Contacts of the helix formed by residues 447 - 459 (chain A) in PDB entry 3L19
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 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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443A LYS 3.8 9.9 + - - -
444A SER* 3.5 9.7 + - - -
445A LEU 3.4 2.6 - - - -
446A LEU* 1.4 79.9 - - - +
448A LYS* 1.3 65.9 + - - +
449A ASP* 2.7 25.0 + - - -
450A LYS* 3.1 34.9 + - - +
451A LEU* 3.1 11.1 + - - +
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Residues in contact with LYS 448 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446A LEU 3.7 1.6 + - - -
447A SER* 1.3 70.5 - - - +
449A ASP* 1.4 57.2 + - - +
451A LEU* 3.1 12.4 + - + +
452A GLU* 2.9 51.6 + - + +
502A PHE* 4.9 16.4 - - + -
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Residues in contact with ASP 449 (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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447A SER* 2.7 27.6 + - - -
448A LYS* 1.4 76.5 - - - +
450A LYS* 1.4 66.5 + - - +
452A GLU* 3.5 14.1 + - - +
453A SER* 2.9 35.7 + - - +
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Residues in contact with LYS 450 (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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358A MET* 4.1 12.7 - - + +
362A LEU* 3.2 51.9 - - + +
363A THR* 3.9 12.1 - - + -
367A GLU* 3.2 28.3 + - - -
444A SER* 2.8 29.6 + - - +
445A LEU* 3.5 18.6 - - + +
447A SER* 3.1 19.5 + - - +
449A ASP* 1.4 83.0 + - - +
451A LEU* 1.4 60.4 + - - +
453A SER* 4.6 0.7 - - - -
454A ALA* 2.9 27.9 + - - +
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Residues in contact with LEU 451 (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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358A MET* 4.1 11.7 - - + -
446A LEU* 3.4 33.0 - - + +
447A SER 3.1 12.8 + - - +
448A LYS* 3.1 10.8 + - + +
450A LYS* 1.4 74.1 - - - +
452A GLU* 1.3 58.3 + - - +
454A ALA* 4.5 1.3 - - - -
455A PHE* 3.0 30.0 + - - +
502A PHE* 3.5 14.6 - - + -
505A PHE* 3.7 9.1 - - + -
506A CYS* 4.0 31.2 - - + +
509A ILE* 3.9 33.0 - - + -
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Residues in contact with GLU 452 (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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448A LYS* 2.9 49.0 + - - +
449A ASP* 3.7 13.0 - - - +
451A LEU* 1.3 73.1 - - - +
453A SER* 1.3 59.6 + - - +
455A PHE* 3.4 2.9 + - - +
456A GLN* 2.9 49.9 + - - +
502A PHE* 3.8 23.9 - - + -
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Residues in contact with SER 453 (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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357A TYR* 4.5 1.9 + - - -
362A LEU* 3.8 28.0 - - - -
449A ASP* 2.9 21.5 + - - +
450A LYS* 4.6 0.7 - - - -
452A GLU* 1.3 70.8 - - - +
454A ALA* 1.3 66.2 + - - +
456A GLN* 3.4 11.8 + - - +
457A LYS* 3.0 22.7 + - - +
366B GLU* 6.1 1.3 - - - -
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Residues in contact with ALA 454 (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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354A ALA 4.8 1.3 - - - +
357A TYR* 3.9 16.8 - - + -
358A MET* 3.5 27.1 - - + -
362A LEU* 3.6 1.9 - - + +
450A LYS 2.9 18.5 + - - +
451A LEU 3.7 4.0 - - - +
453A SER* 1.3 74.8 - - - +
455A PHE* 1.4 62.5 + - - +
457A LYS* 3.1 9.2 + - - +
458A PHE* 3.1 22.9 + - + -
505A PHE* 3.7 18.2 - - + -
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Residues in contact with PHE 455 (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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451A LEU 3.0 18.1 + - - +
452A GLU 3.7 3.4 - - - +
453A SER 3.3 0.2 - - - -
454A ALA* 1.4 75.5 - - - +
456A GLN* 1.3 65.2 + - + +
458A PHE* 3.1 5.6 + - - +
459A ASP* 2.9 47.4 + - + +
464A GLY* 3.3 32.3 - - - -
465A LYS* 4.0 2.7 - - - -
466A ILE* 3.6 22.0 - - + -
500A VAL 3.3 21.1 - - - -
501A ASP 3.4 2.5 - - - -
502A PHE* 3.4 42.6 - + + -
505A PHE* 3.7 24.8 - - + -
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Residues in contact with GLN 456 (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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452A GLU* 2.9 38.6 + - - +
453A SER* 3.8 10.6 + - - +
454A ALA 3.4 0.2 - - - -
455A PHE* 1.3 83.3 - - + +
457A LYS* 1.3 60.4 + - - +
459A ASP* 3.3 21.3 - - + +
460A GLN* 4.8 1.0 - - - -
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Residues in contact with LYS 457 (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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357A TYR* 3.5 35.9 - - + +
453A SER 3.0 12.8 + - - +
454A ALA 3.1 10.5 + - - +
456A GLN* 1.3 79.6 - - - +
458A PHE* 1.3 65.1 + - + +
460A GLN* 4.0 14.0 - - - +
474A VAL* 4.3 8.4 - - + +
366B GLU* 3.0 34.4 + - - +
369B LYS* 3.7 18.2 - - - +
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Residues in contact with PHE 458 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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350A LEU* 4.2 20.9 - - + -
353A ALA* 4.5 4.9 - - + -
354A ALA* 3.7 40.4 - - + -
357A TYR* 4.8 15.7 - + + -
454A ALA* 3.1 26.6 + - + -
455A PHE 3.1 4.0 + - - +
457A LYS* 1.3 81.8 - - + +
459A ASP* 1.3 57.2 + - - +
460A GLN* 3.0 11.6 + - - +
466A ILE* 3.6 28.7 - - + +
470A GLU* 3.5 22.7 - - - +
471A LEU* 4.2 15.7 - - + -
474A VAL* 3.7 35.7 - - + -
475A PHE* 4.8 2.5 - + - -
505A PHE* 4.2 8.5 - + - -
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Residues in contact with ASP 459 (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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2A CA 2.2 33.8 - - - -
455A PHE* 2.9 33.9 + - + +
456A GLN* 3.3 15.7 - - - +
457A LYS 3.5 0.2 - - - -
458A PHE* 1.3 70.5 - - - +
460A GLN* 1.3 64.9 + - - +
461A ASP* 3.1 4.5 - - - +
462A GLY* 3.2 19.8 + - - -
463A ASN* 2.9 6.6 - - - +
464A GLY* 2.8 29.1 + - - -
465A LYS 3.0 9.5 - - - +
466A ILE* 4.0 3.7 - - + +
470A GLU* 4.0 4.5 - - - -
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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