Contacts of the helix formed by residues 431 - 454 (chain C) 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 PRO 431 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427C VAL 3.2 25.6 - - - +
428C GLY 4.5 1.8 - - - -
429C ALA 3.4 3.4 - - - +
430C THR* 1.4 93.4 - - - +
432C TYR* 1.3 60.1 + - - +
433C THR 3.3 0.2 - - - -
434C GLY* 2.8 22.5 + - - -
435C MET* 3.2 8.7 + - - +
509C PRO* 3.6 20.6 - - + +
513C GLY* 3.5 14.7 - - - +
534C VAL* 6.0 0.2 - - - -
538C SER* 3.9 28.0 - - - +
567C PHE* 4.1 21.5 - - + -
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Residues in contact with TYR 432 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C MET* 6.3 1.3 - - + -
428C GLY 4.7 4.2 + - - +
429C ALA* 2.8 25.7 + - + +
431C PRO* 1.3 73.6 - - - +
433C THR* 1.3 65.1 + - + +
434C GLY 3.0 0.5 + - - -
435C MET* 3.1 20.1 + - + +
436C LEU* 2.8 50.3 + - + -
531C ASN* 4.1 26.7 + - - -
535C ALA* 4.1 12.3 - - + +
538C SER* 4.5 4.9 + - - +
539C ILE* 4.7 12.8 - - + -
461D PHE* 3.9 33.9 - + - -
564D ASN* 5.1 7.0 + - + +
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Residues in contact with THR 433 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C GLN* 3.8 24.7 + - + +
393C ASN* 4.1 18.8 - - - +
396C MET* 5.1 14.6 - - + -
429C ALA 2.8 16.3 + - - +
430C THR* 3.0 15.9 + - - -
432C TYR* 1.3 73.9 - - + +
434C GLY* 1.3 55.5 + - - +
436C LEU* 3.5 10.3 - - + +
437C ASN* 2.8 33.8 + - - +
510C HIS* 2.6 35.9 + - - -
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Residues in contact with GLY 434 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430C THR 3.9 1.2 + - - -
431C PRO 2.8 12.6 + - - -
433C THR* 1.3 80.5 + - - +
435C MET* 1.3 57.2 + - - -
437C ASN* 2.9 8.8 - - - +
438C ALA* 2.8 21.7 + - - +
510C HIS* 3.6 16.4 - - - -
513C GLY* 4.2 0.4 - - - -
514C GLU* 3.1 30.2 - - - +
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Residues in contact with MET 435 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431C PRO 3.2 5.7 + - - +
432C TYR* 3.1 36.8 + - + +
434C GLY* 1.3 70.3 - - - +
436C LEU* 1.3 75.5 - - - +
438C ALA 2.9 0.4 + - - +
439C VAL* 2.8 29.9 + - + +
513C GLY 3.9 0.6 - - - -
517C THR* 3.0 37.6 + - + +
531C ASN* 2.7 48.0 - - - +
534C VAL* 3.4 29.4 - - + +
535C ALA* 3.6 18.4 - - - +
538C SER* 4.2 2.2 - - - +
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Residues in contact with LEU 436 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C THR* 4.5 9.6 - - + -
392C GLN* 3.3 25.6 - - + +
432C TYR* 2.8 37.6 + - + +
433C THR* 3.5 9.6 - - + +
435C MET* 1.3 85.6 - - - +
437C ASN* 1.3 65.4 + - - +
439C VAL* 4.2 2.5 - - - -
440C ASN* 2.6 42.7 + - - +
531C ASN* 5.1 1.3 - - - +
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Residues in contact with ASN 437 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388C THR* 4.6 0.7 - - - +
389C ARG* 2.7 43.6 + - - +
392C GLN* 2.7 27.5 + - - +
433C THR 2.8 13.0 + - - +
434C GLY 2.9 14.8 - - - +
436C LEU* 1.3 80.3 - - - +
438C ALA* 1.3 62.3 + - - +
441C LEU* 3.3 25.8 + - - +
467C TYR* 3.9 1.1 - - - -
475C SER* 3.7 5.1 + - - -
510C HIS* 3.4 18.0 + - - -
514C GLU* 2.9 22.2 + - - +
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Residues in contact with ALA 438 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434C GLY 2.8 14.7 + - - +
435C MET 2.9 3.0 + - - -
437C ASN* 1.3 67.2 - - - +
439C VAL* 1.3 58.4 - - - +
440C ASN 2.8 14.4 + - - -
441C LEU 2.8 13.0 + - - -
442C PHE* 2.8 18.1 + - + +
467C TYR* 3.2 22.0 - - + +
514C GLU* 3.7 15.9 - - + +
517C THR* 3.7 25.8 - - + -
518C LEU* 4.7 2.5 - - + +
521C LEU* 4.5 4.3 - - + -
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Residues in contact with VAL 439 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435C MET* 2.8 29.9 + - + +
436C LEU* 3.8 7.9 - - - +
438C ALA* 1.3 73.4 - - - +
440C ASN* 1.3 69.9 + - - +
443C PRO* 3.2 23.1 - - - +
517C THR* 3.9 10.6 - - + +
521C LEU* 3.8 11.9 - - + -
527C PRO* 3.6 40.0 - - + +
528C ASN* 5.1 1.1 - - - -
530C VAL* 4.7 3.1 - - + -
531C ASN* 4.0 27.6 - - + +
557D HIS* 6.5 0.2 - - + -
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Residues in contact with ASN 440 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436C LEU* 2.6 46.8 + - - +
437C ASN 3.5 1.8 + - - +
438C ALA 2.8 5.7 + - - -
439C VAL* 1.3 85.2 - - - +
441C LEU* 1.3 70.9 + - + +
443C PRO* 3.9 4.2 - - - +
444C VAL* 5.4 1.4 - - - +
557D HIS* 4.8 14.0 + - - -
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Residues in contact with LEU 441 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C LEU* 3.3 26.7 - - + -
382C ASN* 6.0 1.6 - - - +
385C ALA* 4.4 22.2 - - + +
389C ARG* 3.2 38.4 - - - +
437C ASN* 3.3 18.1 + - - +
438C ALA 2.8 8.3 + - - +
440C ASN* 1.3 81.8 - - + +
442C PHE* 1.3 58.7 + - - +
443C PRO* 3.3 1.0 - - - +
444C VAL* 3.0 30.5 - - - +
445C LEU* 4.0 6.4 - - + +
467C TYR* 4.1 10.1 - - + -
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Residues in contact with PHE 442 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438C ALA 2.8 23.9 + - - +
441C LEU* 1.3 73.7 - - - +
443C PRO* 1.3 68.7 - - + +
445C LEU* 2.8 29.6 + - + +
446C ARG* 2.8 42.8 + - + -
463C MET* 4.5 5.8 - - + -
464C MET* 4.1 19.3 - - - -
467C TYR* 3.4 48.7 - + + -
518C LEU* 3.6 24.7 - - + -
521C LEU* 4.5 18.2 - - + -
642C PHE* 4.0 20.6 - + - -
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Residues in contact with PRO 443 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439C VAL* 3.2 28.3 - - - +
440C ASN 3.9 4.3 - - - +
441C LEU 3.3 5.6 - - - +
442C PHE* 1.3 91.0 - - + +
444C VAL* 1.3 63.3 + - + +
446C ARG* 3.1 18.1 + - + +
447C ALA* 2.8 28.0 + - - +
521C LEU* 5.0 4.5 - - + -
527C PRO* 4.0 26.0 - - + -
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Residues in contact with VAL 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138C LEU 5.5 1.6 - - - +
139C LEU* 3.9 28.0 - - + -
140C SER* 5.1 9.4 - - - +
378C ASN* 5.3 4.0 - - - +
440C ASN 5.4 1.3 - - - +
441C LEU 3.0 23.8 - - - +
443C PRO* 1.3 76.1 - - + +
445C LEU* 1.3 67.2 + - + +
447C ALA* 3.8 3.3 - - - +
448C VAL* 2.8 36.8 + - + +
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.7 9.2 - - + -
375C VAL* 3.4 47.3 - - + -
378C ASN* 4.9 15.9 - - + +
441C LEU* 4.0 19.5 - - + +
442C PHE* 2.8 20.5 + - + +
444C VAL* 1.3 83.7 - - + +
446C ARG* 1.3 59.8 + - - +
448C VAL* 3.4 3.5 + - - -
449C SER* 2.8 34.6 + - - -
463C MET* 3.4 25.6 - - + +
467C TYR* 4.8 14.6 - - + -
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Residues in contact with ARG 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C PHE* 2.8 37.6 + - + +
443C PRO* 3.3 17.3 + - - +
445C LEU* 1.3 77.4 - - - +
447C ALA* 1.3 55.5 + - - +
449C SER* 3.1 9.9 + - - -
450C ASP* 2.8 35.9 + - - +
521C LEU* 3.3 50.2 + - - +
525C GLN* 2.7 51.8 + - - +
527C PRO* 4.1 10.3 - - - +
642C PHE* 4.9 3.1 - - + -
645C ARG* 3.4 29.6 + - - +
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Residues in contact with ALA 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C THR* 5.2 5.8 - - + +
443C PRO 2.8 18.7 + - - +
444C VAL* 4.0 3.1 - - - +
446C ARG* 1.3 75.9 - - + +
448C VAL* 1.3 59.7 + - - +
450C ASP* 3.1 15.4 - - + +
451C GLN* 2.8 30.0 + - - +
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Residues in contact with VAL 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C THR* 3.7 39.9 - - - +
138C LEU* 4.4 6.7 - - + +
139C LEU* 4.0 30.1 - - + +
374C ARG* 4.5 0.9 - - - +
444C VAL* 2.8 20.3 + - + +
445C LEU 4.0 4.5 - - - +
447C ALA* 1.3 75.5 - - - +
449C SER* 1.3 61.4 + - - +
451C GLN* 4.5 1.3 - - + +
452C GLU* 2.8 58.2 + - + +
458C TYR* 3.8 6.3 - - - +
463C MET* 4.2 6.3 - - + -
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Residues in contact with SER 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C LEU 2.8 12.2 + - - -
446C ARG* 3.1 11.7 - - - -
448C VAL* 1.3 71.3 - - - +
450C ASP* 1.3 67.9 + - - +
453C SER* 2.8 28.9 + - - -
458C TYR* 3.6 14.4 - - - -
460C LYS* 4.3 16.8 - - - -
463C MET* 2.8 46.1 - - - +
642C PHE* 6.3 2.2 - - - -
645C ARG* 5.7 0.7 - - - -
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Residues in contact with ASP 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ARG* 2.8 14.4 + - - +
447C ALA* 3.1 16.4 + - - +
449C SER* 1.3 80.2 - - - +
451C GLN* 1.3 63.4 + - - +
452C GLU 3.0 0.2 + - - -
453C SER 3.4 3.3 + - - -
454C GLN* 3.5 11.4 + - - +
460C LYS* 3.4 31.5 + - - +
645C ARG* 2.5 50.3 + - - -
649C ILE* 5.1 11.2 - - + +
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Residues in contact with GLN 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.9 29.3 - - + +
135C SER* 3.2 40.9 + - - +
136C ASP* 4.0 1.5 - - - -
137C THR* 2.5 45.8 + - - +
447C ALA 2.8 17.2 + - - +
448C VAL* 4.2 2.5 - - + +
450C ASP* 1.3 73.3 - - - +
452C GLU* 1.3 62.4 + - + +
454C GLN* 3.9 15.6 - - - +
455C ASP* 3.9 12.0 - - - +
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Residues in contact with GLU 452 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C THR 6.0 1.3 - - - +
138C LEU* 5.9 4.0 - - + +
151C THR* 3.7 22.8 - - - +
374C ARG* 2.7 35.1 + - - -
448C VAL* 2.8 38.7 + - + +
449C SER 3.9 0.2 - - - +
451C GLN* 1.3 71.1 - - + +
453C SER* 1.3 67.8 + - - +
454C GLN 3.1 1.6 - - - -
455C ASP* 2.8 22.6 + - - +
456C GLY 3.5 5.7 + - - -
457C LEU* 3.8 19.0 - - + +
458C TYR* 3.4 31.0 + - + +
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Residues in contact with SER 453 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C GLN* 4.4 1.7 + - - -
449C SER 2.8 22.1 + - - -
452C GLU* 1.3 72.4 - - - +
454C GLN* 1.3 56.7 + - - +
456C GLY* 2.8 23.4 + - - -
457C LEU 3.8 6.0 + - - +
458C TYR* 2.6 33.8 + - - +
459C GLN* 3.6 9.0 - - - -
460C LYS* 3.5 23.4 + - - +
646C ASP* 4.4 4.7 + - - -
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Residues in contact with GLN 454 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C SER 5.7 0.7 - - - +
102C ARG* 2.8 55.4 + - + +
126C GLN* 3.7 14.9 + - - +
131C TYR* 4.5 5.4 - - + -
133C LEU* 3.9 24.4 - - - +
450C ASP 3.5 14.1 + - - +
451C GLN* 3.9 12.3 + - - +
452C GLU 2.9 0.8 + - - -
453C SER* 1.3 77.9 - - - +
455C ASP* 1.3 62.5 + - - +
456C GLY 3.5 0.2 + - - -
460C LYS* 4.3 7.3 - - - +
649C ILE* 4.7 9.6 - - + +
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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
------------------------------------------------------------
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