Contacts of the helix formed by residues 458 - 468 (chain A) in PDB entry 5JXL
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 ASP 458 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLN* 2.6 30.2 + - - +
457A THR* 1.3 81.0 - - - +
459A PRO* 1.3 64.4 - - + +
460A ALA* 4.5 5.2 - - + +
461A SER* 2.5 11.8 + - - +
462A ALA* 2.4 35.3 + - - +
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Residues in contact with PRO 459 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PRO* 4.4 8.3 - - + -
457A THR 4.1 0.9 - - - +
458A ASP* 1.3 90.0 - - + +
460A ALA* 1.3 59.4 + - + +
462A ALA* 3.6 10.7 - - + +
463A ASN* 2.9 38.5 + - - +
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Residues in contact with ALA 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438A PRO* 3.6 26.2 - - + +
439A MET* 3.1 13.9 - - - +
440A ILE* 3.0 38.0 + - + +
458A ASP* 3.2 3.7 - - + -
459A PRO* 1.3 84.0 - - + +
461A SER* 1.3 59.3 + - - +
464A TYR* 3.7 1.7 + - - +
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Residues in contact with SER 461 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440A ILE* 3.7 15.0 - - - -
447A ALA 4.7 0.9 - - - -
448A PHE* 3.4 34.3 - - - -
449A GLN* 3.7 7.3 + - - -
457A THR* 2.8 18.0 + - - -
458A ASP* 2.5 35.8 + - - +
460A ALA* 1.3 79.9 - - - +
462A ALA* 1.3 57.8 + - - +
463A ASN 3.4 0.4 - - - -
464A TYR* 3.3 3.3 + - - +
465A TRP* 2.9 22.9 + - - +
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Residues in contact with ALA 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ARG 4.9 0.4 - - - -
456A PRO* 3.1 24.5 - - + +
457A THR* 3.6 6.1 - - - -
458A ASP 2.4 24.3 + - - +
459A PRO* 3.2 13.6 + - + +
461A SER* 1.3 66.9 + - - +
463A ASN* 1.3 67.0 + - - +
465A TRP* 3.0 16.5 + - - +
466A ASP* 3.2 18.5 + - - -
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Residues in contact with ASN 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A PRO* 3.5 28.5 - - - +
438A PRO* 2.8 32.5 + - - +
439A MET* 3.9 15.9 - - + +
459A PRO* 2.9 16.5 + - - +
462A ALA* 1.3 78.9 - - - +
464A TYR* 1.3 58.0 + - - +
466A ASP* 3.4 8.2 + - - +
467A ALA* 2.9 29.9 + - - +
471A SER* 5.0 0.2 + - - -
472A LEU* 5.4 0.9 - - - +
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Residues in contact with TYR 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A MET* 3.9 9.4 - - - +
440A ILE* 3.7 39.9 - - + +
442A PRO* 5.6 4.8 - - + +
448A PHE* 3.8 26.7 - + + -
460A ALA 3.7 13.9 + - - +
461A SER 3.3 8.2 + - - +
462A ALA 3.2 0.4 - - - -
463A ASN* 1.3 77.7 - - - +
465A TRP* 1.3 63.7 + - - +
467A ALA* 3.6 7.3 + - - +
468A ILE* 3.3 44.4 - - + +
496A TYR* 3.8 24.5 - + - -
520A GLN* 4.3 10.9 + - - -
542A THR 4.8 1.4 + - - -
543A ILE* 4.1 7.3 - - - +
544A PRO* 3.9 20.9 - - + +
547A ALA* 3.6 13.9 - - + -
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Residues in contact with TRP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448A PHE* 4.5 7.6 - + + -
450A PRO 5.7 1.3 - - - -
453A GLY 4.7 5.9 + - - -
455A ARG* 3.3 64.3 - - + +
461A SER 2.9 13.0 + - - +
462A ALA* 3.0 12.7 + - - +
464A TYR* 1.3 80.2 - - - +
466A ASP* 1.3 84.2 + - - +
468A ILE* 3.2 13.9 + - - +
469A GLN* 2.8 50.6 + - - +
546A ASN 3.8 9.5 + - - -
547A ALA* 4.2 4.5 - - - -
548A GLY 3.1 39.3 + - - +
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Residues in contact with ASP 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455A ARG* 4.0 14.2 + - - -
462A ALA* 3.2 11.5 + - - +
463A ASN* 4.0 10.3 - - - +
465A TRP* 1.3 104.9 - - - +
467A ALA* 1.3 59.9 + - - +
469A GLN* 3.0 21.1 + - - +
471A SER* 2.7 32.3 + - - +
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Residues in contact with ALA 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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439A MET* 4.1 16.8 - - - -
463A ASN 2.9 18.8 + - - +
464A TYR* 3.7 11.9 - - + +
465A TRP 3.1 0.4 - - - -
466A ASP* 1.3 79.5 - - - +
468A ILE* 1.3 58.2 + - + +
469A GLN 2.9 14.2 - - - +
471A SER* 3.3 10.4 + - - -
472A LEU* 4.2 12.1 + - + -
496A TYR* 4.0 33.8 - - + +
517A ASP* 4.9 1.2 - - - +
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Residues in contact with ILE 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464A TYR* 3.3 55.2 - - + +
465A TRP 3.2 7.1 + - - +
466A ASP 3.1 0.8 - - - -
467A ALA* 1.3 76.9 - - + +
469A GLN* 1.3 64.3 + - - +
496A TYR* 5.5 9.6 - - + -
512A THR 4.0 0.5 - - - +
513A PHE* 3.5 47.1 - - + +
514A ASP 4.7 1.4 + - - -
517A ASP* 4.8 5.7 - - - +
518A ILE* 4.2 14.8 - - + -
543A ILE* 4.1 9.6 - - + -
547A ALA* 3.7 16.6 - - + -
548A GLY* 4.4 7.6 - - - +
549A ALA 4.2 6.5 - - - +
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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