Contacts of the helix formed by residues 473 - 485 (chain A) in PDB entry 3N51
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 473 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471A ASP* 3.6 5.4 + - - -
472A VAL* 1.3 75.1 - - - +
474A SER* 1.3 67.6 + - - +
475A GLU* 3.3 12.4 + - - +
476A THR* 3.0 49.3 + - - +
477A TRP* 3.0 13.7 + - - -
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Residues in contact with SER 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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472A VAL 3.3 2.4 + - - -
473A ASP* 1.3 75.3 + - - +
475A GLU* 1.3 65.1 + - - +
477A TRP* 3.4 17.6 + - - +
478A LYS* 3.2 45.2 + - - +
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Residues in contact with GLU 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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473A ASP* 3.3 9.6 + - - +
474A SER* 1.3 81.5 - - - +
476A THR* 1.3 62.6 + - - +
478A LYS* 3.7 21.4 + - - +
479A SER* 3.2 23.2 + - - -
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Residues in contact with THR 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* 4.7 2.5 - - + -
473A ASP* 3.0 34.8 + - - +
475A GLU* 1.3 76.7 - - - +
477A TRP* 1.3 62.8 + - - +
479A SER* 3.2 7.5 + - - -
480A VAL* 3.2 24.2 + - + +
504A LEU* 3.5 24.7 - - + -
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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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460A SER* 3.8 29.4 - - - -
463A LEU* 3.9 19.3 - - + -
464A ALA* 3.7 27.2 + - + +
467A PHE* 3.4 50.2 - + + +
468A GLY 5.4 0.2 - - - +
472A VAL* 3.6 16.1 + - + -
473A ASP 3.0 27.4 + - - -
474A SER* 3.5 17.9 - - - +
476A THR* 1.3 76.5 - - - +
478A LYS* 1.3 90.3 + - + +
480A VAL* 3.4 3.8 + - - +
481A LEU* 2.9 30.3 + - + -
500A MET* 3.3 24.3 - - + +
504A LEU* 4.4 9.2 - - + -
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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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464A ALA* 6.1 0.7 - - - -
474A SER* 3.2 32.8 + - - +
475A GLU* 4.0 22.5 + - - +
476A THR 3.3 0.2 - - - -
477A TRP* 1.3 112.2 - - + +
479A SER* 1.3 59.6 + - - +
481A LEU* 3.3 7.1 + - + +
482A SER* 2.9 28.8 + - - -
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Residues in contact with SER 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 GLU 3.2 18.6 + - - -
476A THR* 3.2 6.7 + - - -
478A LYS* 1.3 76.7 - - - +
480A VAL* 1.3 63.8 + - - +
482A SER* 3.2 9.6 + - - -
483A GLU* 3.1 34.5 + - - +
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Residues in contact with VAL 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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476A THR* 3.2 15.6 + - + +
477A TRP* 3.7 8.7 - - - +
479A SER* 1.3 80.3 - - - +
481A LEU* 1.3 59.1 + - - +
483A GLU* 3.1 19.4 + - - +
484A VAL* 2.9 27.6 + - + +
500A MET* 3.5 31.2 - - + +
503A LYS* 3.5 40.6 - - + +
504A LEU* 4.1 17.5 - - + -
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Residues in contact with LEU 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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460A SER* 4.8 7.0 - - - +
463A LEU* 4.3 14.6 - - + -
477A TRP* 2.9 27.5 + - + +
478A LYS* 3.5 8.5 - - + +
479A SER 3.3 0.2 - - - -
480A VAL* 1.3 76.4 - - - +
482A SER* 1.3 57.5 + - - +
484A VAL* 3.2 7.5 + - + +
485A ASP* 2.9 31.8 + - + +
488A ASN* 3.4 38.4 - - + +
491A GLU 5.6 1.6 - - - +
492A VAL* 3.6 32.1 - - + -
496A GLU* 5.6 1.1 - - + -
500A MET* 3.8 17.9 - - + -
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Residues in contact with SER 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 2.9 13.2 + - - -
479A SER* 3.2 12.5 + - - -
481A LEU* 1.3 76.1 - - - +
483A GLU* 1.3 61.2 + - - +
485A ASP 4.3 5.2 - - - -
486A LYS* 3.2 52.7 + - - +
488A ASN* 4.8 4.9 - - - +
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Residues in contact with GLU 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 SER* 3.1 32.1 + - - +
480A VAL* 3.1 16.5 + - - +
482A SER* 1.3 76.3 - - - +
484A VAL* 1.3 63.4 - - - +
485A ASP* 4.7 0.2 - - - -
486A LYS* 4.5 13.7 + - - +
503A LYS* 3.8 31.4 + - - +
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Residues in contact with VAL 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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480A VAL 2.9 17.3 + - - +
481A LEU* 3.2 12.5 + - + +
483A GLU* 1.3 79.4 - - - +
485A ASP* 1.3 60.9 + - + +
496A GLU* 4.2 24.5 - - + +
499A GLN* 3.6 48.5 - - + +
500A MET* 4.0 14.4 - - + +
503A LYS* 3.8 21.5 - - + +
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Residues in contact with ASP 485 (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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481A LEU* 2.9 12.3 + - + +
482A SER* 3.5 4.1 - - - +
484A VAL* 1.3 86.7 - - + +
486A LYS* 1.3 64.6 + - - +
487A ASN* 2.9 21.9 + - - +
488A ASN* 3.0 45.0 + - + +
496A GLU* 3.7 23.2 - - + +
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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