Contacts of the helix formed by residues 456 - 473 (chain A) in PDB entry 4DKK
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 456 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A PHE* 3.4 15.9 - - + -
454A GLY 3.2 0.8 - - - -
455A LYS* 1.3 100.6 + - - +
457A VAL* 1.3 65.6 + - - +
458A GLU* 3.5 7.3 + - - +
459A SER* 2.6 46.1 + - - -
460A CYS* 3.4 20.6 + - - -
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Residues in contact with VAL 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A ASP* 3.6 26.2 - - + +
436A PHE* 3.4 34.5 - - + -
438A SER* 4.2 2.7 - - - +
456A ASP* 1.3 75.5 - - - +
458A GLU* 1.3 65.1 + - - +
460A CYS* 3.1 7.6 + - - +
461A HIS* 2.9 46.6 + - + +
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Residues in contact with GLU 458 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 3.2 32.5 + - - +
409A SER* 3.2 21.8 + - - -
456A ASP* 3.3 8.1 + - - +
457A VAL* 1.3 79.3 - - - +
459A SER* 1.3 55.6 + - - +
461A HIS* 3.1 16.0 + - - +
462A ASP* 2.9 47.9 + - - +
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Residues in contact with SER 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A ILE 4.5 5.3 - - - +
454A GLY* 4.6 10.3 - - - -
455A LYS* 4.1 12.7 + - - -
456A ASP* 2.6 35.8 + - - -
458A GLU* 1.3 74.8 - - - +
460A CYS* 1.3 64.1 + - - +
462A ASP* 3.3 6.7 + - - +
463A MET 3.0 19.1 + - - -
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Residues in contact with CYS 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436A PHE* 3.2 48.7 - - - -
437A VAL 3.9 1.3 - - - -
438A SER* 3.3 21.3 - - - +
452A GLY* 3.6 21.7 - - - +
453A ILE 3.4 4.7 + - - -
454A GLY 3.4 14.6 - - - -
456A ASP 3.4 4.5 + - - -
457A VAL* 3.1 7.1 + - - +
459A SER* 1.3 76.3 - - - +
461A HIS* 1.3 64.6 + - - +
463A MET 3.4 0.5 + - - -
464A ALA* 3.0 25.8 + - - +
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Residues in contact with HIS 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A SER* 4.7 2.2 - - - -
425A TYR* 3.4 58.8 - + + +
427A ASP* 2.8 30.7 + - - -
438A SER* 3.6 7.6 - - - -
457A VAL* 2.9 27.3 + - + +
458A GLU* 3.1 26.9 + - - +
460A CYS* 1.3 77.6 - - - +
462A ASP* 1.3 57.7 + - - +
464A ALA* 3.3 2.0 + - - +
465A ALA* 2.9 32.8 + - - +
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Residues in contact with ASP 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407A ARG* 3.5 17.2 + - - +
408A PRO* 3.4 26.5 - - + +
409A SER* 2.7 36.2 + - - +
458A GLU* 2.9 31.9 + - - +
459A SER* 3.9 7.0 - - - +
460A CYS 3.3 0.4 - - - -
461A HIS* 1.3 76.9 - - - +
463A MET 1.3 50.5 + - - +
466A LEU* 2.9 36.0 + - - +
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Residues in contact with MET 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451A HIS 4.2 2.2 - - - -
452A GLY* 4.7 3.1 - - - -
459A SER 3.0 15.8 + - - -
460A CYS 3.4 0.8 + - - -
462A ASP* 1.3 74.2 + - - +
464A ALA* 1.3 60.4 - - - +
466A LEU* 3.4 6.4 - - - +
467A ASN* 3.1 29.9 - - - +
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Residues in contact with ALA 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425A TYR* 4.6 2.2 - - + -
438A SER* 4.9 2.7 - - - +
439A LEU 5.1 0.2 - - - -
440A ILE* 3.6 28.6 - - + +
450A SER* 4.1 0.2 - - - -
451A HIS* 3.3 31.1 + - - +
452A GLY* 3.8 0.9 - - - +
460A CYS 3.0 19.0 + - - +
461A HIS* 3.7 5.6 - - - +
463A MET 1.3 73.8 - - - +
465A ALA* 1.3 63.5 + - - +
467A ASN* 3.2 6.8 + - - +
468A ILE* 3.1 24.6 + - - +
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Residues in contact with ALA 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 3.7 6.7 - - - +
409A SER* 3.7 24.7 - - - +
412A LEU* 3.9 10.7 - - + +
425A TYR* 3.6 17.9 - - - +
440A ILE* 3.9 10.0 - - - +
461A HIS 2.9 17.9 + - - +
462A ASP 3.9 0.4 - - - +
464A ALA* 1.3 73.7 - - - +
466A LEU* 1.3 61.8 + - - +
468A ILE* 3.2 3.5 + - - +
469A LEU* 2.8 32.7 + - - +
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 3.7 21.2 - - + +
411A GLN* 5.8 1.3 - - - +
462A ASP 2.9 18.8 + - - +
463A MET 3.5 6.5 - - - +
464A ALA 3.3 0.2 - - - -
465A ALA* 1.3 77.4 - - - +
467A ASN* 1.3 64.2 + - - +
469A LEU* 3.3 10.1 + - + +
470A LYS* 2.9 53.3 + - + +
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Residues in contact with ASN 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A SER* 3.3 21.0 + - - +
451A HIS* 3.2 32.7 + - - -
463A MET 3.1 13.3 - - - +
464A ALA 3.2 4.0 + - - +
466A LEU* 1.3 79.3 - - - +
468A ILE* 1.3 63.1 + - - +
470A LYS* 3.4 15.5 + - - +
471A LEU* 3.0 22.2 + - - +
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Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 3.9 10.8 - - + -
440A ILE* 3.7 16.8 - - + -
442A CYS* 3.4 27.4 - - + -
448A LEU* 3.9 37.5 - - + +
449A ILE 4.7 0.7 - - - -
450A SER* 3.8 18.8 - - - +
464A ALA 3.1 14.4 + - - +
465A ALA 3.2 6.7 + - - +
467A ASN* 1.3 73.5 - - - +
469A LEU* 1.3 59.6 + - - +
471A LEU* 3.1 9.3 + - + +
472A LEU* 2.9 48.2 + - + +
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Residues in contact with LEU 469 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A PRO* 3.6 31.2 - - + +
411A GLN* 3.7 26.9 - - + +
412A LEU* 4.0 21.1 - - + +
415A LEU* 3.8 29.2 - - + -
465A ALA 2.8 18.2 + - - +
466A LEU* 3.7 11.2 - - + +
468A ILE* 1.3 76.4 - - - +
470A LYS* 1.3 56.2 + - + +
472A LEU* 3.4 5.4 + - + +
473A SER* 2.8 35.6 + - - +
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Residues in contact with LYS 470 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466A LEU* 2.9 49.3 + - + +
467A ASN* 3.7 13.5 + - - +
469A LEU* 1.3 75.9 - - + +
471A LEU* 1.3 64.4 + - - +
473A SER* 3.3 11.2 + - - -
474A GLU 3.5 6.9 + - - -
475A LEU* 3.6 33.2 + - + +
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Residues in contact with LEU 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A LEU* 3.7 41.1 - - + -
467A ASN 3.0 14.6 + - - +
468A ILE* 3.5 13.2 - - + +
470A LYS* 1.3 75.9 - - - +
472A LEU* 1.3 63.5 + - + +
474A GLU* 3.0 18.9 + - - +
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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412A LEU* 4.4 1.6 - - + -
415A LEU* 3.8 19.7 - - + -
421A PHE* 3.8 33.0 - - + -
442A CYS* 5.7 0.4 - - + -
448A LEU* 3.7 24.0 - - + -
468A ILE* 2.9 35.2 + - + +
469A LEU* 3.9 4.7 - - - +
471A LEU* 1.3 76.2 - - - +
473A SER* 1.3 60.0 + - - +
474A GLU* 3.2 13.4 + - - +
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Residues in contact with SER 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 2.8 23.2 + - - +
470A LYS 3.5 7.6 - - - -
471A LEU 3.1 0.4 - - - -
472A LEU* 1.3 74.0 - - - +
474A GLU* 1.3 71.6 + - - +
475A LEU* 3.6 25.8 - - - +
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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
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Atomic class I II III IV V VI VII VIII
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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