Contacts of the helix formed by residues 436 - 463 (chain B) in PDB entry 5XA0
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 436 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435B VAL* 1.4 80.7 - - - +
437B PRO* 1.3 60.2 - - - +
438B ALA* 3.3 15.6 + - - +
439B GLU* 3.7 10.5 + - - +
440B VAL* 4.2 4.5 + - - +
441B ARG* 3.1 13.7 + - - -
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Residues in contact with PRO 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASN* 6.1 2.2 - - - +
436B SER* 1.3 71.1 - - - +
438B ALA* 1.3 52.5 + - - +
441B ARG* 1.9 56.0 + - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B SER* 3.3 9.1 + - - +
437B PRO* 1.3 80.2 - - - +
439B GLU* 1.3 51.3 - - - +
441B ARG* 2.9 17.0 + - - +
442B ASP* 2.1 29.7 + - - +
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B THR* 4.9 12.1 - - - +
278B SER* 5.2 9.7 - - - -
281B LEU* 6.4 1.3 - - - -
435B VAL* 2.6 36.4 - - + +
436B SER* 3.7 11.2 + - - +
438B ALA* 1.3 72.3 - - - +
440B VAL* 1.3 65.5 + - + +
441B ARG* 3.0 0.6 - - - +
442B ASP* 2.2 40.6 - - - +
443B LEU* 2.8 23.9 + - + +
509B LEU* 4.5 1.3 - - + +
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Residues in contact with VAL 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LYS* 5.7 16.2 - - + +
239B VAL* 4.9 7.0 - - + -
281B LEU* 3.4 37.5 - - + -
435B VAL* 6.0 2.0 - - + -
436B SER 4.2 2.9 + - - +
439B GLU* 1.3 78.7 - - + +
441B ARG* 1.3 113.8 + - - +
443B LEU* 3.0 10.6 + - + +
444B ASP* 2.9 24.8 + - + +
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Residues in contact with ARG 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.5 12.1 - - + +
126B LEU 5.3 5.2 + - - -
127B LYS 5.1 10.8 - - - +
128B SER 6.0 0.2 - - - +
129B ASN* 4.2 26.6 - - + +
436B SER 3.1 6.7 + - - -
437B PRO* 1.9 51.9 + - - +
438B ALA* 2.9 7.5 + - - +
439B GLU 3.0 3.6 - - - +
440B VAL* 1.3 131.2 - - - +
442B ASP* 1.3 63.9 + - - +
444B ASP* 3.0 3.0 + - - -
445B PHE* 3.0 18.8 + - + +
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Residues in contact with ASP 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B ALA* 2.1 23.1 - - - +
439B GLU* 2.2 30.9 + - - +
441B ARG* 1.3 69.4 - - - +
443B LEU* 1.3 61.7 + - - +
445B PHE* 3.0 7.8 + - - +
446B ALA* 2.9 21.5 + - - +
506B ARG* 6.0 9.0 - - + -
509B LEU* 3.5 12.9 - - + +
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Residues in contact with LEU 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B SER* 2.8 35.0 - - - +
281B LEU* 4.8 19.5 - - + -
439B GLU* 2.8 27.0 + - + +
440B VAL* 3.4 17.0 - - + +
442B ASP* 1.3 72.7 - - - +
444B ASP* 1.3 64.2 + - - +
446B ALA* 3.2 3.6 + - - +
447B ASN* 3.0 25.7 + - - +
509B LEU* 2.8 54.8 - - + +
513B GLN* 5.6 0.2 - - - +
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Residues in contact with ASP 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.1 33.4 - - + +
127B LYS* 5.6 4.9 - - + +
440B VAL* 2.9 17.8 + - + +
441B ARG* 3.5 4.5 - - - +
443B LEU* 1.3 78.3 - - - +
445B PHE* 1.3 56.4 + - - +
447B ASN* 3.8 5.1 - - - +
448B ASP* 2.8 31.7 + - - +
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Residues in contact with PHE 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B LEU* 3.0 57.8 - - + +
33B VAL* 2.9 34.4 - - + +
130B LYS* 5.1 5.6 - - - -
441B ARG 3.0 4.9 + - - +
442B ASP* 3.0 10.3 + - - +
444B ASP* 1.3 74.3 - - - +
446B ALA* 1.3 55.7 + - - +
449B ALA* 2.7 38.3 + - + +
476B LEU* 6.0 1.3 - - + -
479B ASP* 5.3 12.6 - - + -
483B PHE* 4.6 29.2 - + + -
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ASP 2.9 12.0 + - - +
443B LEU 3.4 8.1 - - - +
445B PHE* 1.3 75.1 - - - +
447B ASN* 1.3 51.8 + - - +
449B ALA* 2.9 7.9 + - - +
450B SER* 1.9 41.1 + - - -
509B LEU* 3.8 15.7 - - + -
510B MET* 3.9 10.3 - - + -
513B GLN* 2.7 24.7 - - - +
515B ILE* 4.4 1.8 - - - -
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Residues in contact with ASN 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443B LEU* 3.0 18.1 + - - +
444B ASP* 4.1 6.1 - - - +
446B ALA* 1.3 73.6 - - - +
448B ASP* 1.3 50.2 - - - +
450B SER* 3.2 5.8 + - - -
451B LYS* 1.8 49.6 + - + +
513B GLN* 3.1 31.2 - - + +
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Residues in contact with ASP 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU 4.1 0.4 - - - +
31B GLY* 2.7 17.3 - - - -
32B LEU* 2.6 26.5 + - + +
33B VAL* 2.7 23.5 + - + +
34B ASP* 2.4 36.8 + - - +
444B ASP 2.8 17.7 + - - +
447B ASN* 1.3 73.2 - - - +
449B ALA* 1.3 49.8 + - - +
451B LYS* 2.3 30.3 - - + +
452B VAL* 2.7 16.8 - - - +
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Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 3.0 16.6 - - + +
445B PHE* 2.7 22.8 + - + +
446B ALA* 2.9 6.5 + - - +
448B ASP* 1.3 73.5 - - - +
450B SER* 1.3 47.7 + - - +
451B LYS* 2.8 1.1 - - - -
452B VAL* 2.5 36.9 + - - +
453B LEU* 2.8 8.0 - - + +
476B LEU* 4.1 4.9 - - + -
480B LEU* 5.9 2.5 - - + -
483B PHE* 6.1 4.3 - - + -
515B ILE* 2.8 28.5 - - + -
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Residues in contact with SER 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B ALA 1.9 34.0 + - - -
447B ASN* 3.4 5.8 - - - -
449B ALA* 1.3 66.2 - - - +
451B LYS* 1.3 65.1 + - - -
453B LEU* 2.8 32.5 - - - +
454B GLY* 2.9 9.0 + - - -
513B GLN* 3.1 27.4 - - - +
515B ILE* 2.8 23.9 - - - +
518B GLN* 3.5 8.2 - - - +
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Residues in contact with LYS 451 (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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34B ASP* 3.3 16.8 - - - +
447B ASN* 1.8 44.9 + - + +
448B ASP* 2.3 47.5 - - - +
449B ALA 2.8 4.4 - - - -
450B SER* 1.3 70.1 - - - +
452B VAL* 1.4 82.6 + - - +
454B GLY* 2.9 3.3 + - - +
455B SER* 2.8 25.6 + - - -
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Residues in contact with VAL 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B VAL* 2.8 20.0 - - + +
34B ASP* 2.6 48.0 - - + +
448B ASP* 2.7 11.7 - - - +
449B ALA 2.5 33.1 + - - +
451B LYS* 1.4 87.7 - - - +
453B LEU* 1.3 63.9 + - - +
455B SER* 3.4 3.4 + - - -
456B ILE* 2.7 34.7 + - + +
476B LEU* 3.3 13.9 - - + -
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Residues in contact with LEU 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 2.8 24.9 - - - +
450B SER* 2.8 13.5 - - - +
452B VAL* 1.3 78.1 - - + +
454B GLY* 1.3 56.2 + - - +
456B ILE* 2.9 10.7 + - - +
457B ALA* 2.8 27.1 + - - +
476B LEU* 4.2 17.5 - - + -
515B ILE* 2.9 35.0 - - + +
518B GLN* 2.9 34.5 - - + -
519B ILE* 4.4 8.5 - - + +
522B LEU* 4.0 23.7 - - + +
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Residues in contact with GLY 454 (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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450B SER 2.9 10.7 + - - -
451B LYS* 2.9 10.4 + - - -
453B LEU* 1.3 76.6 - - - +
455B SER* 1.3 56.0 + - - -
457B ALA* 2.9 10.5 + - - +
458B GLY* 2.8 24.3 + - - -
518B GLN* 4.7 12.6 - - - -
522B LEU* 5.9 0.2 - - - -
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Residues in contact with SER 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LYS 2.8 15.8 + - - -
452B VAL* 4.3 2.5 - - - -
454B GLY* 1.3 69.9 - - - -
456B ILE* 1.3 73.7 + - - +
458B GLY* 3.3 6.6 + - - +
459B LYS* 3.1 24.8 + - - +
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Residues in contact with ILE 456 (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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452B VAL* 2.7 28.1 + - + +
453B LEU* 2.9 12.8 + - - +
455B SER* 1.3 76.5 - - - +
457B ALA* 1.3 48.8 + - - +
459B LYS* 2.4 32.6 + - + +
460B LEU* 2.8 28.9 - - + +
465B ILE* 4.9 4.0 - - + -
469B GLU* 2.9 57.0 - - + +
472B SER* 6.4 0.9 - - - -
473B VAL* 4.9 22.2 - - + +
522B LEU* 5.7 4.3 - - + -
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Residues in contact with ALA 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453B LEU 2.8 8.5 + - - +
454B GLY* 2.9 15.7 + - - +
456B ILE* 1.3 71.8 - - - +
458B GLY* 1.3 50.4 - - - +
459B LYS 2.7 1.5 + - - -
460B LEU* 3.0 21.5 - - + +
461B GLU* 3.2 3.1 + - - +
462B LYS* 2.0 32.4 + - - -
522B LEU* 3.4 31.9 - - + +
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Residues in contact with GLY 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B GLY 2.8 15.2 + - - -
455B SER* 3.4 9.4 - - - -
457B ALA* 1.3 63.9 - - - +
459B LYS* 1.4 52.4 - - - +
462B LYS* 1.8 48.3 + - - +
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Residues in contact with LYS 459 (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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455B SER* 3.1 16.0 + - - +
456B ILE* 2.4 26.9 + - + +
457B ALA 2.7 0.6 - - - -
458B GLY* 1.4 66.7 - - - -
460B LEU* 1.4 50.3 + - - -
462B LYS* 2.4 30.0 - - + +
463B GLY* 2.7 28.0 + - - -
464B THR 3.2 10.1 + - - +
469B GLU* 3.5 20.2 - - + +
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Residues in contact with LEU 460 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456B ILE* 2.8 58.3 + - + +
457B ALA* 3.0 35.2 - - + +
459B LYS* 1.4 69.8 - - - +
461B GLU* 1.4 66.8 + - + +
462B LYS* 2.7 7.9 - - - +
463B GLY 3.6 13.4 - - - +
464B THR* 5.0 4.0 - - - +
465B ILE* 4.7 17.5 - - + -
469B GLU* 5.6 0.2 - - - -
522B LEU* 3.5 30.1 - - + +
524B GLN* 4.6 9.9 - - + +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ALA 3.2 4.9 + - - +
460B LEU* 1.4 75.9 - - + +
462B LYS* 1.4 82.9 + - + +
524B GLN* 4.1 31.6 + - + +
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Residues in contact with LYS 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ALA 2.0 26.7 + - - -
458B GLY* 1.8 39.8 + - - +
459B LYS* 2.4 43.1 - - + -
460B LEU 2.9 0.4 - - - -
461B GLU* 1.4 93.3 - - - +
463B GLY* 1.3 70.5 + - - +
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Residues in contact with GLY 463 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B LYS* 2.7 12.8 + - - +
460B LEU 3.6 10.2 - - - +
461B GLU 3.7 0.2 - - - -
462B LYS* 1.3 88.7 - - - +
464B THR* 1.3 61.5 + - - -
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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