Contacts of the strand formed by residues 1625 - 1633 (chain B) in PDB entry 2OPG
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 GLY1625 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1624B MET* 1.3 79.5 - - - +
1626B CYS* 1.3 63.3 + - - +
1709B TYR* 3.3 10.1 + - - -
1710B ARG 3.1 14.1 - - - -
1712B GLU* 3.9 8.1 - - - -
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Residues in contact with CYS1626 (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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1625B GLY* 1.3 75.1 - - - +
1627B GLU* 1.3 63.9 + - - +
1628B THR* 4.3 14.4 - - - -
1708B LEU 3.8 0.2 - - - +
1709B TYR* 3.4 10.4 - - - -
1710B ARG* 2.9 58.5 + - - +
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Residues in contact with GLU1627 (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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1626B CYS* 1.3 76.2 - - - +
1628B THR* 1.3 63.4 + - - +
1678B LEU* 3.8 30.1 - - + +
1686B ARG* 4.4 10.7 + - - -
1707B THR* 4.4 11.9 - - + +
1708B LEU 3.2 5.2 - - - +
1709B TYR* 4.7 7.6 - - + -
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Residues in contact with THR1628 (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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1626B CYS* 4.2 13.8 - - - -
1627B GLU* 1.3 75.8 + - - +
1629B THR* 1.3 67.7 + - - +
1630B ILE* 3.7 25.1 - - + -
1706B LEU 3.7 0.9 - - - +
1707B THR* 3.4 1.4 - - - -
1708B LEU* 2.8 49.6 + - + +
1710B ARG* 5.4 17.4 + - - +
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Residues in contact with THR1629 (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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1628B THR* 1.3 79.0 + - - +
1630B ILE* 1.3 71.6 + - - +
1631B GLU* 5.4 0.2 - - + -
1670B ARG* 5.1 1.2 + - - -
1705B ARG* 3.5 49.4 + - + +
1706B LEU 3.2 10.5 - - - +
1707B THR* 3.1 24.9 + - - +
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Residues in contact with ILE1630 (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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1628B THR* 3.7 18.2 - - + -
1629B THR* 1.3 81.2 - - - +
1631B GLU* 1.3 63.2 + - - +
1632B ILE* 3.6 22.7 - - + -
1668B ASP* 3.9 12.1 - - - +
1670B ARG* 3.8 37.0 - - + +
1671B LEU* 3.6 39.7 - - + -
1704B VAL 3.5 1.0 - - - +
1705B ARG* 3.4 2.4 - - - +
1706B LEU* 2.8 41.5 + - + +
1708B LEU* 4.5 4.9 - - + -
1710B ARG* 6.2 0.7 - - - +
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Residues in contact with GLU1631 (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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1630B ILE* 1.3 76.7 - - - +
1632B ILE* 1.3 62.0 + - - +
1668B ASP* 4.2 0.7 - - - +
1670B ARG* 2.9 22.6 + - - +
1703B ARG* 3.5 36.1 + - + +
1704B VAL 3.1 5.8 - - - +
1705B ARG* 2.9 50.7 + - + +
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Residues in contact with ILE1632 (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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1630B ILE* 3.6 27.1 - - + -
1631B GLU* 1.3 79.3 - - - +
1633B SER* 1.3 63.3 + - - +
1639B LEU* 3.6 26.0 - - + -
1641B LEU* 5.8 0.2 - - + -
1664B ALA* 4.3 3.8 - - + +
1665B ALA* 4.1 25.4 - - + +
1668B ASP* 3.7 24.7 - - + -
1671B LEU* 4.3 13.9 - - + -
1702B GLN 3.5 0.3 - - - +
1703B ARG* 3.7 3.5 - - - -
1704B VAL* 2.8 48.3 + - + +
1706B LEU* 4.8 5.4 - - + -
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Residues in contact with SER1633 (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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1632B ILE* 1.3 72.4 - - - +
1634B LYS* 1.3 65.5 + - - +
1635B GLY* 3.4 4.0 + - - -
1664B ALA* 3.2 16.5 - - - +
1702B GLN* 3.3 12.3 + - - +
1703B ARG* 4.7 4.7 - - - +
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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