Contacts of the helix formed by residues 384 - 416 (chain A) in PDB entry 3IKM
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 384 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A THR* 3.2 18.0 + - - +
382A MET* 3.1 30.1 + - - +
383A LYS* 1.3 81.8 - - - +
385A ILE* 1.3 63.4 - - - +
386A ARG* 3.4 8.5 - - - +
387A GLU* 2.9 31.4 + - - +
388A ASN* 2.7 18.3 + - - +
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Residues in contact with ILE 385 (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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202A CYS* 5.6 7.4 - - + -
210A THR* 5.8 2.2 - - - +
224A CYS* 4.0 25.6 - - - -
228A LEU* 4.5 0.7 - - + -
375A GLU* 4.9 14.6 - - - +
381A THR 4.0 11.6 + - - +
382A MET* 2.8 45.8 - - + -
384A ASP* 1.3 80.2 + - - +
386A ARG* 1.3 66.3 + - + +
388A ASN* 2.9 13.4 + - - +
389A PHE* 2.5 42.4 + - + +
393A MET* 5.0 4.9 - - + +
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Residues in contact with ARG 386 (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 SER* 2.5 32.3 - - - +
228A LEU* 2.9 22.0 - - + +
383A LYS 2.5 40.3 + - - -
384A ASP* 2.9 3.8 + - - +
385A ILE* 1.3 77.0 - - - +
387A GLU* 1.3 110.1 + - - +
389A PHE* 3.4 4.5 - - - -
390A GLN* 2.5 52.5 + - - +
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Residues in contact with GLU 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384A ASP* 2.9 23.2 + - - +
386A ARG* 1.3 129.0 + - - +
388A ASN* 1.3 69.7 + - - +
389A PHE 3.0 0.2 + - - -
390A GLN* 3.1 20.8 + - - +
391A ASP* 3.4 10.4 + - - +
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Residues in contact with ASN 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381A THR* 5.3 3.2 + - - -
384A ASP* 2.7 31.6 + - - +
385A ILE* 2.9 21.4 - - + +
387A GLU* 1.3 81.7 - - - +
389A PHE* 1.3 55.4 + - - +
391A ASP* 3.5 6.7 + - - +
392A LEU* 2.9 28.1 + - - +
393A MET* 3.6 7.2 - - + +
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Residues in contact with PHE 389 (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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169A TRP* 6.4 1.8 - - + -
170A ALA 5.2 11.4 - - - -
171A TRP* 5.3 8.7 - - - -
210A THR 5.6 0.2 - - - -
211A LEU* 3.5 34.5 - - + -
221A TYR* 5.1 4.9 - + + -
222A SER 5.6 1.1 - - - -
224A CYS* 5.9 2.7 - - - -
225A SER* 3.3 20.9 - - - -
385A ILE* 2.5 27.8 + - + +
386A ARG* 2.8 5.3 + - - +
388A ASN* 1.3 69.3 - - - +
390A GLN* 1.3 124.2 + - + +
392A LEU 2.8 1.4 + - - -
393A MET* 2.6 67.9 + - + +
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Residues in contact with GLN 390 (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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169A TRP* 2.4 47.7 - - + +
225A SER* 3.1 4.2 + - - -
386A ARG* 2.5 58.8 + - - +
387A GLU* 3.5 12.4 - - - +
389A PHE* 1.3 109.2 - - + +
391A ASP* 1.3 55.1 + - - +
392A LEU 4.5 0.2 - - - -
393A MET 4.3 0.9 + - - -
394A GLN 5.0 1.0 + - - -
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Residues in contact with ASP 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169A TRP* 2.8 28.9 - - + -
387A GLU 3.4 6.2 + - - +
388A ASN* 3.6 9.9 - - - +
389A PHE 3.1 0.4 - - - -
390A GLN* 1.3 83.0 - - - +
392A LEU* 1.3 64.8 + - + +
394A GLN* 4.8 3.1 + - - +
395A TYR* 3.7 27.4 + - - -
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Residues in contact with LEU 392 (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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371A LYS* 5.0 0.9 - - - -
374A ARG* 2.6 46.7 - - - +
388A ASN 2.9 9.5 + - - +
389A PHE 2.8 7.9 + - - -
391A ASP* 1.3 78.0 - - + +
393A MET* 1.3 75.5 + - + +
394A GLN 2.5 5.3 + - - -
395A TYR* 2.2 83.8 + - + -
396A CYS* 3.4 11.0 - - - -
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Residues in contact with MET 393 (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 LEU* 3.6 18.2 - - + +
213A VAL* 5.4 0.3 - - - +
221A TYR* 4.5 4.9 - - + -
374A ARG* 4.5 4.3 - - - -
375A GLU* 3.1 22.4 - - - +
385A ILE* 5.0 5.4 - - + +
388A ASN* 3.6 7.2 - - + +
389A PHE* 2.6 71.7 + - + +
392A LEU* 1.3 83.7 - - + +
394A GLN* 1.3 60.6 + - - +
395A TYR 3.0 0.4 - - - -
396A CYS* 3.0 39.2 + - + +
397A ALA* 3.2 18.9 + - - +
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Residues in contact with GLN 394 (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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166A PRO* 3.3 28.0 - - + +
167A PRO* 4.9 8.0 + - + +
168A ALA 4.9 2.5 + - - +
169A TRP* 4.4 23.5 - - + +
220A TRP* 5.9 4.0 - - + -
221A TYR* 4.5 9.8 - - + -
389A PHE 4.5 0.6 + - - -
390A GLN 5.0 1.0 + - - -
391A ASP 4.8 5.3 + - - +
392A LEU 2.5 8.7 + - - +
393A MET* 1.3 75.3 - - - +
395A TYR* 1.3 103.5 + - - +
397A ALA* 2.9 23.9 - - + +
398A GLN* 3.0 28.3 + - - +
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Residues in contact with TYR 395 (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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370A PRO* 4.6 9.5 - - + +
371A LYS* 4.8 13.2 - - + +
374A ARG* 5.0 2.7 - - - -
391A ASP* 3.7 18.9 + - - -
392A LEU* 2.2 84.1 + - + +
394A GLN* 1.3 87.7 + - - +
396A CYS* 1.3 68.4 + - - +
398A GLN* 3.1 4.9 + - - +
399A ASP* 2.8 25.6 + - - +
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Residues in contact with CYS 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A LEU* 6.3 0.9 - - + -
213A VAL* 5.8 1.6 - - + -
371A LYS* 3.1 37.0 + - + +
375A GLU* 3.8 14.1 - - - -
392A LEU* 3.4 7.4 - - - +
393A MET* 3.0 46.7 - - + +
395A TYR* 1.3 78.7 - - - +
397A ALA* 1.3 70.4 + - - +
399A ASP* 3.1 0.7 + - - +
400A VAL* 2.9 23.6 + - + +
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Residues in contact with ALA 397 (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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213A VAL* 2.8 20.7 - - + +
221A TYR* 2.5 38.8 - - + +
393A MET 3.2 2.7 + - - +
394A GLN* 2.9 16.1 + - + +
396A CYS* 1.3 77.8 - - - +
398A GLN* 1.3 55.9 + - - +
400A VAL* 2.7 34.8 + - - +
401A TRP* 2.8 10.9 + - + +
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Residues in contact with GLN 398 (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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164A PRO* 3.9 22.9 - - + +
165A LYS 4.8 0.6 - - - -
166A PRO* 2.5 51.7 - - - +
394A GLN* 3.0 25.4 + - - +
395A TYR* 3.6 6.5 - - - +
397A ALA* 1.3 77.5 - - - +
399A ASP* 1.3 67.7 + - - +
401A TRP* 2.6 26.7 + - + +
402A ALA* 3.0 12.9 + - - +
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Residues in contact with ASP 399 (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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368A GLY 4.5 2.6 - - - +
369A PRO* 3.7 0.9 - - - +
370A PRO* 2.6 58.9 - - + +
371A LYS* 3.2 3.9 - - - -
372A GLU* 2.2 32.7 - - - +
395A TYR 2.8 11.3 + - - +
396A CYS 3.5 7.2 - - - +
398A GLN* 1.3 72.3 - - - +
400A VAL* 1.3 56.3 + - - +
402A ALA* 3.4 8.2 + - - +
403A THR* 2.7 39.5 + - - +
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Residues in contact with VAL 400 (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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198A ASP* 3.2 28.0 - - + +
213A VAL* 4.9 1.3 - - + -
270A ASN* 5.5 1.3 - - - +
371A LYS* 2.7 32.5 - - - +
396A CYS* 2.9 11.8 + - + +
397A ALA* 2.7 18.9 + - - +
399A ASP* 1.3 72.7 - - - +
401A TRP* 1.3 59.3 + - + +
403A THR* 2.6 27.9 + - - +
404A HIS* 2.6 51.3 - - + +
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Residues in contact with TRP 401 (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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164A PRO* 6.4 1.3 - - + -
196A VAL* 2.6 63.5 - - + -
197A PHE* 3.1 4.5 - - - -
213A VAL* 2.3 59.1 - - + +
214A ALA* 2.7 16.6 + - - +
215A ILE* 3.2 39.9 - - + -
397A ALA* 2.8 26.1 + - + -
398A GLN* 2.6 23.8 + - + +
400A VAL* 1.3 68.4 - - + +
402A ALA* 1.3 55.3 + - - +
404A HIS* 2.9 15.3 + + + +
405A GLU* 2.5 39.4 + - - +
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Residues in contact with ALA 402 (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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366A VAL* 4.8 16.8 - - + -
398A GLN 3.0 12.1 + - - +
399A ASP* 3.6 12.3 - - - +
401A TRP* 1.3 69.5 - - - +
403A THR* 1.3 57.9 + - - +
405A GLU* 2.6 10.2 + - - -
406A VAL* 2.2 52.2 + - + -
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Residues in contact with THR 403 (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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270A ASN* 2.7 27.4 + - - +
355A SER* 3.6 23.1 - - - +
359A ALA* 5.4 1.3 - - - -
399A ASP* 2.7 24.2 - - - +
400A VAL* 2.6 26.1 + - - +
402A ALA* 1.3 71.0 - - - +
404A HIS* 1.3 81.0 + - - +
406A VAL* 3.6 4.0 - - - +
407A PHE* 2.7 45.5 + - - -
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Residues in contact with HIS 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196A VAL* 3.1 34.2 - - + +
197A PHE 3.6 9.5 + - - -
198A ASP* 4.1 1.5 - - + +
268A GLY 3.6 3.9 + - - +
269A HIS* 3.4 24.5 - + + -
270A ASN* 3.0 40.9 + - - -
274A ASP* 5.1 3.6 - - - -
294A THR* 4.4 4.6 - - - +
400A VAL* 2.6 48.2 - - + +
401A TRP* 2.9 18.6 + + + +
403A THR* 1.3 83.7 + - - +
405A GLU* 1.3 59.2 - - + +
407A PHE* 4.2 0.5 - - - +
408A GLN* 2.8 33.7 + - - +
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Residues in contact with GLU 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU* 4.7 12.5 - - - +
160A ALA* 6.1 0.2 - - - +
196A VAL* 5.4 4.4 - - - +
215A ILE* 3.5 42.2 - - + +
363A ARG* 2.8 14.0 + - - +
401A TRP 2.5 12.8 + - - +
402A ALA* 2.6 10.7 + - - +
404A HIS* 1.3 74.8 - - + +
406A VAL* 1.3 61.3 + - + +
408A GLN* 4.5 2.7 - - - -
409A GLN* 3.1 53.9 + - - +
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Residues in contact with VAL 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
359A ALA* 3.7 17.9 - - + -
362A HIS* 4.2 4.0 - - + +
363A ARG* 2.6 56.7 + - + +
365A TYR 6.0 0.7 - - - +
366A VAL* 5.9 3.4 - - + -
402A ALA* 2.2 59.8 + - + +
403A THR* 2.9 4.3 + - - +
405A GLU* 1.3 63.5 - - + +
407A PHE* 1.3 96.1 + - + +
410A GLN* 3.7 7.6 - - - +
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Residues in contact with PHE 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ASN* 4.9 5.6 - - + -
294A THR* 3.8 32.8 - - - +
298A HIS* 5.6 0.4 - - + -
355A SER* 2.7 58.1 - - - -
358A LEU* 3.3 17.9 - - + -
359A ALA* 3.1 34.1 - - + -
362A HIS* 4.5 14.4 + + + -
403A THR* 2.7 28.4 + - - +
406A VAL* 1.3 84.4 - - + +
408A GLN* 1.3 50.7 + - - +
410A GLN* 3.2 1.7 - - - +
411A LEU* 2.4 50.0 + - + +
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Residues in contact with GLN 408 (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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157A LEU* 5.2 5.7 - - - +
158A LEU* 4.1 25.5 - - + +
196A VAL* 4.2 13.5 - - - +
266A VAL* 6.3 0.8 - - - +
268A GLY* 3.1 39.2 - - - +
294A THR* 3.2 14.6 - - - +
404A HIS 2.8 21.6 + - - +
405A GLU* 4.0 3.8 - - - +
407A PHE* 1.3 73.8 - - - +
409A GLN* 1.3 54.2 + - + +
410A GLN 2.9 4.9 - - - -
411A LEU* 2.9 21.8 - - + +
412A PRO* 2.5 36.7 - - - +
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Residues in contact with GLN 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157A LEU 4.8 1.6 + - - -
158A LEU* 2.3 48.8 + - + +
159A GLN* 4.5 1.4 + - - +
160A ALA 4.1 13.5 + - - -
363A ARG* 2.9 26.5 + - - +
405A GLU* 3.1 36.8 + - - +
408A GLN* 1.3 75.4 - - + +
410A GLN* 1.3 57.1 + - - +
412A PRO* 3.7 5.7 - - - +
413A LEU* 3.5 19.6 - - - +
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Residues in contact with GLN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A HIS* 3.4 41.1 + - - +
363A ARG* 3.3 32.7 - - - +
406A VAL 3.7 6.1 - - - +
407A PHE 3.2 1.0 + - - -
408A GLN 2.9 0.2 - - - -
409A GLN* 1.3 78.7 - - - +
411A LEU* 1.3 54.3 + - - +
412A PRO* 3.1 6.5 - - - +
413A LEU* 4.4 7.0 - - - +
414A PHE* 2.4 56.5 - - + -
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Residues in contact with LEU 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.9 0.7 - - + -
294A THR* 3.4 21.3 - - + -
297A MET* 2.8 48.5 - - + -
301A ILE* 6.2 0.7 - - - -
362A HIS* 4.5 9.9 - - + +
407A PHE* 2.4 25.8 + - + +
408A GLN* 2.9 47.3 - - + +
410A GLN* 1.3 67.4 - - - +
412A PRO* 1.3 90.0 - - + +
414A PHE* 4.8 0.7 - - - -
415A LEU* 2.6 42.0 + - + +
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Residues in contact with PRO 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.2 22.4 - - + -
408A GLN 2.5 30.7 - - - +
409A GLN 3.9 4.0 - - - +
410A GLN 3.1 7.9 - - - +
411A LEU* 1.3 89.9 - - + +
413A LEU* 1.3 78.2 + - + +
415A LEU* 2.5 40.1 + - + +
416A GLU* 2.8 24.2 + - + +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 5.9 1.8 - - + -
409A GLN 3.5 19.1 - - - +
410A GLN* 4.4 13.0 - - - +
412A PRO* 1.3 95.6 - - + +
414A PHE* 1.3 69.7 + - + +
416A GLU* 3.4 20.1 - - - +
417A ARG* 2.9 34.1 + - - +
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Residues in contact with PHE 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A ILE* 2.8 35.0 - - + +
362A HIS* 4.7 11.9 - + - -
410A GLN* 2.4 62.8 - - + -
411A LEU* 4.9 1.6 - - - +
412A PRO 3.3 0.4 - - - -
413A LEU* 1.3 82.1 - - + +
415A LEU* 1.3 59.0 + - - +
417A ARG* 2.5 59.3 + - - +
418A CYS* 3.4 3.1 + - - -
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Residues in contact with LEU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A MET* 3.2 48.5 - - + +
300A ALA* 5.1 3.4 - - + -
301A ILE* 3.8 31.6 - - + +
411A LEU* 2.6 28.0 - - + +
412A PRO* 2.5 20.5 + - + +
414A PHE* 1.3 66.7 - - - +
416A GLU* 1.3 52.7 + - + +
417A ARG 2.7 4.5 - - - -
418A CYS* 2.7 35.1 + - - +
424A LEU* 5.9 5.3 - - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 5.7 4.5 - - - +
412A PRO* 2.8 25.5 + - + +
413A LEU* 3.4 24.8 + - - +
415A LEU* 1.3 72.0 - - + +
417A ARG* 1.3 55.4 + - - +
418A CYS 2.8 6.3 - - - -
419A PRO* 2.9 30.5 - - + +
420A HIS 5.5 0.9 - - - +
424A LEU* 5.5 14.4 - - + -
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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) + - + + + + + -
------------------------------------------------------------
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