Contacts of the strand formed by residues 457 - 461 (chain F) in PDB entry 3PRJ
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 PHE 457 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425F TYR* 3.6 25.4 - + + -
428F ILE* 4.3 8.7 - - + -
429F HIS* 3.7 25.8 - + + -
432F MET* 3.8 16.2 - - - -
436F ALA* 3.5 32.1 - - + -
438F ILE* 3.6 35.4 - - + -
452F LEU* 2.9 46.8 + - + +
453F GLN* 3.8 21.7 - - - +
455F ILE* 4.3 6.5 - - + -
456F GLY* 1.3 79.8 - - - +
458F GLN* 1.3 65.6 + - - +
459F ILE* 3.7 4.2 + - + -
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Residues in contact with GLN 458 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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435F PRO* 4.8 13.4 - - + +
436F ALA 2.8 10.6 + - - +
437F PHE* 3.3 43.7 - - + -
438F ILE 3.0 24.9 + - - +
453F GLN* 5.8 0.2 - - - -
456F GLY 3.8 2.6 + - - +
457F PHE* 1.3 72.7 - - - +
459F ILE* 1.3 59.5 + - - +
460F GLU* 4.0 3.5 + - - +
466F VAL* 4.0 24.0 - - - +
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Residues in contact with ILE 459 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438F ILE* 3.7 28.7 - - + +
440F ASP* 4.7 7.6 - - + -
445F LEU* 4.6 7.9 - - + -
449F HIS* 3.6 38.5 - - + +
452F LEU* 4.5 19.7 - - + -
453F GLN* 3.8 43.5 + - + +
457F PHE* 4.0 11.4 - - + +
458F GLN* 1.3 75.6 - - - +
460F GLU* 1.3 70.8 + - - +
461F THR* 5.3 1.0 - - - +
466F VAL* 4.4 12.6 - - - +
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Residues in contact with GLU 460 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F PHE* 5.3 1.1 - - - -
317F ARG* 3.3 28.8 + - - +
321F SER* 3.2 24.1 + - - -
437F PHE* 4.9 7.7 - - + -
438F ILE 3.0 9.4 + - - +
439F PHE* 3.3 25.4 - - + -
440F ASP* 2.9 23.0 + - - +
458F GLN* 4.9 5.2 + - - +
459F ILE* 1.3 81.6 - - - +
461F THR* 1.3 61.0 + - - +
465F LYS* 5.0 0.3 - - - -
466F VAL* 3.1 42.1 + - + +
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Residues in contact with THR 461 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F PHE* 5.4 1.6 - - - -
317F ARG* 2.7 22.6 + - - +
440F ASP* 3.1 27.9 + - - +
443F ARG* 3.1 28.1 - - - +
446F ASP* 4.6 0.2 + - - -
449F HIS* 3.9 31.0 - - + +
459F ILE* 5.3 1.1 - - - +
460F GLU* 1.3 76.7 - - - +
462F ILE* 1.3 67.9 + - - +
464F LYS* 3.4 36.9 + - + +
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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