Contacts of the helix formed by residues 400 - 428 (chain D) in PDB entry 3FAL
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 LEU 400 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C GLU* 3.5 36.1 - - + +
397C TYR* 4.0 28.3 - - + -
398C ALA* 4.4 15.3 - - + +
401C GLU* 6.0 0.9 - - - +
398D ASP* 3.3 3.2 + - - +
399D PRO* 1.3 81.0 - - + +
401D MET* 1.3 64.4 + - - +
402D PHE 3.2 0.4 - - - -
403D PRO* 3.2 10.6 - - + +
404D ARG* 2.9 50.2 + - + +
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Residues in contact with MET 401 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 3.9 38.8 - - + +
349D LEU* 3.8 26.2 - - + -
391D VAL* 4.1 7.9 - - + -
395D HIS* 3.9 27.6 - - + +
398D ASP* 3.1 43.6 + - - +
399D PRO 3.0 0.2 + - - -
400D LEU* 1.3 76.7 - - - +
402D PHE* 1.3 56.8 + - - +
404D ARG* 3.7 10.8 - - - +
405D MET* 2.9 48.3 + - + +
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Residues in contact with PHE 402 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415C PHE* 4.7 11.2 - + - -
416C ALA* 3.8 15.3 - - + -
384D VAL* 4.0 18.2 - - + -
387D LEU* 3.8 27.8 - - + -
388D HIS* 3.1 64.8 - + + +
391D VAL* 3.8 15.0 - - + +
399D PRO 3.3 5.5 + - - +
401D MET* 1.3 75.6 - - - +
403D PRO* 1.3 75.3 - - + +
405D MET* 3.2 10.3 + - + +
406D LEU* 3.1 48.2 + - + +
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Residues in contact with PRO 403 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397C TYR* 3.7 31.4 - - + -
401C GLU* 4.9 4.7 - - - +
415C PHE* 3.9 18.8 - - + -
419C LEU* 3.9 25.1 - - + -
399D PRO 3.4 9.4 - - - +
400D LEU* 3.2 21.1 - - + +
402D PHE* 1.3 99.8 - - + +
404D ARG* 1.3 59.2 + - - +
406D LEU* 3.4 1.3 + - + +
407D MET* 3.0 30.1 + - - +
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Residues in contact with ARG 404 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C GLU* 5.4 1.8 - - - -
394C GLU* 2.7 48.0 + - - +
397C TYR* 4.2 12.3 - - + -
347D LEU* 3.9 31.1 - - + +
398D ASP* 3.2 32.5 + - - -
400D LEU* 2.9 38.0 + - + +
401D MET* 3.7 9.7 - - - +
403D PRO* 1.3 75.8 - - - +
405D MET* 1.3 62.0 + - - +
407D MET* 3.4 7.3 + - - +
408D LYS* 3.3 28.3 + - - +
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Residues in contact with MET 405 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347D LEU* 4.3 5.6 - - + -
349D LEU* 3.5 43.1 - - + -
353D GLU* 4.3 7.4 - - - -
357D LEU* 4.0 20.1 - - + +
387D LEU* 3.9 33.2 - - + -
391D VAL* 2.9 37.7 - - + -
401D MET* 2.9 25.1 + - + +
402D PHE* 3.2 9.8 + - - +
404D ARG* 1.3 77.0 - - - +
406D LEU* 1.3 61.8 + - - +
408D LYS* 3.2 23.3 + - - +
409D LEU 3.8 2.1 + - - -
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Residues in contact with LEU 406 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C ALA* 4.2 9.2 - - + -
419C LEU* 4.3 17.5 - - + -
420C LEU* 3.8 29.2 - - + -
423C PRO* 5.0 1.4 - - - +
357D LEU* 5.2 0.4 - - + -
360D ILE* 4.8 5.6 - - + -
384D VAL* 4.8 7.2 - - + -
387D LEU* 4.6 11.7 - - + -
402D PHE* 3.1 53.6 + - + +
403D PRO 3.4 3.8 + - - +
405D MET* 1.3 72.1 - - - +
407D MET* 1.3 67.6 + - + +
409D LEU* 2.9 48.5 + - + +
410D VAL* 3.8 4.7 + - - +
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Residues in contact with MET 407 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373C ILE* 4.3 7.6 - - - -
393C ARG* 4.0 19.5 - - - +
397C TYR* 3.1 31.0 - - + +
419C LEU* 3.8 33.9 - - + +
422C LEU* 3.7 27.1 - - - -
403D PRO 3.0 27.8 + - - +
404D ARG* 3.8 6.3 - - - +
405D MET 3.3 0.2 - - - -
406D LEU* 1.3 78.5 - - - +
408D LYS* 1.3 58.8 + - + +
410D VAL* 2.9 40.6 + - + +
411D SER* 3.3 8.3 + - - -
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Residues in contact with LYS 408 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298D LEU* 5.6 2.7 - - + -
340D PHE* 4.1 17.5 + - + -
343D ALA* 3.8 23.7 + - - +
344D MET* 3.7 39.7 - - - +
347D LEU* 4.1 20.9 - - + -
357D LEU* 5.3 5.2 - - + -
404D ARG* 3.3 16.2 + - - +
405D MET* 3.3 15.3 - - - +
406D LEU 3.1 0.8 - - - -
407D MET* 1.3 78.5 - - + +
409D LEU* 1.3 59.5 + - + +
411D SER* 3.4 11.7 + - - +
412D LEU* 3.1 27.7 + - - +
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Residues in contact with LEU 409 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420C LEU* 4.9 6.5 - - + -
423C PRO* 4.0 16.9 - - + +
294D GLU* 5.0 2.3 - - - +
298D LEU* 5.3 0.4 - - + -
357D LEU* 4.2 22.0 - - + +
360D ILE* 3.7 26.2 - - + -
361D SER* 4.1 28.3 - - - -
405D MET 4.3 4.5 - - - +
406D LEU* 2.9 39.2 + - + +
408D LYS* 1.3 78.5 - - + +
410D VAL* 1.3 57.3 + - - +
412D LEU* 3.7 22.3 + - + +
413D ARG* 3.5 20.9 + - - +
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Residues in contact with VAL 410 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C GLU* 5.6 0.2 - - - +
393C ARG* 6.0 2.9 - - - +
419C LEU 5.2 0.4 - - - +
422C LEU* 3.6 32.3 - - + +
423C PRO* 3.9 17.9 - - + -
426C ARG* 3.6 47.1 + - + +
406D LEU 4.2 1.8 - - - +
407D MET* 2.9 32.5 + - + +
409D LEU* 1.3 75.0 - - - +
411D SER* 1.3 65.9 + - - +
413D ARG* 3.1 19.6 + - - +
414D THR 3.6 3.1 + - - -
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Residues in contact with SER 411 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C ASP* 4.5 11.7 + - - -
426C ARG* 4.4 11.8 + - - +
340D PHE* 4.0 21.9 - - - -
407D MET 3.3 10.0 + - - -
408D LYS* 3.6 15.8 + - - +
410D VAL* 1.3 78.3 - - - +
412D LEU* 1.3 64.7 + - - +
414D THR* 3.1 7.4 + - - -
415D LEU* 3.0 27.6 + - - +
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Residues in contact with LEU 412 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294D GLU* 3.7 53.1 - - + +
297D LEU* 4.0 16.4 - - + +
298D LEU* 3.9 29.4 - - + -
340D PHE* 3.8 24.7 - - + -
361D SER* 4.7 0.9 - - - +
408D LYS 3.1 20.2 + - - +
409D LEU* 3.7 23.6 - - + +
410D VAL 3.2 0.4 - - - -
411D SER* 1.3 76.0 - - - +
413D ARG* 1.3 58.8 + - - +
415D LEU* 3.2 7.1 + - + +
416D SER* 2.8 31.6 + - - -
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Residues in contact with ARG 413 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348C ARG* 5.0 0.8 - - - +
423C PRO* 3.4 37.8 + - + +
424C ALA 4.6 0.2 - - - +
426C ARG* 4.1 11.2 - - + -
427C SER* 3.0 33.5 + - - +
430C LEU* 3.6 11.0 - - + +
294D GLU* 3.4 16.6 + - - -
364D SER* 3.7 19.6 + - - -
366D ASP* 2.7 42.8 + - - -
367D ARG* 3.4 18.3 - - - +
409D LEU* 3.5 15.6 + - - +
410D VAL 3.1 8.4 + - - +
412D LEU* 1.3 77.2 - - - +
414D THR* 1.3 61.5 + - - +
416D SER* 3.5 6.8 + - - -
417D SER* 3.2 15.8 + - - -
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Residues in contact with THR 414 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426C ARG* 2.7 39.8 + - - +
430C LEU* 4.0 16.8 - - + +
410D VAL 3.6 1.0 + - - -
411D SER* 3.1 11.1 + - - +
413D ARG* 1.3 78.6 - - - +
415D LEU* 1.3 63.3 + - + +
417D SER* 3.0 6.6 + - - -
418D VAL* 2.8 37.5 + - + +
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Residues in contact with LEU 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297D LEU* 3.6 27.6 - - + +
333D PHE* 5.2 1.2 - - - -
336D PRO* 3.7 36.6 - - + +
337D ILE* 4.3 10.2 - - + +
340D PHE* 3.5 47.3 - - + -
411D SER* 3.0 20.2 + - - +
412D LEU* 3.7 8.3 - - + +
414D THR* 1.3 78.4 - - + +
416D SER* 1.3 60.6 + - - +
418D VAL* 3.3 9.4 + - + +
419D HIS* 2.8 29.8 + - - +
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Residues in contact with SER 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290D THR* 4.9 6.4 + - - +
293D ILE* 3.2 33.0 - - - +
294D GLU* 4.6 8.5 + - - +
297D LEU* 4.9 0.4 - - - +
412D LEU 2.8 17.6 + - - -
413D ARG* 3.6 9.4 - - - -
415D LEU* 1.3 77.9 - - - +
417D SER* 1.3 57.3 + - - +
419D HIS* 3.2 5.2 + - - +
420D SER* 3.0 28.1 + - - -
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Residues in contact with SER 417 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C LEU* 4.2 27.7 - - - +
413D ARG 3.2 10.5 + - - -
414D THR* 3.0 10.4 + - - -
416D SER* 1.3 77.3 - - - +
418D VAL* 1.3 66.4 + - - +
420D SER* 3.0 22.8 + - - -
421D GLU* 3.1 22.7 + - - +
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Residues in contact with VAL 418 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D GLN* 5.3 1.4 + - - +
332D GLU* 3.3 27.1 - - + +
333D PHE* 3.8 18.6 - - + +
336D PRO* 4.7 9.9 - - + -
337D ILE* 6.0 0.7 - - + -
414D THR* 2.8 30.6 + - + +
415D LEU* 3.6 15.3 - - + +
417D SER* 1.3 75.3 - - - +
419D HIS* 1.3 62.3 + - - +
421D GLU* 3.2 21.7 + - - +
422D GLN* 3.1 19.6 + - - +
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Residues in contact with HIS 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D LO2 2.8 47.7 + + - -
293D ILE* 3.5 34.8 - - + +
297D LEU* 5.6 0.7 - - + -
333D PHE* 3.5 22.4 - + + -
415D LEU 2.8 18.6 + - - +
416D SER 3.5 5.4 + - - +
418D VAL* 1.3 76.6 - - - +
420D SER* 1.3 67.1 + - - +
422D GLN* 3.0 5.4 + - - +
423D VAL* 3.0 35.3 + - + +
441D TRP* 3.5 38.3 - + + -
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Residues in contact with SER 420 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416D SER 3.0 12.9 + - - -
417D SER* 3.0 20.3 + - - -
419D HIS* 1.3 82.7 + - - +
421D GLU* 1.3 61.4 + - - +
423D VAL* 3.2 17.1 + - - +
424D PHE* 3.2 12.8 + - - +
441D TRP 5.5 6.1 - - - -
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Residues in contact with GLU 421 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330D GLN* 4.1 10.5 + - - +
332D GLU* 6.0 3.1 - - - +
417D SER* 3.1 33.8 + - - +
418D VAL* 3.5 19.6 + - - +
419D HIS 3.2 0.2 - - - -
420D SER* 1.3 76.4 + - - +
422D GLN* 1.3 62.3 + - - +
424D PHE* 3.3 8.8 + - - +
425D ALA* 3.0 22.5 + - - +
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Residues in contact with GLN 422 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D LO2 3.5 23.1 - - + -
328D GLY 4.9 0.6 + - - -
329D LEU* 3.5 17.0 - - + +
330D GLN* 3.0 44.7 + - - +
333D PHE* 3.2 40.2 - - + +
418D VAL 3.1 5.7 + - - +
419D HIS 3.0 11.4 + - - +
421D GLU* 1.3 77.3 - - - +
423D VAL* 1.3 61.2 + - - +
425D ALA* 3.3 9.3 + - - +
426D LEU* 3.1 29.3 + - + +
429D GLN* 5.5 0.2 + - - -
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Residues in contact with VAL 423 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D LO2 3.9 15.0 - - - -
419D HIS* 3.0 45.4 + - + +
420D SER* 3.2 10.3 + - - +
422D GLN* 1.3 76.4 - - - +
424D PHE* 1.3 63.4 + - - +
426D LEU* 3.3 13.8 + - + +
427D ARG* 3.5 21.1 + - + +
433D LEU* 3.8 21.8 - - + -
441D TRP* 4.3 8.3 - - + +
442D ASP* 3.8 29.2 - - - +
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Residues in contact with PHE 424 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 3.9 28.0 - - + -
305A TRP* 3.8 34.5 - + - -
420D SER 3.2 10.3 + - - +
421D GLU* 3.7 10.1 - - - +
423D VAL* 1.3 79.2 - - - +
425D ALA* 1.3 67.3 + - - +
427D ARG* 3.0 40.0 + - - +
428D LEU* 3.5 27.1 + - + -
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Residues in contact with ALA 425 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A VAL* 6.0 1.0 - - - +
302A ARG* 5.1 9.2 - - + -
330D GLN* 3.7 24.0 - - - +
421D GLU 3.0 13.8 + - - +
422D GLN* 3.3 16.5 + - - +
424D PHE* 1.3 83.2 - - + +
426D LEU* 1.3 63.3 + - - +
428D LEU* 3.1 24.2 + - - +
429D GLN* 3.8 12.2 + - - +
----------------------------------------------------------
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Residues in contact with LEU 426 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1D LO2 3.4 31.6 - - - -
252D PHE* 3.2 31.9 - - + -
327D ALA 5.3 0.2 - - - +
328D GLY 4.1 9.6 - - - +
329D LEU* 4.1 8.1 - - + -
422D GLN* 3.1 24.4 + - - +
423D VAL* 3.6 8.3 - - - +
424D PHE 3.1 0.4 - - - -
425D ALA* 1.3 73.3 - - - +
427D ARG* 1.3 60.6 + - - +
429D GLN* 2.8 47.5 + - - +
431D LYS* 3.3 36.4 + - + +
433D LEU* 5.4 2.5 - - + -
----------------------------------------------------------
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Residues in contact with ARG 427 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ASP* 3.7 19.8 + - - -
276A LEU* 4.0 23.0 - - + +
277A PHE* 3.7 43.6 - - + -
423D VAL* 3.7 18.8 + - + +
424D PHE* 3.0 25.5 + - - +
426D LEU* 1.3 72.6 - - - +
428D LEU* 1.3 57.8 + - - +
429D GLN 2.8 22.3 - - - +
431D LYS 4.1 6.5 - - - +
432D LYS* 5.6 2.7 - - - -
442D ASP* 2.8 61.3 + - - +
443D VAL* 3.8 14.5 - - - +
----------------------------------------------------------
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Residues in contact with LEU 428 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A LEU* 3.4 49.0 - - + +
279A LEU* 5.2 5.6 - - + +
280A VAL* 3.7 15.0 + - - +
301A LEU* 4.3 16.5 - - + +
302A ARG* 3.9 27.1 - - + +
305A TRP* 3.4 36.6 - - + +
424D PHE* 3.5 25.0 + - + +
425D ALA* 3.1 15.3 + - - +
427D ARG* 1.3 76.6 - - - +
429D GLN* 1.3 60.8 + - + +
----------------------------------------------------------
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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