Contacts of the helix formed by residues 362 - 387 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B PRO* 3.1 27.0 - - - +
361B MET 3.0 24.7 - - - -
362B SER* 4.8 0.7 - - - +
259D ILE* 4.9 0.3 - - - +
360D PRO 3.6 3.9 + - - -
361D MET* 1.3 80.2 - - - +
363D LYS* 1.3 60.7 - - - +
364D GLU* 3.7 7.6 - - - -
365D LEU* 3.5 18.2 + - - +
366D GLU* 2.9 31.3 + - - +
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Residues in contact with LYS 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B MET 4.5 1.4 + - - -
362D SER* 1.3 75.3 - - - +
364D GLU* 1.3 73.0 + - + +
366D GLU* 3.2 42.6 + - - +
367D THR* 2.9 55.5 + - - +
370D ALA* 6.2 0.4 - - - +
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PRO* 3.4 32.4 - - + +
361B MET* 4.4 5.6 + - - +
259D ILE* 4.2 11.9 - - + +
362D SER* 3.2 7.4 - - - +
363D LYS* 1.3 92.4 + - + +
365D LEU* 1.3 58.9 + - - +
367D THR* 3.4 5.8 + - - -
368D GLU* 3.0 23.9 + - - +
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Residues in contact with LEU 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259D ILE* 3.8 22.8 - - + +
262D ILE* 4.3 7.2 - - + -
263D ALA* 3.7 36.6 - - + +
266D ARG* 3.9 20.2 - - - +
359D MET* 4.4 9.4 - - + -
360D PRO 4.1 14.4 - - - +
361D MET* 3.7 26.7 - - + -
362D SER* 3.5 16.6 + - - +
363D LYS 3.3 0.2 - - - -
364D GLU* 1.3 71.9 - - - +
366D GLU* 1.3 67.6 + - - +
368D GLU 3.2 0.5 + - - -
369D MET* 2.8 37.5 + - + +
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Residues in contact with GLU 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361D MET* 3.8 15.6 - - - +
362D SER 2.9 16.5 + - - +
363D LYS* 3.3 39.9 + - - +
365D LEU* 1.3 77.6 - - - +
367D THR* 1.3 55.8 + - - +
369D MET* 3.4 6.6 + - - +
370D ALA* 2.9 30.3 + - + +
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Residues in contact with THR 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363D LYS* 2.9 43.4 + - - +
364D GLU* 3.6 6.7 - - - -
365D LEU 3.2 0.2 - - - -
366D GLU* 1.3 77.1 - - - +
368D GLU* 1.3 62.8 + - - +
370D ALA* 3.2 7.2 + - - +
371D VAL* 3.0 28.4 + - + +
445D TYR* 4.4 20.2 - - + +
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Residues in contact with GLU 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259D ILE* 4.5 7.8 - - + +
260D GLN* 4.2 21.3 + - - +
263D ALA* 3.8 19.5 - - + -
364D GLU 3.0 16.6 + - - +
365D LEU 3.9 2.9 - - - +
367D THR* 1.3 75.1 - - - +
369D MET* 1.3 65.7 + - - +
371D VAL* 3.2 14.8 + - - +
372D ILE* 3.0 35.2 + - + +
427D CYS* 4.6 3.8 - - - -
429D ARG* 2.7 46.8 + - - -
445D TYR* 4.7 5.5 + - - -
449D ARG* 5.3 1.0 + - - -
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Residues in contact with MET 369 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263D ALA* 3.7 18.8 - - + -
266D ARG* 3.9 21.3 - - + -
267D CYS* 3.4 20.9 - - - +
270D GLU* 3.5 35.2 - - - +
361D MET* 4.2 16.6 - - + +
365D LEU* 2.8 36.8 + - + +
366D GLU* 3.7 5.8 - - - +
368D GLU* 1.3 75.0 - - - +
370D ALA* 1.3 58.5 + - - +
372D ILE 3.3 0.2 + - - -
373D LYS* 2.9 41.1 + - + +
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Residues in contact with ALA 370 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LYS* 6.2 0.2 - - - +
366D GLU* 2.9 19.5 + - + +
367D THR* 3.2 7.4 + - - +
369D MET* 1.3 76.6 - - - +
371D VAL* 1.3 61.8 + - + +
373D LYS* 4.0 5.1 - - - +
374D ALA* 3.0 26.0 + - - +
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Residues in contact with VAL 371 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367D THR* 3.0 21.9 + - + +
368D GLU* 3.2 24.7 + - - +
370D ALA* 1.3 76.6 - - + +
372D ILE* 1.3 60.2 + - + +
374D ALA* 3.3 5.3 + - - +
375D GLU* 2.9 53.9 + - + +
429D ARG* 4.3 8.7 - - - +
442D ILE* 5.9 0.2 - - - +
445D TYR* 3.7 35.7 - - + -
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Residues in contact with ILE 372 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PRO* 3.9 24.9 - - + -
227D SER* 4.0 4.4 - - - +
230D ASN* 3.9 15.9 - - - +
260D GLN* 4.0 6.7 - - + +
263D ALA* 3.8 16.4 - - + -
264D ALA* 3.7 28.7 - - - +
267D CYS* 3.8 24.2 - - + -
368D GLU* 3.0 29.7 + - + +
371D VAL* 1.3 77.4 - - + +
373D LYS* 1.3 62.5 + - - +
375D GLU* 3.8 8.3 - - - +
376D THR* 2.8 36.3 + - - +
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Residues in contact with LYS 373 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267D CYS* 3.6 23.3 - - - +
270D GLU* 2.7 45.3 + - - +
271D GLN* 3.3 36.9 + - + +
274D GLU* 5.3 4.1 + - - +
369D MET* 2.9 26.7 + - + +
370D ALA* 4.1 5.2 - - - +
372D ILE* 1.3 76.4 - - - +
374D ALA* 1.3 55.9 + - - +
377D LYS* 2.9 31.4 + - - +
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Residues in contact with ALA 374 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370D ALA 3.0 19.2 + - - +
371D VAL* 3.7 4.7 - - - +
372D ILE 3.2 0.2 - - - -
373D LYS* 1.3 74.6 - - - +
375D GLU* 1.3 66.4 + - - +
377D LYS* 3.4 6.7 + - - +
378D CYS* 3.0 27.4 + - - -
442D ILE* 4.1 16.6 - - + -
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Residues in contact with GLU 375 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D SER* 2.6 38.4 + - - +
371D VAL* 2.9 39.5 + - + +
372D ILE* 4.7 3.8 - - - +
374D ALA* 1.3 75.0 - - - +
376D THR* 1.3 64.5 + - - +
378D CYS* 3.3 11.8 + - - +
379D ILE* 3.3 11.8 + - - +
429D ARG* 5.3 2.1 + - - -
430D TYR* 3.6 8.8 - - - -
438D PHE* 3.5 25.3 - - + -
442D ILE* 3.6 24.7 - - + +
445D TYR* 5.6 0.2 - - - -
446D ASN* 3.2 26.2 + - - +
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Residues in contact with THR 376 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D SER* 3.4 24.2 - - - -
230D ASN* 4.1 4.2 - - + +
231D ALA* 4.1 15.7 - - - +
234D ILE* 3.8 23.1 - - + -
271D GLN* 3.6 22.5 + - - +
372D ILE* 2.8 26.6 + - - +
373D LYS 3.7 0.2 - - - -
375D GLU* 1.3 75.9 - - - +
377D LYS* 1.3 63.9 + - - +
379D ILE* 3.1 7.2 + - - +
380D LEU* 3.0 31.5 + - + +
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Residues in contact with LYS 377 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D GLN* 4.5 7.4 - - - +
275D TYR* 4.2 17.3 + - - +
373D LYS 2.9 18.7 + - - +
374D ALA* 3.8 7.2 - - - +
376D THR* 1.3 78.0 - - - +
378D CYS* 1.3 58.6 + - - +
381D ASP* 2.7 66.3 + - - +
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Residues in contact with CYS 378 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D ALA* 3.0 21.0 + - - -
375D GLU 3.4 9.2 - - - +
376D THR 3.2 0.2 - - - -
377D LYS* 1.3 79.2 - - - +
379D ILE* 1.3 61.1 + - + +
381D ASP* 3.8 5.8 - - - +
382D LYS* 3.2 24.1 + - - +
437D PRO* 3.9 13.8 - - - +
438D PHE* 4.0 21.1 - - + -
439D THR* 4.5 12.6 - - - -
442D ILE* 3.4 24.7 - - - -
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Residues in contact with ILE 379 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D SER 3.9 21.5 - - - +
228D MET* 3.8 28.3 - - + -
231D ALA* 3.8 16.8 - - + -
375D GLU 3.3 13.9 + - - +
376D THR* 3.1 6.6 + - - +
378D CYS* 1.3 73.3 - - - +
380D LEU* 1.3 66.6 + - - +
382D LYS* 3.3 4.0 + - - +
383D MET* 3.0 39.1 + - + +
403D VAL* 4.3 15.1 - - + +
404D MET* 4.3 5.8 - - + -
430D TYR* 4.2 3.8 - - - +
436D VAL* 4.1 16.2 - - + -
437D PRO* 4.2 10.3 - - + -
438D PHE* 4.1 12.8 - - + -
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Residues in contact with LEU 380 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ALA* 3.8 14.6 - - + +
234D ILE* 3.9 21.3 - - + -
235D THR* 3.5 26.0 - - - +
238D LEU* 5.8 0.7 - - + -
275D TYR* 3.5 44.4 - - + +
376D THR* 3.0 37.6 + - + +
377D LYS 4.1 0.4 - - - +
379D ILE* 1.3 72.5 - - - +
381D ASP* 1.3 63.9 + - - +
383D MET* 3.1 13.8 + - - +
384D PHE* 2.9 34.9 + - + -
391D LEU* 4.9 7.4 - - + -
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Residues in contact with ASP 381 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D TYR* 4.2 6.2 + - - -
377D LYS* 2.7 65.2 + - - +
378D CYS* 3.8 6.7 - - - +
380D LEU* 1.3 72.1 - - - +
382D LYS* 1.3 63.0 + - - +
384D PHE* 3.3 8.5 + - - +
385D GLU* 3.0 24.7 + - - +
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Residues in contact with LYS 382 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378D CYS 3.2 15.8 + - - +
379D ILE 3.7 3.6 - - - +
380D LEU 3.2 0.2 - - - -
381D ASP* 1.3 79.0 - - - +
383D MET* 1.3 57.5 + - - +
385D GLU* 3.2 36.0 + - - +
386D LEU* 2.9 55.6 + - + +
403D VAL* 3.8 31.4 - - + -
437D PRO* 3.8 20.6 - - + -
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Residues in contact with MET 383 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D THR* 3.4 20.0 - - + +
379D ILE* 3.0 27.9 + - - +
380D LEU* 3.4 18.4 - - - +
382D LYS* 1.3 75.3 - - - +
384D PHE* 1.3 63.4 + - - +
386D LEU* 3.4 3.6 + - - -
387D GLY* 3.1 18.0 + - - -
390D ASP 4.5 0.3 - - - +
391D LEU* 4.0 14.6 - - + -
394D GLY* 3.2 20.8 - - - +
395D THR* 3.3 31.2 - - - +
398D ALA* 3.7 19.7 - - + -
403D VAL* 4.5 2.7 - - + -
404D MET* 3.5 36.3 - - + +
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Residues in contact with PHE 384 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D LEU* 4.4 6.3 - - + -
275D TYR* 4.1 20.6 - + - -
279D TYR* 3.3 48.0 - + - -
380D LEU* 2.9 31.4 + - + -
381D ASP* 3.8 9.4 - - - +
383D MET* 1.3 76.3 - - - +
385D GLU* 1.3 64.4 + - - +
387D GLY 3.3 0.9 + - - -
388D LYS 3.0 3.5 + - - -
389D GLY* 2.9 54.0 + - - -
390D ASP 5.3 1.3 - - - -
391D LEU* 3.8 44.0 - - + -
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Residues in contact with GLU 385 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381D ASP 3.0 16.4 + - - +
382D LYS* 3.2 40.2 + - - +
384D PHE* 1.3 77.4 - - - +
386D LEU* 1.3 64.2 + - + +
388D LYS* 3.0 23.1 + - - +
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Residues in contact with LEU 386 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382D LYS* 2.9 45.3 + - + +
383D MET 3.9 3.1 - - - +
384D PHE 3.4 0.2 - - - -
385D GLU* 1.3 77.7 - - + +
387D GLY* 1.3 61.7 + - - +
388D LYS* 3.2 11.5 + - - +
394D GLY* 4.4 2.0 - - - +
397D LYS* 3.2 38.9 - - + +
398D ALA* 3.8 25.4 - - + +
401D THR* 3.8 26.9 - - + +
403D VAL* 4.2 12.6 - - + -
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Residues in contact with GLY 387 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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383D MET 3.1 10.7 + - - -
384D PHE 3.8 0.9 - - - -
386D LEU* 1.3 75.4 - - - +
388D LYS* 1.3 70.9 + - - +
389D GLY 3.2 2.9 - - - -
390D ASP* 2.9 38.9 + - - +
393D ILE* 4.1 12.7 - - - +
394D GLY* 3.5 11.4 - - - -
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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