Contacts of the strand formed by residues 1827 - 1833 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1815E GLY* 3.6 1.9 - - - -
1816E PHE* 3.2 26.3 + - - +
1817E TYR* 5.8 1.3 - - - -
1823E ASP 3.2 26.8 + - - +
1824E LEU* 3.2 12.3 + - + +
1825E ASP 3.1 14.3 + - - +
1826E GLU* 1.3 84.2 + - - +
1828E GLU* 1.3 60.4 + - - +
1829E PHE* 3.6 22.9 - - + -
1950E ASN* 4.9 12.1 + - + +
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Residues in contact with GLU1828 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813E ARG* 3.0 46.0 + - + -
1814E VAL 3.6 4.5 - - - +
1815E GLY* 4.1 5.5 - - - -
1817E TYR* 3.6 22.4 + - + +
1826E GLU 5.6 0.4 - - - +
1827E GLN* 1.3 75.0 + - - +
1829E PHE* 1.3 58.4 + - - +
1881E GLN* 4.1 2.6 - - - +
1936E LEU* 5.4 0.4 - - - -
1950E ASN* 3.1 7.0 - - - +
1951E VAL* 2.4 58.7 + - + +
1954E LYS* 3.3 25.1 + - - -
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Residues in contact with PHE1829 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1813E ARG* 3.6 6.6 - - - +
1814E VAL* 2.6 41.3 + - - +
1816E PHE* 4.1 17.3 - + - -
1824E LEU* 3.6 33.9 - - + -
1827E GLN* 3.6 20.6 - - + -
1828E GLU* 1.3 79.8 - - - +
1830E VAL* 1.3 63.1 + - - +
1831E TYR* 3.9 16.8 - + + -
1948E ARG* 3.5 37.7 - - + -
1949E VAL* 3.1 19.3 - - - +
1950E ASN* 3.9 14.6 - - + -
1951E VAL* 4.2 0.4 - - - +
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Residues in contact with VAL1830 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811E TYR* 4.4 14.4 - - + -
1812E PHE 3.3 9.2 - - - +
1813E ARG* 4.7 2.9 - - - -
1829E PHE* 1.3 77.4 - - - +
1831E TYR* 1.3 63.6 + - - +
1885E VAL* 4.4 4.7 - - + -
1910E PHE* 4.2 38.4 - - + -
1936E LEU* 4.6 11.2 - - + -
1938E THR* 3.6 29.4 - - + -
1942E PHE* 3.6 9.7 - - + -
1948E ARG* 3.4 15.9 - - - -
1949E VAL* 2.7 12.2 + - + +
1951E VAL* 3.7 16.2 - - + -
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Residues in contact with TYR1831 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1811E TYR* 3.3 4.7 - - - +
1812E PHE* 2.7 37.2 + - - +
1814E VAL* 3.4 39.9 - - + -
1816E PHE* 3.2 17.5 - + - -
1829E PHE* 3.9 10.5 - - + -
1830E VAL* 1.3 74.5 - - - +
1832E LYS* 1.3 60.4 + - - +
1833E GLU* 3.8 20.7 + - - +
1842E ILE* 4.5 10.1 - - + -
1845E ARG* 4.3 10.1 - - - -
1846E LEU* 4.0 21.8 - - + +
1850E TYR* 4.2 1.2 + - - -
1947E THR* 3.4 11.0 - - - -
1948E ARG* 2.7 54.8 + - + -
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Residues in contact with LYS1832 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1808E PHE 3.8 8.5 + - - -
1809E GLY* 5.5 1.1 - - - -
1810E THR 3.5 4.5 - - - +
1811E TYR* 3.3 33.8 + - + +
1830E VAL 3.6 2.4 + - - -
1831E TYR* 1.3 69.5 - - - +
1833E GLU* 1.3 77.0 + - - +
1834E PRO* 4.7 0.5 - - - +
1904E ASN* 3.9 21.6 + - - +
1942E PHE* 3.4 35.0 - - + +
1943E PRO* 3.9 21.0 - - + +
1944E TYR 5.9 0.2 - - - +
1946E LYS 5.8 0.9 - - - +
1947E THR* 2.9 31.0 + - + +
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Residues in contact with GLU1833 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1809E GLY* 4.5 1.4 - - - -
1810E THR* 2.9 28.2 + - - +
1812E PHE* 4.0 17.9 - - + -
1831E TYR* 3.8 14.7 + - - +
1832E LYS* 1.3 89.0 - - - +
1834E PRO* 1.3 80.7 - - + +
1835E ALA 3.6 0.5 + - - -
1837E THR* 3.4 32.2 - - + +
1842E ILE* 4.3 9.2 - - + -
1845E ARG* 2.7 43.1 + - - -
1947E THR* 6.0 0.5 - - - -
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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