Contacts of the helix formed by residues 460 - 469 (chain A) in PDB entry 5ODS
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 SER 460 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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429A LYS* 3.4 42.3 + - - +
433A LEU* 4.9 5.5 - - - +
458A GLU 4.2 1.6 + - - -
459A CYS* 1.3 75.2 - - - +
461A GLU* 1.3 66.6 + - - +
462A GLU* 3.5 15.5 + - - +
463A LEU* 3.7 16.5 + - - +
464A GLY 4.0 2.4 + - - -
478A VAL* 4.4 1.7 - - - +
479A TYR* 5.5 0.2 - - - -
482A ALA* 3.7 16.0 - - - +
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Residues in contact with GLU 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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460A SER* 1.3 72.5 + - - +
462A GLU* 1.3 60.8 + - - +
463A LEU 3.0 2.2 - - - -
464A GLY* 2.8 21.7 + - - -
465A ASP* 3.0 35.1 + - - +
479A TYR* 3.7 19.1 - - + -
482A ALA* 4.4 4.2 - - - +
484A VAL* 4.0 26.6 - - + +
486A ASN* 4.2 6.2 - - - +
487A LYS* 3.1 32.2 + - + +
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Residues in contact with GLU 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A LEU* 3.8 22.9 - - + +
437A ARG* 3.5 22.7 + - - -
460A SER* 3.5 9.0 + - - +
461A GLU* 1.3 79.2 - - - +
463A LEU* 1.3 58.1 + - - +
465A ASP* 3.0 27.9 - - - +
466A LEU* 3.4 18.1 + - + +
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Residues in contact with LEU 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429A LYS 6.1 0.2 - - - +
432A SER* 4.1 16.6 - - - +
433A LEU* 3.8 22.4 - - + +
436A CYS* 3.9 30.5 - - + -
448A LEU* 5.6 1.3 - - + -
452A LEU* 6.0 0.4 - - + -
457A LEU* 3.9 27.8 - - + -
459A CYS* 4.5 11.4 - - + -
460A SER* 3.7 13.2 + - - +
461A GLU 3.0 0.6 - - - -
462A GLU* 1.3 78.8 - - - +
464A GLY* 1.3 59.3 + - - +
466A LEU* 3.1 9.1 + - + +
467A VAL* 2.8 40.9 + - + +
478A VAL* 3.9 21.1 - - + -
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Residues in contact with GLY 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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461A GLU 2.8 10.6 + - - -
463A LEU* 1.3 79.5 - - - +
465A ASP* 1.3 55.0 + - - -
467A VAL* 3.1 11.8 - - - +
468A LYS* 2.8 29.8 + - - +
475A ALA* 3.5 2.5 - - - +
478A VAL* 3.7 16.3 - - - +
479A TYR* 3.2 22.4 - - - -
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Residues in contact with ASP 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A GLU* 3.0 33.9 + - - +
462A GLU* 3.0 28.1 - - - +
464A GLY* 1.3 73.8 - - - +
466A LEU* 1.3 67.2 + - - +
468A LYS* 3.8 9.6 - - + +
469A SER* 2.8 23.4 + - - -
479A TYR* 2.9 16.1 + - - +
487A LYS* 3.9 9.7 + - - +
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Residues in contact with LEU 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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433A LEU* 4.4 11.2 - - + +
436A CYS 5.6 0.2 - - - -
437A ARG* 3.6 57.4 - - + +
440A LEU* 4.6 13.8 - - + +
462A GLU* 3.4 21.3 + - + +
463A LEU* 3.1 16.0 + - + +
465A ASP* 1.3 87.8 + - - +
467A VAL* 1.3 58.6 + - + +
469A SER* 2.6 25.2 + - - +
470A VAL* 4.5 1.6 + - - +
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Residues in contact with VAL 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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440A LEU* 3.6 32.1 - - + -
448A LEU* 3.7 22.7 - - + -
463A LEU* 2.8 31.3 + - + +
464A GLY* 3.1 19.3 - - - +
466A LEU* 1.3 68.8 - - - +
468A LYS* 1.3 66.0 + - - +
469A SER 3.0 3.4 + - - -
470A VAL* 3.1 14.6 + - + +
471A ASP* 3.2 15.6 + - - +
474A LEU* 4.8 6.1 - - + -
475A ALA* 3.6 24.9 - - - +
478A VAL* 3.9 10.1 - - + -
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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 GLY 2.8 19.9 + - - +
465A ASP* 3.8 12.3 - - + +
466A LEU 3.3 0.2 - - - -
467A VAL* 1.3 78.4 - - - +
469A SER* 1.3 61.9 + - - +
470A VAL 3.1 2.6 + - - -
471A ASP 3.7 8.3 + - - -
472A PRO* 3.8 29.6 - - + +
475A ALA* 3.6 17.3 - - + -
479A TYR* 4.6 12.1 - - + +
490A GLN* 5.7 3.8 + - - +
491A CYS* 5.7 5.2 - - - -
494A GLU* 4.8 13.4 + - - +
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Residues in contact with SER 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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465A ASP 2.8 13.9 + - - -
466A LEU* 2.6 27.6 + - - +
468A LYS* 1.3 75.0 - - - +
470A VAL* 1.3 57.0 + - - +
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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