Contacts of the strand formed by residues 1827 - 1833 (chain A) in PDB entry 6AJL
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 GLN1827 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1814A VAL 4.1 0.7 - - - +
1815A GLY* 3.8 0.7 - - - -
1816A PHE* 3.0 27.2 + - - +
1817A TYR* 5.2 0.9 - - - -
1823A ASP* 3.5 22.2 + - - +
1824A LEU* 2.7 27.0 + - - +
1825A ASP 3.0 2.0 + - - +
1826A GLU* 1.3 77.6 - - - +
1828A GLU* 1.3 61.5 + - - +
1829A PHE* 3.5 30.7 - - + -
1950A ASN* 4.5 14.1 + - + +
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Residues in contact with GLU1828 (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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1813A ARG* 3.3 38.4 + - + +
1814A VAL 3.3 11.9 - - - +
1815A GLY* 3.8 11.2 - - - -
1817A TYR* 4.1 15.6 + - + +
1826A GLU 5.5 0.4 - - - +
1827A GLN* 1.3 76.7 - - - +
1829A PHE* 1.3 62.1 + - - +
1881A GLN* 4.2 3.1 - - - +
1936A LEU* 4.7 1.0 - - - +
1950A ASN* 3.1 6.4 - - - +
1951A VAL* 2.9 54.1 + - + +
1954A LYS* 3.7 18.5 + - - -
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Residues in contact with PHE1829 (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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1813A ARG* 3.3 7.8 - - - +
1814A VAL 2.7 39.5 + - - +
1816A PHE* 3.9 23.3 - + - -
1824A LEU* 3.4 30.5 - - + -
1827A GLN* 3.5 29.2 - - + -
1828A GLU* 1.3 77.2 - - - +
1830A VAL* 1.3 62.0 + - - +
1831A TYR* 3.9 18.4 - + + -
1948A ARG* 3.2 46.9 - - + -
1949A VAL* 3.7 4.5 - - - +
1950A ASN* 3.5 31.6 - - + -
1951A VAL* 4.1 1.5 - - - +
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Residues in contact with VAL1830 (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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1811A TYR* 4.3 5.4 - - + -
1812A PHE 3.2 9.9 - - - +
1813A ARG* 4.4 3.6 - - - +
1829A PHE* 1.3 77.1 - - - +
1831A TYR* 1.3 68.9 + - - +
1885A VAL* 4.6 2.2 - - + -
1910A PHE* 4.2 31.4 - - + -
1936A LEU* 4.2 16.8 - - + -
1938A THR* 3.9 21.3 - - + -
1942A PHE* 3.4 21.9 - - + -
1948A ARG* 3.3 2.6 - - - -
1949A VAL 2.9 32.2 + - - +
1951A VAL* 4.2 10.5 - - + -
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Residues in contact with TYR1831 (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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1810A THR 3.8 0.2 - - - +
1811A TYR* 3.2 10.6 - - - +
1812A PHE 2.6 34.5 + - - +
1814A VAL* 3.5 32.8 - - + -
1816A PHE* 3.9 13.2 - - - -
1829A PHE* 3.9 11.4 - + + -
1830A VAL* 1.3 75.6 - - - +
1832A LYS* 1.3 58.3 + - - +
1833A GLU* 4.0 10.5 - - + +
1842A ILE* 4.3 15.9 - - + -
1845A ARG* 3.8 27.4 - - - -
1846A LEU* 4.5 20.1 - - + +
1947A THR* 3.9 9.4 - - - -
1948A ARG* 3.1 52.1 + - + +
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Residues in contact with LYS1832 (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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1808A PHE 3.8 7.4 - - - -
1809A GLY* 5.1 1.6 - - - -
1810A THR 3.6 2.5 - - - +
1811A TYR* 3.5 42.6 + - + +
1831A TYR* 1.3 73.9 - - - +
1833A GLU* 1.3 76.3 + - - +
1834A PRO* 4.7 1.0 - - - +
1904A ASN* 3.7 21.2 + - - +
1942A PHE* 3.7 17.0 - - + -
1943A PRO* 4.1 20.0 - - + +
1947A THR* 3.0 36.0 + - + +
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Residues in contact with GLU1833 (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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1809A GLY* 4.0 3.8 - - - -
1810A THR* 2.7 29.3 + - - +
1812A PHE* 4.1 23.3 - - + -
1831A TYR* 4.1 10.7 - - + -
1832A LYS* 1.3 88.4 - - - +
1834A PRO* 1.3 79.0 - - + +
1835A ALA 3.8 0.3 + - - -
1837A THR* 3.4 27.8 - - + +
1842A ILE* 4.3 8.7 - - + -
1845A ARG* 2.9 43.1 + - - -
1947A THR* 5.7 1.0 + - - -
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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