Contacts of the helix formed by residues 492 - 501 (chain A) in PDB entry 3ODX
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 ILE 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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417A ARG* 4.4 2.5 - - - +
421A ILE* 3.5 52.5 - - + -
424A LEU* 4.8 3.4 - - + -
478A LEU* 4.4 18.8 - - + -
481A ARG* 3.9 7.0 - - + +
489A ILE* 4.9 5.8 - - + -
491A GLU* 1.3 77.3 - - - +
493A GLY* 1.3 75.8 + - - +
494A ASP* 3.3 8.0 + - - -
495A VAL* 3.0 17.9 + - + +
496A LEU* 3.0 33.6 + - + +
575A ILE* 4.3 12.8 - - + -
584A GLU* 2.6 3.6 + - - +
588A VAL* 3.7 19.3 - - + -
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Residues in contact with GLY 493 (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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492A ILE* 1.3 77.1 - - - +
494A ASP* 1.3 64.0 + - - +
496A LEU* 2.8 18.5 + - - +
497A LEU* 2.9 15.1 + - - +
584A GLU* 2.8 11.7 + - - -
587A LYS* 3.6 29.2 - - - -
588A VAL* 3.7 12.8 - - - -
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Residues in contact with ASP 494 (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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481A ARG* 2.6 42.4 + - - -
491A GLU* 4.2 7.0 - - - +
492A ILE* 3.5 6.6 + - - -
493A GLY* 1.3 69.3 - - - +
495A VAL* 1.3 78.6 + - - +
497A LEU* 3.6 6.9 + - - +
498A ALA* 3.1 22.7 + - - +
584A GLU* 5.0 0.2 + - - -
587A LYS* 3.5 26.7 - - + +
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Residues in contact with VAL 495 (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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474A PHE* 4.6 5.8 - - + -
477A ARG* 3.5 35.5 - - + +
478A LEU* 4.2 20.4 - - + +
481A ARG* 3.7 36.3 - - + +
492A ILE* 3.0 12.3 + - + +
494A ASP* 1.3 92.8 + - - +
496A LEU* 1.3 66.9 + - + +
498A ALA* 3.0 22.3 + - - +
499A ARG* 3.3 5.0 + - - +
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Residues in contact with LEU 496 (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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424A LEU* 4.7 8.5 - - + -
474A PHE* 4.6 16.6 - - + -
478A LEU* 4.7 0.9 - - + -
492A ILE* 3.0 40.6 + - + +
493A GLY 2.8 11.9 + - - +
495A VAL* 1.3 77.1 - - + +
497A LEU* 1.3 64.6 + - - +
499A ARG* 2.8 13.3 + - - -
500A PHE* 3.0 23.7 + - + +
572A LEU* 3.4 39.5 - - + -
575A ILE* 5.4 3.6 - - + -
588A VAL* 4.3 19.1 - - + -
591A ALA* 3.6 17.7 - - + -
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Residues in contact with LEU 497 (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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493A GLY 2.9 21.1 + - - +
494A ASP* 3.9 6.7 - - - +
496A LEU* 1.3 73.8 - - - +
498A ALA* 1.3 58.2 + - - +
500A PHE* 5.1 0.7 - - - -
501A ASP* 2.9 62.7 + - + +
587A LYS* 3.1 47.3 - - + +
590A LEU* 3.8 16.4 - - + -
591A ALA* 3.8 14.1 - - + +
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Residues in contact with ALA 498 (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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477A ARG* 3.5 37.2 + - - +
494A ASP 3.1 13.7 + - - +
495A VAL* 3.0 16.2 + - - +
497A LEU* 1.3 77.6 - - - +
499A ARG* 1.3 55.0 + - - +
501A ASP 5.1 0.2 - - - -
504A GLU* 3.1 27.6 - - - +
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Residues in contact with ARG 499 (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 VAL* 4.4 7.6 - - + +
473A LEU* 6.3 1.8 - - + -
474A PHE* 2.9 71.3 - - + +
477A ARG* 5.2 4.9 - - - +
495A VAL 3.3 3.1 + - - +
496A LEU 2.8 8.3 + - - +
498A ALA* 1.3 80.6 - - - +
500A PHE* 1.3 128.0 + - - +
501A ASP 3.5 1.1 - - - -
504A GLU* 3.2 26.3 - - + +
505A GLY* 3.3 1.6 - - - -
508A PHE* 3.2 47.0 - - + +
568A TYR* 3.8 7.8 - - - -
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Residues in contact with PHE 500 (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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474A PHE* 4.2 4.7 - + - -
496A LEU* 3.0 21.1 + - + +
499A ARG* 1.3 130.3 - - - +
501A ASP* 1.3 58.6 + - + +
505A GLY* 3.1 15.5 - - - -
508A PHE* 3.9 11.4 - + - -
568A TYR* 3.8 17.7 - + - -
572A LEU* 4.3 13.0 - - + -
591A ALA* 4.7 3.1 - - + +
594A CYS* 3.5 28.4 - - + +
595A CYS* 3.2 34.3 - - + -
598A ILE* 3.8 26.1 - - + +
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Residues in contact with ASP 501 (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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497A LEU* 2.9 49.7 + - + +
498A ALA* 4.7 0.7 - - - +
500A PHE* 1.3 79.7 - - - +
502A GLY* 1.3 75.3 + - - +
503A ALA 3.6 0.9 + - - -
504A GLU* 3.8 4.5 + - - +
505A GLY* 2.9 13.9 + - - -
590A LEU* 3.8 11.4 - - - +
594A CYS* 3.8 21.8 - - - -
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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