Contacts of the helix formed by residues 455 - 467 (chain N) in PDB entry 5L4K
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 GLY 455 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450N HIS* 5.9 0.4 + - - -
453N HIS 3.1 6.4 + - - -
454N GLY* 1.3 72.7 - - - -
456N ASP* 1.3 66.0 + - - +
457N ILE* 3.2 6.4 + - - +
458N ILE* 3.3 16.7 + - - +
459N ASP* 3.8 8.3 - - - +
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Residues in contact with ASP 456 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455N GLY* 1.3 73.5 - - - +
457N ILE* 1.3 62.4 + - + +
458N ILE 3.3 0.2 - - - -
459N ASP* 3.3 11.4 + - - +
460N TYR* 3.0 25.9 + - - +
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Residues in contact with ILE 457 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416N GLU 5.5 0.2 - - - +
420N LEU* 3.8 40.8 - - + -
446N LEU* 4.0 15.7 - - + +
450N HIS* 3.5 55.0 - - + +
454N GLY* 4.6 0.9 - - - -
455N GLY 3.0 7.9 - - - +
456N ASP* 1.3 81.9 - - + +
458N ILE* 1.3 59.0 + - - +
460N TYR* 3.6 4.9 - - + +
461N LEU* 2.9 46.6 + - + +
484N ALA* 4.4 4.0 - - + -
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Residues in contact with ILE 458 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454N GLY* 3.0 37.7 - - - +
455N GLY* 3.8 6.5 - - - +
456N ASP 3.3 0.6 - - - -
457N ILE* 1.3 77.1 - - - +
459N ASP* 1.3 58.8 + - - +
461N LEU* 3.5 3.7 + - - +
462N LEU* 2.9 27.1 + - + +
481N LEU* 4.1 15.7 - - + +
484N ALA* 3.6 25.8 - - + +
485N ALA* 4.3 9.9 - - + -
488N THR* 5.5 3.8 - - + -
490N ARG* 3.7 46.7 - - - +
493N VAL* 4.4 3.4 - - + -
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Residues in contact with ASP 459 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455N GLY 3.8 10.2 - - - +
456N ASP* 3.3 13.1 + - - +
457N ILE 3.3 0.4 - - - -
458N ILE* 1.3 79.3 - - - +
460N TYR* 1.3 66.2 + - - +
462N LEU* 3.0 9.0 + - - +
463N ASN* 2.9 34.9 + - - +
490N ARG* 4.4 14.5 + - - -
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Residues in contact with TYR 460 (chain N).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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420N LEU* 3.8 18.6 - - + -
427N LEU* 3.4 33.1 - - + +
428N PRO* 4.8 3.8 + - - +
443N LEU* 4.7 1.6 - - + -
446N LEU* 3.2 37.0 - - + -
456N ASP 3.0 13.8 + - - +
457N ILE* 3.6 11.7 - - + +
459N ASP* 1.3 77.2 - - - +
461N LEU* 1.3 61.1 + - + +
463N ASN* 3.2 9.7 + - + +
464N GLN* 3.0 60.0 + - + +
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Residues in contact with LEU 461 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443N LEU* 3.9 43.1 - - + +
446N LEU* 4.1 13.2 - - + -
447N GLY 4.5 5.2 - - - +
457N ILE* 2.9 31.1 + - + +
458N ILE 4.0 2.9 - - - +
460N TYR* 1.3 76.0 - - + +
462N LEU* 1.3 58.8 + - - +
464N GLN* 3.1 3.4 + - + +
465N LEU* 2.9 36.1 + - + +
477N GLY 5.2 1.6 - - - +
480N GLY* 3.5 29.6 - - - +
481N LEU* 3.8 19.3 - - + +
484N ALA* 3.8 17.0 - - + -
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Residues in contact with LEU 462 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458N ILE 2.9 15.7 + - - +
459N ASP* 3.0 9.2 + - - +
461N LEU* 1.3 78.6 - - - +
463N ASN* 1.3 57.2 + - - +
465N LEU* 4.3 1.9 - - - +
466N LYS* 2.9 32.0 + - + +
481N LEU* 3.7 24.9 - - + -
490N ARG* 4.4 12.6 - - - +
492N ASP* 4.8 11.7 - - + -
493N VAL* 3.4 37.7 - - + +
496N LEU* 3.9 16.4 - - + +
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Residues in contact with ASN 463 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459N ASP* 2.9 26.4 + - - +
460N TYR* 3.7 10.7 - - + +
462N LEU* 1.3 76.6 - - - +
464N GLN* 1.3 59.9 + - + +
466N LYS* 4.0 7.3 - - - +
467N ASN* 2.7 41.4 + - - +
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Residues in contact with GLN 464 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428N PRO* 2.9 35.8 - - - +
429N LYS* 4.7 18.2 - - - +
443N LEU* 3.5 35.8 - - + +
460N TYR* 3.0 46.8 + - + +
461N LEU* 3.1 8.9 + - - +
463N ASN* 1.3 80.1 + - - +
465N LEU* 1.3 61.0 + - + +
467N ASN* 3.2 17.1 - - - +
468N ALA* 3.4 13.3 - - - +
473N VAL* 4.3 8.0 - - - +
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Residues in contact with LEU 465 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443N LEU* 4.5 2.0 - - + -
461N LEU* 2.9 32.5 + - + +
464N GLN* 1.3 82.0 - - + +
466N LYS* 1.3 66.5 + - - +
467N ASN 3.3 0.4 - - - -
468N ALA* 3.2 16.2 + - + +
473N VAL 4.1 1.8 - - - +
474N ARG* 3.6 43.1 - - + +
477N GLY* 3.6 28.9 - - - +
478N SER* 3.8 15.7 - - - +
481N LEU* 4.3 16.4 - - + -
496N LEU* 4.0 20.8 - - + +
497N LEU* 5.4 2.0 - - + -
500N ASN* 4.9 9.0 + - - +
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Residues in contact with LYS 466 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462N LEU* 2.9 22.1 + - + +
463N ASN* 4.4 7.6 - - - +
464N GLN 3.5 0.2 - - - -
465N LEU* 1.3 79.5 - - - +
467N ASN* 1.3 59.4 + - + +
468N ALA 3.5 4.0 + - - +
496N LEU* 4.1 28.2 - - + +
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Residues in contact with ASN 467 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429N LYS* 4.9 17.8 - - - +
463N ASN* 2.7 32.5 + - - +
464N GLN* 3.2 17.6 - - - +
466N LYS* 1.3 77.3 - - + +
468N ALA* 1.3 62.2 + - - +
469N SER* 3.7 6.4 + - - -
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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