Contacts of the strand formed by residues 1748 - 1755 (chain D) in PDB entry 3SUA
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 PRO1748 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1746D TYR* 4.7 7.2 - - + +
1747D ARG* 1.3 89.1 - - + +
1749D LEU* 1.3 63.7 + - - +
1750D THR* 4.8 2.7 + - - +
1771D VAL 4.1 5.8 - - - +
1772D LEU* 4.1 15.7 - - + -
1843D ASP* 3.4 9.7 - - - +
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Residues in contact with LEU1749 (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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1747D ARG* 3.6 2.8 + - + +
1748D PRO* 1.3 75.8 - - - +
1750D THR* 1.3 66.8 + - - +
1751D LEU* 4.0 4.9 - - + +
1770D LYS* 3.5 3.3 - - - +
1771D VAL* 3.0 44.6 + - + +
1773D ASP* 3.7 35.0 - - + +
1836D LEU* 3.8 30.3 - - + -
1841D VAL* 4.1 13.2 - - + +
1842D PRO* 3.8 9.0 - - + +
1843D ASP* 3.2 34.8 - - + +
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Residues in contact with THR1750 (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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1748D PRO* 4.8 2.9 + - - +
1749D LEU* 1.3 78.1 + - - +
1751D LEU* 1.3 60.7 + - - +
1752D ASN 4.2 0.2 + - - -
1768D PRO* 4.9 14.5 - - + +
1769D VAL 3.3 9.6 - - - +
1770D LYS* 3.4 33.1 - - + +
1843D ASP* 2.9 20.9 + - - +
1844D GLY* 3.3 17.5 + - - -
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Residues in contact with LEU1751 (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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1749D LEU* 5.1 3.6 - - + -
1750D THR* 1.3 75.9 - - - +
1752D ASN* 1.4 64.6 + - - +
1753D ALA* 3.2 10.1 + - + +
1768D PRO* 4.5 1.6 - - - -
1769D VAL* 3.0 33.5 + - + +
1771D VAL* 3.8 26.7 - - + -
1780D ALA* 6.2 0.9 - - + -
1784D MET* 4.4 13.2 - - + -
1836D LEU* 3.9 17.5 - - + -
1841D VAL* 4.8 6.7 - - + -
1842D PRO 4.9 2.5 - - - +
1844D GLY 4.0 5.4 - - - +
1845D ALA* 3.3 20.2 - - + +
1847D VAL* 3.4 36.8 - - + -
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Residues in contact with ASN1752 (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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1750D THR 4.2 1.4 + - - -
1751D LEU* 1.4 68.7 - - - +
1753D ALA* 1.3 57.4 + - - +
1754D LEU* 3.4 19.9 - - - +
1766D GLY* 3.5 27.5 - - - +
1767D VAL 4.0 4.2 - - - -
1768D PRO* 4.3 9.6 - - + +
1844D GLY* 4.2 14.9 - - - +
1845D ALA 3.2 15.8 + - - +
1846D THR* 3.4 19.2 + - - +
1847D VAL 3.2 12.3 + - - +
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Residues in contact with ALA1753 (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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1751D LEU* 3.2 4.8 + - + -
1752D ASN* 1.3 73.1 - - - +
1754D LEU* 1.3 61.8 + - - +
1766D GLY* 3.3 0.7 - - - -
1767D VAL* 2.8 47.6 + - - +
1769D VAL* 3.7 21.3 - - + -
1784D MET* 3.7 24.7 - - + -
1788D LEU* 3.8 13.7 - - + +
1847D VAL 3.2 4.7 - - - -
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Residues in contact with LEU1754 (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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1752D ASN* 3.4 29.4 - - - +
1753D ALA* 1.3 74.6 - - - +
1755D LEU* 1.3 61.4 + - - +
1756D ALA* 4.7 3.8 - - + +
1764D ALA* 3.7 43.5 - - + +
1765D GLN* 3.9 2.7 - - - +
1766D GLY* 3.7 17.7 - - - +
1784D MET* 4.8 0.2 - - - +
1788D LEU* 4.1 7.7 - - - +
1808D ARG* 4.5 9.0 - - - +
1846D THR* 3.8 12.1 - - + -
1847D VAL 2.9 6.4 + - - +
1848D ALA* 3.4 18.6 - - + -
1849D LEU* 3.0 23.0 + - - +
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Residues in contact with LEU1755 (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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1754D LEU* 1.3 76.6 - - - +
1756D ALA* 1.3 58.8 + - - +
1757D VAL* 3.4 26.4 + - + -
1764D ALA* 4.3 15.8 - - - +
1765D GLN 4.3 4.8 + - - +
1785D LEU* 4.6 2.5 - - + -
1788D LEU* 3.7 25.4 - - + +
1789D TYR* 3.2 44.9 - - + +
1803D LEU* 5.0 2.2 - - + -
1849D LEU* 3.9 33.9 - - + -
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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