Contacts of the helix formed by residues 215 - 242 (chain A) in PDB entry 5MKE
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 LYS 215 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A TYR* 1.3 76.9 + - + +
217A LEU* 3.1 40.0 - - + +
218A LYS* 2.8 38.0 + - - +
219A SER* 3.0 9.4 + - - -
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Residues in contact with TYR 216 (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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215A LYS* 1.3 88.1 - - + +
217A LEU* 1.3 53.6 + - + +
219A SER* 2.6 18.5 + - - -
220A VAL* 2.6 49.4 + - + +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LYS* 3.1 34.1 - - + +
216A TYR* 1.3 77.6 - - + +
218A LYS* 1.3 57.0 + - - +
220A VAL* 4.3 10.3 - - + -
221A LEU* 3.2 35.0 - - + +
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Residues in contact with LYS 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LYS 2.8 28.0 + - - +
217A LEU* 1.3 73.1 - - - +
219A SER* 1.3 58.4 + - - +
222A ARG* 3.1 47.2 + - + +
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Residues in contact with SER 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A LYS 3.0 6.6 + - - -
216A TYR* 2.6 33.7 + - - -
218A LYS* 1.3 76.4 - - - +
220A VAL* 1.3 64.4 + - - -
222A ARG* 3.5 4.0 - - - +
223A GLU* 3.3 20.1 + - - +
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Residues in contact with VAL 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 2.6 38.8 + - + +
217A LEU* 4.3 11.9 - - + -
219A SER* 1.3 72.2 - - - +
221A LEU* 1.3 62.4 + - + +
223A GLU* 2.8 20.6 + - + +
224A LEU* 2.3 57.6 + - + +
579A PHE* 6.1 4.9 - - + -
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Residues in contact with LEU 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A LEU* 3.2 27.0 + - + +
219A SER 3.6 0.2 - - - -
220A VAL* 1.3 81.2 - - + +
222A ARG* 1.3 52.4 + - - +
224A LEU* 3.3 18.6 - - + +
225A VAL* 2.3 58.0 + - + +
228A LEU* 5.6 4.3 - - + -
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Residues in contact with ARG 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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218A LYS* 3.1 40.5 + - + +
219A SER* 3.5 5.6 - - - +
221A LEU* 1.3 78.2 - - - +
223A GLU* 1.3 63.3 + - - +
225A VAL* 3.1 19.3 - - - +
226A THR* 3.0 53.5 + - - +
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Residues in contact with GLU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER 3.3 5.8 + - - +
220A VAL* 2.8 36.9 + - + +
222A ARG* 1.3 75.8 - - + +
224A LEU* 1.3 56.6 + - + +
226A THR* 2.1 36.9 + - + +
227A TYR* 2.6 60.5 + - + -
487A TYR* 4.7 7.7 - - + +
490A GLU* 5.4 1.7 - - - +
576A PHE* 5.5 1.4 - - - -
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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
----------------------------------------------------------
220A VAL* 2.3 51.5 + - + +
221A LEU* 3.3 29.2 - - + +
223A GLU* 1.3 68.5 - - + +
225A VAL* 1.3 50.4 + - - +
227A TYR* 2.9 10.4 + - + +
228A LEU* 2.4 46.5 + - + +
576A PHE* 3.5 52.7 - - + +
579A PHE* 4.5 17.0 - - + -
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Residues in contact with VAL 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 2.3 54.7 + - + +
222A ARG* 3.1 23.1 - - - +
224A LEU* 1.3 67.3 - - - +
226A THR* 1.3 53.7 + - + +
228A LEU* 2.9 17.4 + - + +
229A LEU* 2.6 57.2 + - + +
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Residues in contact with THR 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 ARG* 3.0 36.2 + - - +
223A GLU* 2.1 40.3 + - - +
225A VAL* 1.3 72.7 - - + +
227A TYR* 1.3 54.9 + - - -
229A LEU* 4.5 2.5 - - - +
230A PHE* 2.8 37.2 + - - +
483A PHE* 3.5 20.4 - - + -
487A TYR* 2.7 27.6 + - + -
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Residues in contact with TYR 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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223A GLU* 2.6 77.0 + - + -
224A LEU* 3.2 11.0 - - + +
226A THR* 1.3 74.6 + - - +
228A LEU* 1.3 62.4 + - + +
230A PHE* 5.0 2.9 - - - -
231A LEU* 3.0 28.1 + - - +
487A TYR* 4.3 23.4 - + - -
490A GLU* 5.5 0.3 + - - -
491A GLU* 5.3 4.2 + - - -
572A LYS* 3.3 39.9 + - + -
576A PHE* 3.2 34.5 - + + -
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Residues in contact with LEU 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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221A LEU* 5.6 4.3 - - + -
224A LEU* 2.4 38.8 + - + +
225A VAL* 2.9 30.0 + - + +
227A TYR* 1.3 67.8 - - + +
229A LEU* 1.3 69.7 + - + +
231A LEU* 3.0 24.1 - - + +
232A ILE* 3.0 14.1 - - + +
576A PHE* 6.4 2.0 - - + -
1006A CHS 5.3 7.6 - - + +
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Residues in contact with LEU 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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225A VAL* 2.6 42.5 + - + +
226A THR* 4.4 2.7 - - - +
228A LEU* 1.3 77.0 - - + +
230A PHE* 1.3 55.0 + - - +
231A LEU 2.9 4.5 - - - -
232A ILE* 2.7 38.2 + - + +
233A VAL* 3.2 13.1 + - + +
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Residues in contact with PHE 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 THR 2.8 22.8 + - - +
227A TYR* 5.5 2.5 - - - -
229A LEU* 1.3 73.5 - - - +
231A LEU* 1.3 66.0 + - - +
233A VAL* 3.2 31.3 + - + +
234A LEU* 3.4 43.3 + - + +
480A PHE* 3.5 16.2 - - + -
483A PHE* 3.4 35.0 - + + -
484A ILE* 3.3 40.6 - - + -
487A TYR* 5.0 5.6 - + - -
514A ILE* 6.2 4.0 - - + -
569A VAL* 5.5 6.7 - - + -
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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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227A TYR 3.0 19.4 + - - +
228A LEU* 3.0 18.8 - - + +
229A LEU 2.9 0.4 + - - -
230A PHE* 1.3 81.8 - - - +
232A ILE* 1.3 63.8 + - + +
234A LEU* 3.6 2.3 + - - +
235A CYS* 3.1 30.9 + - - -
569A VAL* 5.3 19.1 - - + +
570A TRP* 4.3 20.9 - - + +
572A LYS* 6.6 0.2 - - + -
573A LEU* 4.2 29.2 - - + +
1006A CHS 3.7 41.5 - - + +
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Residues in contact with ILE 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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228A LEU* 3.0 29.2 - - + +
229A LEU* 2.7 22.9 + - + +
231A LEU* 1.3 73.4 - - + +
233A VAL* 1.3 49.0 + - - +
235A CYS 3.1 0.2 + - - -
236A ILE* 2.2 66.2 + - + +
1006A CHS 3.4 63.5 - - + +
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Residues in contact with VAL 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 LEU* 3.2 7.8 + - + +
230A PHE* 3.3 43.7 - - + +
231A LEU 3.1 0.4 - - - -
232A ILE* 1.3 74.2 - - - +
234A LEU* 1.3 62.0 + - + +
236A ILE* 2.8 15.2 + - + +
237A LEU* 2.7 29.1 + - + +
476A CYS* 4.1 29.5 - - + -
479A ILE* 6.3 1.6 - - + -
480A PHE* 4.4 17.3 - - + -
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Residues in contact with LEU 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A PHE* 3.4 45.4 + - + +
231A LEU 4.4 3.4 - - - +
233A VAL* 1.3 78.1 - - - +
235A CYS* 1.3 58.0 + - - +
237A LEU* 3.2 25.6 + - + +
238A THR* 2.8 36.6 + - + +
480A PHE* 4.8 14.1 - - + -
484A ILE* 5.6 0.9 - - + -
514A ILE* 6.5 0.2 - - + -
565A THR* 5.8 2.2 - - - +
566A VAL* 5.7 9.9 - - + -
569A VAL* 4.7 24.7 - - + -
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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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231A LEU* 3.1 33.6 + - - -
232A ILE 3.1 7.8 + - - +
234A LEU* 1.3 75.4 - - - +
236A ILE* 1.3 52.4 + - - +
238A THR* 2.4 10.6 + - - -
239A TYR* 2.3 40.9 + - + +
566A VAL* 5.8 2.7 - - - -
569A VAL* 6.5 0.9 - - - -
570A TRP* 4.5 4.0 - - - -
1005A CHS 6.5 0.7 - - - -
1006A CHS 3.2 33.0 - - - +
613B GLN* 4.3 21.1 - - - -
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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
----------------------------------------------------------
232A ILE* 2.2 60.6 + - + +
233A VAL* 2.8 11.4 + - + +
235A CYS* 1.3 65.5 - - - +
237A LEU* 1.3 55.1 + - + +
239A TYR* 3.9 10.8 - - + -
240A GLY* 2.2 41.4 + - - -
472A PHE 5.7 3.4 - - - +
473A LEU* 6.0 2.5 - - - -
476A CYS* 4.5 17.9 - - - -
1006A CHS 4.1 6.9 + - - +
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Residues in contact with LEU 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 VAL 2.7 17.8 + - - +
234A LEU* 3.2 29.6 + - + +
236A ILE* 1.3 73.2 - - + +
238A THR* 1.3 56.4 + - + +
240A GLY* 4.7 0.2 - - - -
241A MET* 2.2 60.6 + - + +
461A LYS* 5.1 0.9 - - - +
464A ARG* 3.7 27.1 - - - +
473A LEU* 4.2 24.2 - - + +
476A CYS* 4.3 11.7 - - - -
480A PHE* 3.5 33.4 - - + -
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Residues in contact with THR 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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234A LEU* 2.8 22.2 + - + +
235A CYS* 2.4 27.7 + - - -
237A LEU* 1.3 71.1 - - + +
239A TYR* 1.3 58.1 + - - +
241A MET* 3.4 20.4 - - + +
242A MET* 2.7 37.0 + - - +
562A ALA* 6.5 0.9 - - + -
566A VAL* 5.0 7.9 - - + -
616B TYR* 5.6 4.7 - - - -
617B LEU* 4.5 31.7 - - + +
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Residues in contact with TYR 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* 2.3 33.8 + - + +
236A ILE* 3.6 8.7 - - + +
238A THR* 1.3 69.2 + - - -
240A GLY* 1.3 62.8 + - - +
242A MET 2.8 21.2 - - - +
243A SER* 3.6 11.1 + - - -
244A SER 6.2 0.7 - - - -
1005A CHS 3.9 31.9 - - + +
1006A CHS 3.2 42.0 - - - +
616B TYR* 6.3 1.1 - - - -
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Residues in contact with GLY 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A ILE* 2.2 29.0 + - - -
237A LEU* 4.7 0.4 - - - -
239A TYR* 1.3 71.7 - - - +
241A MET* 1.3 64.7 + - - +
242A MET* 3.1 3.0 + - - -
243A SER* 4.4 2.6 + - - -
473A LEU* 5.7 9.4 - - - +
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Residues in contact with MET 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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237A LEU* 2.2 64.2 + - + +
238A THR* 3.4 18.8 - - + +
240A GLY* 1.3 67.8 - - - +
242A MET* 1.3 93.8 + - + +
243A SER 4.3 0.3 + - - -
246A VAL* 5.1 0.5 - - - +
433A ILE* 6.0 0.2 - - - +
435A LEU* 4.1 9.2 - - - +
461A LYS* 3.3 57.8 - - + +
473A LEU* 5.6 8.8 - - + +
558A PHE* 5.3 13.2 - - + -
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Residues in contact with MET 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 THR* 2.7 26.6 + - - +
239A TYR* 2.8 15.8 - - - +
241A MET* 1.3 125.1 - - + +
243A SER* 1.3 65.2 + - - +
246A VAL* 4.1 16.6 - - + -
435A LEU* 3.7 22.2 - - + -
459A PRO* 5.6 8.5 - - + +
460A LEU* 5.2 3.4 - - - -
461A LYS* 4.5 18.2 - - + +
555A GLN* 5.6 7.0 - - - +
559A ASN* 5.5 10.1 - - - +
616B TYR* 3.9 15.4 + - + +
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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) + - + + + + + -
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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