Contacts of the helix formed by residues 447 - 451 (chain B) in PDB entry 4OL0
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 ILE 447 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373B LEU* 5.9 0.7 - - + -
407B VAL* 5.0 7.6 - - + +
411B ILE* 3.9 32.8 - - + -
416B SER* 3.1 36.6 - - - +
419B CYS* 4.0 16.8 - - - -
420B PHE* 4.7 6.7 - - + +
423B LEU* 4.1 5.8 - - + -
443B ILE* 3.3 35.9 - - + +
444B MET* 3.0 4.9 + - - +
446B ALA* 1.3 86.1 - - + +
448B ALA* 1.3 65.7 + - - +
449B LYS 3.3 2.5 - - - -
450B SER* 2.8 21.9 + - - -
451B VAL* 3.6 6.2 - - + +
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Residues in contact with ALA 448 (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 PHE* 4.4 8.3 - - + -
444B MET 2.9 15.8 + - - +
445B ALA 3.9 1.0 + - - +
446B ALA 3.8 0.4 - - - -
447B ILE* 1.3 76.0 - - - +
449B LYS* 1.3 62.3 + - - +
450B SER 3.1 1.4 + - - -
451B VAL* 3.2 26.2 + - - +
459B LEU* 5.7 2.3 - - - +
484B LEU* 4.2 5.6 - - + -
487B GLU* 3.7 29.2 - - + +
488B MET* 4.0 18.8 - - + +
491B VAL* 5.8 3.3 - - - +
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Residues in contact with LYS 449 (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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445B ALA 5.2 0.2 + - - -
447B ILE 3.1 1.4 + - - -
448B ALA* 1.3 78.2 - - - +
450B SER* 1.3 60.6 + - - +
451B VAL 3.3 4.5 - - - +
487B GLU* 3.3 38.2 + - - +
489B SER* 4.4 4.9 - - - -
490B GLU* 3.7 36.3 + - + +
525B ASN* 3.4 36.2 + - - +
529B VAL* 4.6 0.2 - - - +
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Residues in contact with SER 450 (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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408B LYS* 5.1 6.1 + - - +
411B ILE* 4.5 17.2 - - - +
416B SER* 3.3 22.6 + - - -
446B ALA 5.2 1.9 + - - -
447B ILE* 2.8 16.4 + - - -
449B LYS* 1.3 79.4 - - - +
451B VAL* 1.3 62.6 - - - +
452B ASP 3.8 1.2 + - - -
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Residues in contact with VAL 451 (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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416B SER* 3.9 12.8 - - - +
417B MET* 3.8 15.7 - - + +
420B PHE* 4.1 26.5 - - + -
447B ILE 3.6 11.0 - - - +
448B ALA* 3.2 24.1 + - - +
449B LYS 4.3 4.5 - - - +
450B SER* 1.3 81.1 - - - +
452B ASP* 1.3 77.1 + - - +
453B PRO* 3.5 6.8 - - - +
455B ASN* 3.8 20.0 - - - +
459B LEU* 3.9 17.0 - - + +
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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