Contacts of the strand formed by residues 473 - 478 (chain B) in PDB entry 2YA6
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 ALA 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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465B THR* 4.4 7.0 - - + -
466B VAL 4.0 4.5 - - - -
467B TYR* 3.7 31.0 - - + +
468B THR* 5.3 0.5 - - - +
472B LYS* 1.3 77.9 - - - +
474B THR* 1.3 64.8 + - - +
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Residues in contact with THR 474 (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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451B ARG* 5.9 1.1 - - - +
458B TYR* 4.4 11.7 - - + -
465B THR* 4.0 14.2 - - - +
466B VAL* 2.6 39.5 + - + +
468B THR* 3.8 30.5 - - + +
473B ALA* 1.3 76.5 - - - +
475B ASP* 1.3 65.2 + - - +
476B TYR* 3.1 30.1 + - + +
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Residues in contact with ASP 475 (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 THR* 1.3 75.5 - - - +
476B TYR* 1.3 63.6 + - + +
477B ARG* 4.0 2.1 + - - +
495B LYS* 3.7 31.3 + - + -
496B GLY* 3.5 22.1 + - - +
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Residues in contact with TYR 476 (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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451B ARG* 3.3 30.1 + - - -
465B THR* 3.8 3.5 - - - +
466B VAL* 3.0 34.0 + - + -
474B THR* 3.1 29.0 + - + +
475B ASP* 1.3 80.6 - - + +
477B ARG* 1.3 64.3 + - - +
493B LEU* 3.7 22.2 - - + -
494B TYR 3.3 9.0 - - - +
495B LYS* 4.0 29.8 + - + +
500B LEU* 3.6 23.6 - - + -
512B PRO* 4.1 8.2 - - + +
513B PHE* 3.6 29.6 - + + -
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Residues in contact with ARG 477 (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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463B ASN 4.9 7.1 + - - +
464B GLY 3.3 15.5 - - - +
465B THR* 4.4 5.2 - - + +
466B VAL* 4.3 0.7 - - - -
475B ASP 5.1 2.7 - - - +
476B TYR* 1.3 76.7 - - - +
478B VAL* 1.3 68.5 + - - +
479B VAL* 4.3 13.7 - - - +
493B LEU* 3.5 6.6 - - - +
494B TYR* 2.9 70.5 + - + +
496B GLY* 3.2 26.5 + - - +
497B ASP* 3.5 15.8 + - - -
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Residues in contact with VAL 478 (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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449B LEU* 4.0 0.9 - - + -
460B ILE* 4.0 22.2 - - + -
463B ASN 4.2 3.5 - - - +
464B GLY* 2.7 26.6 + - - +
466B VAL* 3.9 14.6 - - + -
477B ARG* 1.3 82.5 + - - +
479B VAL* 1.3 74.3 + - - +
480B VAL* 2.9 18.0 + - + +
491B GLY* 3.9 8.7 - - - -
492B ASP 3.4 4.5 - - - +
493B LEU* 3.9 18.4 - - + -
503B ILE* 3.7 33.2 - - + -
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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