Contacts of the helix formed by residues 413 - 435 (chain D) in PDB entry 5DO7
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 413 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D ASN* 3.2 17.9 + - - +
409D ASN* 2.8 8.9 + - - +
410D ASP* 3.4 24.0 - - - +
411D PHE 3.2 1.1 - - - -
412D ARG* 1.3 74.8 - - - +
414D LEU* 1.3 61.4 + - - +
415D PRO* 3.2 24.1 - - - +
416D THR* 2.3 41.4 + - - +
417D LEU* 3.3 20.4 - - - +
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Residues in contact with LEU 414 (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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438B HIS* 3.7 25.1 - - + +
517B TRP* 4.9 20.9 - - + +
411D PHE 5.2 3.6 - - - +
412D ARG 3.3 8.0 + - - +
413D ASP* 1.3 75.4 - - - +
415D PRO* 1.3 71.5 - - + +
417D LEU* 2.8 25.5 + - + +
418D LEU* 2.5 45.6 + - + +
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Residues in contact with PRO 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B PHE* 4.3 8.1 - - + -
438B HIS* 3.7 30.7 - - + +
439B GLY* 4.9 5.6 - - - +
412D ARG 5.3 0.2 - - - +
413D ASP* 3.2 14.1 - - - +
414D LEU* 1.3 96.0 - - + +
416D THR* 1.3 65.9 + - + +
418D LEU* 3.4 9.8 + - + +
419D ILE* 3.0 28.5 + - - +
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Residues in contact with THR 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ASP* 4.6 6.1 + - - -
413D ASP* 2.3 40.8 + - - +
415D PRO* 1.3 79.0 - - + +
417D LEU* 1.3 60.9 + - - +
419D ILE* 2.8 30.6 + - - +
420D HIS* 2.8 37.2 + - - +
470D LYS* 6.5 0.4 - - - -
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Residues in contact with LEU 417 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410D ASP* 4.2 19.3 - - - +
411D PHE* 4.0 37.7 - - + +
413D ASP 3.3 15.5 - - - +
414D LEU* 2.8 20.7 + - + +
416D THR* 1.3 84.5 + - - +
418D LEU* 1.3 60.1 + - - +
420D HIS* 3.6 5.7 + - + +
421D GLY* 3.4 17.0 + - - -
503D GLU* 4.0 35.7 - - + +
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Residues in contact with LEU 418 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B PHE* 5.2 0.3 - - - -
436B PHE* 4.6 2.7 - - + -
438B HIS* 3.9 10.1 - - + +
517B TRP* 4.0 16.8 - - + +
518B LEU* 3.8 51.0 - - + +
414D LEU* 2.5 65.6 + - + +
415D PRO* 3.5 10.5 - - + +
417D LEU* 1.3 71.1 - - - +
419D ILE* 1.3 70.7 + - + +
421D GLY* 3.5 2.0 + - - -
422D ALA* 2.8 23.8 + - - +
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Residues in contact with ILE 419 (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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433B PHE* 4.1 21.3 - - + -
436B PHE* 3.4 35.2 - - + -
415D PRO 3.0 17.0 - - - +
416D THR* 2.8 9.3 + - - +
418D LEU* 1.3 76.4 - - - +
420D HIS* 1.3 58.1 + - + +
422D ALA* 2.7 6.4 + - - +
423D GLU* 2.4 66.8 + - + +
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Residues in contact with HIS 420 (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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416D THR* 2.8 41.3 + - - +
417D LEU* 3.6 7.4 + - + +
419D ILE* 1.3 76.6 - - + +
421D GLY* 1.3 65.0 + - - +
423D GLU* 2.8 27.7 + - - +
424D ALA* 2.8 24.4 + - - +
466D ASP* 2.9 47.3 + - + -
470D LYS* 4.6 6.4 - - - -
503D GLU* 3.8 23.3 - - + +
507D TYR* 4.1 18.0 - - + -
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Residues in contact with GLY 421 (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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417D LEU 3.4 11.2 + - - -
418D LEU 3.7 3.4 - - - -
419D ILE 3.2 0.4 - - - -
420D HIS* 1.3 76.4 - - - +
422D ALA* 1.3 50.6 + - - +
424D ALA* 4.9 2.0 - - - -
425D CYS* 2.6 41.0 + - - +
507D TYR* 5.9 3.3 - - - +
510D ILE* 3.6 17.2 - - - +
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Residues in contact with ALA 422 (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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429B MET* 4.2 12.6 - - - -
433B PHE* 3.4 35.2 - - + -
418D LEU 2.8 12.7 + - - +
419D ILE* 2.7 12.1 + - + +
421D GLY* 1.3 69.8 - - - -
423D GLU* 1.3 54.8 + - - +
425D CYS* 2.8 27.4 + - - +
426D LEU* 2.8 32.9 + - + +
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Residues in contact with GLU 423 (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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419D ILE* 2.4 48.4 + - + +
420D HIS* 2.8 32.0 + - - +
422D ALA* 1.3 66.7 - - - +
424D ALA* 1.3 61.3 + - - +
426D LEU* 4.9 4.3 - - - +
427D MET* 3.9 25.2 + - - +
462D ASN* 3.0 35.6 + - - +
466D ASP* 5.1 0.2 - - - +
507D TYR* 4.6 2.6 + - - +
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Residues in contact with ALA 424 (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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420D HIS 2.8 13.5 + - - +
421D GLY* 3.7 2.7 - - - +
423D GLU* 1.3 73.8 - - - +
425D CYS* 1.3 72.5 + - - +
426D LEU 2.7 4.1 + - - -
427D MET* 2.8 14.8 + - - +
428D SER 3.2 6.2 + - - -
459D ILE* 4.7 1.8 - - - -
507D TYR* 3.7 47.3 + - + +
510D ILE* 4.3 5.2 - - + -
511D TYR* 3.9 18.6 - - + -
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Residues in contact with CYS 425 (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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425B CYS* 4.4 2.0 - - - -
429B MET* 3.6 23.8 - - + -
421D GLY 2.6 24.1 + - - +
422D ALA* 2.8 8.6 + - - +
424D ALA* 1.3 73.6 - - - +
426D LEU* 1.3 59.1 + - - +
428D SER* 2.8 20.3 + - - -
429D MET* 3.0 40.8 + - - +
510D ILE* 3.4 24.8 - - + +
514D PRO* 5.6 0.6 - - - +
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Residues in contact with LEU 426 (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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426B LEU* 3.5 31.6 - - + -
429B MET* 3.7 33.7 - - + -
433B PHE* 5.3 6.3 - - + -
422D ALA* 2.8 31.5 + - + +
423D GLU* 4.9 3.6 - - - +
424D ALA 2.7 4.0 + - - -
425D CYS* 1.3 72.9 - - - +
427D MET* 1.3 67.0 + - - +
429D MET* 2.8 16.4 + - + +
430D THR* 2.8 21.9 + - + +
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Residues in contact with MET 427 (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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536C LEU* 4.4 21.5 - - + -
423D GLU 3.9 15.3 + - - +
424D ALA 2.8 12.0 + - - +
426D LEU* 1.3 73.9 - - - +
428D SER* 1.3 62.7 + - - +
430D THR* 2.8 9.2 + - - +
431D ILE* 2.8 28.6 + - - +
458D LEU* 3.7 29.2 - - + +
459D ILE* 4.0 24.9 - - - -
461D PHE 5.4 1.3 - - - -
462D ASN* 3.7 36.8 - - + +
511D TYR* 3.8 12.3 - - + -
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Residues in contact with SER 428 (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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424D ALA 3.2 1.6 + - - -
425D CYS 2.8 14.5 + - - -
427D MET* 1.3 73.2 - - - +
429D MET* 1.3 66.1 + - - +
431D ILE* 4.6 0.4 - - - -
432D GLY* 2.8 22.5 + - - -
510D ILE 3.8 8.7 - - - -
511D TYR* 2.9 30.7 + - - -
514D PRO* 3.2 11.0 - - - +
515D THR* 2.8 45.8 + - - -
518D LEU* 4.1 1.6 - - - +
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Residues in contact with MET 429 (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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422B ALA* 4.2 19.3 - - - -
425B CYS* 3.4 23.8 - - - -
426B LEU* 3.7 28.5 - - + -
425D CYS* 3.0 40.9 + - - +
426D LEU* 2.8 13.3 + - + +
428D SER* 1.3 77.5 - - - +
430D THR* 1.3 60.7 + - + +
432D GLY* 3.5 0.7 - - - -
433D PHE* 2.8 42.4 + - + -
514D PRO* 5.3 6.7 - - + +
518D LEU* 3.5 15.7 - - - +
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Residues in contact with THR 430 (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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559C PHE* 3.8 22.8 - - + -
426D LEU* 2.8 24.5 + - + +
427D MET* 2.8 15.6 + - - +
429D MET* 1.3 71.1 - - + +
431D ILE* 1.3 77.6 + - - +
433D PHE* 2.9 4.2 + - - +
434D LEU* 2.8 27.2 + - - +
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Residues in contact with ILE 431 (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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543C LEU* 5.8 4.9 - - + -
427D MET* 2.8 16.9 + - - +
428D SER 3.8 2.0 - - - +
430D THR* 1.3 82.1 + - - +
432D GLY* 1.3 67.3 + - - +
434D LEU* 3.3 4.5 + - - +
435D TYR* 3.2 28.3 + - + +
451D LEU* 3.9 17.5 - - + -
454D MET* 4.3 5.4 - - + -
455D ILE* 4.1 15.3 - - + +
458D LEU* 3.8 32.1 - - + -
511D TYR* 3.8 24.5 - - + +
515D THR* 3.8 25.1 - - + +
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Residues in contact with GLY 432 (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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428D SER 2.8 18.1 + - - -
429D MET 3.5 3.8 - - - -
430D THR 3.0 0.4 + - - -
431D ILE* 1.3 72.3 - - - +
433D PHE* 1.3 67.3 + - - +
435D TYR* 2.8 15.8 + - - +
436D PHE* 2.8 11.6 + - - -
515D THR* 4.3 8.7 - - - -
518D LEU* 3.6 26.1 - - - +
519D ALA* 4.4 4.4 + - - -
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Residues in contact with PHE 433 (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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418B LEU 5.1 0.2 - - - -
419B ILE* 4.0 25.1 - - + -
422B ALA* 3.4 32.8 - - + -
426B LEU* 5.5 5.6 - - + -
556C PRO* 3.2 10.5 - - + +
558C PRO* 5.5 10.1 - - + -
559C PHE* 3.4 21.3 - + + -
429D MET* 2.8 28.3 + - + +
430D THR* 2.9 3.3 + - - +
432D GLY* 1.3 70.2 - - - -
434D LEU* 1.3 58.1 + - - +
436D PHE* 2.7 38.1 + + - +
518D LEU* 3.3 31.6 - - + -
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Residues in contact with LEU 434 (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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543C LEU* 3.6 18.8 - - + -
544C VAL* 3.2 36.1 - - + -
550C ARG* 3.0 47.2 + - + +
555C MET* 4.6 4.0 - - + -
556C PRO* 3.6 5.0 - - + +
559C PHE* 3.1 27.8 - - + -
430D THR* 2.8 16.5 + - - +
431D ILE* 3.5 6.5 - - - +
433D PHE* 1.3 77.4 - - - +
435D TYR* 1.3 87.8 + - + +
436D PHE 3.4 0.2 - - - -
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Residues in contact with TYR 435 (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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543C LEU* 4.2 9.0 - - + +
549C LEU* 3.1 35.2 + - - +
550C ARG* 4.2 12.6 - - + +
431D ILE* 3.2 20.7 + - + +
432D GLY 2.8 6.8 + - - +
434D LEU* 1.3 98.9 - - + +
436D PHE* 1.3 67.4 + - - +
437D GLY* 3.0 4.0 + - - -
443D LEU* 3.7 27.1 - - + +
447D ASP* 3.5 28.9 - - + -
450D ALA* 3.6 11.8 - - - +
451D LEU* 3.3 47.4 + - + -
454D MET* 4.2 9.3 - - + +
519D ALA* 3.5 8.6 - - + +
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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
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Atomic class I II III IV V VI VII VIII
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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