Contacts of the helix formed by residues 471 - 481 (chain A) in PDB entry 3OPY
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 471 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401A GLU* 4.9 1.8 - - - -
458A VAL* 4.5 0.4 - - - -
469A PRO* 5.3 9.2 - - + +
470A ILE* 1.3 77.1 - - - +
472A SER* 1.3 64.7 + - - +
473A GLU* 3.8 9.7 + - - +
474A GLU* 2.9 56.3 + - - +
475A VAL* 3.2 10.7 + - - +
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Residues in contact with SER 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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399A VAL* 3.7 27.5 - - - +
401A GLU* 3.4 29.4 + - - +
458A VAL* 4.3 7.4 - - - -
471A THR* 1.3 72.1 - - - +
473A GLU* 1.3 59.3 + - - +
475A VAL* 3.4 3.4 + - - +
476A LYS* 2.9 28.6 + - - +
488A ILE* 3.4 16.2 - - - +
490A ARG* 3.4 22.5 + - - -
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Residues in contact with GLU 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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471A THR* 3.1 9.8 - - - +
472A SER* 1.3 77.6 + - - +
474A GLU* 1.4 63.2 + - - +
476A LYS* 3.3 27.7 + - - +
477A ASP* 3.1 43.1 + - - +
488A ILE* 3.3 22.1 - - - +
490A ARG* 4.1 15.9 + - - +
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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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435A TRP* 3.9 22.5 + - + -
436A LYS* 5.4 9.0 + - - +
469A PRO* 3.4 20.3 - - - +
470A ILE* 3.5 8.3 - - - +
471A THR* 2.9 43.9 + - - +
473A GLU* 1.4 79.0 - - - +
475A VAL* 1.4 61.2 + - - +
477A ASP* 3.4 12.2 + - - +
478A VAL* 3.3 25.7 + - - +
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Residues in contact with VAL 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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399A VAL* 4.1 11.9 - - + -
424A PHE* 3.7 15.5 - - + -
435A TRP* 4.1 2.0 - - + -
439A LEU* 3.7 13.9 - - + -
456A VAL* 3.7 29.6 - - + -
458A VAL* 3.8 11.9 - - + -
470A ILE* 3.6 22.7 - - + -
471A THR 3.2 14.8 + - - +
472A SER 3.6 7.4 - - - +
473A GLU 3.3 0.2 - - - -
474A GLU* 1.4 71.6 - - - +
476A LYS* 1.4 64.1 + - - +
478A VAL* 3.1 19.6 + - - +
479A LEU* 3.2 15.9 + - + +
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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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399A VAL* 4.2 1.7 - - + +
472A SER 2.9 17.0 + - - +
473A GLU* 3.3 29.8 + - - +
475A VAL* 1.4 69.4 - - - +
477A ASP* 1.3 63.5 + - - +
479A LEU* 3.2 5.4 + - - +
480A VAL* 2.9 45.0 + - + +
486A THR* 3.2 48.3 + - + +
487A ARG* 4.8 9.9 - - - +
488A ILE* 3.7 28.0 - - + +
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Residues in contact with ASP 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 GLU* 3.1 35.9 + - - +
474A GLU* 3.4 12.8 - - - +
476A LYS* 1.3 79.5 - - - +
478A VAL* 1.4 60.5 + - + +
480A VAL* 3.5 8.8 + - - +
481A GLU* 3.2 30.4 + - - +
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Residues in contact with VAL 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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435A TRP* 3.8 15.3 - - + -
436A LYS* 3.4 61.0 - - + +
439A LEU* 4.0 13.9 - - + -
440A LYS* 3.8 15.3 - - + -
474A GLU 3.3 16.6 - - - +
475A VAL 3.1 7.7 + - - +
477A ASP* 1.4 75.2 - - + +
479A LEU* 1.3 61.2 + - + +
481A GLU* 3.1 29.2 + - - +
482A ILE* 3.6 9.1 + - - +
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Residues in contact with LEU 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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397A ALA* 4.1 14.1 - - + -
398A PHE 5.0 1.6 - - - +
399A VAL* 3.8 17.3 - - + -
439A LEU* 3.9 16.8 - - + +
440A LYS* 5.8 1.3 - - - +
443A CYS* 3.8 31.6 - - + -
454A THR* 4.7 2.2 - - + -
456A VAL* 3.9 15.3 - - + -
475A VAL* 3.5 11.4 - - + +
476A LYS 3.2 3.4 + - - +
478A VAL* 1.3 73.9 - - + +
480A VAL* 1.3 63.7 + - - +
482A ILE* 3.2 19.4 + - + +
484A LEU* 3.3 27.0 + - + +
486A THR* 3.4 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 LYS* 2.9 36.0 + - + +
477A ASP* 3.8 9.4 - - - +
478A VAL 3.3 0.6 - - - -
479A LEU* 1.3 75.3 - - - +
481A GLU* 1.4 57.8 + - + +
483A GLY* 3.0 22.0 + - - -
484A LEU 3.4 19.1 + - - +
485A ASP* 5.1 1.1 - - - -
486A THR* 3.5 17.0 - - - +
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Residues in contact with GLU 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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436A LYS* 5.4 7.5 - - - +
440A LYS* 3.0 30.1 + - - +
477A ASP* 3.2 18.0 + - - +
478A VAL* 3.1 25.1 - - - +
480A VAL* 1.4 74.1 - - + +
482A ILE* 1.3 61.8 + - - +
483A GLY 3.3 1.8 - - - -
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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