Contacts of the helix formed by residues 221 - 245 (chain A) in PDB entry 3KMR
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 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212A ASN* 3.8 4.6 + - - +
213A SER* 3.0 41.5 + - - +
218A VAL* 3.9 5.1 - - + +
220A LEU* 1.3 72.4 - - - +
222A ILE* 1.3 59.3 + - - +
223A ASP* 3.1 14.7 + - - +
224A LEU* 2.9 33.2 + - + +
225A TRP* 2.8 29.5 + - - +
299A ASN* 2.8 19.8 + - + +
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Residues in contact with ILE 222 (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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220A LEU* 3.9 8.9 + - + +
221A ASP* 1.3 72.5 + - - +
223A ASP* 1.3 67.2 + - - +
225A TRP* 3.1 11.5 + - + +
226A ASP* 2.8 56.9 + - - +
403A PRO* 3.4 39.3 - - + -
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Residues in contact with ASP 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A ASN* 4.0 22.7 + - - +
221A ASP* 3.1 9.9 + - - +
222A ILE* 1.3 85.8 - - - +
224A LEU* 1.3 62.6 + - - +
226A ASP* 3.5 13.2 + - - +
227A LYS* 3.2 35.0 + - - +
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 3.9 17.0 - - + -
212A ASN* 3.6 37.0 - - + +
213A SER* 3.5 24.9 - - - +
221A ASP* 2.9 20.3 + - + +
223A ASP* 1.3 73.4 - - - +
225A TRP* 1.3 59.9 + - - +
227A LYS* 3.1 12.0 + - + +
228A PHE* 2.8 32.9 + - - +
290A LEU* 5.4 0.4 - - + -
292A LEU* 4.0 18.6 - - + -
296A GLN* 3.9 24.7 - - + +
299A ASN* 4.2 1.3 - - + -
300A ALA* 3.9 13.2 - - + +
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Residues in contact with TRP 225 (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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1A EQN 3.9 22.4 - - + -
220A LEU* 3.9 9.6 - - + -
221A ASP 2.8 18.1 + - - +
222A ILE* 3.5 19.1 - - + +
224A LEU* 1.3 71.2 - - - +
226A ASP* 1.3 71.6 + - - +
228A PHE* 4.0 7.2 - + - -
229A SER* 2.8 56.6 + - - -
300A ALA 3.3 29.9 + - - +
398A LEU* 3.9 24.0 - - + -
402A ILE* 3.6 41.3 - - + +
403A PRO* 4.7 1.7 - - + +
405A SER 5.7 0.4 + - - -
406A MET* 3.8 35.7 - - + -
407A PRO* 4.6 6.4 - - + +
410A ILE* 5.3 0.4 - - + -
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Residues in contact with ASP 226 (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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222A ILE* 2.8 47.4 + - - +
223A ASP* 3.6 12.5 - - - +
225A TRP* 1.3 77.9 + - - +
227A LYS* 1.3 63.1 + - + +
229A SER* 3.3 7.1 + - - -
230A GLU* 3.2 24.4 + - - +
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Residues in contact with LYS 227 (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 TYR* 5.9 3.6 - - + +
210A THR* 3.8 12.5 + - - -
212A ASN* 2.8 28.5 + - - +
223A ASP* 3.2 19.3 + - - +
224A LEU* 3.1 13.2 + - + +
226A ASP* 1.3 75.9 - - + +
228A PHE* 1.3 59.0 + - - +
230A GLU* 3.4 5.2 + - - +
231A LEU* 3.0 36.4 + - + +
290A LEU* 4.2 28.7 - - + +
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Residues in contact with PHE 228 (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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1A EQN 3.4 68.6 - + + -
224A LEU 2.8 20.4 + - - +
225A TRP* 3.8 12.8 - + - +
227A LYS* 1.3 71.5 - - - +
229A SER* 1.3 58.2 + - - +
231A LEU* 3.4 7.0 + - - +
232A SER* 2.9 34.9 + - - -
286A PHE* 3.7 24.9 - + + -
290A LEU* 5.4 1.5 - - - +
292A LEU* 5.6 2.7 - - + -
300A ALA* 3.3 34.5 - - + -
301A GLY* 4.3 5.6 - - - -
302A PHE* 3.4 32.5 - + - -
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Residues in contact with SER 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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1A EQN 4.9 0.2 - - - -
225A TRP* 2.8 57.8 + - - -
226A ASP* 3.3 9.7 + - - -
228A PHE* 1.3 75.2 - - - +
230A GLU* 1.3 59.3 + - - +
232A SER* 3.2 8.7 + - - -
233A THR* 3.0 32.4 + - - -
407A PRO* 4.1 19.7 - - - +
410A ILE* 3.7 4.3 - - - +
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Residues in contact with GLU 230 (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 ASP 3.2 16.7 + - - +
227A LYS* 3.6 6.1 - - - +
229A SER* 1.3 81.0 + - - +
231A LEU* 1.3 63.1 + - + +
233A THR* 3.3 14.4 + - - +
234A LYS* 2.1 57.0 + - - +
407A PRO* 6.1 0.4 - - - -
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Residues in contact with LEU 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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1A EQN 3.6 19.9 - - + +
227A LYS* 3.0 22.8 + - + +
228A PHE* 3.7 5.8 - - - +
230A GLU* 1.3 77.4 - - + +
232A SER* 1.3 57.5 + - - +
234A LYS* 3.3 17.4 + - + +
235A CYS* 2.9 28.4 + - - +
286A PHE* 3.7 30.1 - - + -
287A SER* 4.5 2.5 - - - +
288A ASP* 3.7 40.6 - - + +
290A LEU* 3.8 22.4 - - + -
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Residues in contact with SER 232 (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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1A EQN 3.2 54.7 + - - +
228A PHE* 2.9 24.5 + - - -
229A SER 3.5 6.1 - - - -
230A GLU 3.2 0.2 - - - -
231A LEU* 1.3 74.3 - - - +
233A THR* 1.3 60.1 + - - +
235A CYS* 3.2 2.4 + - - +
236A ILE* 2.9 35.8 + - - +
269A LEU* 4.4 3.4 - - - +
410A ILE* 4.1 13.9 - - - -
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Residues in contact with THR 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 SER 3.0 13.6 + - - -
230A GLU* 3.5 19.4 - - - +
232A SER* 1.3 75.2 - - - +
234A LYS* 1.3 63.6 + - + +
236A ILE* 3.2 13.0 + - - +
237A ILE* 3.2 30.7 + - + +
407A PRO* 3.9 15.7 - - + +
409A LEU* 3.9 22.6 - - + +
410A ILE* 3.8 13.9 + - - +
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Residues in contact with LYS 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 GLU* 2.1 53.5 + - - +
231A LEU* 3.3 20.8 + - + +
233A THR* 1.3 76.3 - - + +
235A CYS* 1.3 61.7 + - - +
237A ILE* 3.3 15.4 + - + +
238A LYS* 3.2 26.2 + - + +
287A SER* 6.6 0.4 - - - -
288A ASP* 6.5 0.4 - - + -
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Residues in contact with CYS 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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1A EQN 3.8 32.1 - - + +
231A LEU 2.9 16.3 + - - +
232A SER 3.2 2.4 + - - +
234A LYS* 1.3 73.6 - - - +
236A ILE* 1.3 61.5 + - - +
238A LYS* 3.3 7.4 + - - +
239A THR* 2.9 31.5 + - - -
269A LEU* 3.2 31.0 - - + -
272A ARG* 3.8 31.9 - - - -
287A SER* 5.5 2.2 - - - +
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Residues in contact with ILE 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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1A EQN 5.5 1.6 - - + -
232A SER* 2.9 22.2 + - - +
233A THR* 3.2 6.7 + - - +
235A CYS* 1.3 76.0 - - - +
237A ILE* 1.3 62.7 + - - +
239A THR* 3.1 8.9 + - - -
240A VAL* 3.0 29.3 + - + +
265A CYS* 3.9 21.5 - - - -
269A LEU* 4.3 11.9 - - + -
409A LEU* 3.7 21.1 - - + -
410A ILE* 3.9 31.2 - - + +
413A MET* 3.7 41.7 - - + -
414A LEU* 5.9 0.2 - - + -
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Residues in contact with ILE 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 THR* 3.2 24.9 + - + +
234A LYS* 3.5 13.0 - - + +
235A CYS 3.2 0.2 - - - -
236A ILE* 1.3 77.2 - - - +
238A LYS* 1.3 64.9 + - + +
240A VAL* 3.3 4.0 + - - +
241A GLU* 3.1 40.0 + - + +
409A LEU* 3.7 17.9 - - + -
631C ILE* 6.4 0.2 - - + -
635C LEU* 4.2 30.9 - - + +
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Residues in contact with LYS 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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197A GLU 5.2 5.1 + - - -
198A THR* 3.6 35.9 - - - +
234A LYS 3.2 16.3 + - - +
235A CYS* 3.3 9.4 + - - +
237A ILE* 1.3 78.4 - - + +
239A THR* 1.3 55.7 + - - +
241A GLU* 3.3 31.8 + - - +
242A PHE* 2.9 28.9 + - - +
272A ARG* 3.9 7.2 - - - +
287A SER* 6.6 0.2 - - - -
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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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235A CYS* 2.9 25.8 + - - -
236A ILE* 3.1 12.5 + - - -
238A LYS* 1.3 75.8 - - - +
240A VAL* 1.3 57.5 + - - +
242A PHE* 3.3 11.0 + - + +
243A ALA* 2.9 26.7 + - + +
261A LEU* 4.4 13.2 - - + -
265A CYS* 5.6 6.7 - - - +
268A ILE* 3.7 49.4 - - + +
269A LEU* 4.3 4.4 - - - +
272A ARG* 4.3 5.4 + - - +
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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
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236A ILE* 3.0 20.7 + - + +
237A ILE 3.6 7.0 - - - +
239A THR* 1.3 74.1 - - - +
241A GLU* 1.3 64.7 + - + +
243A ALA* 3.2 7.4 + - - +
244A LYS* 3.0 38.9 + - - +
261A LEU* 4.4 13.0 - - + -
413A MET* 5.5 0.7 - - + -
632C LEU* 3.7 24.5 - - + -
635C LEU* 3.9 30.5 - - + -
636C LEU* 3.9 26.9 - - + -
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Residues in contact with GLU 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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197A GLU 5.5 0.3 - - - +
198A THR* 4.0 11.4 - - + +
237A ILE* 3.1 34.6 + - + +
238A LYS* 3.3 41.2 + - - +
240A VAL* 1.3 76.9 - - + +
242A PHE* 1.3 63.8 + - - +
244A LYS* 3.4 23.0 + - - +
245A GLN* 3.4 22.1 + - - +
635C LEU* 6.5 0.7 - - + -
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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
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191A VAL 4.2 3.6 - - - -
194A ALA* 3.5 27.4 - - + -
195A HIS* 3.6 27.4 - - + -
198A THR* 3.6 16.0 - - - +
238A LYS 2.9 12.8 + - - +
239A THR* 3.4 12.8 - - + +
241A GLU* 1.3 75.8 - - - +
243A ALA* 1.3 66.3 + - + +
245A GLN* 2.9 21.3 + - - +
246A LEU* 3.5 32.4 + - + +
268A ILE* 4.9 13.0 - - + -
272A ARG* 3.9 11.4 - - - +
327A GLY 3.5 22.9 - - - -
330A SER* 3.7 24.9 - - - -
331A ALA 4.0 5.8 - - - -
334A LEU* 5.1 1.3 - - + -
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Residues in contact with ALA 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 THR 2.9 17.6 + - - +
240A VAL* 3.2 5.6 + - - +
242A PHE* 1.3 75.5 - - - +
244A LYS* 1.3 62.6 + - - +
246A LEU* 3.0 17.1 + - - +
249A PHE* 3.3 37.4 - - + +
261A LEU* 3.9 12.3 - - + -
334A LEU* 3.5 31.2 - - + -
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Residues in contact with LYS 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 VAL* 3.0 26.1 + - - +
241A GLU* 3.7 18.9 - - - +
242A PHE 3.2 0.6 - - - -
243A ALA* 1.3 74.5 - - - +
245A GLN* 1.3 61.2 + - + +
246A LEU 3.4 3.7 + - - +
249A PHE* 4.4 1.6 - - + -
250A THR* 4.0 31.2 + - + +
635C LEU 2.8 28.8 + - - +
636C LEU* 3.8 32.8 - - + +
637C GLN 4.2 4.8 + - - -
638C GLU* 3.6 22.0 - - - +
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Residues in contact with GLN 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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190A LYS* 4.8 9.2 + - - +
193A LYS* 4.6 10.1 - - - +
194A ALA* 3.7 31.8 - - + +
197A GLU* 3.6 23.2 + - - +
198A THR* 3.7 21.7 - - - +
241A GLU* 3.4 17.6 - - - +
242A PHE 2.9 9.4 + - - +
244A LYS* 1.3 77.8 - - + +
246A LEU* 1.3 64.3 + - - +
247A PRO* 3.5 8.3 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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