Contacts of the helix formed by residues 362 - 387 (chain B) in PDB entry 1CCW
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 SER 362 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259B ILE* 4.9 0.3 - - - +
359B MET* 5.8 0.2 - - - -
360B PRO 3.6 3.5 + - - -
361B MET* 1.3 74.9 - - - +
363B LYS* 1.3 58.4 + - - +
364B GLU 3.7 0.6 + - - -
365B LEU* 3.5 19.6 + - - +
366B GLU* 2.9 30.4 + - - +
360D PRO* 3.2 33.0 - - - +
361D MET 2.9 27.1 - - - -
362D SER* 4.8 1.1 - - - +
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Residues in contact with LYS 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B SER* 1.3 74.0 - - - +
364B GLU* 1.3 58.0 + - - +
366B GLU* 2.8 33.4 + - - +
367B THR* 2.8 46.0 + - - +
361D MET 4.5 1.4 + - - -
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Residues in contact with GLU 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ASN* 5.0 3.6 + - - +
259B ILE* 3.3 32.8 - - + +
362B SER* 3.2 8.5 + - - +
363B LYS* 1.3 79.9 - - - +
365B LEU* 1.3 54.6 + - - +
367B THR* 3.4 6.2 + - - -
368B GLU* 3.0 28.5 + - + +
425B LEU* 5.7 7.8 - - - +
358D ARG 4.7 6.8 - - - +
360D PRO* 4.0 20.8 - - + +
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Residues in contact with LEU 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 3.9 22.6 - - + +
262B ILE* 4.1 7.6 - - + -
263B ALA* 3.7 37.5 - - + +
266B ARG* 3.9 25.1 - - - +
359B MET* 4.4 9.0 - - + -
360B PRO 4.1 15.7 - - - +
361B MET* 4.2 12.8 - - + -
362B SER* 3.4 18.2 + - - +
363B LYS 3.4 0.2 - - - -
364B GLU* 1.3 73.0 - - - +
366B GLU* 1.3 62.3 + - - +
368B GLU* 3.3 0.8 + - - -
369B MET* 2.9 48.1 + - + +
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B MET* 6.1 3.1 - - + +
362B SER 2.9 18.0 + - - +
363B LYS* 2.8 44.6 + - - +
365B LEU* 1.3 79.2 - - - +
367B THR* 1.3 58.3 + - - +
369B MET* 3.4 8.8 + - - +
370B ALA* 2.9 30.1 + - + +
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Residues in contact with THR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363B LYS* 2.8 36.1 + - - +
364B GLU* 3.6 7.6 - - - +
366B GLU* 1.3 78.5 + - - +
368B GLU* 1.3 63.2 + - - +
370B ALA* 3.2 7.3 + - - +
371B VAL* 3.1 28.6 + - + +
445B TYR* 4.4 20.2 - - + +
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Residues in contact with GLU 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259B ILE* 4.5 7.9 - - + -
260B GLN* 4.1 22.1 + - - +
263B ALA* 3.8 20.0 - - + -
364B GLU* 3.0 17.3 + - + +
365B LEU 3.9 2.9 - - - +
367B THR* 1.3 75.7 - - - +
369B MET* 1.3 66.3 + - - +
371B VAL* 3.3 11.9 + - - +
372B ILE* 2.9 39.1 + - + +
427B CYS* 4.6 3.8 - - - -
429B ARG* 2.8 44.6 + - - -
445B TYR* 4.6 5.9 + - - -
449B ARG* 5.3 1.0 + - - -
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Residues in contact with MET 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263B ALA* 3.7 20.0 - - + -
266B ARG* 3.8 29.2 - - + -
267B CYS* 3.4 23.9 - - - -
270B GLU* 3.5 29.4 - - - +
361B MET* 6.0 3.8 - - - +
365B LEU* 2.9 40.3 + - + +
366B GLU* 3.7 7.6 - - - +
368B GLU* 1.3 77.2 - - - +
370B ALA* 1.3 63.0 + - - +
372B ILE 3.3 0.7 + - - -
373B LYS* 2.9 30.0 + - - +
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366B GLU* 2.9 18.4 + - + +
367B THR* 3.2 7.6 + - - +
369B MET* 1.3 75.0 - - - +
371B VAL* 1.3 64.0 + - + +
373B LYS* 3.5 4.9 + - - +
374B ALA* 2.9 26.3 + - - +
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Residues in contact with VAL 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B THR* 3.1 22.2 + - + +
368B GLU* 3.5 21.5 - - - +
369B MET 3.2 0.2 - - - -
370B ALA* 1.3 77.8 - - + +
372B ILE* 1.3 65.1 + - + +
374B ALA* 3.7 4.2 - - - +
375B GLU* 3.0 48.8 + - + +
429B ARG* 4.3 4.5 - - - +
442B ILE* 6.2 0.2 - - + -
445B TYR* 3.7 40.8 - - + -
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Residues in contact with ILE 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B PRO* 3.9 23.8 - - + -
227B SER* 4.4 4.7 - - - +
230B ASN* 3.9 15.5 - - - +
260B GLN* 4.0 5.8 - - + +
263B ALA* 3.8 12.1 - - + -
264B ALA* 3.7 28.7 - - - +
267B CYS* 3.8 23.8 - - + -
368B GLU* 2.9 35.4 + - + +
371B VAL* 1.3 77.9 - - + +
373B LYS* 1.3 63.0 + - - +
375B GLU* 3.4 8.7 + - - +
376B THR* 2.8 36.5 + - - +
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Residues in contact with LYS 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B CYS* 3.6 22.4 - - - +
270B GLU* 2.7 44.9 + - - +
271B GLN* 3.4 38.0 + - + +
274B GLU* 5.3 4.3 + - - +
369B MET* 2.9 25.4 + - - +
370B ALA* 4.0 4.7 - - - +
372B ILE* 1.3 74.6 - - - +
374B ALA* 1.3 58.4 + - - +
376B THR* 3.8 0.2 - - - -
377B LYS* 2.9 32.0 + - - +
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Residues in contact with ALA 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B ALA 2.9 18.3 + - - +
371B VAL* 3.7 4.7 - - - +
373B LYS* 1.3 74.7 - - - +
375B GLU* 1.3 66.6 + - - +
377B LYS* 3.4 8.0 + - - +
378B CYS* 3.0 27.2 + - - -
442B ILE* 4.1 17.5 - - + -
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Residues in contact with GLU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER* 2.6 40.7 + - - +
371B VAL* 3.0 39.7 + - + +
372B ILE* 3.8 3.9 - - - +
374B ALA* 1.3 76.0 - - - +
376B THR* 1.3 63.5 + - - +
378B CYS 3.2 8.8 + - - -
379B ILE* 3.3 11.3 + - - +
429B ARG* 5.3 2.0 + - - -
430B TYR* 3.6 7.5 - - - -
438B PHE* 3.4 28.9 - - + -
442B ILE* 3.6 24.3 - - + +
446B ASN* 3.1 29.4 + - - +
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Residues in contact with THR 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227B SER* 3.4 23.4 - - - -
230B ASN* 4.2 4.2 - - + +
231B ALA* 3.9 17.9 - - - +
234B ILE* 3.8 21.8 - - + -
271B GLN* 3.5 22.8 + - - +
372B ILE* 2.8 26.9 + - - +
373B LYS 3.8 0.2 - - - -
375B GLU* 1.3 75.0 - - - +
377B LYS* 1.3 59.4 + - - +
379B ILE* 3.2 6.0 + - - +
380B LEU* 2.9 36.0 + - + +
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Residues in contact with LYS 377 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B GLN* 4.5 7.8 - - - +
275B TYR* 4.3 16.2 - - - +
373B LYS 2.9 19.2 + - - +
374B ALA* 3.8 7.4 - - - +
376B THR* 1.3 74.4 - - - +
378B CYS* 1.3 60.8 + - - +
381B ASP* 2.7 70.3 + - - +
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Residues in contact with CYS 378 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B ALA 3.0 13.9 + - - -
375B GLU 3.2 8.0 + - - +
377B LYS* 1.3 76.7 - - - +
379B ILE* 1.3 62.1 + - - +
381B ASP* 3.8 5.9 - - - +
382B LYS* 3.1 23.7 + - - +
437B PRO* 3.6 27.5 - - - +
438B PHE* 3.9 12.3 - - + -
439B THR* 4.4 11.2 - - - -
442B ILE* 3.4 32.5 - - - -
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Residues in contact with ILE 379 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B SER 4.0 20.4 - - - +
228B MET* 3.8 27.6 - - + -
231B ALA* 3.8 17.3 - - + -
375B GLU 3.3 14.1 + - - +
376B THR* 3.2 6.6 + - - +
378B CYS* 1.3 73.6 - - - +
380B LEU* 1.3 65.2 + - - +
382B LYS* 3.1 4.9 + - - +
383B MET* 3.1 38.6 + - - +
403B VAL* 4.2 16.0 - - + +
404B MET* 4.4 5.4 - - + -
430B TYR* 4.2 5.8 - - - +
436B VAL* 4.1 9.2 - - + -
437B PRO* 4.2 9.2 - - + -
438B PHE* 4.0 18.4 - - + -
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Residues in contact with LEU 380 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ALA* 3.9 13.7 - - + +
234B ILE* 3.9 21.1 - - + -
235B THR* 3.5 25.4 - - - +
238B LEU* 5.8 0.7 - - + -
275B TYR* 3.6 44.6 - - + +
376B THR* 2.9 36.7 + - + +
377B LYS* 4.1 0.4 - - - +
379B ILE* 1.3 71.2 - - - +
381B ASP* 1.3 67.7 + - - +
383B MET* 3.2 14.4 + - + +
384B PHE* 3.0 33.4 + - + -
391B LEU* 4.9 7.2 - - + -
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Residues in contact with ASP 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B TYR* 4.1 8.1 + - - -
377B LYS* 2.7 63.5 + - - +
378B CYS* 3.8 6.4 + - - +
380B LEU* 1.3 73.7 - - - +
382B LYS* 1.3 62.5 + - - +
384B PHE* 3.4 7.0 + - - +
385B GLU* 3.1 36.4 + - - +
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Residues in contact with LYS 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B CYS 3.1 18.3 + - - +
379B ILE 3.1 4.2 + - - +
381B ASP* 1.3 76.9 - - - +
383B MET* 1.3 58.2 + - - +
385B GLU* 3.1 22.7 + - + +
386B LEU* 2.8 50.5 + - + +
403B VAL* 3.7 31.0 - - + -
437B PRO* 3.9 18.6 - - + -
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Residues in contact with MET 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B THR* 3.4 20.0 - - + +
379B ILE* 3.1 22.4 + - - +
380B LEU* 3.2 19.5 + - - +
382B LYS* 1.3 78.0 - - - +
384B PHE* 1.3 61.8 + - - +
386B LEU* 3.4 3.1 + - - -
387B GLY* 3.0 18.5 + - - -
390B ASP 4.5 0.5 - - - +
391B LEU* 3.9 14.6 - - + -
394B GLY* 3.2 19.2 - - - +
395B THR* 3.3 33.4 - - - +
398B ALA* 3.8 20.4 - - + -
403B VAL* 4.5 3.8 - - + -
404B MET* 3.7 32.5 - - + +
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Residues in contact with PHE 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238B LEU* 4.3 5.6 - - + -
275B TYR* 4.1 20.4 - + - -
279B TYR* 3.2 48.2 - + - -
380B LEU* 3.0 31.4 + - + -
381B ASP* 3.8 8.3 - - - +
383B MET* 1.3 75.9 - - - +
385B GLU* 1.3 62.2 + - + +
387B GLY 3.3 0.7 + - - -
388B LYS* 3.1 2.9 + - - -
389B GLY* 2.8 55.1 + - - +
390B ASP 5.2 1.6 - - - -
391B LEU* 3.8 45.3 - - + -
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Residues in contact with GLU 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
381B ASP* 3.1 27.8 + - - +
382B LYS* 3.1 29.0 + - + +
384B PHE* 1.3 77.2 - - - +
386B LEU* 1.3 62.4 + - + +
388B LYS* 3.0 19.0 + - - +
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Residues in contact with LEU 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382B LYS* 2.8 52.3 + - + +
383B MET 3.8 3.6 - - - +
385B GLU* 1.3 73.0 - - - +
387B GLY* 1.3 60.9 + - - +
388B LYS* 3.2 11.7 + - - +
394B GLY* 4.3 2.2 - - - +
397B LYS* 3.3 38.2 - - + +
398B ALA* 3.8 24.9 - - + +
401B THR* 3.8 29.6 - - + +
403B VAL* 4.2 2.5 - - + -
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Residues in contact with GLY 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B MET 3.0 11.4 + - - -
384B PHE 3.3 0.4 + - - -
386B LEU* 1.3 76.8 - - - +
388B LYS* 1.3 70.6 + - - +
389B GLY 3.2 3.1 - - - -
390B ASP* 3.0 36.9 + - - +
393B ILE* 4.1 13.5 - - - +
394B GLY* 3.6 11.8 - - - -
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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