Contacts of the helix formed by residues 457 - 469 (chain A) in PDB entry 5DSG
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 ASN 457 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 5.2 2.4 - - - +
397A LYS* 4.6 16.9 - - - +
398A VAL* 5.2 3.4 - - - +
401A THR* 4.0 14.9 + - + +
453A TYR* 3.3 23.0 + - - +
454A ALA 3.6 14.0 - - - +
455A LEU 3.3 2.2 - - - -
456A CYS* 1.3 82.6 - - - +
458A ALA* 1.3 76.5 + - - +
459A THR* 2.8 24.6 + - - -
460A PHE* 3.5 30.0 - - + -
461A LYS* 3.6 6.6 + - - +
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Residues in contact with ALA 458 (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 LYS* 6.1 0.2 - - - +
457A ASN* 1.3 75.1 + - - +
459A THR* 1.3 62.2 + - - +
460A PHE 3.4 0.4 - - - -
461A LYS* 3.7 8.5 - - + +
462A LYS* 2.9 30.7 + - - +
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Residues in contact with THR 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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60A ASN* 3.4 25.6 - - - +
62A GLN* 4.8 11.9 - - + +
63A LEU* 3.8 20.6 - - + -
457A ASN* 2.8 11.5 + - - -
458A ALA* 1.3 77.1 - - - +
460A PHE* 1.3 55.4 + - - +
462A LYS* 3.5 5.1 + - + +
463A THR* 2.3 38.3 + - - -
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Residues in contact with PHE 460 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A VAL* 4.3 11.0 - - + -
56A SER* 4.1 14.6 - - - -
57A ILE* 3.9 22.7 - - + -
63A LEU* 3.8 28.3 - - + -
68A ASN* 3.8 29.4 - - - -
71A LEU* 4.6 11.0 - - + -
401A THR* 6.2 0.9 - - + -
453A TYR* 3.6 43.5 - + + +
457A ASN* 3.5 30.2 + - + -
458A ALA 3.4 0.4 - - - -
459A THR* 1.3 78.9 - - - +
461A LYS* 1.3 57.4 + - - +
463A THR* 3.5 3.7 + - - -
464A PHE* 2.9 45.3 + + + -
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Residues in contact with LYS 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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454A ALA* 3.5 31.5 + - + +
457A ASN 3.6 10.9 + - - +
458A ALA* 3.5 8.2 + - + +
459A THR 3.2 0.2 - - - -
460A PHE* 1.3 76.5 - - - +
462A LYS* 1.3 61.2 + - - +
464A PHE* 3.1 12.9 + - + +
465A ARG* 2.9 27.9 + - + +
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Residues in contact with LYS 462 (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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458A ALA 2.9 19.4 + - - +
459A THR* 3.9 5.8 - - + +
461A LYS* 1.3 75.6 - - - +
463A THR* 1.3 57.9 + - - +
465A ARG* 3.4 8.3 + - - +
466A HIS* 2.9 28.6 + - - +
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Residues in contact with THR 463 (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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56A SER* 3.6 40.6 - - - +
59A VAL* 5.4 3.8 - - + -
60A ASN* 3.4 27.5 + - + +
63A LEU* 3.8 2.4 - - - +
459A THR* 2.3 27.5 + - - +
460A PHE* 3.7 5.4 - - - -
462A LYS* 1.3 75.5 - - - +
464A PHE* 1.3 58.9 + - - +
466A HIS* 3.3 8.5 + - + +
467A LEU* 2.9 40.6 + - + +
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Residues in contact with PHE 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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49A GLY* 4.7 1.1 - - - -
52A LEU* 3.3 37.9 - - + -
53A VAL* 3.6 25.1 - - + -
56A SER* 3.1 27.6 - - - -
450A PRO* 4.0 9.4 - - + -
453A TYR* 4.6 1.3 - - + -
454A ALA* 3.6 36.1 - - + -
460A PHE* 2.9 33.2 + + + -
461A LYS* 3.2 8.5 - - + +
463A THR* 1.3 75.3 - - - +
465A ARG* 1.3 58.0 + - - +
467A LEU* 2.9 6.3 + - - -
468A LEU* 2.9 43.0 + - + +
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Residues in contact with ARG 465 (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 LYS* 2.9 14.4 + - + +
462A LYS* 3.7 10.8 - - - +
464A PHE* 1.3 76.1 - - - +
466A HIS* 1.3 61.0 + - - +
467A LEU 3.5 0.2 + - - -
468A LEU* 3.8 13.3 + - - +
469A LEU* 3.9 21.1 + - - +
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Residues in contact with HIS 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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462A LYS 2.9 17.3 + - - +
463A THR* 3.6 10.5 - - + +
464A PHE 3.1 0.2 - - - -
465A ARG* 1.3 77.2 - - - +
467A LEU* 1.3 61.3 + - + +
469A LEU* 3.8 1.8 + - - +
470A CYS* 3.3 33.7 + - - +
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Residues in contact with LEU 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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52A LEU* 3.7 19.7 - - + +
55A LEU* 3.7 20.9 - - + -
56A SER* 3.4 44.0 - - - +
59A VAL* 4.2 26.9 - - + -
463A THR* 2.9 23.3 + - + +
464A PHE* 2.9 4.9 + - - +
466A HIS* 1.3 78.0 - - + +
468A LEU* 1.3 64.5 + - - +
469A LEU 3.1 2.7 - - - -
470A CYS* 3.2 27.6 + - + +
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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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52A LEU* 3.7 39.9 - - + -
464A PHE* 2.9 29.6 + - + +
465A ARG* 3.8 8.2 + - - +
466A HIS 3.5 0.4 - - - -
467A LEU* 1.3 76.5 - - - +
469A LEU* 1.3 68.4 + - + +
470A CYS 3.5 0.6 + - - -
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Residues in contact with LEU 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 ARG 3.9 16.3 + - - +
466A HIS* 3.8 3.8 + - - +
467A LEU 3.1 0.6 - - - -
468A LEU* 1.3 87.7 - - + +
470A CYS* 1.3 69.6 + - - +
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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