Contacts of the helix formed by residues 466 - 478 (chain A) in PDB entry 3DDN
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 GLY 466 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A ARG 3.4 0.6 + - - -
465A PRO* 1.3 71.2 - - - +
467A ALA* 1.3 63.9 + - - +
468A LEU* 3.3 3.1 - - - -
469A GLY* 3.2 6.9 + - - -
470A LYS* 3.0 30.8 + - - +
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Residues in contact with ALA 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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461A TYR* 3.4 35.2 - - + +
463A ASP 3.7 4.0 - - - +
464A ARG 2.9 19.9 + - - +
465A PRO 3.1 1.9 - - - -
466A GLY* 1.3 77.7 - - - +
468A LEU* 1.3 63.4 + - - +
470A LYS* 3.2 4.5 + - - +
471A ILE* 2.9 31.7 + - + +
518A VAL* 3.6 17.9 - - + -
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Residues in contact with LEU 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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461A TYR* 5.1 1.8 + - - -
466A GLY* 3.3 0.9 - - - -
467A ALA* 1.3 77.4 - - - +
469A GLY* 1.3 56.5 + - - +
471A ILE* 3.5 5.5 + - + +
472A GLY* 3.0 30.6 + - - +
487A LEU* 3.8 35.0 - - + -
498A ILE* 4.5 12.3 - - + -
500A LEU* 5.7 4.5 - - + -
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Residues in contact with GLY 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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466A GLY* 3.2 9.8 + - - -
467A ALA 3.2 0.8 - - - -
468A LEU* 1.3 76.4 - - - +
470A LYS* 1.3 57.3 + - - +
472A GLY* 3.8 0.6 - - - -
473A THR* 2.6 40.8 + - - -
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Residues in contact with LYS 470 (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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463A ASP* 3.7 22.6 + - - -
465A PRO 4.0 15.8 + - - -
466A GLY* 3.0 23.2 + - - +
467A ALA* 3.2 6.7 + - - +
469A GLY* 1.3 74.5 - - - +
471A ILE* 1.3 63.0 + - - +
473A THR* 3.8 3.9 - - - -
474A LEU* 3.0 31.6 + - + +
517A ALA* 3.7 35.9 + - + +
518A VAL* 4.4 7.6 - - + -
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Residues in contact with ILE 471 (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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459A ILE* 4.2 18.6 - - + -
461A TYR* 4.7 7.9 - - + +
467A ALA* 2.9 30.8 + - + +
468A LEU* 4.0 4.3 - - + +
470A LYS* 1.3 76.7 - - - +
472A GLY* 1.3 64.1 + - - +
473A THR 3.2 0.2 + - - -
474A LEU* 3.3 5.2 + - - +
475A LEU* 3.0 43.1 + - + +
498A ILE* 4.2 31.2 - - + -
500A LEU* 4.4 11.7 - - + -
514A ILE* 4.1 21.9 - - + +
517A ALA* 6.4 0.2 - - + -
518A VAL* 4.0 20.9 - - + -
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Residues in contact with GLY 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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468A LEU* 3.0 19.0 + - - +
469A GLY 4.0 0.4 - - - -
471A ILE* 1.3 78.5 - - - +
473A THR* 1.3 57.2 + - - +
475A LEU* 3.9 1.1 - - - +
476A GLY* 3.1 24.3 + - - -
482A ILE* 4.0 24.2 - - - +
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Residues in contact with THR 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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469A GLY* 2.6 25.8 + - - -
470A LYS* 3.8 4.5 - - - -
472A GLY* 1.3 75.6 - - - +
474A LEU* 1.3 60.9 + - + +
476A GLY 3.4 0.7 + - - -
477A THR* 2.9 42.9 + - - +
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Residues in contact with LEU 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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470A LYS* 3.0 23.2 + - + +
471A ILE 3.8 2.9 - - - +
473A THR* 1.3 77.3 - - + +
475A LEU* 1.3 62.1 + - - +
477A THR* 3.4 8.1 + - + -
478A ALA* 3.0 22.3 + - - +
510A VAL* 4.5 8.3 - - + +
513A ALA* 3.8 17.0 - - + +
514A ILE* 3.7 45.1 - - + +
517A ALA* 3.8 18.6 - - + -
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Residues in contact with LEU 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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457A LEU* 4.2 13.2 - - + -
471A ILE* 3.0 43.2 + - + +
472A GLY 3.9 3.4 - - - +
474A LEU* 1.3 76.0 - - - +
476A GLY* 1.3 59.6 + - - +
478A ALA* 3.2 11.9 + - - +
480A VAL* 2.9 44.6 + - + +
482A ILE* 3.9 28.7 - - + -
500A LEU* 4.4 4.9 - - + -
502A LEU* 4.5 5.4 - - + -
506A VAL* 4.2 27.4 - - + -
510A VAL* 4.6 1.8 - - + -
514A ILE* 3.6 21.3 - - + -
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Residues in contact with GLY 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 GLY 3.1 18.5 + - - -
473A THR* 3.8 0.7 - - - -
475A LEU* 1.3 74.6 - - - +
477A THR* 1.3 63.7 + - - +
479A GLY* 3.2 12.0 + - - -
480A VAL 4.1 9.6 - - - -
482A ILE* 6.3 0.4 - - - -
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Residues in contact with THR 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 THR* 2.9 28.9 + - - +
474A LEU* 3.7 9.2 - - + -
476A GLY* 1.3 78.8 - - - +
478A ALA* 1.3 59.3 + - - +
479A GLY* 3.1 1.8 + - - -
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Residues in contact with ALA 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474A LEU 3.0 13.8 + - - +
475A LEU* 3.2 10.7 + - - +
477A THR* 1.3 75.1 - - - +
479A GLY* 1.3 61.4 + - - +
480A VAL* 3.5 14.8 + - + +
504A GLN* 5.0 4.0 + - - -
507A PRO* 5.1 6.3 - - + +
510A VAL* 4.4 26.5 - - + -
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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