Contacts of the helix formed by residues 494 - 500 (chain D) in PDB entry 5DO7
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 PHE 494 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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399D PHE* 3.3 37.8 - + - -
490D GLY* 3.0 32.5 - - - -
492D TYR 2.4 9.8 + - - -
493D PHE* 1.4 119.9 - + + +
495D ALA* 1.3 65.0 + - - +
496D LYS 3.3 1.3 - - - -
497D ILE* 4.0 10.5 - - + -
498D LEU* 3.7 30.9 + - + +
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Residues in contact with ALA 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D PHE* 3.9 7.6 - - - -
402D LEU* 4.1 12.3 - - + -
403D ILE* 3.1 30.2 - - - +
406D GLN* 4.8 3.5 - - - +
491D PRO 2.7 25.7 + - - +
492D TYR* 2.2 54.0 + - + +
494D PHE* 1.3 71.6 - - - +
496D LYS* 1.3 58.0 + - - +
499D GLY* 4.2 0.2 - - - -
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Residues in contact with LYS 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D GLN* 4.2 21.0 + - - +
467D VAL* 5.3 0.4 - - + -
470D LYS* 6.1 0.7 - - + -
471D CYS* 4.3 11.4 - - + +
474D GLU* 2.6 32.3 + - - +
477D MET* 4.3 4.4 - - - +
492D TYR* 3.5 30.1 + - + +
495D ALA* 1.3 75.9 - - - +
497D ILE* 1.3 62.0 + - - +
498D LEU 3.0 2.7 - - - -
499D GLY* 2.6 29.0 + - - +
500D GLU* 3.2 35.6 + - - +
547D LEU* 3.9 23.3 - - + -
658D TYR* 3.2 24.8 + - + +
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Residues in contact with ILE 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493D PHE* 2.8 30.5 - - + +
494D PHE* 4.0 5.6 + - + -
495D ALA 3.6 0.4 - - - -
496D LYS* 1.3 76.6 - - - +
498D LEU* 1.3 72.5 + - + +
500D GLU* 4.5 5.3 + - - +
501D LEU* 3.9 18.2 + - + +
540D PHE* 3.8 31.2 - - + -
544D ILE* 4.7 8.7 - - + -
547D LEU* 4.2 22.0 - - + -
655D MET* 4.0 30.3 - - + +
658D TYR* 4.1 13.2 - - + -
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Residues in contact with LEU 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399D PHE* 3.7 26.2 - - + -
403D ILE* 3.7 13.9 - - + -
407D ILE* 4.8 1.4 - - - +
494D PHE* 3.7 30.4 + - + +
496D LYS 3.0 0.6 - - - -
497D ILE* 1.3 89.6 - - + +
499D GLY* 1.3 56.6 + - - +
501D LEU* 2.8 40.0 + - + +
502D PRO* 3.5 5.4 - - - +
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Residues in contact with GLY 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403D ILE* 3.1 25.5 - - - +
406D GLN* 4.0 25.2 + - - -
407D ILE* 3.7 23.8 - - - +
410D ASP* 4.9 3.1 - - - +
411D PHE* 5.7 1.6 - - - -
496D LYS 2.6 14.0 + - - -
498D LEU* 1.3 71.7 - - - +
500D GLU* 1.3 59.8 + - - +
502D PRO* 3.7 2.6 - - - +
503D GLU* 5.7 0.3 - - - +
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Residues in contact with GLU 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D GLN* 4.5 4.4 + - - +
410D ASP* 5.1 5.8 - - - +
467D VAL* 3.8 24.3 - - - +
470D LYS* 3.8 33.7 - - - +
496D LYS* 3.2 40.2 + - - +
497D ILE* 4.9 4.9 - - - +
499D GLY* 1.3 75.1 - - - +
501D LEU* 1.3 66.9 + - - +
502D PRO 3.4 0.2 - - - -
503D GLU* 2.8 25.1 + - - +
504D HIS 3.1 7.3 + - - -
543D ARG* 3.9 29.4 - - - +
547D LEU* 4.2 9.9 - - - +
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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