Contacts of the helix formed by residues 413 - 440 (chain B) in PDB entry 1G4Y
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414B THR* 1.3 64.9 + - - +
415B GLN* 3.2 15.1 + - - +
416B LEU* 2.7 45.7 + - + +
417B THR* 3.1 25.1 + - - -
473B LEU* 5.9 0.9 - - + -
50R ASP* 2.6 37.7 - - + +
53R ASN* 5.0 15.1 - - - +
54R GLU* 5.6 4.4 + - - -
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Residues in contact with THR 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 1.3 73.6 + - - +
415B GLN* 1.3 64.5 + - - +
417B THR* 3.3 6.4 + - - -
418B LYS* 2.8 31.4 + - - +
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Residues in contact with GLN 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 3.2 13.9 - - - +
414B THR* 1.3 83.4 + - - +
416B LEU* 1.3 59.3 + - + +
418B LYS* 3.4 9.7 + - + +
419B ARG* 3.0 52.1 + - + +
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP* 2.7 31.7 + - + +
414B THR 3.3 0.2 - - - -
415B GLN* 1.3 72.0 - - + +
417B THR* 1.3 61.5 + - - +
419B ARG* 3.1 24.1 + - - +
420B VAL* 2.9 32.5 + - - +
466B VAL* 3.8 29.2 - - + +
469B GLU* 4.3 20.6 - - + -
470B GLN* 3.7 23.8 - - - +
473B LEU* 4.0 21.1 - - + -
50R ASP* 5.7 1.6 - - - +
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Residues in contact with THR 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413B ASP 3.1 14.2 + - - -
414B THR* 3.3 10.4 + - - -
416B LEU* 1.3 79.5 - - - +
418B LYS* 1.3 59.7 + - - +
420B VAL* 3.1 10.1 + - + +
421B LYS* 2.9 46.3 + - + +
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Residues in contact with LYS 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B THR 2.8 19.0 + - - +
415B GLN* 3.4 9.6 - - + +
417B THR* 1.3 79.8 - - - +
419B ARG* 1.3 65.9 + - + +
421B LYS* 4.0 6.2 - - + +
422B ASN* 3.1 55.4 + - - +
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Residues in contact with ARG 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLN* 3.0 36.2 + - + +
416B LEU* 3.1 22.6 + - - +
418B LYS* 1.3 79.3 - - + +
420B VAL* 1.3 62.5 + - - +
422B ASN* 4.0 3.9 - - - +
423B ALA* 3.0 27.8 + - - +
462B GLN* 6.5 1.1 - - + -
466B VAL* 3.9 21.5 - - + -
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Residues in contact with VAL 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416B LEU 2.9 20.4 + - - +
417B THR* 3.4 10.3 - - + +
419B ARG* 1.3 76.1 - - - +
421B LYS* 1.3 60.8 + - + +
423B ALA 3.2 0.5 + - - -
424B ALA* 2.7 43.6 + - + +
463B LEU* 3.7 20.7 - - + +
466B VAL* 3.5 27.6 - - + -
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Residues in contact with LYS 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B THR* 2.9 39.0 + - + +
418B LYS* 4.1 5.8 - - + +
420B VAL* 1.3 77.8 - - + +
422B ASN* 1.3 65.3 + - - +
424B ALA* 4.0 5.0 - - + +
425B ALA* 3.0 25.5 + - - +
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Residues in contact with ASN 422 (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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418B LYS* 3.1 54.4 + - - +
419B ARG* 4.0 3.7 - - - +
421B LYS* 1.3 78.4 - - - +
423B ALA* 1.3 58.2 + - - +
425B ALA* 3.7 5.4 - - - +
426B ASN* 3.0 37.0 + - - +
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Residues in contact with ALA 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B ARG 3.0 19.9 + - - +
422B ASN* 1.3 74.6 - - - +
424B ALA* 1.3 65.6 + - - +
426B ASN* 3.1 5.0 + - - +
427B VAL* 3.0 25.5 + - - +
459B ALA* 3.6 5.7 - - - +
462B GLN* 3.6 35.4 - - + +
463B LEU* 3.6 23.6 - - + +
466B VAL* 6.2 0.4 - - + -
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Residues in contact with ALA 424 (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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420B VAL* 2.7 27.4 + - + +
421B LYS* 4.0 5.2 - - + +
423B ALA* 1.3 72.2 - - - +
425B ALA* 1.3 64.9 + - - +
427B VAL* 3.1 3.9 + - - +
428B LEU* 3.1 31.8 + - + +
463B LEU* 3.9 19.9 - - + +
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Residues in contact with ALA 425 (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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421B LYS 3.0 18.3 + - - +
422B ASN* 3.7 6.5 - - - +
424B ALA* 1.3 76.1 - - - +
426B ASN* 1.3 62.7 + - - +
428B LEU* 3.3 13.3 + - - +
429B ARG* 2.9 26.5 + - - +
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Residues in contact with ASN 426 (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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422B ASN* 3.0 24.9 + - - +
423B ALA* 3.1 6.3 + - - +
425B ALA* 1.3 78.8 - - - +
427B VAL* 1.3 60.3 + - - +
429B ARG* 3.9 20.7 - - + -
430B GLU* 2.9 41.2 + - + +
455B LYS 5.4 0.4 - - - +
458B GLN* 5.8 2.2 + - - -
459B ALA* 3.8 14.1 - - + -
462B GLN* 5.2 4.6 + - - -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B ALA 3.0 18.7 + - - +
424B ALA* 3.1 8.0 + - - +
426B ASN* 1.3 76.1 - - - +
428B LEU* 1.3 70.7 + - + +
430B GLU* 4.4 0.2 - - - +
431B THR* 2.9 41.0 + - - +
456B PHE* 4.3 7.7 - - + -
459B ALA* 3.6 22.7 - - + -
460B ILE* 3.9 25.8 - - + +
463B LEU* 3.8 22.0 - - + -
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Residues in contact with LEU 428 (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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424B ALA* 3.1 22.3 + - + +
425B ALA* 3.5 12.6 - - - +
426B ASN 3.2 0.2 - - - -
427B VAL* 1.3 84.5 - - + +
429B ARG* 1.3 63.4 + - - +
431B THR* 4.0 4.0 - - - -
432B TRP* 3.0 26.0 + - - +
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Residues in contact with ARG 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B ALA 2.9 16.9 + - - +
426B ASN* 3.6 21.1 - - - +
427B VAL 3.3 0.2 - - - -
428B LEU* 1.3 78.1 - - - +
430B GLU* 1.3 93.0 + - - +
432B TRP* 3.6 6.3 - - - +
433B LEU* 3.0 45.8 + - + +
455B LYS* 4.3 5.0 - - - +
799B SO4 2.9 42.0 + - - -
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Residues in contact with GLU 430 (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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426B ASN* 2.9 24.4 + - + +
427B VAL 4.4 0.4 - - - +
429B ARG* 1.3 106.1 + - - +
431B THR* 1.3 61.0 + - - +
433B LEU* 3.7 1.8 - - - +
434B ILE* 2.9 37.5 + - - +
452B HIS* 2.8 36.9 + - - +
455B LYS* 3.4 37.2 - - + +
456B PHE* 3.7 21.1 - - + -
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Residues in contact with THR 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B VAL* 2.9 29.3 + - - +
428B LEU* 4.0 4.3 - - - -
430B GLU* 1.3 76.1 - - - +
432B TRP* 1.3 65.1 - - - +
434B ILE* 3.8 4.4 - - - +
435B TYR* 2.9 26.6 + - + +
456B PHE* 3.4 24.2 - - + -
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Residues in contact with TRP 432 (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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428B LEU 3.0 19.0 + - - +
429B ARG* 3.6 5.4 - - - +
431B THR* 1.3 77.7 - - - +
433B LEU* 1.3 79.1 + - + +
435B TYR* 3.2 30.5 + + - +
436B LYS* 2.8 50.3 + - + +
440B LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 433 (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 ARG* 3.0 49.4 + - + +
430B GLU* 4.1 3.1 - - - +
431B THR 3.3 0.2 - - - -
432B TRP* 1.3 101.2 - - + +
434B ILE* 1.3 61.6 + - - +
436B LYS* 4.4 10.8 - - + +
437B ASN* 2.8 38.4 + - - +
452B HIS* 3.7 42.6 - - + +
799B SO4 5.5 0.7 - - - +
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Residues in contact with ILE 434 (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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430B GLU 2.9 25.9 + - - +
431B THR* 3.8 4.7 - - - +
433B LEU* 1.3 68.2 - - - +
435B TYR* 1.3 69.1 + - - +
437B ASN* 3.3 3.5 + - - -
438B THR* 2.9 42.8 + - + +
449B VAL* 4.8 7.2 - - + +
452B HIS* 3.7 23.8 - - + +
453B GLN* 3.8 26.0 - - + +
456B PHE* 3.6 35.0 - - + -
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Residues in contact with TYR 435 (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 THR* 2.9 21.8 + - + +
432B TRP* 3.5 24.2 - + - +
434B ILE* 1.3 79.5 - - - +
436B LYS* 1.3 58.4 + - - +
438B THR* 3.2 4.7 + - - -
439B LYS* 2.8 82.6 + - + +
440B LEU* 3.7 30.6 + - + +
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Residues in contact with LYS 436 (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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432B TRP* 2.8 52.6 + - + +
433B LEU* 3.9 14.1 - - + +
435B TYR* 1.3 74.6 - - - +
437B ASN* 1.3 66.7 + - - +
440B LEU* 3.0 42.1 + - + -
441B VAL* 3.2 24.2 - - + +
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Residues in contact with ASN 437 (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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433B LEU* 2.8 38.6 + - - +
434B ILE* 3.3 3.3 + - - +
436B LYS* 1.3 86.6 - - - +
438B THR* 1.3 59.1 + - - +
441B VAL* 3.3 26.1 - - - +
444B ILE* 3.6 19.2 - - - +
445B ASP* 4.5 5.7 + - - +
448B LYS* 3.7 32.5 + - + +
449B VAL* 4.2 16.8 - - + +
452B HIS* 4.1 15.3 + - + -
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Residues in contact with THR 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
434B ILE* 2.9 33.9 + - + +
435B TYR* 3.6 4.2 + - - -
437B ASN* 1.3 76.3 - - - +
439B LYS* 1.3 74.4 + - - +
441B VAL* 4.9 0.7 - - - -
444B ILE* 4.0 27.6 - - + +
449B VAL* 3.6 36.3 - - + -
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Residues in contact with LYS 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B TYR* 2.8 50.8 + - + +
436B LYS 3.6 0.2 + - - -
437B ASN 3.7 0.2 - - - -
438B THR* 1.3 96.9 - - - +
440B LEU* 1.3 69.0 + - + +
441B VAL* 3.5 6.3 + - - +
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Residues in contact with LEU 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432B TRP* 3.7 30.1 - - + -
435B TYR* 3.8 34.3 - - + +
436B LYS* 3.0 20.2 + - + +
439B LYS* 1.3 84.8 - - + +
441B VAL* 1.3 65.9 + - - +
442B LYS* 5.4 1.2 + - - +
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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