Contacts of the strand formed by residues 1646 - 1652 (chain A) in PDB entry 5A31
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 GLN1646 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1637A LEU* 4.3 13.2 - - - +
1638A TYR 3.4 12.6 - - - +
1639A LYS* 4.3 9.3 - - + +
1644A TYR 3.3 3.4 + - - -
1645A GLU* 1.3 82.7 - - + +
1647A THR* 1.3 68.5 + - - +
1664A LYS* 3.2 44.3 + - - +
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Residues in contact with THR1647 (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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1637A LEU* 3.2 7.8 - - - -
1638A TYR* 3.0 48.6 + - - +
1644A TYR* 4.0 22.5 - - + +
1645A GLU 5.1 0.2 - - - -
1646A GLN* 1.3 83.7 + - - +
1648A LYS* 1.3 60.8 + - - +
6T GLN* 3.7 26.4 + - - +
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Residues in contact with LYS1648 (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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1635A GLU* 4.0 33.4 + - + +
1636A VAL 3.2 3.6 - - - +
1637A LEU* 3.6 38.2 - - + +
1647A THR* 1.3 73.8 - - - +
1649A GLU* 1.3 60.5 + - - +
1665A GLN* 5.3 1.6 - - - +
6T GLN* 4.0 11.5 + - - +
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Residues in contact with GLU1649 (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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1635A GLU* 4.6 1.8 - - - -
1636A VAL* 2.9 31.7 + - + +
1638A TYR* 2.5 43.0 + - + +
1647A THR 4.2 0.2 - - - -
1648A LYS* 1.3 75.4 - - - +
1650A GLU* 1.3 68.2 + - - +
1651A LEU* 3.5 20.0 - - - +
6T GLN* 3.5 42.0 - - - +
7T LEU 3.6 17.5 + - - +
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Residues in contact with GLU1650 (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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1633A LEU* 3.8 33.7 - - + +
1634A LEU 3.2 15.9 - - - +
1635A GLU* 4.6 10.8 - - + +
1649A GLU* 1.3 81.2 - - - +
1651A LEU* 1.3 62.9 + - - +
1669A LYS* 4.6 15.8 + - + +
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Residues in contact with LEU1651 (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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1633A LEU* 3.6 6.9 - - - +
1634A LEU* 2.7 53.6 + - + +
1636A VAL* 3.7 29.8 - - + -
1638A TYR* 5.6 1.1 - - - +
1649A GLU* 3.5 33.7 - - - +
1650A GLU* 1.3 75.4 - - - +
1652A MET* 1.3 64.0 + - - +
1655A THR* 5.0 17.5 - - + +
1656A LEU 4.8 13.2 - - - +
1657A LEU* 5.1 8.7 - - + -
1658A PRO* 5.3 6.3 - - + -
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Residues in contact with MET1652 (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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1631A TYR* 3.9 25.4 - - + -
1632A ALA 3.7 15.0 - - - +
1633A LEU* 3.6 25.5 - - + +
1634A LEU* 5.3 0.7 - - - +
1651A LEU* 1.3 74.6 - - - +
1653A ALA* 1.3 67.0 + - - +
1654A PRO* 3.4 4.4 - - + -
1655A THR* 3.4 23.7 + - - +
1708A TYR* 3.8 39.7 - - + -
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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