Contacts of the helix formed by residues 472 - 484 (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 THR 472 (chain A).
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Specific contacts
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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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Residues in contact with LEU 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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118A PRO* 3.8 16.8 - - + +
119A VAL* 4.3 12.8 - - - +
120A ASP* 3.8 31.2 - - - +
469A PHE* 3.1 14.1 + - + +
472A THR* 1.3 82.6 + - - +
474A GLU* 1.3 64.2 + - - +
476A GLU* 3.1 14.3 + - + +
477A TRP* 2.9 64.6 + - + +
480A GLN* 6.1 0.4 - - - +
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Residues in contact with GLU 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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107A GLN* 2.9 13.9 + - - -
110A ILE* 3.6 22.2 - - + -
469A PHE* 2.9 22.8 + - + +
470A LYS* 2.7 51.5 + - - +
473A LEU* 1.3 72.4 - - - +
475A GLN* 1.3 72.9 + - - +
477A TRP* 3.2 15.3 - - + +
478A LYS* 2.8 52.6 + - + +
496A ASP* 4.3 2.1 - - - +
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Residues in contact with GLN 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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470A LYS* 3.0 26.2 + - - +
471A GLN* 4.0 13.5 - - - +
472A THR 3.1 8.5 + - - +
474A GLU* 1.3 93.0 + - - +
476A GLU* 1.3 61.0 + - - +
478A LYS* 3.9 15.9 - - - +
479A LYS* 2.8 56.4 + - - +
496A ASP* 5.0 5.7 + - - -
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Residues in contact with GLU 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 THR* 3.1 18.5 + - - +
473A LEU* 3.1 19.7 + - + +
475A GLN* 1.3 73.5 - - - +
477A TRP* 1.3 64.3 + - - +
479A LYS* 3.4 30.0 - - - +
480A GLN* 2.9 49.8 + - - +
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Residues in contact with TRP 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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110A ILE* 4.8 13.2 - - + -
120A ASP 6.1 0.2 - - - -
131A TRP* 4.1 9.9 - + - -
155A TRP* 3.7 31.9 - + - -
156A ALA* 3.9 29.7 + - + -
159A GLY* 3.4 42.0 - - - +
160A ASP* 3.7 13.8 - - + +
163A VAL* 5.4 1.1 - - + -
469A PHE* 3.8 17.9 - + - -
473A LEU* 2.9 57.4 + - + +
474A GLU* 3.2 17.0 - - + +
476A GLU* 1.3 76.0 - - - +
478A LYS* 1.3 59.6 + - + +
480A GLN* 4.5 8.1 - - - -
481A ALA* 2.9 31.6 + - - +
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Residues in contact with LYS 478 (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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106A LEU* 5.1 3.0 - - - +
107A GLN* 3.0 22.1 + - - -
110A ILE* 3.6 18.8 - - - +
163A VAL* 5.5 4.0 - - + -
474A GLU* 2.8 41.2 + - - +
475A GLN* 4.0 18.8 - - - +
477A TRP* 1.3 77.5 - - + +
479A LYS* 1.3 67.4 + - + +
481A ALA* 3.8 1.1 - - - +
482A ILE* 3.0 32.4 + - + +
487A LEU* 4.1 17.7 - - + -
492A LEU* 3.7 34.8 - - + -
495A VAL* 5.3 1.3 - - - -
496A ASP* 6.0 1.8 - - - -
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Residues in contact with LYS 479 (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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475A GLN* 2.8 41.8 + - - +
476A GLU* 3.4 34.3 - - - +
478A LYS* 1.3 78.4 - - + +
480A GLN* 1.3 56.9 + - + +
482A ILE* 3.2 8.2 + - - +
483A ALA* 2.9 28.9 + - - +
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Residues in contact with GLN 480 (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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160A ASP* 3.3 31.6 + - - +
473A LEU* 6.1 0.2 - - - +
476A GLU* 2.9 47.6 + - - +
477A TRP* 3.8 7.7 - - - +
479A LYS* 1.3 70.6 - - + +
481A ALA* 1.3 57.1 + - - +
483A ALA* 3.1 8.7 + - - +
484A LYS* 2.8 43.7 + - + +
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Residues in contact with ALA 481 (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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160A ASP 3.5 22.7 + - - +
163A VAL* 3.7 24.2 - - + -
477A TRP 2.9 18.1 + - - +
478A LYS 3.8 2.5 - - - +
480A GLN* 1.3 77.8 - - - +
482A ILE* 1.3 58.8 + - - +
484A LYS* 3.5 5.9 + - - +
485A GLY 3.1 3.1 + - - -
486A ARG* 2.8 30.7 + - + +
487A LEU* 3.2 14.8 + - + -
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Residues in contact with ILE 482 (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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478A LYS* 3.0 27.0 + - + +
479A LYS* 3.6 6.7 - - - +
481A ALA* 1.3 72.8 - - - +
483A ALA* 1.3 67.3 + - - +
485A GLY* 3.3 11.3 + - - -
487A LEU* 3.4 40.2 - - + +
489A PRO* 4.0 33.0 - - + -
492A LEU* 4.4 7.2 - - + -
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Residues in contact with ALA 483 (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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479A LYS 2.9 14.2 + - - +
480A GLN* 3.4 11.0 - - - +
482A ILE* 1.3 79.9 - - - +
484A LYS* 1.3 62.5 + - + +
485A GLY* 3.1 1.4 + - - -
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Residues in contact with LYS 484 (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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160A ASP* 3.0 52.3 + - - -
161A GLU* 3.1 22.3 + - - +
480A GLN* 2.8 25.1 + - + +
481A ALA* 4.0 6.5 - - - +
482A ILE 3.4 0.2 - - - -
483A ALA* 1.3 74.4 - - + +
485A GLY* 1.3 59.1 + - - +
486A ARG* 3.8 19.3 + - + +
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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