Contacts of the helix formed by residues 451 - 471 (chain B) in PDB entry 5MJ6
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 451 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B TYR* 4.2 1.8 - - - -
450B SER* 1.3 76.7 - - - +
452B MET* 1.3 64.9 + - - +
453B ALA* 3.3 17.4 + - - +
454B ASP* 3.2 15.5 + - - -
455B ARG* 3.0 21.0 + - - +
817B ARG* 4.7 1.6 - - - -
857B THR* 3.3 33.8 - - - -
858B ASP* 3.9 7.0 - - - -
892B LYS* 3.5 19.0 - - - +
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Residues in contact with MET 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B SER* 1.3 75.4 - - - +
453B ALA* 1.3 57.5 + - - +
455B ARG* 3.1 23.1 + - + -
456B LYS* 3.0 36.1 + - + +
505B LEU* 3.5 33.0 - - + -
814B PRO* 3.6 41.7 - - + +
817B ARG* 3.9 33.8 - - + +
818B GLU* 4.4 10.8 - - + -
858B ASP* 3.4 16.7 + - - +
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Residues in contact with ALA 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B SER* 3.1 11.0 + - - +
452B MET* 1.3 81.0 - - - +
454B ASP* 1.3 56.3 + - - +
456B LYS* 3.1 6.3 + - - +
457B LEU* 2.7 36.7 + - - +
818B GLU* 3.9 20.8 + - + +
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLU 5.7 4.0 - - - +
444B LEU 6.1 0.9 - - - +
445B TYR* 4.5 2.6 - - + -
450B SER* 3.8 14.8 - - - +
451B SER* 3.2 16.6 + - - +
453B ALA* 1.3 75.0 - - - +
455B ARG* 1.3 66.2 + - - +
457B LEU* 3.7 18.0 - - + +
458B VAL* 3.2 30.5 + - + +
888B ALA* 3.3 24.7 - - + +
892B LYS* 2.6 32.8 + - - +
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Residues in contact with ARG 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 3.4 41.9 + - + +
445B TYR* 2.6 58.8 + - + -
447B SER* 5.3 1.4 - - - -
451B SER 3.0 13.1 + - - +
452B MET* 3.3 32.8 - - + +
453B ALA 3.1 0.2 - - - -
454B ASP* 1.3 80.0 - - - +
456B LYS* 1.3 60.6 + - - +
458B VAL* 3.5 3.3 + - - +
459B THR* 2.8 27.8 + - - +
505B LEU* 4.6 8.8 - - + +
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Residues in contact with LYS 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B MET* 3.0 32.5 + - + +
453B ALA* 3.5 7.4 - - - +
455B ARG* 1.3 76.4 - - - +
457B LEU* 1.3 55.3 + - - +
459B THR* 3.3 6.4 + - - -
460B LYS* 2.9 41.2 + - + +
505B LEU* 3.4 30.6 + - + +
506B SER 3.4 20.7 + - - -
507B SER* 4.5 10.3 - - - +
509B GLU* 4.7 2.2 + - - -
510B ASP* 3.4 32.4 + - - +
814B PRO* 5.1 0.7 - - + -
818B GLU* 2.7 38.7 + - - +
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Residues in contact with LEU 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B GLU* 4.6 11.9 - - + +
442B THR* 3.6 36.8 - - + -
453B ALA 2.7 19.1 + - - +
454B ASP* 3.7 22.0 - - - +
456B LYS* 1.3 74.0 - - - +
458B VAL* 1.3 63.0 + - - +
460B LYS* 3.7 9.5 - - - +
461B ILE* 3.1 21.4 + - + +
1127B 7O2 3.5 27.4 - - + -
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Residues in contact with VAL 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 3.9 24.9 - - + -
393B ALA* 4.9 0.9 - - - -
441B GLU 4.5 2.9 - - - +
442B THR* 3.6 31.2 - - - +
443B LEU 3.6 16.6 - - - +
444B LEU 3.9 18.6 - - - +
445B TYR* 4.3 6.7 - - + -
454B ASP* 3.2 19.1 + - + +
455B ARG 3.9 3.4 - - - +
457B LEU* 1.3 78.8 - - + +
459B THR* 1.3 64.4 + - - +
461B ILE* 3.8 1.0 - - - +
462B ILE* 3.2 38.0 + - + +
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Residues in contact with THR 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B TYR* 2.7 27.2 + - - +
396B THR* 4.0 18.4 - - + -
400B LEU* 4.2 1.5 - - + +
455B ARG 2.8 14.8 + - - -
456B LYS 3.7 5.8 - - - -
457B LEU 3.2 0.2 - - - -
458B VAL* 1.3 78.4 - - - +
460B LYS* 1.3 62.4 + - - +
462B ILE* 3.5 2.1 + - - +
463B ALA* 3.1 22.3 + - - +
498B LEU* 3.7 24.0 - - + -
502B PHE* 4.0 12.1 - - + -
505B LEU* 3.8 22.9 - - + +
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Residues in contact with LYS 460 (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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456B LYS* 2.9 27.5 + - + +
457B LEU* 3.7 7.3 - - - +
459B THR* 1.3 77.2 - - - +
461B ILE* 1.3 58.5 + - - +
463B ALA* 3.1 4.4 + - - +
464B HIS* 2.8 28.9 + - - +
494B GLU* 3.3 21.2 - - + +
495B TYR* 3.2 29.5 + - + +
498B LEU* 3.5 26.4 - - + +
507B SER* 4.6 4.7 - - - +
510B ASP* 3.2 30.9 + - - +
1127B 7O2 4.4 15.3 - - + -
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Residues in contact with ILE 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428B GLY 3.8 11.9 - - - -
429B ALA* 3.8 26.7 - - + +
438B PHE* 3.6 15.9 - - + -
442B THR* 3.2 35.9 - - - +
457B LEU 3.1 7.4 + - - +
458B VAL 3.8 5.8 - - - +
460B LYS* 1.3 79.3 - - - +
462B ILE* 1.3 62.6 + - + +
464B HIS* 3.3 4.0 + - + +
465B GLU* 2.9 39.7 + - - +
1127B 7O2 3.4 51.8 - - + -
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Residues in contact with ILE 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393B ALA* 3.8 29.8 - - - +
396B THR* 4.1 9.4 - - + -
397B THR* 3.7 24.9 - - - +
400B LEU* 3.9 15.7 - - + -
419B LEU* 4.2 7.6 - - + -
438B PHE* 4.5 8.5 - - + -
443B LEU* 3.8 30.7 - - + -
458B VAL* 3.2 23.5 + - + +
459B THR 3.9 3.1 - - - +
460B LYS 3.2 0.4 - - - -
461B ILE* 1.3 76.6 - - + +
463B ALA* 1.3 66.2 + - - +
465B GLU* 3.4 1.4 + - - +
466B LEU* 2.9 32.6 + - + +
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Residues in contact with ALA 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400B LEU* 3.6 20.6 - - + +
404B PHE* 3.6 10.2 - - - -
459B THR 3.1 15.2 + - - +
460B LYS* 3.4 9.0 - - - +
462B ILE* 1.3 78.6 - - - +
464B HIS* 1.3 61.5 + - - +
466B LEU* 4.7 0.2 - - - -
467B ALA* 3.0 24.6 + - - +
494B GLU* 4.2 10.9 - - - +
497B SER* 3.8 20.9 - - - +
498B LEU* 4.1 9.2 - - + -
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Residues in contact with HIS 464 (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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460B LYS 2.8 16.5 + - - +
461B ILE* 3.6 9.4 - - + +
462B ILE 3.2 0.2 - - - -
463B ALA* 1.3 73.4 - - - +
465B GLU* 1.3 72.6 + - - +
467B ALA* 3.2 5.2 + - - +
468B HIS* 3.2 23.3 + + - -
487B GLU* 3.9 2.5 - - - -
490B ALA* 3.5 21.3 + - + +
491B THR* 3.4 24.0 - - - -
494B GLU* 2.8 32.3 + - - +
549B TYR* 4.1 1.1 - + - -
1126B ZN 2.1 36.8 - - - -
1127B 7O2 3.2 33.4 + + + -
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Residues in contact with GLU 465 (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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429B ALA* 3.4 15.7 - - + +
430B MET 3.2 23.4 + - - +
431B GLU* 3.3 5.1 + - + +
436B LEU* 3.5 24.0 - - + -
438B PHE* 3.6 23.3 - - + -
461B ILE* 2.9 26.7 + - - +
462B ILE 4.1 1.6 - - - +
464B HIS* 1.3 81.7 - - - +
466B LEU* 1.3 60.5 + - - +
468B HIS* 3.3 9.9 + - - +
469B GLN* 3.2 22.0 + - - -
1127B 7O2 3.1 39.6 + - - +
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Residues in contact with LEU 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397B THR* 3.7 28.3 - - + +
400B LEU* 3.7 29.6 - - + -
401B LEU* 3.8 13.0 - - + +
404B PHE* 3.9 14.1 - - + -
417B LEU* 4.0 26.2 - - + -
419B LEU* 5.0 0.9 - - + -
436B LEU* 3.9 19.7 - - + -
462B ILE* 2.9 26.2 + - + +
465B GLU* 1.3 74.7 - - - +
467B ALA* 1.3 66.1 + - - +
469B GLN* 3.0 25.2 + - + +
470B TRP* 3.3 14.8 - - + -
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Residues in contact with ALA 467 (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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404B PHE* 3.9 10.7 - - + -
408B PHE* 4.7 2.2 - - - -
463B ALA 3.0 20.4 + - - +
464B HIS 3.5 5.2 - - - +
466B LEU* 1.3 74.8 - - - +
468B HIS* 1.3 63.0 + - - +
469B GLN 3.0 1.4 + - - -
470B TRP* 3.2 12.1 + - - +
471B PHE* 3.1 22.2 + - + +
490B ALA* 3.9 17.5 - - - +
493B MET* 3.8 30.5 - - + -
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Residues in contact with HIS 468 (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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431B GLU* 3.4 34.9 + - + -
464B HIS* 3.2 18.8 + + - -
465B GLU* 3.4 12.1 - - - +
466B LEU 3.1 0.8 - - - -
467B ALA* 1.3 76.9 - - - +
469B GLN* 1.3 65.0 + - - +
470B TRP 3.2 0.6 + - - -
471B PHE 3.0 25.7 + - - -
472B GLY* 4.3 1.8 - - - -
473B ASN* 3.1 24.8 + - - +
486B ASN* 3.5 13.9 - - + -
487B GLU* 3.2 19.7 + - - -
490B ALA* 3.4 14.3 - - + +
1126B ZN 2.1 37.3 - - - -
1127B 7O2 3.1 11.8 + - - -
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Residues in contact with GLN 469 (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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412B TYR* 3.8 24.5 - - + -
417B LEU* 4.9 0.4 - - + -
431B GLU* 3.2 26.1 + - - +
433B TRP* 3.2 32.5 - - - +
434B GLY 3.4 12.3 + - - -
436B LEU* 3.6 16.2 - - - +
465B GLU 3.2 19.7 + - - +
466B LEU* 3.0 29.9 + - + +
468B HIS* 1.3 76.0 - - - +
470B TRP* 1.3 69.9 + - + +
473B ASN* 3.3 10.7 - - - +
474B LEU* 3.1 24.4 + - - +
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Residues in contact with TRP 470 (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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401B LEU* 4.4 15.3 - - + -
404B PHE* 3.6 26.0 - + + -
405B GLN* 3.8 24.5 - - + -
408B PHE* 3.4 34.5 - + + +
410B ILE* 3.2 36.2 + - + +
411B GLN 4.4 2.3 + - - -
412B TYR* 4.3 13.2 - + + -
466B LEU* 3.3 25.6 - - + -
467B ALA 3.2 4.5 + - - +
468B HIS 3.2 0.2 - - - -
469B GLN* 1.3 89.2 - - + +
471B PHE* 1.3 66.9 + - + +
472B GLY 3.1 2.1 + - - -
474B LEU* 3.2 25.1 + - + +
475B VAL* 3.0 31.0 + - - +
576B LEU* 4.0 21.2 - - + +
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Residues in contact with PHE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B PHE* 3.4 39.3 - + - -
467B ALA 3.1 12.3 + - - +
468B HIS* 3.0 27.0 + - - -
470B TRP* 1.3 77.2 - - + +
472B GLY* 1.3 55.4 + - - +
475B VAL* 3.9 3.8 - - + -
485B LEU 4.4 4.7 - - - +
486B ASN* 3.7 13.4 - - - +
489B PHE* 3.4 64.2 - + + -
490B ALA 4.6 3.1 - - - +
493B MET* 4.3 6.1 - - + -
572B VAL* 3.9 20.4 - - + -
575B TYR* 3.9 26.5 - + - -
576B LEU* 4.1 15.7 - - + -
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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) + - + + + + + -
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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