Contacts of the helix formed by residues 466 - 470 (chain B) in PDB entry 5OF4
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 466 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461B LEU* 5.7 2.1 - - - +
463B PRO* 3.5 9.2 + - + +
464B LEU 3.3 0.6 - - - -
465B ASP* 1.3 91.0 - - + +
467B TYR* 1.3 63.8 + - - +
468B PRO* 3.4 1.8 - - - -
469B LYS* 3.8 17.0 + - + +
470B ILE* 4.9 2.4 + - - +
640B LEU* 6.2 0.9 - - + -
647B ARG* 4.4 17.0 - - - +
650B ASP* 3.3 25.4 - - - +
651B PHE* 3.9 18.8 - - + -
654B PHE* 3.7 58.3 - - + -
690B ARG* 4.3 11.4 - - - +
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Residues in contact with TYR 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.3 27.9 + + - -
39B VAL* 4.1 18.2 - - + -
448B PHE* 3.2 28.6 - + - -
456B ILE* 4.8 7.4 - - + -
461B LEU* 5.7 8.8 - - + +
463B PRO 4.6 0.8 + - - -
464B LEU* 3.8 17.7 + - + +
465B ASP 3.4 0.2 - - - -
466B ILE* 1.3 77.8 - - - +
468B PRO* 1.4 63.5 - - + +
469B LYS 3.1 1.6 - - - -
470B ILE* 2.7 52.9 + - + +
471B LEU 3.4 0.5 + - - -
472B ASP* 3.2 43.0 - - + +
474B HIS* 3.3 32.8 - + + +
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Residues in contact with PRO 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B LEU 4.6 1.8 - - - +
465B ASP* 3.3 22.2 - - - +
466B ILE* 3.6 0.7 - - - -
467B TYR* 1.4 91.6 - - + +
469B LYS* 1.3 63.3 + - - -
470B ILE 3.1 0.7 - - - -
471B LEU* 3.3 38.8 - - + +
474B HIS* 5.4 6.5 - - + +
640B LEU* 5.3 0.9 - - - +
643B GLN* 5.6 1.0 - - - +
644B PHE* 3.5 35.6 - - + -
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Residues in contact with LYS 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP* 3.7 18.3 - - + +
244B ILE* 4.1 11.1 - - - +
438B MET 3.3 24.5 + - - +
440B ALA* 3.4 33.7 + - + +
441B SER 4.4 1.6 + - - -
466B ILE* 3.8 25.4 + - + +
467B TYR 2.9 1.6 + - - -
468B PRO* 1.3 77.9 - - - +
470B ILE* 1.3 61.5 + - + +
471B LEU* 3.7 6.6 + - - +
636B ARG* 3.9 26.7 - - - +
640B LEU* 3.6 40.1 - - + +
644B PHE* 5.2 0.6 - - - -
651B PHE* 4.1 14.1 - - + -
654B PHE* 6.2 0.2 - - + -
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Residues in contact with ILE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ILE* 4.0 32.3 - - + -
240B ASP* 5.7 2.2 - - + +
440B ALA* 4.6 13.7 - - + -
441B SER* 4.1 12.1 - - - -
444B ILE* 3.6 31.0 - - + -
448B PHE* 4.3 0.4 - - + -
456B ILE* 4.5 11.7 - - + -
466B ILE 5.5 1.8 - - - +
467B TYR* 2.7 44.8 + - + +
469B LYS* 1.3 79.5 - - + +
471B LEU* 1.3 63.3 + - - +
472B ASP* 3.2 22.3 + - - +
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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
------------------------------------------------------------
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