Contacts of the helix formed by residues 461 - 472 (chain Z) in PDB entry 5LN3
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 PRO 461 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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434Z TYR* 6.1 0.2 - - - +
458Z GLU* 3.7 20.1 - - + +
459Z CYS 4.2 3.6 - - - +
460Z ASP* 1.3 84.6 - - - +
462Z ALA* 1.4 62.0 + - - +
463Z LEU* 3.3 4.0 - - + +
464Z ALA* 3.4 31.8 + - + +
465Z LEU* 3.7 13.4 + - - +
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Residues in contact with ALA 462 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448Z CYS* 6.5 1.3 - - + -
452Z ASN* 6.3 0.2 - - - +
458Z GLU* 3.7 9.5 + - - +
460Z ASP* 3.0 9.9 + - - +
461Z PRO* 1.4 68.7 - - - +
463Z LEU* 1.4 59.9 + - - +
464Z ALA 3.4 0.2 + - - -
465Z LEU* 3.4 13.1 + - + +
466Z LEU* 2.9 29.8 + - - +
481Z SER* 4.1 6.4 + - - +
484Z GLY 5.6 1.1 - - - -
485Z LEU* 3.7 33.8 - - + +
488Z ALA* 4.9 9.4 - - + -
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Residues in contact with LEU 463 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456Z ARG* 4.9 1.1 - - - +
458Z GLU* 4.0 25.6 - - - +
461Z PRO* 5.0 3.6 - - + -
462Z ALA* 1.4 76.9 - - - +
464Z ALA* 1.3 59.1 + - - +
466Z LEU* 3.4 1.2 + - - +
467Z SER* 2.8 33.2 + - - +
485Z LEU* 4.1 10.3 - - + +
489Z TYR* 3.7 35.4 - - + +
496Z ASP* 5.1 14.8 - - + +
497Z VAL* 6.0 2.0 - - + +
500Z LEU* 4.0 22.6 - - + +
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Residues in contact with ALA 464 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461Z PRO* 3.4 27.3 + - + +
462Z ALA 3.2 1.0 - - - -
463Z LEU* 1.3 79.3 - - - +
465Z LEU* 1.4 55.2 + - + +
467Z SER* 3.6 5.1 + - - -
468Z ASP* 2.8 36.5 + - - +
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Residues in contact with LEU 465 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433Z LEU* 4.1 8.3 - - + -
434Z TYR* 3.5 35.2 - - + +
441Z LYS* 6.4 1.1 - - - -
445Z LEU* 3.9 20.4 - - + -
448Z CYS* 5.4 0.7 - - - -
460Z ASP* 3.4 26.7 - - - +
461Z PRO 3.7 12.5 + - - +
462Z ALA* 3.4 11.6 + - + +
464Z ALA* 1.4 73.3 - - + +
466Z LEU* 1.4 65.9 + - - +
468Z ASP* 3.2 21.7 + - - +
469Z TYR* 3.1 37.0 + - + +
481Z SER* 4.3 7.6 - - - +
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Residues in contact with LEU 466 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462Z ALA 2.9 19.2 + - - +
463Z LEU 4.0 2.9 - - - +
465Z LEU* 1.4 77.0 - - - +
467Z SER* 1.4 60.6 + - - +
469Z TYR* 3.5 10.3 + - - +
470Z VAL* 3.6 15.2 + - + +
478Z ARG* 3.7 33.0 - - + +
481Z SER* 3.9 15.2 + - - +
482Z ILE* 3.7 29.6 - - + -
485Z LEU* 3.6 22.2 - - + -
500Z LEU* 3.5 33.9 - - + +
501Z LEU* 4.2 7.6 - - + -
504Z VAL* 5.2 2.2 - - + -
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Residues in contact with SER 467 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463Z LEU* 2.8 23.1 + - - +
464Z ALA* 3.7 6.5 - - - -
465Z LEU 3.3 0.2 - - - -
466Z LEU* 1.4 73.7 - - - +
468Z ASP* 1.4 65.3 + - - +
470Z VAL* 3.4 14.6 + - - +
471Z LEU* 3.5 18.7 + - - +
500Z LEU* 3.6 22.7 - - - +
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Residues in contact with ASP 468 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464Z ALA* 2.8 23.3 - - - +
465Z LEU* 3.4 15.3 - - - +
467Z SER* 1.4 78.8 - - - +
469Z TYR* 1.3 67.7 + - + +
471Z LEU* 3.2 13.3 + - - +
472Z HIS* 3.0 45.4 + - + +
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Residues in contact with TYR 469 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433Z LEU* 5.3 1.0 - - - +
441Z LYS* 4.5 18.0 - - - +
445Z LEU* 3.3 24.2 - - + +
465Z LEU* 3.1 35.0 + - + +
466Z LEU* 3.8 10.1 - - - +
467Z SER 3.3 0.6 - - - -
468Z ASP* 1.3 80.5 - - + +
470Z VAL* 1.4 64.9 + - - +
472Z HIS* 3.3 22.3 + - - +
474Z SER* 3.6 38.6 + - - +
477Z MET* 3.9 27.3 - - + +
478Z ARG* 3.9 29.0 + - + -
481Z SER* 3.8 23.1 - - - -
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Residues in contact with VAL 470 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466Z LEU* 3.6 15.6 + - + +
467Z SER* 3.4 10.2 + - - +
468Z ASP 3.4 0.8 - - - -
469Z TYR* 1.4 74.5 - - - +
471Z LEU* 1.4 64.7 + - + +
472Z HIS 3.4 5.4 - - - +
478Z ARG* 4.3 22.1 + - - +
500Z LEU* 5.2 10.3 - - + +
503Z PRO* 5.1 15.7 - - + -
504Z VAL* 4.0 26.9 - - + -
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Residues in contact with LEU 471 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467Z SER* 3.5 15.2 + - - +
468Z ASP* 3.2 14.6 + - - +
469Z TYR 3.2 0.4 - - - -
470Z VAL* 1.4 76.3 - - + +
472Z HIS* 1.4 74.0 + - + +
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Residues in contact with HIS 472 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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468Z ASP* 3.0 38.0 + - + +
469Z TYR* 3.3 12.6 + - - +
470Z VAL 3.4 9.2 - - - +
471Z LEU* 1.4 90.8 - - + +
473Z ASN* 1.4 68.1 + - - +
474Z SER* 3.6 14.6 + - - +
478Z ARG* 4.9 2.4 + - - -
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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