Contacts of the strand formed by residues 449 - 453 (chain A) in PDB entry 6PAU
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 VAL 449 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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298A HIS* 4.0 13.2 - - + -
299A ARG 3.3 22.0 - - - +
301A LEU* 3.9 5.6 - - - +
306A LEU* 4.1 21.5 - - + -
311A PHE* 4.1 14.8 - - + -
416A LEU* 5.0 5.4 - - + -
417A LYS 3.4 2.3 + - - +
418A ALA* 3.5 25.5 - - + -
419A ALA* 3.0 26.0 + - - +
447A PHE* 3.5 3.9 - - - +
448A ASP* 1.3 79.6 - - - +
450A PHE* 1.3 63.5 + - - +
451A ASN* 3.6 21.5 - - - +
8C ILE* 5.1 0.2 - - + -
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Residues in contact with PHE 450 (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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299A ARG 2.8 37.2 + - - +
301A LEU* 4.3 7.6 - - + -
399A SER 5.3 0.9 - - - -
400A PHE* 3.9 31.4 - + + -
419A ALA* 3.6 16.2 - - + -
421A SER* 3.9 27.4 - - - -
435A MET* 4.0 22.9 - - + -
438A ALA* 4.2 15.7 - - + -
439A LEU* 3.5 29.2 - - + -
442A ALA* 3.8 13.0 - - + -
449A VAL* 1.3 72.3 - - - +
451A ASN* 1.3 71.8 + - - +
452A ALA* 4.7 0.2 - - + -
467A PHE* 3.5 20.4 - + - -
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Residues in contact with ASN 451 (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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296A TYR* 4.6 4.7 - - + -
297A TRP 3.4 5.6 - - - +
298A HIS* 2.9 29.2 + - - +
311A PHE* 4.5 3.7 - - - -
418A ALA* 3.8 14.1 - - - +
419A ALA 2.8 11.1 + - - +
420A TYR* 3.2 49.6 + - + -
421A SER* 2.9 27.2 + - - -
449A VAL* 3.6 17.2 - - - +
450A PHE* 1.3 79.0 - - - +
452A ALA* 1.3 64.2 + - - +
6C SER 5.5 0.8 + - - -
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Residues in contact with ALA 452 (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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296A TYR* 3.7 6.1 - - - -
297A TRP* 2.8 36.0 + - - +
420A TYR* 6.1 0.2 - - - -
421A SER* 3.8 22.0 - - - +
450A PHE* 4.7 0.7 - - + -
451A ASN* 1.3 78.3 - - - +
453A LEU* 1.3 68.3 + - - +
458A ASN* 4.2 6.3 - - - +
461A PHE* 4.9 2.9 - - + -
462A LEU* 4.2 7.9 - - + -
467A PHE* 3.8 20.9 - - + -
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Residues in contact with LEU 453 (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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294A CYS* 4.0 14.8 - - + -
295A ARG 3.4 12.6 - - - +
296A TYR* 3.4 52.0 - - + +
421A SER* 5.4 0.6 + - - -
452A ALA* 1.3 77.5 - - - +
454A ASP* 1.3 58.3 + - - +
455A LEU* 3.2 26.0 - - + +
458A ASN* 2.8 28.6 + - - +
462A LEU* 4.1 3.4 - - - +
474A LEU* 4.1 14.6 - - + -
476A TYR* 3.8 22.2 - - - +
494A VAL* 5.3 11.7 - - + -
503A GOL 6.0 0.2 - - - -
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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