Contacts of the helix formed by residues 493 - 501 (chain B) 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 GLY 493 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B ILE* 1.3 82.9 - - - +
494B ASP* 1.3 63.6 + - - -
496B LEU* 2.9 20.2 + - - +
497B LEU* 2.9 13.6 + - - +
584B GLU* 3.1 5.1 + - - -
587B LYS* 3.8 20.6 - - - -
588B VAL* 3.7 21.3 - - - -
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Residues in contact with ASP 494 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B ARG* 3.1 33.1 + - - -
491B GLU* 3.9 16.4 - - - +
492B ILE 2.4 31.8 + - - +
493B GLY* 1.3 69.4 - - - -
495B VAL* 1.3 58.0 + - - +
497B LEU* 3.4 8.9 + - - +
498B ALA* 2.9 29.5 + - - +
584B GLU* 5.3 0.2 + - - -
587B LYS* 3.7 23.7 - - + +
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Residues in contact with VAL 495 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PHE* 4.8 4.4 - - + -
477B ARG* 3.7 33.8 - - + +
478B LEU* 4.0 25.1 - - + +
481B ARG* 3.7 33.2 - - + +
492B ILE* 2.7 21.8 + - + +
494B ASP* 1.3 82.5 + - - +
496B LEU* 1.3 68.7 + - + +
498B ALA* 3.0 22.6 + - - +
499B ARG* 3.2 7.3 + - - +
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Residues in contact with LEU 496 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424B LEU* 4.5 17.5 - - + -
474B PHE* 4.7 11.2 - - + -
478B LEU* 4.8 1.3 - - + -
492B ILE* 3.8 26.7 - - + -
493B GLY 2.9 7.8 + - - +
495B VAL* 1.3 74.8 - - + +
497B LEU* 1.3 54.3 + - - +
499B ARG 2.7 22.5 + - - -
500B PHE* 2.9 24.6 + - + -
572B LEU* 3.6 38.1 - - + -
575B ILE* 5.6 4.0 - - + -
588B VAL* 4.1 28.9 - - + -
591B ALA* 3.6 17.3 - - + -
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Residues in contact with LEU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493B GLY 2.9 16.8 + - - +
494B ASP* 3.9 7.6 - - - +
496B LEU* 1.3 70.4 - - - +
498B ALA* 1.3 58.0 + - - +
500B PHE* 5.0 0.2 - - - -
501B ASP* 2.7 55.5 + - + +
587B LYS* 3.6 55.6 - - + +
590B LEU* 3.7 24.9 - - + -
591B ALA* 3.6 20.9 - - + +
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Residues in contact with ALA 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B ARG* 3.5 39.4 + - - +
494B ASP 2.9 14.3 + - - +
495B VAL* 3.0 13.9 + - - +
497B LEU* 1.3 75.1 - - - +
499B ARG* 1.3 57.9 + - - +
501B ASP 4.8 0.9 - - - -
504B GLU* 3.2 27.0 - - - +
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Residues in contact with ARG 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470B VAL* 4.7 4.7 - - + +
471B HIS* 5.7 0.2 - - - +
474B PHE* 3.0 72.5 - - + +
477B ARG* 5.4 3.1 - - - +
495B VAL 3.2 4.1 + - - +
496B LEU 2.7 15.4 + - - +
498B ALA* 1.3 74.0 - - - +
500B PHE* 1.3 127.3 + - + +
501B ASP 3.6 0.7 - - - -
504B GLU* 3.4 23.6 - - + +
505B GLY* 3.4 1.3 + - - -
508B PHE* 3.5 46.0 - - + +
568B TYR* 3.7 16.0 - - - -
572B LEU* 5.2 1.2 - - - +
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Residues in contact with PHE 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474B PHE* 4.5 3.4 - + - -
496B LEU* 2.9 23.0 + - + +
497B LEU* 5.0 0.4 - - - -
499B ARG* 1.3 137.0 - - + +
501B ASP* 1.3 59.4 + - + +
505B GLY* 3.1 18.4 - - - -
508B PHE* 4.3 5.2 - + - -
568B TYR* 4.1 11.0 - + - -
572B LEU* 4.2 10.8 - - + -
591B ALA* 4.5 2.9 - - - +
594B CYS* 3.6 26.9 - - + +
595B CYS* 3.0 35.4 - - + -
598B ILE* 3.5 29.5 - - + +
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Residues in contact with ASP 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497B LEU* 2.7 43.3 + - + +
498B ALA* 4.7 1.0 - - - +
500B PHE* 1.3 75.2 - - - +
502B GLY* 1.3 72.6 + - - +
503B ALA 3.6 1.0 + - - -
504B GLU* 3.9 4.7 + - - +
505B GLY* 3.3 7.4 + - - -
590B LEU* 4.1 18.9 - - - +
594B CYS* 3.8 20.7 - - - -
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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