Contacts of the helix formed by residues 248 - 270 (chain A) in PDB entry 5TIN
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 ALA 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244A ILE* 4.1 9.6 - - + -
245A ASN* 3.0 20.2 + - + +
247A ASP* 1.3 74.3 - - - +
249A ALA* 1.3 64.3 + - - +
250A PRO* 3.4 7.0 - - + -
251A ALA* 3.3 18.0 + - + -
252A ARG* 3.1 23.2 + - - +
301A TYR* 4.2 2.0 - - - -
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Residues in contact with ALA 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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247A ASP 3.0 10.7 + - - +
248A ALA* 1.3 71.9 - - - +
250A PRO* 1.3 67.9 - - + +
252A ARG* 3.8 0.3 - - - -
253A VAL* 2.9 34.5 + - + +
301A TYR* 3.1 25.5 - - + +
305A ASN* 4.1 9.6 - - - +
244B ILE* 5.2 0.9 - - + -
248B ALA* 3.8 25.6 - - + -
251B ALA* 4.1 5.2 - - + -
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Residues in contact with PRO 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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247A ASP 4.9 1.1 - - - +
248A ALA* 3.6 4.7 - - - -
249A ALA* 1.3 96.3 - - + +
251A ALA* 1.3 55.0 + - - +
253A VAL* 4.6 0.2 - - + -
254A ALA* 3.0 30.8 + - - +
248B ALA* 5.2 2.7 - - + -
250B PRO* 4.1 35.2 - - + +
251B ALA* 4.0 16.2 - - + +
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Residues in contact with ALA 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A ILE* 4.4 11.4 - - + -
248A ALA* 3.3 22.1 + - + +
249A ALA 3.2 0.6 - - - -
250A PRO* 1.3 80.6 - - + +
252A ARG* 1.3 58.9 + - - +
254A ALA* 3.4 6.6 + - - +
255A LEU* 3.0 33.4 + - + +
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Residues in contact with ARG 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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241A SER* 3.0 60.6 + - - +
242A PHE* 3.6 6.7 - - - +
244A ILE* 3.1 24.8 + - + -
245A ASN 3.5 22.6 + - - -
246A MET* 4.2 1.4 - - - +
248A ALA 3.1 8.6 + - - +
249A ALA 4.1 0.2 - - - +
251A ALA* 1.3 76.8 - - - +
253A VAL* 1.3 65.2 + - - +
255A LEU* 3.6 6.5 + - - +
256A GLY* 3.2 17.2 + - - -
298A LEU* 4.7 3.8 - - - +
300A GLU* 3.9 6.3 + - - -
301A TYR* 3.0 59.8 - - + +
323A ASP* 2.6 41.1 + - - -
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Residues in contact with VAL 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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249A ALA* 2.9 20.4 + - + +
250A PRO 4.3 0.9 - - - +
252A ARG* 1.3 73.7 - - - +
254A ALA* 1.3 60.9 + - - +
256A GLY* 3.2 1.6 + - - -
257A ILE* 2.9 49.4 + - + +
298A LEU* 4.4 12.9 - - + +
301A TYR* 3.9 22.2 - - + -
244B ILE* 4.4 15.3 - - + -
251B ALA* 3.8 34.8 - - + +
254B ALA* 5.2 0.9 - - + -
255B LEU* 4.0 13.2 - - + -
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Residues in contact with ALA 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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250A PRO 3.0 21.4 + - - +
251A ALA* 3.6 6.5 - - - +
253A VAL* 1.3 77.4 - - - +
255A LEU* 1.3 59.3 + - - +
257A ILE* 4.6 8.3 - - - -
258A THR* 2.8 39.4 + - + +
254B ALA* 6.0 4.0 - - + +
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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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237A LEU* 3.2 44.6 - - + +
238A SER* 5.0 2.9 - - - +
240A VAL* 3.6 23.1 - - + -
241A SER* 3.7 28.0 - - - +
244A ILE* 4.4 9.9 - - + -
251A ALA* 3.0 19.1 + - + +
252A ARG* 3.6 10.3 - - - +
254A ALA* 1.3 76.6 - - - +
256A GLY* 1.3 58.4 + - - +
258A THR* 3.5 4.2 + - - +
259A THR* 2.8 33.9 + - + +
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Residues in contact with GLY 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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238A SER* 6.1 0.7 - - - -
241A SER* 5.9 0.2 - - - -
252A ARG 3.2 8.6 + - - -
253A VAL 3.2 6.5 + - - -
255A LEU* 1.3 78.2 - - - +
257A ILE* 1.3 64.5 + - - +
259A THR* 3.2 4.6 + - - -
260A VAL* 3.1 29.8 + - - +
294A VAL 5.1 1.1 - - - -
297A ALA* 5.9 1.1 - - - -
298A LEU* 4.0 30.5 - - - -
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Residues in contact with ILE 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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253A VAL* 2.9 42.1 + - + +
254A ALA* 3.9 6.3 - - - +
256A GLY* 1.3 72.1 - - - +
258A THR* 1.3 65.7 + - + +
260A VAL* 3.6 4.3 - - - +
261A LEU* 2.8 43.3 + - + +
298A LEU* 4.4 3.5 - - + +
237B LEU* 4.7 8.3 - - + -
254B ALA* 3.8 13.5 - - + -
255B LEU* 3.7 43.3 - - + +
258B THR* 3.3 32.5 - - + +
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Residues in contact with THR 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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237A LEU* 5.3 5.4 - - - +
254A ALA* 2.8 26.5 + - + +
255A LEU* 3.5 7.4 + - - +
257A ILE* 1.3 83.5 - - + +
259A THR* 1.3 62.3 + - - +
261A LEU* 4.1 6.0 - - + +
262A THR* 2.8 38.2 + - - -
258B THR* 6.4 0.4 - - + -
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Residues in contact with THR 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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234A ILE* 3.6 33.5 - - + +
237A LEU* 3.9 23.8 - - + -
238A SER* 3.9 19.6 - - - +
255A LEU 2.8 23.2 + - - +
256A GLY* 3.2 8.5 + - - -
258A THR* 1.3 75.9 + - - +
260A VAL* 1.3 62.5 + - - +
262A THR* 4.6 0.4 - - - -
263A MET* 3.0 30.8 + - - +
294A VAL* 3.3 20.9 + - - +
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Residues in contact with VAL 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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256A GLY 3.1 20.1 + - - +
257A ILE* 3.6 4.9 - - - +
259A THR* 1.3 76.5 + - - +
261A LEU* 1.3 65.6 + - + +
263A MET* 3.3 6.1 + - - +
264A THR* 3.1 25.8 + - + +
291A LEU* 3.8 9.5 - - + +
294A VAL* 3.4 21.8 - - + +
295A PHE* 3.8 40.6 - - + -
298A LEU* 4.6 9.0 - - + -
233B LEU* 5.8 2.9 - - + +
234B ILE* 5.3 3.1 - - + -
237B LEU* 4.1 19.1 - - + -
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Residues in contact with LEU 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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257A ILE* 2.8 41.1 + - + +
258A THR* 4.1 6.1 - - + +
260A VAL* 1.3 70.3 - - - +
262A THR* 1.3 65.4 + - - +
264A THR* 2.6 22.2 + - - +
265A THR* 3.2 13.2 + - + +
234B ILE* 3.6 28.7 - - + -
237B LEU* 4.3 12.8 - - + -
258B THR* 3.9 16.6 - - + +
262B THR* 3.4 31.4 - - + +
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Residues in contact with THR 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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234A ILE* 3.7 34.0 - - + +
258A THR* 2.8 26.1 + - - -
259A THR* 4.0 3.4 - - - -
261A LEU* 1.3 77.5 - - - +
263A MET* 1.3 57.9 + - - +
265A THR* 3.0 10.7 + - - +
266A GLN* 2.8 38.1 + - - +
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Residues in contact with MET 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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231A SER* 3.5 22.0 - - - +
234A ILE* 4.0 26.0 - - - -
235A VAL* 5.1 1.8 - - - -
259A THR 3.0 17.6 + - - +
260A VAL* 3.4 6.3 - - - +
261A LEU 3.2 0.2 - - - -
262A THR* 1.3 78.7 - - - +
264A THR* 1.3 55.8 + - - +
266A GLN* 3.5 12.9 - - + +
267A SER* 3.0 26.5 + - - -
287A MET* 3.4 35.4 - - - +
290A CYS* 3.7 20.9 - - + +
291A LEU* 3.7 37.3 - - + +
294A VAL* 4.6 4.3 - - + -
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Residues in contact with THR 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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260A VAL* 3.1 16.2 + - + +
261A LEU* 2.6 27.2 + - - +
263A MET* 1.3 73.9 - - - +
265A THR* 1.3 62.7 + - - +
267A SER* 3.3 7.2 + - - -
268A SER* 3.0 26.9 + - - -
291A LEU* 4.1 22.0 - - + -
230B PRO* 5.1 21.6 - - + +
233B LEU* 5.4 4.3 - - + -
234B ILE* 4.8 17.5 - - + +
262B THR* 5.2 5.1 - - - +
266B GLN* 5.6 3.8 + - - -
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Residues in contact with THR 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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261A LEU 3.2 12.0 + - - +
262A THR* 3.0 23.3 + - - +
264A THR* 1.3 76.6 + - - +
266A GLN* 1.3 55.5 + - - +
268A SER* 3.1 9.3 + - - -
269A GLY* 2.8 33.6 + - - -
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Residues in contact with GLN 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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226A GLN 3.9 13.5 + - - -
227A MET* 4.1 9.6 + - - +
230A PRO* 3.8 27.9 - - - +
231A SER* 4.3 6.7 - - - -
234A ILE* 4.8 3.2 - - - +
262A THR* 2.8 32.8 + - - +
263A MET* 3.5 29.4 - - + +
265A THR* 1.3 78.2 + - - +
267A SER* 1.3 60.5 + - - +
269A GLY* 3.8 2.1 - - - -
270A SER* 3.1 23.0 + - - -
287A MET* 4.0 12.6 - - + +
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Residues in contact with SER 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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263A MET 3.0 18.8 + - - -
264A THR* 3.4 8.7 - - - -
265A THR 3.1 0.2 - - - -
266A GLN* 1.3 74.1 - - - +
268A SER* 1.3 64.0 + - - +
270A SER* 2.6 21.8 + - - -
271A ARG* 3.3 26.2 + - - -
287A MET* 4.0 28.9 - - - +
291A LEU* 5.6 6.2 - - - +
225B ILE* 5.3 1.7 + - - +
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Residues in contact with SER 268 (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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264A THR 3.0 14.1 + - - -
265A THR* 3.1 16.5 + - - +
267A SER* 1.3 75.0 + - - +
269A GLY* 1.3 60.4 + - - +
271A ARG* 3.2 26.6 + - - +
272A ALA* 3.4 11.5 + - - +
226B GLN* 3.5 29.6 + - - +
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Residues in contact with GLY 269 (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* 4.6 7.0 - - - +
265A THR 2.8 17.9 + - - -
266A GLN* 3.8 2.9 - - - -
268A SER* 1.3 79.0 + - - +
270A SER* 1.3 57.8 + - - +
271A ARG 3.2 1.3 + - - -
272A ALA* 3.4 19.7 + - - +
273A SER 5.0 0.3 + - - -
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Residues in contact with SER 270 (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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145A PHE* 4.3 7.1 - - - -
227A MET* 4.0 30.1 - - - +
266A GLN 3.1 13.1 + - - -
267A SER 2.6 20.9 + - - -
269A GLY* 1.3 76.0 - - - +
271A ARG* 1.3 65.9 + - - +
272A ALA 3.6 0.2 - - - -
273A SER 5.4 0.4 - - - -
274A LEU* 3.9 12.6 - - - +
283A ILE* 3.9 28.7 - - - +
284A ASP* 4.5 0.5 + - - -
287A MET* 4.0 11.7 - - - +
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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