Contacts of the helix formed by residues 237 - 274 (chain A) in PDB entry 2KSB
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 HIS 237 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A ASP* 2.7 25.9 + - - +
235A ARG* 3.6 0.7 + - - +
236A TYR* 1.4 122.6 + + - +
238A GLU* 1.3 58.1 + - - +
239A GLN* 2.9 39.8 + - - +
240A VAL* 3.0 5.2 + - + +
241A SER* 2.9 23.2 + - - -
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Residues in contact with GLU 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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231A ASP* 2.6 21.9 + - + +
237A HIS* 1.3 68.7 + - - +
239A GLN* 1.3 70.8 + - + +
241A SER* 2.6 25.9 + - - +
242A ALA* 2.6 24.4 + - - +
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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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237A HIS* 2.9 47.1 + - - +
238A GLU* 1.3 86.0 + - + +
240A VAL* 1.3 69.3 + - + +
242A ALA* 3.2 8.0 + - - +
243A LYS* 2.9 44.9 + - + +
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Residues in contact with VAL 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A LEU* 4.1 10.6 - - + +
236A TYR* 2.7 35.4 - - + +
237A HIS* 3.0 13.3 + - + +
239A GLN* 1.3 85.9 - - + +
241A SER* 1.3 59.7 + - - +
243A LYS* 3.5 15.4 + - - +
244A ARG* 2.9 49.9 + - - +
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Residues in contact with SER 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 2.9 35.4 + - - +
229A PRO 4.8 1.9 + - - -
230A GLY 4.1 1.6 - - - -
231A ASP* 3.8 12.6 + - - -
235A ARG* 2.9 28.3 - - - -
237A HIS 2.9 7.3 + - - -
238A GLU* 2.6 28.2 + - - +
240A VAL* 1.3 76.1 - - - +
242A ALA* 1.3 62.5 + - - +
244A ARG* 3.2 14.4 + - - +
245A LYS* 4.0 4.4 + - - +
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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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238A GLU 2.6 20.2 + - - +
239A GLN* 3.2 9.8 + - - +
241A SER* 1.3 72.2 + - - +
243A LYS* 1.3 67.3 + - + +
245A LYS* 3.0 33.7 + - + +
246A VAL* 3.6 7.0 + - - +
311A ARG* 4.6 18.1 + - - +
331A TYR* 4.9 8.3 - - - +
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Residues in contact with LYS 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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62A ARG* 6.1 1.0 - - - +
65A THR* 5.7 7.1 - - - +
130A ARG* 5.1 18.0 + - - +
133A ALA* 6.1 3.4 - - + -
223A LEU* 4.3 12.8 - - + -
239A GLN* 2.9 39.3 + - + +
240A VAL* 3.7 8.7 - - - +
241A SER 3.3 0.2 - - - -
242A ALA* 1.3 73.6 - - + +
244A ARG* 1.3 61.5 + - - +
245A LYS 3.0 2.2 - - - -
246A VAL* 2.8 31.7 + - + +
247A VAL* 3.0 11.8 + - - +
311A ARG* 5.9 4.0 - - - +
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Residues in contact with ARG 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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223A LEU* 2.9 52.2 - - + +
224A TRP 4.4 7.9 - - - +
225A ALA 5.4 0.6 - - - +
226A SER 3.6 10.1 + - - -
227A GLU* 3.4 38.1 - - + -
234A ASP 3.3 13.7 + - - -
235A ARG* 2.9 41.9 - - - +
236A TYR 4.3 1.4 - - - +
240A VAL* 2.9 38.0 + - - +
241A SER* 3.2 0.6 - - - +
242A ALA 3.2 0.6 - - - -
243A LYS* 1.3 78.0 - - - +
245A LYS* 1.3 58.7 + - - +
247A VAL* 2.7 31.0 - - + +
248A LYS* 3.2 9.5 + - - +
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Residues in contact with LYS 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A GLU* 3.9 27.9 + - + +
229A PRO* 4.8 17.6 + - - +
241A SER* 4.0 7.2 - - - +
242A ALA* 3.0 21.6 + - - +
243A LYS 3.0 0.2 - - - -
244A ARG* 1.3 78.0 - - - +
246A VAL* 1.3 62.2 + - + +
248A LYS* 2.7 49.5 - - - +
249A MET* 3.2 8.3 + - - +
308A LEU 5.1 6.4 - - - +
309A ASN* 5.8 8.0 - - + +
310A ASP* 5.1 9.6 - - - +
331A TYR* 4.8 12.8 - - - +
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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
----------------------------------------------------------
67A THR* 4.8 4.5 - - + +
130A ARG* 3.8 11.4 - - - +
242A ALA 4.0 9.6 - - - +
243A LYS* 2.8 20.3 + - + +
245A LYS* 1.3 74.9 - - + +
247A VAL* 1.3 66.4 + - - +
249A MET* 3.3 6.8 + - + +
250A MET* 2.9 55.3 + - + +
309A ASN* 6.4 3.1 - - + -
311A ARG* 5.5 13.2 - - - +
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Residues in contact with VAL 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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130A ARG* 3.7 31.4 - - + +
134A ILE* 5.0 4.5 - - + -
216A TYR* 6.0 1.3 - - + -
219A VAL* 4.2 24.2 - - + -
223A LEU* 5.2 10.1 - - + +
224A TRP 4.8 10.8 - - - +
225A ALA* 6.2 0.4 - - - -
243A LYS 3.0 8.7 + - - +
244A ARG* 2.7 36.3 - - + +
246A VAL* 1.3 78.1 - - - +
248A LYS* 1.3 59.7 + - + +
250A MET* 3.0 4.2 + - + +
251A ILE* 2.9 45.5 + - + +
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Residues in contact with LYS 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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225A ALA* 5.8 10.5 - - - +
227A GLU* 5.7 2.8 + - + -
244A ARG 3.6 6.3 - - - +
245A LYS* 2.7 54.6 - - - +
247A VAL* 1.3 82.9 - - + +
249A MET* 1.3 62.8 + - - +
251A ILE* 3.0 17.4 + - + +
252A VAL* 2.9 20.4 + - - +
308A LEU* 4.4 27.1 + - + +
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Residues in contact with MET 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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71A LEU* 4.6 5.4 - - + -
245A LYS 3.2 6.8 + - - +
246A VAL* 3.7 9.4 - - + +
247A VAL 3.2 0.2 - - - -
248A LYS* 1.3 81.6 - - - +
250A MET* 1.3 64.5 + - + +
252A VAL* 2.7 29.8 - - + +
253A VAL* 2.8 16.4 + - + +
301A ASN* 5.6 0.2 - - + -
304A ILE* 3.7 22.0 - - + -
305A TYR* 3.0 50.3 - - + -
308A LEU* 3.7 27.4 - - + -
309A ASN* 3.3 30.1 - - + +
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Residues in contact with MET 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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67A THR* 2.9 33.0 - - + -
71A LEU* 4.8 3.8 - - + -
123A MET* 5.3 0.3 - - - +
126A VAL* 3.1 31.2 - - + -
130A ARG* 2.9 51.8 - - + +
246A VAL* 2.9 29.3 + - + +
247A VAL* 3.0 8.3 + - + +
249A MET* 1.3 77.8 - - + +
251A ILE* 1.3 62.0 + - + +
253A VAL* 3.3 10.7 + - + +
254A VAL* 3.1 29.9 + - + +
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Residues in contact with ILE 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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216A TYR* 3.5 44.9 - - + +
219A VAL* 6.3 0.2 - - + -
224A TRP 6.4 1.1 - - - -
225A ALA* 6.1 7.0 - - + +
247A VAL* 2.9 34.5 + - + +
248A LYS* 3.0 17.9 + - + +
250A MET* 1.3 77.4 - - + +
252A VAL* 1.3 62.6 + - - +
254A VAL* 3.0 10.4 + - + +
255A CYS* 2.9 34.9 + - - -
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Residues in contact with VAL 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 LYS 2.9 9.2 + - - +
249A MET* 2.7 33.4 + - - +
251A ILE* 1.3 76.5 - - - +
253A VAL* 1.3 68.9 + - + +
255A CYS* 3.0 11.3 + - + +
256A THR* 2.9 27.4 + - - +
304A ILE* 4.1 20.4 - - + -
308A LEU* 4.0 22.7 - - + -
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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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74A LEU* 4.4 12.8 - - + -
123A MET* 3.5 25.1 - - + -
249A MET* 2.8 42.3 + - + +
250A MET* 3.5 11.2 - - + +
252A VAL* 1.3 75.3 - - - +
254A VAL* 1.3 59.7 + - - +
256A THR* 2.7 26.8 - - - +
257A PHE* 3.1 8.7 + - - +
300A TYR* 4.4 11.0 - - + +
301A ASN* 5.0 3.6 - - + -
304A ILE* 2.9 29.4 - - + -
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Residues in contact with VAL 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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123A MET* 4.3 22.7 - - + +
127A ALA* 6.3 0.4 - - + -
209A LEU* 6.2 4.0 - - + -
212A ILE* 4.1 35.0 - - + -
250A MET* 3.1 17.7 - - + +
251A ILE* 3.0 10.0 + - + +
253A VAL* 1.3 75.6 - - - +
255A CYS* 1.3 66.3 + - - +
257A PHE* 3.0 11.2 + - + +
258A ALA* 2.9 25.2 + - + +
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Residues in contact with CYS 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 ILE* 2.9 41.9 + - - -
252A VAL* 3.0 12.1 + - + +
254A VAL* 1.3 78.2 - - - +
256A THR* 1.3 63.1 + - - +
258A ALA* 3.1 7.8 + - - +
259A ILE* 3.0 23.6 + - - +
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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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252A VAL* 2.9 16.5 + - - +
253A VAL* 2.7 30.3 - - - +
255A CYS* 1.3 76.2 - - - +
257A PHE* 1.3 59.9 + - - +
259A ILE* 2.7 30.2 - - - +
260A CYS* 3.0 13.2 + - - -
300A TYR* 2.9 50.8 - - + +
304A ILE* 5.0 4.9 - - + -
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Residues in contact with PHE 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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116A VAL* 4.3 7.6 - - + -
119A SER* 3.7 25.1 - - - -
120A ILE* 3.5 43.5 - - + -
123A MET* 4.9 13.5 - - + -
205A TYR* 3.9 17.7 - + - -
209A LEU* 6.5 0.7 - - + -
212A ILE* 6.2 0.9 - - + -
253A VAL 3.4 9.9 - - - +
254A VAL* 3.1 16.4 - - + +
256A THR* 1.3 81.4 - - - +
258A ALA* 1.3 67.4 + - + +
260A CYS* 3.2 2.0 + - - -
261A TRP* 3.0 57.3 + + + +
297A SER* 5.5 0.4 - - - -
300A TYR* 3.4 22.0 - - - +
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Residues in contact with ALA 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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205A TYR* 4.3 12.6 - - - +
209A LEU* 5.3 10.8 - - + -
254A VAL* 2.9 16.1 + - + +
255A CYS* 3.7 9.4 - - - +
257A PHE* 1.3 80.6 - - + +
259A ILE* 1.3 61.4 + - - +
262A LEU* 2.7 42.3 + - + +
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Residues in contact with ILE 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 CYS 3.0 11.0 + - - +
256A THR* 2.7 35.7 - - - +
258A ALA* 1.3 77.2 - - - +
260A CYS* 1.3 76.2 + - - +
262A LEU* 5.0 0.7 - - - -
263A PRO* 3.0 27.4 - - + +
293A LEU* 4.5 5.4 - - + +
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Residues in contact with CYS 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 17.8 + - - +
257A PHE 3.8 2.7 - - - +
259A ILE* 1.3 91.6 - - - +
261A TRP* 1.3 59.6 + - - +
263A PRO* 4.1 3.1 - - - +
290A ILE* 4.5 5.7 - - - +
293A LEU* 3.9 34.8 - - - +
294A ALA* 4.0 11.5 + - - +
296A SER* 4.9 4.3 - - - -
297A SER* 2.9 42.8 - - - +
300A TYR* 4.1 8.1 - - - -
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Residues in contact with TRP 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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81A MET* 4.6 11.7 - - + -
116A VAL* 3.0 47.0 - - + +
119A SER* 5.6 0.6 - - - -
181A MET* 6.0 3.8 - - + -
205A TYR* 4.3 7.9 - - + -
257A PHE* 3.0 57.9 + + + +
258A ALA 4.5 0.2 - - - +
260A CYS* 1.3 73.5 - - - +
262A LEU* 1.3 65.0 + - - +
263A PRO 3.2 2.7 - - - -
264A PHE* 2.8 34.4 + + + +
265A HIS* 3.1 33.4 + + + +
291A MET* 5.2 11.2 - - + -
294A ALA* 2.9 43.1 - - + -
295A MET* 5.5 4.3 - - - -
297A SER* 3.6 17.4 + - - -
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Residues in contact with LEU 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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205A TYR* 3.6 30.7 + - + +
206A PHE* 5.0 11.2 - - + -
209A LEU* 4.6 7.4 - - + -
258A ALA* 2.7 29.2 + - + +
259A ILE* 5.0 0.9 - - + -
261A TRP* 1.3 72.8 - - - +
263A PRO* 1.3 70.6 - - + +
265A HIS* 3.1 5.9 + - + -
266A ILE* 2.9 28.4 + - + +
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Residues in contact with PRO 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 ILE* 3.0 28.7 - - + +
260A CYS 4.1 2.5 - - - +
261A TRP 3.6 1.6 - - - -
262A LEU* 1.3 98.9 - - + +
264A PHE* 1.3 59.6 + - - +
266A ILE* 2.7 15.2 - - + +
267A PHE* 2.7 32.2 - - + -
290A ILE* 3.5 22.9 - - + -
293A LEU* 5.1 7.2 - - + -
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Residues in contact with PHE 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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181A MET* 3.2 34.8 - - + -
184A TRP* 2.9 32.5 - + - -
261A TRP* 2.8 32.0 + + + +
263A PRO* 1.3 76.4 - - - +
265A HIS* 1.3 57.4 + + - +
267A PHE* 3.2 4.6 + - + -
268A PHE* 2.7 41.6 + + - +
287A TYR* 3.4 24.0 - + - -
290A ILE* 2.8 35.7 - - + +
291A MET* 3.6 31.2 - - + -
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Residues in contact with HIS 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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116A VAL* 4.4 12.0 - - + +
117A PHE* 5.9 4.0 - + - -
201A THR* 4.4 8.1 - - + +
204A ILE* 5.6 3.1 - - + -
205A TYR* 2.9 74.0 - + + +
206A PHE* 4.4 9.0 - - + -
261A TRP* 3.1 42.8 + + + +
262A LEU* 3.1 5.7 + - + +
264A PHE* 1.3 78.2 - + + +
266A ILE* 1.3 62.7 + - - +
268A PHE* 2.8 34.1 - + - +
269A LEU* 3.2 12.8 + - - +
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Residues in contact with ILE 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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206A PHE* 5.4 8.3 - - + -
262A LEU* 2.9 19.5 + - + +
263A PRO* 2.7 32.1 - - + +
265A HIS* 1.3 76.7 - - - +
267A PHE* 1.3 79.0 + - + +
269A LEU* 3.1 16.3 + - + +
270A LEU* 3.0 50.5 + - + +
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Residues in contact with PHE 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 PRO* 2.7 31.5 + - + +
264A PHE* 3.7 6.7 - - + +
266A ILE* 1.3 91.5 - - + +
268A PHE* 1.3 67.8 + - - +
270A LEU* 4.6 5.6 - - + -
271A PRO* 2.8 32.1 - - + +
279A LEU* 4.3 30.1 - - + -
280A LYS* 6.5 0.2 - - + -
286A VAL* 3.4 32.8 - - + -
287A TYR* 3.1 27.0 + + + -
290A ILE* 4.3 15.5 - - + -
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Residues in contact with PHE 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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113A ILE* 5.7 2.2 - - + -
181A MET* 4.0 9.6 - - + -
182A ILE* 2.9 32.5 - - + -
184A TRP* 2.9 32.9 - + - +
197A HIS* 2.8 63.7 - + - -
200A VAL* 4.8 9.6 - - + -
201A THR* 2.8 30.3 - - + -
264A PHE* 2.7 24.4 + + - +
265A HIS* 2.8 29.4 - + - +
267A PHE* 1.3 79.7 - - - +
269A LEU* 1.3 56.3 + - - +
272A TYR 3.6 5.9 + - - -
287A TYR* 3.2 11.6 + - - -
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Residues in contact with LEU 269 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A HIS* 3.2 24.9 - - + +
198A ILE* 5.1 4.0 - - + -
201A THR* 3.3 26.0 - - + +
202A VAL* 5.7 6.7 - - + -
206A PHE* 3.8 29.8 - - + -
265A HIS 3.7 8.1 - - - +
266A ILE* 3.1 14.0 + - + +
268A PHE* 1.3 79.2 - - - +
270A LEU* 1.4 64.5 + - + +
272A TYR* 2.7 27.3 + - + +
273A ILE* 3.1 13.2 + - + +
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Residues in contact with LEU 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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266A ILE* 3.0 43.3 + - + +
267A PHE* 4.6 9.2 - - + -
269A LEU* 1.4 77.9 - - + +
271A PRO* 1.3 76.6 - - + +
273A ILE* 2.8 38.2 - - + +
274A ASN* 3.0 5.4 + - - +
279A LEU* 3.3 38.3 - - + +
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Residues in contact with PRO 271 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP* 4.0 11.9 - - + +
185A PRO* 5.8 1.8 - - + -
267A PHE* 2.8 33.2 - - + +
268A PHE 4.5 1.8 - - - +
269A LEU 3.3 0.2 - - - -
270A LEU* 1.3 91.8 - - + +
272A TYR* 1.3 61.8 + - - +
274A ASN 3.8 8.5 - - - +
275A PRO* 2.9 32.0 - - + +
279A LEU* 4.5 8.3 - - + -
282A PHE* 3.6 38.1 - - + -
287A TYR* 3.8 13.0 - - + +
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184A TRP 3.9 10.2 + - - +
193A GLU* 3.5 24.5 - - - -
194A LYS* 2.8 59.6 - - + +
197A HIS* 2.8 42.4 - + + +
198A ILE* 3.5 24.5 - - + +
268A PHE 3.6 2.8 + - - -
269A LEU* 2.7 15.4 + - + +
271A PRO* 1.3 72.0 - - - +
273A ILE* 1.3 75.2 + - + +
275A PRO* 3.0 17.8 - - - +
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Residues in contact with ILE 273 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 3.1 8.5 + - + +
270A LEU* 2.8 35.7 + - + +
272A TYR* 1.3 98.0 - - + +
274A ASN* 1.3 88.7 + - + +
275A PRO* 3.1 6.4 - - - +
279A LEU* 5.8 2.9 - - + -
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Residues in contact with ASN 274 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A LEU 3.0 3.7 + - - +
271A PRO* 3.1 12.9 - - - +
273A ILE* 1.3 98.2 + - + +
275A PRO* 1.3 67.5 + - - +
277A LEU* 2.7 62.0 + - - +
278A TYR 4.4 7.7 - - - +
279A LEU* 6.1 3.1 - - + -
282A PHE* 5.7 1.2 - - - -
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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