ILE* 4.8 0.8 - - - +
210B MSE 3.7 17.6 - - - -
252B SER* 5.5 1.3 + - - -
253B ILE* 3.6 24.8 - - - +
256B MSE 3.2 25.8 - - - +
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Residues in contact with ILE 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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192A PRO* 4.4 21.3 - - + +
207A ASP* 5.2 7.4 - - - +
210A MSE 4.4 20.9 - - + -
249A MSE 3.0 14.6 + - - +
250A ASN* 3.2 16.8 + - - +
252A SER* 1.3 74.6 - - - +
254A THR* 1.3 58.9 + - - +
255A LEU 3.3 0.2 + - - -
256A MSE 3.3 8.5 + - - +
257A THR* 2.4 41.5 + - - +
249B MSE 3.8 31.9 - - + +
252B SER* 3.5 24.7 - - - +
253B ILE* 6.5 0.2 - - + -
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Residues in contact with THR 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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234A ASN* 3.5 35.2 - - + +
235A PRO 3.9 13.9 + - - +
236A LEU* 4.5 7.6 - - + -
250A ASN* 2.8 25.6 + - - +
251A GLN* 3.4 14.7 - - - -
253A ILE* 1.3 74.0 - - - +
255A LEU* 1.3 63.5 + - - +
257A THR* 3.4 6.8 - - - -
258A ARG* 3.0 29.5 + - - +
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Residues in contact with LEU 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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236A LEU* 3.9 22.4 - - + -
251A GLN* 2.8 33.2 + - + +
252A SER* 2.8 14.5 + - - +
254A THR* 1.3 78.4 - - - +
256A MSE 1.3 56.8 + - - +
258A ARG* 3.5 8.9 + - + +
259A LYS* 3.2 24.6 + - - +
166B THR* 5.1 3.4 - - + -
168B ILE* 4.9 8.5 - - + +
170B THR 4.2 1.6 - - - +
171B GLY* 3.6 38.4 - - - +
210B MSE 5.0 8.3 - - + -
211B VAL* 5.8 1.3 - - + -
256B MSE 4.2 14.1 - - + -
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Residues in contact with MSE 256 (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 MSE 3.3 39.6 - - + +
211A VAL* 5.3 3.6 - - + -
252A SER 3.2 11.0 + - - +
253A ILE* 3.5 11.9 - - - +
255A LEU* 1.3 74.3 - - - +
257A THR* 1.3 68.6 + - - +
259A LYS* 3.7 7.5 - - - +
260A ASN* 3.1 27.9 + - - +
252B SER* 3.5 35.7 - - - +
255B LEU* 4.3 11.7 - - + -
256B MSE 3.9 43.0 - - + +
259B LYS* 5.6 9.7 + - + -
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Residues in contact with THR 257 (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 ASP* 5.6 0.5 + - - -
209A GLY* 3.5 22.6 + - - +
210A MSE 4.2 0.9 - - - -
213A ASN* 3.7 24.0 - - - +
234A ASN* 3.8 18.6 - - - +
253A ILE* 2.4 34.8 + - - +
254A THR* 3.4 8.9 - - - -
256A MSE 1.3 77.9 - - - +
258A ARG* 1.3 51.9 + - - +
260A ASN* 3.4 12.1 - - - +
261A SER* 2.3 36.2 + - - -
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Residues in contact with ARG 258 (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 ASN* 2.7 54.4 + - + +
235A PRO* 3.8 5.3 - - - +
236A LEU* 3.1 34.7 - - - +
254A THR* 3.0 22.5 + - - +
255A LEU* 3.7 10.7 - - + +
257A THR* 1.3 73.0 - - - +
259A LYS* 1.3 56.3 + - - +
261A SER* 3.3 6.9 - - - -
262A GLU* 2.7 59.6 + - - +
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Residues in contact with LYS 259 (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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255A LEU 3.2 14.7 + - - +
256A MSE 3.3 9.6 + - - +
258A ARG* 1.3 79.6 - - - +
260A ASN* 1.3 59.9 + - - +
262A GLU* 3.5 12.9 + - - +
263A ALA* 3.3 21.7 + - - +
256B MSE 5.9 5.8 - - + -
259B LYS* 5.2 22.6 + - + +
260B ASN* 4.6 23.0 - - - +
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Residues in contact with ASN 260 (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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209A GLY 2.8 25.3 + - - -
210A MSE 3.2 20.5 + - - +
211A VAL* 3.3 20.8 - - - +
212A ASP* 3.7 2.0 - - - -
213A ASN* 3.0 22.9 + - - +
214A ILE 4.4 0.5 + - - -
256A MSE 3.1 19.8 + - - +
257A THR 3.4 5.0 + - - +
259A LYS* 1.3 72.9 - - - +
261A SER* 1.3 68.8 + - - +
262A GLU 3.4 0.2 - - - -
263A ALA* 3.6 7.2 - - - +
264A GLN* 3.3 27.5 + - - +
259B LYS* 4.5 16.0 - - - +
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Residues in contact with SER 261 (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 ASN* 3.3 24.9 + - - +
214A ILE* 3.7 25.5 - - - +
231A ASP* 5.6 0.4 - - - -
234A ASN* 4.3 3.2 + - - -
257A THR* 2.3 26.1 + - - +
258A ARG* 3.2 10.6 + - - -
260A ASN* 1.3 81.5 + - - +
262A GLU* 1.3 64.1 + - - +
264A GLN* 3.5 2.6 + - - +
265A LEU* 3.1 28.8 + - - +
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Residues in contact with GLU 262 (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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258A ARG* 2.7 49.2 + - - +
259A LYS* 3.5 12.0 + - - +
260A ASN 3.4 0.2 - - - -
261A SER* 1.3 72.4 - - - +
263A ALA* 1.3 59.3 + - - +
265A LEU* 3.4 12.1 + - + +
266A ALA* 2.9 28.6 + - - +
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Residues in contact with ALA 263 (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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259A LYS 3.3 12.0 + - - +
260A ASN* 3.6 13.5 - - - +
262A GLU* 1.3 77.0 - - - +
264A GLN* 1.3 64.3 + - + +
266A ALA* 3.0 25.4 - - - +
267A THR* 3.5 11.3 - - - +
259B LYS* 6.1 2.0 - - - +
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Residues in contact with GLN 264 (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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212A ASP* 3.4 12.7 + - - +
214A ILE* 3.4 24.5 - - + +
216A VAL* 3.3 18.7 + - + +
217A ASP* 3.1 55.5 + - - +
260A ASN* 3.3 15.1 + - + +
261A SER 3.8 3.8 - - - +
263A ALA* 1.3 77.4 - - + +
265A LEU* 1.3 60.6 + - - +
266A ALA 3.1 1.3 - - - -
267A THR* 2.8 41.4 + - - +
268A LEU* 3.9 1.9 + - - +
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Residues in contact with LEU 265 (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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214A ILE* 4.0 15.0 - - + -
216A VAL* 5.5 0.4 - - + -
229A VAL* 4.2 12.8 - - + -
231A ASP* 3.6 23.8 - - + +
261A SER* 3.1 22.8 + - - +
262A GLU* 3.7 12.3 - - + +
264A GLN* 1.3 75.8 - - - +
266A ALA* 1.3 60.1 + - - +
267A THR 3.3 0.5 + - - -
268A LEU* 3.3 33.2 + - + +
274A LEU* 3.8 31.2 - - + -
276A GLN* 4.5 9.4 - - - +
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Residues in contact with ALA 266 (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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262A GLU 2.9 13.2 + - - +
263A ALA* 3.0 18.6 - - - +
264A GLN 3.1 0.2 - - - -
265A LEU* 1.3 79.5 - - - +
267A THR* 1.3 56.6 + - + +
268A LEU 3.2 9.2 + - - +
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Residues in contact with THR 267 (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 VAL* 4.0 8.3 - - - +
220A ARG* 3.1 32.9 + - - -
263A ALA 3.5 15.7 - - - +
264A GLN* 2.8 30.3 + - - +
266A ALA* 1.3 76.6 - - + +
268A LEU* 1.3 62.7 + - - +
269A LYS* 3.7 8.0 + - - +
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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