Contacts of the strand formed by residues 560 - 563 (chain F) in PDB entry 2VKX
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 560 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514E THR* 5.6 3.6 - - + -
562E THR* 5.1 4.7 - - + -
564E VAL* 4.5 7.6 - - + -
516F GLN* 4.5 21.1 - - + +
517F VAL 3.1 25.4 - - - +
518F GLN* 3.8 23.1 - - + +
519F PHE* 4.7 1.3 - - - -
555F ALA* 3.7 6.7 - - - +
558F GLU* 2.9 48.7 - - + +
559F GLY* 1.3 84.7 - - - +
561F VAL* 1.3 71.5 + - - +
562F THR* 4.2 15.9 - - - +
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Residues in contact with VAL 561 (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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515F ALA 3.7 0.2 - - - +
516F GLN* 3.5 2.3 - - - -
517F VAL* 2.8 56.2 + - + +
519F PHE* 3.4 31.0 - - + -
533F TYR* 5.5 1.6 - - + -
535F ALA* 5.3 1.3 - - + -
550F TYR* 4.2 35.4 - - + -
555F ALA* 4.2 14.6 - - + -
560F ILE* 1.3 77.3 - - - +
562F THR* 1.3 64.6 + - - +
563F ILE* 4.2 2.8 + - + -
576F LEU* 4.3 14.8 - - + -
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Residues in contact with THR 562 (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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516E GLN* 4.3 10.8 - - - +
558E GLU* 3.7 21.5 + - - +
560E ILE* 4.8 4.0 - - + -
562E THR* 4.3 10.0 + - - +
514F THR* 4.0 12.1 - - - -
515F ALA 3.3 10.3 - - - +
516F GLN* 3.9 15.6 + - - +
550F TYR* 2.6 29.6 + - - -
560F ILE* 4.2 10.2 - - - +
561F VAL* 1.3 79.2 + - - +
563F ILE* 1.3 68.3 + - - +
564F VAL* 3.8 14.8 + - + +
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Residues in contact with ILE 563 (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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514F THR* 3.3 6.1 - - - -
515F ALA* 3.2 38.0 + - + +
517F VAL* 4.6 9.9 - - + -
535F ALA* 4.6 12.6 - - + -
537F TRP* 3.9 45.8 - - + -
550F TYR* 3.5 11.2 - - + +
561F VAL* 4.2 3.1 - - + -
562F THR* 1.3 74.7 - - - +
564F VAL* 1.3 60.0 + - - +
566F LEU* 4.0 9.0 - - + -
574F VAL* 4.6 13.2 - - + -
593F PHE* 3.5 34.5 - - + -
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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