Contacts of the helix formed by residues 466 - 477 (chain A) in PDB entry 6BFN
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 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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463A ASP 3.0 12.9 + - - +
464A ALA 3.0 0.8 + - - -
465A TRP* 1.3 97.8 - - + +
467A ALA* 1.3 65.1 + - - +
468A PRO* 3.5 0.9 - - - -
469A ILE* 3.4 6.5 + - - +
470A ALA* 3.0 24.1 + - - +
495A GLN* 4.2 14.8 - - + +
498A CYS* 3.6 28.2 - - + -
499A CYS* 4.8 2.7 - - - -
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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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463A ASP 4.0 1.2 + - - -
464A ALA* 2.9 19.5 + - - +
466A ALA* 1.3 79.0 - - - +
468A PRO* 1.4 67.9 - - + +
470A ALA* 3.3 6.1 + - - +
471A MET* 3.1 20.1 + - - +
491A LEU* 5.3 1.0 - - - +
495A GLN* 4.4 14.1 - - - +
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Residues in contact with PRO 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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445A ALA* 5.0 8.1 - - + -
447A VAL* 4.1 21.3 - - + -
464A ALA 3.8 4.3 - - - +
465A TRP* 3.5 17.0 - - - +
467A ALA* 1.4 94.5 - - + +
469A ILE* 1.3 64.1 + - + +
471A MET* 3.0 19.6 + - + +
472A GLN* 3.0 18.4 + - - +
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Residues in contact with ILE 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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438A VAL* 4.1 13.9 - - + +
441A GLU* 4.0 22.2 - - + -
442A ALA* 3.7 30.3 - - + +
445A ALA* 5.2 3.6 - - + -
447A VAL* 3.8 19.3 - - + -
465A TRP* 3.7 37.0 - - + +
466A ALA* 3.6 7.0 - - - +
467A ALA 3.3 0.2 - - - -
468A PRO* 1.3 77.4 - - + +
470A ALA* 1.3 64.1 + - - +
472A GLN* 2.9 12.9 + - - +
473A ILE* 2.9 28.2 + - + +
498A CYS* 3.7 16.6 - - - -
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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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466A ALA 3.0 13.8 + - - +
467A ALA* 3.6 9.4 - - - +
469A ILE* 1.3 74.6 - - - +
471A MET* 1.3 53.6 + - - +
473A ILE* 3.0 15.9 + - - +
474A TYR* 2.7 34.8 + - - +
490A GLY 5.5 0.3 - - - +
491A LEU* 4.0 17.2 - - + +
494A GLY* 3.9 4.7 - - - -
495A GLN* 3.6 31.2 - - + +
498A CYS* 4.3 1.1 - - - -
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Residues in contact with MET 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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467A ALA 3.1 11.1 + - - +
468A PRO* 3.0 15.1 + - + +
470A ALA* 1.3 74.8 - - - +
472A GLN* 1.3 62.3 + - - +
474A TYR* 3.0 8.8 + - + +
475A LYS* 2.8 67.1 + - + +
491A LEU* 3.7 37.2 - - + +
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Residues in contact with GLN 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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441A GLU* 3.4 25.7 - - + +
444A GLU* 4.5 4.0 - - - +
445A ALA* 5.4 10.3 - - + -
468A PRO 3.0 15.9 + - - +
469A ILE* 2.9 11.8 + - - +
471A MET* 1.3 85.6 - - - +
473A ILE* 1.3 63.8 + - - +
475A LYS* 3.0 10.1 + - - +
476A LYS* 2.9 55.7 + - - +
477A HIS* 4.5 0.2 - - - -
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Residues in contact with ILE 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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415A LEU* 4.2 28.7 - - + -
418A LEU* 4.7 10.1 - - + -
419A ALA* 6.3 1.1 - - + -
437A LEU* 4.6 8.7 - - + -
438A VAL* 4.9 6.7 - - + -
441A GLU* 4.9 4.5 - - + -
469A ILE* 2.9 24.1 + - + +
470A ALA* 3.3 14.4 - - - +
472A GLN* 1.3 72.9 - - - +
474A TYR* 1.3 62.9 + - - +
476A LYS 3.0 0.2 + - - -
477A HIS* 2.9 53.0 + - + -
478A LEU* 3.7 19.8 + - + +
494A GLY* 4.5 10.1 - - - +
498A CYS* 4.3 17.3 - - - -
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Residues in contact with TYR 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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470A ALA 2.7 12.3 + - - +
471A MET* 3.4 10.5 - - - +
473A ILE* 1.3 78.2 - - - +
475A LYS* 1.3 89.5 + - + +
476A LYS 3.5 0.2 + - - -
478A LEU* 3.7 42.3 - - + +
485A CYS* 2.7 32.8 + - + -
486A PRO 4.2 2.0 - - - -
487A PRO* 3.5 36.0 - - + +
490A GLY* 3.9 19.3 - - - +
491A LEU* 3.7 21.5 - - + -
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Residues in contact with LYS 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 MET* 2.8 42.6 + - + +
472A GLN* 3.0 12.5 + - - +
474A TYR* 1.3 96.2 - - + +
476A LYS* 1.3 68.5 + - + +
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Residues in contact with LYS 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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441A GLU* 3.0 38.2 + - - -
444A GLU* 3.5 18.4 + - - -
472A GLN* 2.9 37.8 + - - +
473A ILE 3.0 1.0 + - - -
475A LYS* 1.3 90.9 - - + +
477A HIS* 1.3 77.7 + - + +
478A LEU 3.4 5.5 + - - +
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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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419A ALA* 3.2 28.3 - - + +
421A GLN* 5.4 0.5 - - - +
437A LEU* 3.7 41.0 - - + +
441A GLU* 2.8 29.8 + - - -
472A GLN 4.3 0.7 - - - -
473A ILE* 2.9 39.7 + - + +
476A LYS* 1.3 88.3 - - + +
478A LEU* 1.3 64.6 + - - -
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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