Contacts of the helix formed by residues 464 - 477 (chain A) in PDB entry 3J8B
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 ALA 464 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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456A THR* 5.2 13.8 - - - -
461A PHE* 5.2 0.7 - - - -
463A ASP* 1.3 73.1 - - - +
465A PHE* 1.3 60.7 + - - +
467A LEU* 3.4 9.4 + - - +
468A GLU* 3.3 18.0 + - - +
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Residues in contact with PHE 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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463A ASP* 3.2 4.5 - - + +
464A ALA* 1.3 76.2 - - - +
466A GLN* 1.3 60.1 + - - +
467A LEU 3.1 0.2 - - - -
468A GLU* 3.3 9.4 + - - +
469A ARG* 3.0 25.8 + - - +
600C MET* 4.8 17.5 - - + -
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Residues in contact with GLN 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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461A PHE* 5.1 1.1 - - + -
462A VAL* 4.8 9.4 - - + +
463A ASP* 3.0 28.4 + - + +
465A PHE* 1.3 75.5 - - - +
467A LEU* 1.3 58.1 + - - +
469A ARG* 3.3 9.8 - - - +
470A ALA* 3.0 26.7 + - - +
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Residues in contact with LEU 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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456A THR* 4.8 17.9 - - - -
459A VAL 5.4 1.3 - - - +
461A PHE* 3.4 28.2 - - + +
463A ASP 3.0 5.4 + - - +
464A ALA* 3.5 12.3 - - - +
466A GLN* 1.3 75.2 - - - +
468A GLU* 1.3 65.5 + - - +
470A ALA* 3.2 8.2 + - - +
471A ILE* 3.0 23.1 + - - +
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Residues in contact with GLU 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 ALA 3.3 8.6 + - - +
465A PHE* 3.3 11.6 + - - +
467A LEU* 1.3 74.8 - - - +
469A ARG* 1.3 65.0 + - - +
471A ILE* 3.2 8.1 + - - +
472A VAL* 3.0 23.7 + - - +
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Residues in contact with ARG 469 (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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465A PHE 3.0 13.4 + - - +
466A GLN* 3.3 14.8 - - - +
468A GLU* 1.3 75.3 - - - +
470A ALA* 1.3 59.0 + - - +
472A VAL* 3.3 7.2 + - - +
473A ASP* 3.0 28.2 + - - +
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Residues in contact with ALA 470 (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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436A ILE* 5.3 13.7 - - + -
466A GLN 3.0 13.4 + - - +
467A LEU* 3.2 11.6 + - - +
469A ARG* 1.3 76.0 - - - +
471A ILE* 1.3 58.8 + - - +
473A ASP* 3.2 7.8 + - - +
474A ALA* 2.9 29.8 + - - +
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Residues in contact with ILE 471 (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 LEU* 5.4 9.9 - - + -
467A LEU 3.0 12.8 + - - +
468A GLU* 3.5 11.4 - - - +
470A ALA* 1.3 77.4 - - - +
472A VAL* 1.3 60.5 + - - +
474A ALA* 3.4 8.4 + - - +
475A ALA* 3.1 20.3 + - - +
480A LEU* 5.7 1.2 - - - +
482A VAL* 5.8 2.1 - - - +
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Residues in contact with VAL 472 (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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468A GLU 3.0 12.5 + - - +
469A ARG* 3.7 8.7 - - - +
471A ILE* 1.3 74.2 - - - +
473A ASP* 1.3 60.9 + - - +
475A ALA* 3.0 9.7 + - - +
476A ARG* 2.8 29.1 + - - +
585C TYR* 6.0 6.3 - - + -
588C VAL* 6.1 5.2 - - + -
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Residues in contact with ASP 473 (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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469A ARG 3.0 17.5 + - - +
470A ALA* 3.5 9.2 - - - +
472A VAL* 1.3 78.4 - - - +
474A ALA* 1.3 61.0 + - - +
476A ARG* 3.2 7.4 + - - +
477A HIS* 3.1 26.0 + - - +
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Residues in contact with ALA 474 (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 LEU* 5.5 10.1 - - + +
440A LEU* 4.7 16.6 - - + -
470A ALA 2.9 16.8 + - - +
471A ILE* 3.5 9.9 - - - +
473A ASP* 1.3 76.3 - - - +
475A ALA* 1.3 56.9 + - - +
477A HIS* 3.7 3.6 + - - +
478A CYS 3.3 2.6 + - - -
479A ASP* 2.8 45.8 + - + +
480A LEU* 4.4 7.9 - - + -
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Residues in contact with ALA 475 (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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471A ILE 3.1 12.9 + - - +
472A VAL* 3.0 14.0 + - - +
474A ALA* 1.3 75.7 - - - +
476A ARG* 1.3 59.9 + - - +
478A CYS* 3.0 17.8 + - - +
480A LEU* 3.2 22.1 - - + +
481A GLN* 5.2 0.2 - - - -
482A VAL* 4.8 17.0 - - + +
588C VAL* 5.4 10.8 - - + -
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Residues in contact with ARG 476 (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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472A VAL 2.8 17.2 + - - +
473A ASP* 3.2 8.0 + - - +
475A ALA* 1.3 72.8 - - - +
477A HIS* 1.3 58.0 + - - +
478A CYS* 3.0 5.9 + - - +
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Residues in contact with HIS 477 (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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473A ASP 3.1 16.8 + - - +
474A ALA* 4.2 5.2 - - - +
475A ALA 3.3 0.2 - - - -
476A ARG* 1.3 74.2 - - - +
478A CYS* 1.3 68.8 + - - +
479A ASP* 3.4 5.8 + - + +
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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