Contacts of the helix formed by residues 237 - 261 (chain A) in PDB entry 2Q8I
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 VAL 237 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A ILE* 5.6 2.2 - - + -
163A MET* 3.9 30.7 - - + -
186A SER* 3.3 32.1 - - - +
187A ILE* 4.2 5.4 - - + -
236A TYR* 1.3 94.6 - - + +
238A PRO* 1.3 69.1 - - + +
239A SER* 3.1 12.1 - - - +
240A HIS* 3.1 38.4 + - + +
241A LEU 3.3 1.2 + - - -
338A PHE* 4.2 17.3 - - + -
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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
----------------------------------------------------------
183A HIS* 3.7 24.7 - - + +
186A SER 3.2 17.0 - - - +
188A ASP* 3.9 13.5 - - + +
191A CYS* 4.5 16.4 - - - -
196A VAL* 4.1 11.8 - - + +
236A TYR 3.2 9.8 - - - +
237A VAL* 1.3 81.8 - - + +
239A SER* 1.3 57.7 + - - +
241A LEU* 3.2 9.5 + - + +
242A PHE* 2.8 30.0 + - - +
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Residues in contact with SER 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186A SER* 5.8 0.9 - - - -
237A VAL* 3.1 7.9 - - - +
238A PRO* 1.3 81.0 - - - +
240A HIS* 1.3 71.0 + - - +
242A PHE* 3.7 8.9 - - - +
243A HIS* 3.0 27.5 + - - +
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Residues in contact with HIS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A ILE* 4.0 5.9 + - + +
163A MET* 4.6 10.1 + - + +
236A TYR* 3.9 13.6 + - + +
237A VAL* 3.1 40.8 + - + +
239A SER* 1.3 80.9 - - - +
241A LEU* 1.3 65.5 + - - +
243A HIS* 3.4 5.1 + - - +
244A MET* 3.1 33.4 + - + +
334A TYR* 3.5 40.9 + + + +
337A TYR* 3.9 32.1 - + - -
338A PHE* 4.4 5.0 - + - -
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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
----------------------------------------------------------
191A CYS* 4.3 22.9 - - - -
193A VAL* 4.4 22.7 - - + -
196A VAL* 4.1 10.8 - - + -
234A VAL* 5.1 1.6 - - + -
236A TYR* 4.1 8.7 - - + -
237A VAL 3.3 6.7 + - - +
238A PRO* 3.2 9.3 + - + +
240A HIS* 1.3 75.9 - - - +
242A PHE* 1.3 66.6 + - - +
244A MET* 3.1 21.2 + - + +
245A LEU* 2.9 49.3 + - + +
283A ILE* 3.9 18.6 - - + -
356A ILE* 4.7 4.9 - - + -
358A LEU* 4.3 17.5 - - + -
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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
----------------------------------------------------------
196A VAL* 3.7 18.3 - - + +
199A ASP* 3.8 15.5 - - + -
200A ALA* 3.6 30.4 - - + +
203A THR* 3.7 28.7 - - + -
238A PRO 2.8 17.1 + - - +
239A SER* 3.7 10.3 - - - +
241A LEU* 1.3 76.0 - - - +
243A HIS* 1.3 59.8 + - - +
245A LEU* 3.0 4.8 + - - +
246A PHE* 2.8 53.1 + + + +
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Residues in contact with HIS 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 SER 3.0 19.3 + - - +
240A HIS* 3.6 7.9 - - - +
241A LEU 3.3 0.2 - - - -
242A PHE* 1.3 82.3 - - - +
244A MET* 1.3 66.8 + - - +
246A PHE* 3.4 5.7 + + - +
247A GLU* 3.3 33.4 + - + +
327A GLY* 4.9 2.0 + - - -
330A ILE* 4.2 14.1 - - + +
331A SER* 3.9 15.5 + - - -
334A TYR* 3.9 38.7 + + + -
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Residues in contact with MET 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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236A TYR* 4.0 12.1 - - + +
240A HIS 3.1 21.5 + - - +
241A LEU* 3.1 21.7 + - + +
243A HIS* 1.3 78.2 - - - +
245A LEU* 1.3 62.1 + - - +
247A GLU* 3.3 3.3 + - - +
248A LEU* 3.3 27.3 + - - +
331A SER* 3.5 40.1 + - - +
334A TYR* 3.8 10.8 - - + -
335A ALA* 3.6 24.7 - - - +
342A LEU* 4.8 1.6 - - + -
356A ILE* 4.0 22.0 - - + -
358A LEU* 4.0 23.6 - - + -
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Residues in contact with LEU 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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196A VAL* 3.9 16.6 - - + -
197A VAL* 3.8 36.1 - - + +
200A ALA* 3.5 13.9 - - + -
241A LEU* 2.9 46.2 + - + +
244A MET* 1.3 74.8 - - - +
246A PHE* 1.3 66.6 + - - +
248A LEU* 3.3 5.2 + - - +
249A PHE* 2.9 36.7 + - + -
283A ILE* 4.0 20.9 - - + -
285A ILE* 4.1 13.0 - - + -
356A ILE* 4.0 12.8 - - + -
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Residues in contact with PHE 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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200A ALA* 3.8 12.5 - - + +
203A THR* 3.7 28.7 - - + -
204A ALA* 3.7 29.4 - - + -
207A LEU* 3.6 24.0 - - + -
242A PHE* 2.8 33.9 + + + +
243A HIS* 3.7 6.3 - + - +
244A MET 3.2 0.2 - - - -
245A LEU* 1.3 77.0 - - - +
247A GLU* 1.3 79.1 + - + +
249A PHE* 3.4 1.4 + - - +
250A LYS* 2.9 48.7 + - + +
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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
----------------------------------------------------------
243A HIS* 3.3 25.3 + - + +
244A MET 3.8 2.2 - - - +
245A LEU 3.3 0.2 - - - -
246A PHE* 1.3 89.1 - - + +
248A LEU* 1.3 67.4 + - + +
250A LYS* 3.0 33.3 + - - +
251A ASN* 3.1 34.5 + - - +
325A GLY 4.8 1.7 + - - -
327A GLY* 3.4 30.6 - - - +
328A LEU* 5.3 0.7 - - - -
331A SER* 3.4 27.4 - - - +
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Residues in contact with LEU 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A MET 3.3 10.1 + - - +
245A LEU 3.3 3.5 + - - +
247A GLU* 1.3 78.6 - - + +
249A PHE* 1.3 58.6 + - - +
251A ASN* 3.2 4.1 + - - +
252A SER* 2.8 32.5 + - - -
285A ILE* 3.7 26.9 - - + -
328A LEU* 4.2 23.3 - - + -
331A SER* 5.5 1.3 - - - -
342A LEU* 4.0 15.7 - - + -
354A ALA* 4.1 23.6 - - + -
356A ILE* 3.7 37.2 - - + -
408A RDC 3.6 22.5 + - + +
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Residues in contact with PHE 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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197A VAL* 3.5 35.4 - - + -
200A ALA 4.1 0.9 - - - -
201A TYR* 3.3 49.6 - + + -
204A ALA* 4.1 13.9 - - + -
218A LEU* 4.1 1.8 - - + -
245A LEU* 2.9 40.3 + - + +
246A PHE 3.8 2.7 - - - +
248A LEU* 1.3 74.1 - - - +
250A LYS* 1.3 66.2 + - - +
252A SER* 3.2 2.6 + - - -
253A MET* 2.8 28.8 + - + +
270A VAL* 4.1 5.8 - - + -
272A THR* 3.5 26.5 - - + -
285A ILE* 3.7 31.4 - - + -
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Residues in contact with LYS 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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204A ALA* 3.9 15.8 - - + +
207A LEU* 5.6 6.1 - - + -
208A CYS* 6.5 0.2 - - - -
246A PHE* 2.9 34.2 + - + +
247A GLU* 3.0 36.4 + - - +
249A PHE* 1.3 76.6 - - - +
251A ASN* 1.3 81.8 + - - +
253A MET* 4.0 3.7 - - - +
254A ARG* 3.1 29.5 + - + +
325A GLY 5.1 7.3 - - - +
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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 GLU* 3.1 20.6 + - - +
248A LEU* 4.6 1.4 - - - +
250A LYS* 1.3 94.7 + - - +
252A SER* 1.3 59.5 + - - +
254A ARG* 3.5 0.7 + - - -
255A ALA* 2.9 31.4 + - - +
328A LEU* 4.6 10.5 - - - +
408A RDC 3.3 83.3 + - + +
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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 LEU 2.8 18.0 + - - -
249A PHE* 3.6 5.2 - - - -
251A ASN* 1.3 77.0 - - - +
253A MET* 1.3 55.2 + - - +
255A ALA* 3.3 2.6 + - - +
256A THR* 2.7 38.5 + - - -
270A VAL* 4.0 19.7 - - - -
285A ILE* 3.8 14.1 + - - +
287A ASP* 2.7 36.8 + - - +
408A RDC 3.6 5.4 + - - -
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Residues in contact with MET 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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201A TYR* 2.8 66.6 - - + +
204A ALA* 3.9 12.1 - - + +
205A LYS* 3.8 27.1 - - + +
208A CYS* 3.8 22.2 - - + -
216A PRO* 3.6 23.8 - - + +
249A PHE* 2.8 21.9 + - + +
250A LYS* 4.0 4.3 - - - +
252A SER* 1.3 69.8 - - - +
254A ARG* 1.3 61.7 + - - +
256A THR* 3.1 1.7 + - - -
257A VAL* 2.8 35.8 + - - +
270A VAL* 4.6 2.2 - - + -
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Residues in contact with ARG 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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208A CYS* 4.8 0.2 - - - -
212A TYR* 3.2 40.7 + - + +
250A LYS* 3.1 23.4 + - + +
251A ASN* 3.9 3.6 + - - +
253A MET* 1.3 76.8 - - - +
255A ALA* 1.3 63.3 + - - +
257A VAL* 4.8 0.4 - - - -
258A GLU* 3.0 46.1 + - - +
408A RDC 3.9 30.5 - - + +
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Residues in contact with ALA 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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251A ASN 2.9 19.8 + - - +
252A SER 3.6 4.0 - - - +
253A MET 3.2 0.2 - - - -
254A ARG* 1.3 78.7 - - - +
256A THR* 1.3 62.5 + - - +
258A GLU* 3.5 2.5 + - - +
259A LEU* 3.2 18.5 + - - +
287A ASP* 4.6 0.2 - - - +
289A GLY* 3.5 26.3 - - - +
408A RDC 3.5 45.4 + - + +
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Residues in contact with THR 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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216A PRO* 3.7 16.6 - - + -
252A SER 2.7 25.5 + - - -
253A MET 3.6 2.7 - - - -
255A ALA* 1.3 70.1 - - - +
257A VAL* 1.3 68.7 + - - +
259A LEU 3.2 1.6 + - - -
260A TYR* 3.0 30.9 + - + +
267A TYR* 4.3 7.4 - - + -
268A PRO* 3.6 45.0 + - + +
269A ALA 5.3 0.6 + - - +
270A VAL* 4.0 5.2 - - - +
287A ASP* 4.0 15.6 - - - +
288A LEU 4.4 1.9 + - - -
289A GLY* 4.0 11.0 + - - -
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Residues in contact with VAL 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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208A CYS* 4.2 3.8 - - - -
212A TYR* 3.6 41.5 - - + +
214A VAL* 4.0 24.5 - - + +
215A ALA* 4.1 2.9 - - - -
216A PRO* 3.9 22.4 - - + -
253A MET 2.8 20.9 + - - +
254A ARG 4.3 1.8 - - - +
256A THR* 1.3 72.0 - - - +
258A GLU* 1.3 64.1 + - - +
261A GLU* 3.1 30.1 + - + +
267A TYR* 3.8 19.2 - - + +
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Residues in contact with GLU 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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211A TYR* 5.4 0.7 - - - -
212A TYR* 2.8 41.1 + - + +
254A ARG* 3.0 40.6 + - - +
255A ALA* 4.3 2.7 - - - +
256A THR 3.2 0.2 - - - -
257A VAL* 1.3 77.0 - - - +
259A LEU* 1.3 61.8 + - - +
261A GLU* 3.6 23.5 - - - +
262A ASP* 5.0 0.7 + - - +
408A RDC 4.5 5.9 - - - +
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Residues in contact with LEU 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 ALA 3.2 17.8 + - - +
256A THR 3.9 2.7 - - - +
258A GLU* 1.3 77.8 - - - +
260A TYR* 1.3 71.7 + - + +
261A GLU 3.5 0.7 + - - -
262A ASP* 4.6 2.6 + - - +
263A ARG* 3.4 40.3 + - - +
288A LEU 3.4 23.3 - - - +
289A GLY 3.9 4.7 - - - +
290A GLY* 3.6 22.2 - - - +
349A GLY 5.5 3.6 - - - +
350A VAL 4.8 1.6 - - - +
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Residues in contact with TYR 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 THR* 3.0 23.3 + - + +
257A VAL 3.9 1.1 - - - -
259A LEU* 1.3 89.2 - - + +
261A GLU* 1.3 63.5 + - - +
262A ASP 3.2 2.8 + - - -
263A ARG* 3.5 41.0 + - + +
265A GLU* 3.7 27.1 - - + -
266A GLY 3.4 21.6 + - - +
267A TYR* 3.7 26.1 + - + -
268A PRO* 3.6 31.0 - - + +
288A LEU* 3.6 31.4 + - - +
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Residues in contact with GLU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A TYR* 5.0 10.4 - - - -
257A VAL* 3.1 16.4 + - + +
258A GLU* 3.6 25.7 - - - +
259A LEU 3.5 0.8 - - - -
260A TYR* 1.3 79.6 - - - +
262A ASP* 1.3 78.4 + - - +
263A ARG 3.4 5.3 + - - +
267A TYR* 3.7 13.0 + - - +
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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