Contacts of the helix formed by residues 413 - 419 (chain B) in PDB entry 2JED
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 LYS 413 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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411B LEU 3.7 1.4 + - - -
412B LYS* 1.3 70.4 - - - +
414B ASP* 1.3 61.6 + - - +
416B VAL* 3.4 5.6 + - - +
417B LEU* 3.1 25.6 + - - +
449B GLN* 2.7 29.8 + - - -
450B THR 2.8 25.0 + - - -
451B LYS 3.6 14.8 - - - +
452B GLU* 2.9 20.1 + - - +
453B ASN 3.7 4.3 - - - -
454B LEU* 3.7 30.7 - - + +
686B MET* 3.9 18.9 - - + +
688B GLN* 2.7 28.6 + - - +
691B PHE* 3.7 26.4 - - + -
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Residues in contact with ASP 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LYS* 4.2 4.3 - - + -
413B LYS* 1.3 77.4 - - - +
415B VAL* 1.3 65.4 + - + +
417B LEU* 3.4 5.4 + - - +
418B MET* 3.2 40.6 + - - +
452B GLU 4.5 0.8 + - - -
680B ARG* 3.2 38.2 + - - +
682B LEU* 3.9 23.4 - - + +
684B ASN 4.7 6.2 - - - +
686B MET* 4.4 9.9 - - + +
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Residues in contact with VAL 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LYS* 3.2 34.0 + - + +
414B ASP* 1.3 80.7 - - + +
416B VAL* 1.3 67.7 + - + +
418B MET* 3.2 19.0 + - + +
419B ASP* 2.9 41.9 + - - +
680B ARG* 5.2 1.1 - - - +
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Residues in contact with VAL 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
411B LEU* 4.0 36.1 - - + -
412B LYS 3.0 19.6 + - - +
413B LYS* 3.6 9.9 - - - +
415B VAL* 1.3 74.7 - - - +
417B LEU* 1.3 58.4 + - - +
419B ASP* 3.5 5.1 + - - -
420B ASP 3.1 6.9 + - - -
421B ASP* 2.9 58.4 + - + +
422B VAL* 3.7 5.6 - - + +
425B THR* 3.8 7.0 - - - +
454B LEU* 4.4 4.9 - - + -
691B PHE* 3.8 20.6 - - + -
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Residues in contact with LEU 417 (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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413B LYS 3.1 17.0 + - - +
414B ASP* 3.8 6.3 - - - +
416B VAL* 1.3 76.2 - - - +
418B MET* 1.3 59.8 + - + +
420B ASP* 3.2 18.9 + - - +
422B VAL* 4.1 13.7 - - + -
686B MET* 4.9 18.4 - - + -
687B ASP 6.2 0.2 - - - +
690B MET* 3.9 25.8 - - - -
691B PHE* 5.7 0.7 - - + -
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Residues in contact with MET 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B ASP* 3.2 44.3 + - - +
415B VAL* 3.2 18.2 + - + +
417B LEU* 1.3 78.3 - - + +
419B ASP* 1.3 61.2 + - - +
420B ASP* 3.2 2.8 + - - +
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Residues in contact with ASP 419 (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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415B VAL* 2.9 37.7 + - - +
416B VAL* 3.9 5.1 + - - +
418B MET* 1.3 76.6 - - - +
420B ASP* 1.3 69.6 + - - +
421B ASP* 3.4 26.5 - - + +
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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