Contacts of the helix formed by residues 458 - 472 (chain A) in PDB entry 3BNF
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
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Residue Dist Surf HB Arom Phob DC
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456A LYS 3.8 4.2 + - - +
457A VAL* 1.3 70.2 - - - +
459A MET* 1.3 60.8 - - - +
460A GLU* 4.0 9.7 + - - +
461A ALA* 3.1 39.3 + - + +
462A PHE* 3.1 25.3 + - + -
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Residues in contact with MET 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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94A LYS* 3.8 17.3 - - - +
113A LEU* 4.0 17.7 - - + -
448A LYS* 3.9 21.8 - - + +
449A GLU* 5.9 2.5 - - + +
452A GLN* 3.1 42.6 - - - +
457A VAL* 3.0 11.9 + - + +
458A ASP* 1.3 73.0 - - - +
460A GLU* 1.3 53.4 + - + +
462A PHE* 2.9 11.2 + - + +
463A ILE* 2.7 56.3 + - + +
500A SER* 5.9 1.6 - - - -
501A TYR* 6.1 0.9 - - - -
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Residues in contact with GLU 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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458A ASP* 4.1 9.2 - - - +
459A MET* 1.3 77.9 - - + +
461A ALA* 1.3 61.6 + - - +
463A ILE* 3.4 10.3 + - + +
464A ALA* 3.0 24.6 + - - +
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Residues in contact with ALA 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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458A ASP* 3.1 35.0 + - + +
460A GLU* 1.3 76.7 - - - +
462A PHE* 1.3 66.5 + - + +
464A ALA* 3.3 7.2 + - - +
465A GLU* 3.2 25.6 + - - +
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Residues in contact with PHE 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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94A LYS* 3.6 45.1 - - + -
113A LEU* 4.0 16.8 - - + +
456A LYS 5.6 0.7 - - - -
457A VAL* 3.9 13.7 - - + -
458A ASP* 3.1 40.8 + - + -
459A MET* 2.9 11.7 + - - +
461A ALA* 1.3 84.3 - - + +
463A ILE* 1.3 57.1 + - - +
465A GLU* 3.6 23.0 + - - +
466A LYS* 2.9 28.8 + - - +
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Residues in contact with ILE 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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113A LEU* 4.0 20.4 - - + -
459A MET* 2.7 48.4 + - + +
460A GLU* 3.8 8.7 - - + +
462A PHE* 1.3 71.9 - - - +
464A ALA* 1.3 65.2 + - - +
466A LYS* 3.1 2.5 + - - +
467A LEU* 2.9 36.8 + - + +
501A TYR* 3.6 45.3 - - + +
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Residues in contact with ALA 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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460A GLU 3.0 17.2 + - - +
461A ALA* 3.7 7.4 - - - +
462A PHE 3.3 0.4 - - - -
463A ILE* 1.3 80.2 - - - +
465A GLU* 1.3 61.9 + - - +
467A LEU* 3.3 9.9 + - - +
468A LYS* 3.2 23.7 + - - +
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Residues in contact with GLU 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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94A LYS* 5.6 0.3 + - - -
116A GLY* 4.8 5.4 - - - -
117A ALA* 3.2 41.2 + - + +
461A ALA 3.2 15.3 + - - +
462A PHE* 3.7 24.8 - - - +
464A ALA* 1.3 77.7 - - - +
466A LYS* 1.3 60.8 + - - +
468A LYS* 3.5 11.7 - - - +
469A PHE 3.3 12.3 + - - -
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Residues in contact with LYS 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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110A ILE 2.8 28.5 + - - -
111A ASN* 3.2 15.5 - - - +
112A THR 3.0 8.3 + - - +
113A LEU* 3.8 16.2 - - + -
115A THR* 3.0 18.0 + - - -
116A GLY* 2.7 33.0 + - - +
117A ALA* 4.2 4.3 - - - -
462A PHE 2.9 18.9 + - - +
463A ILE* 3.3 5.8 - - - +
465A GLU* 1.3 76.3 - - - +
467A LEU* 1.3 63.7 + - - +
469A PHE* 3.0 18.9 + - + +
470A LYS* 3.0 23.1 + - + +
501A TYR* 3.3 21.8 - - + +
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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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463A ILE* 2.9 30.7 + - + +
464A ALA* 3.3 10.3 + - - +
466A LYS* 1.3 77.0 - - - +
468A LYS* 1.3 53.2 + - - +
470A LYS* 3.2 11.1 + - + +
471A GLN* 2.8 60.7 + - - +
501A TYR* 3.9 25.8 - - + -
502A TYR* 4.4 12.3 - - + -
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Residues in contact with LYS 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 3.2 11.0 + - - +
465A GLU* 3.5 15.7 - - - +
467A LEU* 1.3 77.8 - - - +
469A PHE* 1.3 59.4 + - - +
471A GLN* 3.2 11.6 + - - -
472A THR* 3.0 41.7 + - + +
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Residues in contact with PHE 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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110A ILE* 3.8 33.0 - - + -
116A GLY 4.0 9.2 - - - -
117A ALA* 3.7 25.1 - - + -
118A PRO* 3.3 41.1 - - + +
155A TRP* 3.8 20.2 - + - -
465A GLU 3.3 2.0 + - - -
466A LYS* 3.0 18.7 + - - +
468A LYS* 1.3 79.3 - - - +
470A LYS* 1.3 65.6 + - + +
472A THR* 4.1 4.7 - - - -
473A LEU* 3.1 15.5 + - + +
474A GLU* 2.9 42.2 + - + -
477A TRP* 3.8 22.9 - + - -
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Residues in contact with LYS 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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107A GLN* 3.6 0.4 - - - +
110A ILE* 5.2 0.4 - - + -
111A ASN* 2.9 22.0 + - - +
466A LYS* 3.0 19.0 + - + +
467A LEU* 3.2 14.5 + - + +
469A PHE* 1.3 88.2 - - + +
471A GLN* 1.3 61.4 + - + +
472A THR 3.5 0.3 + - - -
474A GLU* 2.7 40.7 + - - +
475A GLN* 3.0 34.0 + - - +
496A ASP* 2.8 23.4 + - - -
501A TYR* 3.5 26.2 - - + +
502A TYR* 3.1 27.1 - - + -
504A LYS* 6.1 0.4 - - - +
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Residues in contact with GLN 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 LEU* 2.8 47.7 + - - +
468A LYS* 3.7 9.9 + - - +
469A PHE 3.2 0.4 - - - -
470A LYS* 1.3 82.0 - - + +
472A THR* 1.3 64.8 + - + +
475A GLN* 4.0 12.0 - - - +
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Residues in contact with THR 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 LYS* 3.0 29.7 + - + +
469A PHE* 3.2 3.2 + - - -
471A GLN* 1.3 86.0 - - + +
473A LEU* 1.3 77.4 + - - +
474A GLU 3.4 0.4 - - - -
475A GLN* 3.1 7.6 + - - +
476A GLU* 3.1 28.5 + - - +
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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