Contacts of the helix formed by residues 892 - 900 (chain J) in PDB entry 4XLN
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 ASP 892 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887J GLY* 3.7 4.1 - - - +
890J VAL* 3.4 22.3 - - - +
891J GLY* 1.3 77.5 - - - +
893J GLU* 1.3 61.5 + - - +
894J LYS* 3.2 25.5 + - + +
895J VAL* 3.3 29.9 - - - +
896J ALA* 3.7 5.9 + - - +
922J LEU* 4.9 3.6 - - - +
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Residues in contact with GLU 893 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868J TYR* 2.9 31.0 + - - +
869J LEU* 4.2 20.7 - - + +
883J ALA 4.7 1.1 - - - +
884J ARG* 4.6 12.3 - - - +
887J GLY* 3.6 26.5 + - - -
888J GLU 5.9 0.2 - - - -
892J ASP* 1.3 70.7 - - - +
894J LYS* 1.3 61.2 + - - +
895J VAL 3.5 0.2 - - - -
896J ALA* 3.7 3.8 - - + -
897J GLN* 2.9 31.7 + - - +
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Residues in contact with LYS 894 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869J LEU* 5.2 5.8 - - - -
892J ASP* 3.9 24.0 - - + +
893J GLU* 1.3 80.0 - - - +
895J VAL* 1.3 76.4 + - - +
897J GLN* 3.9 2.5 - - - +
898J GLU* 2.9 32.4 + - - +
921J ARG* 5.6 8.2 - - - +
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Residues in contact with VAL 895 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890J VAL* 4.5 3.6 - - + -
892J ASP* 3.3 35.0 - - - +
894J LYS* 1.3 85.6 - - - +
896J ALA* 1.3 62.8 + - - +
898J GLU* 3.1 26.3 - - - +
899J LEU* 2.9 35.2 + - + +
921J ARG* 3.6 35.4 - - - +
922J LEU* 4.2 27.6 - - + -
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Residues in contact with ALA 896 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883J ALA 4.6 1.6 - - - +
886J VAL* 4.2 7.0 - - + +
887J GLY* 3.5 35.7 - - - +
890J VAL* 5.2 4.3 - - + -
892J ASP 3.9 2.9 - - - +
893J GLU* 3.7 8.0 - - + +
894J LYS 3.1 0.2 - - - -
895J VAL* 1.3 78.4 - - + +
897J GLN* 1.3 56.6 + - - +
898J GLU 2.9 3.1 - - - -
899J LEU* 2.8 32.5 + - - +
900J ILE* 3.0 27.9 - - + +
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Residues in contact with GLN 897 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868J TYR* 3.5 38.8 + - + +
869J LEU* 3.6 26.6 - - + +
871J ARG* 4.6 19.1 + - - +
873J LEU* 4.3 10.3 - - - +
883J ALA* 4.8 2.9 + - + -
893J GLU 2.9 21.4 + - - +
894J LYS 4.2 1.7 - - - +
896J ALA* 1.3 73.6 - - - +
898J GLU* 1.3 64.3 + - - +
900J ILE* 3.8 20.5 - - - +
902J MET* 3.9 23.5 - - - +
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Residues in contact with GLU 898 (chain J).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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894J LYS* 2.9 22.4 + - - +
895J VAL* 3.1 32.2 - - - +
897J GLN* 1.3 82.0 + - - +
899J LEU* 1.3 67.4 + - - +
900J ILE 3.7 2.4 + - - +
921J ARG* 3.8 27.4 + - - +
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Residues in contact with LEU 899 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886J VAL* 5.2 2.2 - - + -
895J VAL* 2.9 26.3 + - + +
896J ALA* 2.8 26.5 + - - +
898J GLU* 1.3 78.1 - - - +
900J ILE* 1.3 60.7 + - + -
901J GLN* 3.8 7.4 + - - -
914J LEU* 3.3 39.0 - - + +
917J GLN* 4.0 41.1 - - + +
918J ALA* 4.5 2.0 - - + +
921J ARG* 4.3 6.1 - - + -
922J LEU* 4.0 26.0 - - + -
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Residues in contact with ILE 900 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882J PHE* 3.5 24.0 - - + -
883J ALA* 4.2 13.5 - - - -
886J VAL* 3.6 36.3 - - + -
896J ALA* 3.0 27.9 + - + +
897J GLN* 3.8 12.9 + - - +
898J GLU 3.5 2.3 - - - +
899J LEU* 1.3 82.3 - - + +
901J GLN* 1.3 70.9 + - - +
902J MET* 3.5 26.0 + - + +
906J GLN* 4.2 5.6 - - - +
914J LEU* 3.6 22.0 - - + -
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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