Contacts of the strand formed by residues 542 - 545 (chain D) in PDB entry 2DB3
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 VAL 542 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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485D LEU* 4.2 18.4 - - + -
489D ALA* 3.8 27.1 - - + +
492D THR* 3.5 9.0 - - + +
494D VAL* 4.1 11.4 - - + -
509D LEU* 4.4 0.4 - - + -
514D PHE* 4.5 9.9 - - + -
515D PRO* 3.1 5.0 + - + +
516D THR* 3.2 21.7 - - + +
517D THR* 3.1 28.2 + - - +
535D PHE* 4.0 2.2 - - - -
540D MET 3.7 0.4 - - - -
541D LYS* 1.3 87.3 + - + +
543D LEU* 1.3 63.9 + - - +
544D ILE* 3.8 23.3 - - + -
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Residues in contact with LEU 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492D THR 3.0 8.7 + - - +
493D ILE* 3.2 33.6 - - + +
494D VAL 2.7 32.2 + - - -
517D THR* 3.7 9.0 - - + +
518D SER* 3.7 22.4 - - - +
519D ILE* 3.8 15.5 - - + +
531D ALA* 4.7 4.0 - - + +
532D LEU* 4.0 23.3 - - + -
535D PHE* 3.7 34.5 - - + -
542D VAL* 1.3 72.7 - - - +
544D ILE* 1.3 72.2 + - - +
545D ALA* 4.5 0.9 - - + -
549D ALA* 5.2 1.3 - - + -
553D LEU* 6.2 0.2 - - + -
555D ILE* 5.7 2.2 - - + -
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Residues in contact with ILE 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494D VAL* 3.4 30.7 - - + +
496D VAL* 4.0 14.1 - - + -
502D ALA* 3.5 36.1 - - + +
505D LEU* 4.3 7.6 - - + -
506D ALA* 3.9 15.0 - - - +
509D LEU* 3.8 24.0 - - + -
516D THR* 3.7 17.5 - - + -
517D THR 3.1 7.0 + - - +
518D SER* 3.2 5.4 - - - -
519D ILE 3.0 24.4 + - - +
542D VAL* 3.8 9.0 - - + -
543D LEU* 1.3 75.8 - - - +
545D ALA* 1.3 63.2 + - - +
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Residues in contact with ALA 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D ILE* 4.5 9.6 - - + -
494D VAL 2.8 9.3 + - - +
495D PHE* 3.2 13.0 - - + -
496D VAL* 2.8 38.5 + - - +
502D ALA* 4.6 1.3 - - - -
519D ILE* 3.4 27.4 - - + -
543D LEU* 3.9 0.9 + - + -
544D ILE* 1.3 77.1 - - - +
546D THR* 1.3 65.2 + - - +
549D ALA* 3.9 11.9 - - + -
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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