Contacts of the helix formed by residues 444 - 466 (chain B) in PDB entry 4EMX
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 LYS 444 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440B HIS* 4.1 35.8 + - + +
441B PRO* 2.9 21.3 + - + +
443B ALA* 1.3 79.4 - - + +
445B ARG* 1.3 63.3 + - - +
446B MET 3.6 1.8 - - - -
447B PRO* 3.6 13.8 - - - +
448B CYS* 3.4 19.6 + - - +
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Residues in contact with ARG 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B ILE* 4.0 19.5 - - + -
389B LYS* 4.4 14.3 + - - +
392B CYS* 3.8 30.2 - - - +
396B GLU* 3.9 8.1 + - - +
437B CYS* 3.4 24.3 - - + +
438B CYS* 3.3 21.2 + - - -
440B HIS* 3.2 21.3 + - + +
441B PRO 3.3 5.4 + - - +
442B GLU* 3.6 40.0 - - - +
443B ALA 3.6 1.2 - - - +
444B LYS* 1.3 78.0 - - - +
446B MET* 1.3 56.2 + - - +
448B CYS* 3.5 1.8 + - - +
449B ALA* 2.7 38.6 + - - +
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Residues in contact with MET 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340B ASP 3.9 11.9 + - - +
341B TYR* 4.5 3.8 - - + -
342B SER* 3.6 29.2 - - - -
345B LEU* 3.9 21.3 - - + -
381B VAL* 4.2 6.7 - - + +
384B PRO* 3.9 26.0 - - + -
385B GLN* 3.9 34.3 - - + +
388B ILE* 4.6 15.0 - - + +
443B ALA 5.2 1.0 - - - +
445B ARG* 1.3 72.9 - - - +
447B PRO* 1.4 68.9 - - + +
450B GLU* 2.6 45.1 + - + +
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Residues in contact with PRO 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221B GLN* 5.2 2.7 - - - +
339B PRO 3.3 25.6 - - - +
340B ASP* 3.3 22.9 - - - +
341B TYR 3.8 7.9 - - - +
342B SER* 3.7 15.1 - - - -
444B LYS* 3.6 19.3 - - - +
446B MET* 1.4 87.4 - - - +
448B CYS* 1.3 62.4 + - - +
451B ASP* 3.1 33.8 + - - +
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Residues in contact with CYS 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LYS* 3.7 20.1 - - - +
437B CYS* 2.1 53.4 - - + -
440B HIS* 4.1 13.5 - - + +
444B LYS 3.4 18.3 + - - +
445B ARG 3.5 2.0 + - - +
446B MET 3.2 0.4 - - - -
447B PRO* 1.3 80.9 - - - +
449B ALA* 1.3 62.0 + - - +
452B TYR* 3.1 25.5 + - - +
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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
----------------------------------------------------------
388B ILE* 4.2 29.2 - - + -
433B VAL* 3.7 18.2 - - + +
437B CYS* 3.5 15.0 - - + -
438B CYS* 6.5 0.2 - - - -
445B ARG 2.7 21.9 + - - +
448B CYS* 1.3 76.0 - - - +
450B GLU* 1.3 57.9 + - - +
452B TYR* 3.4 2.3 + - - +
453B LEU* 2.9 33.9 + - + +
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Residues in contact with GLU 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342B SER* 2.8 24.4 + - - -
344B VAL* 3.6 7.5 - - + +
348B ARG* 2.6 34.8 + - - -
384B PRO* 3.6 17.4 - - + +
388B ILE* 5.1 5.4 - - + +
446B MET* 2.6 27.7 + - + +
449B ALA* 1.3 75.9 - - - +
451B ASP* 1.3 57.7 + - - +
453B LEU* 3.4 7.2 + - + +
454B SER* 2.9 26.3 + - - -
485B ARG* 2.8 45.3 + - + +
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Residues in contact with ASP 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.8 0.9 - - - +
214B TRP* 5.4 3.2 + - - -
218B ARG* 5.6 0.9 - - - -
342B SER* 3.7 4.5 - - - -
343B VAL* 2.9 48.5 + - - +
344B VAL* 3.5 21.7 + - - +
447B PRO* 3.1 25.8 + - - +
450B GLU* 1.3 74.8 - - - +
452B TYR* 1.3 64.4 + - - +
454B SER* 3.2 18.9 + - - -
455B VAL* 3.3 14.0 + - - +
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Residues in contact with TYR 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA* 6.0 5.2 - - + -
429B ASN* 3.2 35.5 + - - +
430B LEU* 4.9 0.7 - - - -
432B LYS* 4.0 15.1 - - + +
433B VAL* 3.6 35.4 - - + -
436B LYS* 3.9 36.1 - - + -
448B CYS 3.1 22.3 + - - +
449B ALA 3.7 2.2 - - - +
451B ASP* 1.3 74.9 - - - +
453B LEU* 1.3 66.9 + - + +
455B VAL* 3.0 26.3 + - + +
456B VAL* 3.1 30.8 + - + +
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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
----------------------------------------------------------
387B LEU* 4.4 3.4 - - + -
388B ILE* 4.3 19.1 - - + -
430B LEU* 3.7 25.8 - - + +
433B VAL* 4.3 26.9 - - + -
449B ALA* 2.9 22.9 + - + +
450B GLU* 3.4 11.2 + - - +
452B TYR* 1.3 77.1 - - + +
454B SER* 1.3 63.4 + - - +
456B VAL* 4.5 3.1 - - - +
457B LEU* 2.9 34.1 + - + +
485B ARG* 3.8 33.9 - - + -
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Residues in contact with SER 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B LEU* 4.1 21.4 - - - +
344B VAL* 3.2 30.6 - - - +
450B GLU 2.9 15.6 + - - -
451B ASP* 3.2 15.9 + - - -
452B TYR 3.1 0.4 - - - -
453B LEU* 1.3 74.4 - - - +
455B VAL* 1.3 63.0 + - - +
457B LEU* 4.1 4.6 - - - +
458B ASN* 3.1 24.1 + - - +
481B LEU 5.5 1.4 + - - -
484B ARG* 5.2 5.4 + - - +
485B ARG* 5.3 5.9 - - - +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ALA 5.1 0.9 - - - +
194B ALA* 3.5 38.5 - - + +
195B LYS* 4.0 23.1 - - + +
198B LEU* 3.5 27.4 - - + -
451B ASP 3.6 10.8 - - - +
452B TYR* 3.0 22.3 + - + +
454B SER* 1.3 77.3 - - - +
456B VAL* 1.3 66.6 + - + +
458B ASN* 3.4 5.5 + - - +
459B GLN* 3.2 21.0 + - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426B VAL* 3.6 32.4 - - + +
429B ASN* 4.0 20.4 - - + +
430B LEU* 3.6 24.0 - - + +
452B TYR* 3.1 46.8 + - + +
453B LEU* 4.0 1.1 - - - +
455B VAL* 1.3 76.2 - - + +
457B LEU* 1.3 63.8 + - - +
459B GLN* 3.1 19.5 + - + +
460B LEU* 3.1 12.0 + - - +
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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
----------------------------------------------------------
411B TYR* 4.2 22.9 - - + +
426B VAL* 5.1 1.6 - - + -
430B LEU* 4.4 16.8 - - + -
453B LEU* 2.9 27.8 + - + +
454B SER* 4.2 3.6 - - - +
456B VAL* 1.3 72.3 - - - +
458B ASN* 1.3 58.2 + - - +
460B LEU* 3.2 17.0 + - + +
461B CYS* 2.8 32.0 + - - -
484B ARG* 4.9 9.0 - - + -
485B ARG* 3.8 41.1 - - + +
488B PHE* 4.0 35.9 - - + -
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Residues in contact with ASN 458 (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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194B ALA 5.0 0.4 + - - -
197B ARG* 3.4 32.1 + - - +
198B LEU* 3.6 19.9 - - + +
201B ALA* 3.4 18.6 - - - +
454B SER 3.1 18.3 + - - +
455B VAL 3.5 5.6 + - - +
456B VAL 3.2 0.2 - - - -
457B LEU* 1.3 78.8 - - - +
459B GLN* 1.3 53.1 + - - +
461B CYS* 3.1 2.3 + - - +
462B VAL* 2.8 47.3 + - - +
484B ARG* 2.6 34.4 + - - +
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Residues in contact with GLN 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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190B LYS 5.3 0.2 - - - +
193B SER* 5.4 2.5 + - - -
194B ALA* 3.5 36.1 + - + +
197B ARG* 4.2 20.2 - - - +
426B VAL* 4.8 4.7 - - + -
429B ASN* 5.0 13.6 + - - +
455B VAL 3.2 14.5 + - - +
456B VAL* 3.1 14.9 + - + +
458B ASN* 1.3 76.9 - - - +
460B LEU* 1.3 55.5 + - - +
462B VAL* 3.3 8.6 + - - +
463B LEU* 2.8 49.6 + - + +
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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
----------------------------------------------------------
411B TYR* 4.9 9.4 - - + -
415B VAL* 5.3 4.5 - - + -
418B VAL* 4.2 17.9 - - + -
422B THR* 3.8 20.6 - - + -
423B LEU* 5.6 4.3 - - + -
426B VAL* 3.6 33.5 - - + +
456B VAL 3.1 5.0 + - - +
457B LEU* 3.5 19.3 - - + +
459B GLN* 1.3 75.7 - - - +
461B CYS* 1.3 63.4 + - - +
463B LEU* 3.4 2.9 + - - +
464B HIS* 3.0 30.0 + - + +
473B VAL* 4.3 17.0 - - + -
488B PHE* 3.7 32.1 - - + -
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Residues in contact with CYS 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B LEU 2.8 22.4 + - - -
458B ASN* 3.1 9.6 + - - +
460B LEU* 1.3 70.9 - - - +
462B VAL* 1.3 59.5 + - + +
464B HIS* 4.0 1.9 - - - +
465B GLU* 3.1 31.4 + - - +
473B VAL* 4.8 1.8 - - - -
477B CYS* 2.0 59.0 - - + +
484B ARG* 3.6 26.0 - - - +
488B PHE* 4.2 9.2 - - - -
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Residues in contact with VAL 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 3.8 27.4 - - + +
197B ARG* 3.4 37.5 - - + +
201B ALA* 4.7 4.3 - - + -
205B LYS* 5.6 1.8 - - - -
458B ASN* 2.8 37.8 + - - +
459B GLN* 3.4 25.6 - - - +
461B CYS* 1.3 70.8 - - + +
463B LEU* 1.3 70.6 + - + +
464B HIS 3.4 0.5 + - - -
465B GLU* 3.5 27.4 + - - +
466B LYS* 3.7 9.0 + - - +
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Residues in contact with LEU 463 (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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108B ASP* 4.5 15.7 - - + +
109B ASN* 3.9 34.7 - - + +
422B THR* 3.9 39.0 + - + +
425B GLU* 5.1 9.2 - - + -
426B VAL* 4.6 7.4 - - + -
459B GLN* 2.8 39.4 + - + +
460B LEU 4.0 0.2 - - - +
462B VAL* 1.3 78.8 - - + +
464B HIS* 1.3 58.3 + - - +
466B LYS* 3.7 16.3 - - - +
467B THR* 4.5 1.6 + - - -
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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
----------------------------------------------------------
418B VAL* 4.2 10.5 - - + +
422B THR* 5.4 3.1 - - + -
460B LEU* 3.0 22.4 + - + +
461B CYS 4.0 2.2 - - - +
463B LEU* 1.3 76.7 - - - +
465B GLU* 1.3 63.7 + - + +
466B LYS 3.1 5.8 - - - -
467B THR 3.1 26.4 + - - -
468B PRO* 3.2 6.1 - - + +
469B VAL* 3.2 24.8 + - + +
470B SER* 2.9 55.9 + - - -
473B VAL* 3.6 25.2 - - + +
474B THR* 3.3 17.5 + - - -
477B CYS* 6.0 0.2 - - - -
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Residues in contact with GLU 465 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ASP* 5.1 0.7 - - - +
197B ARG* 4.4 6.2 + - - -
205B LYS* 3.2 38.7 + - - -
461B CYS 3.1 19.2 + - - +
462B VAL* 3.5 27.6 - - - +
464B HIS* 1.3 78.5 - - + +
466B LYS* 1.3 66.6 + - - +
467B THR* 3.3 0.6 + - - -
468B PRO* 3.9 16.5 - - - +
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Residues in contact with LYS 466 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B ASP* 3.0 29.7 + - - +
108B ASP* 5.5 2.7 - - + +
109B ASN* 2.6 44.1 + - + +
111B ASN* 4.4 11.3 - - - +
462B VAL 3.7 6.9 + - - +
463B LEU* 3.7 15.7 - - - +
465B GLU* 1.3 84.0 - - - +
467B THR* 1.3 68.3 + - - +
468B PRO* 4.3 1.9 - - - +
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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