Contacts of the helix formed by residues 892 - 900 (chain N) in PDB entry 5D4C
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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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887N ALA 3.6 3.8 + - - +
890N VAL* 3.1 13.2 - - + +
891N GLU* 1.3 79.4 - - - +
893N GLU* 1.3 62.2 + - - +
894N LYS* 3.3 28.8 + - - -
895N VAL* 3.2 32.1 + - + +
896N ALA* 3.1 27.2 + - - +
922N LEU* 4.7 10.7 - - + +
926N LYS* 4.7 5.8 + - - +
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Residues in contact with GLU 893 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868N TYR* 3.2 38.8 + - + +
869N MET* 4.8 10.2 - - + +
887N ALA* 4.2 19.9 + - + +
891N GLU 4.2 0.8 - - - -
892N ASP* 1.3 72.4 + - - +
894N LYS* 1.3 70.0 + - + +
896N ALA* 3.6 1.0 + - - +
897N TRP* 2.9 31.2 + - + +
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Residues in contact with LYS 894 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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869N MET* 4.8 17.0 - - + -
892N ASP* 3.3 17.9 + - - +
893N GLU* 1.3 82.2 - - + +
895N VAL* 1.3 68.4 + - + +
897N TRP* 3.2 8.2 + - - +
898N GLU* 3.0 32.4 + - - +
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Residues in contact with VAL 895 (chain N).
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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892N ASP* 3.2 31.5 + - + +
894N LYS* 1.3 78.7 - - + +
896N ALA* 1.3 58.9 + - - +
898N GLU* 2.9 28.2 + - - +
899N LEU* 2.9 24.8 + - + +
921N ARG* 4.0 37.0 - - + +
922N LEU* 3.9 22.9 - - + -
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Residues in contact with ALA 896 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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883N ALA 5.2 2.0 - - - +
886N VAL* 3.8 11.8 - - + +
887N ALA* 3.7 25.8 - - + +
890N VAL* 3.7 12.9 - - + +
892N ASP 3.1 21.3 + - - +
893N GLU 3.9 2.0 - - - +
895N VAL* 1.3 77.1 - - - +
897N TRP* 1.3 62.4 + - - +
899N LEU* 3.5 12.0 + - - +
900N ILE* 3.4 30.8 + - - +
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Residues in contact with TRP 897 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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868N TYR* 3.5 34.3 - + - +
869N MET* 3.6 26.9 - - + -
871N LYS* 3.2 33.1 - - + +
873N LEU* 3.6 24.2 - - + -
880N ILE* 5.0 0.7 - - + -
883N ALA* 4.2 20.2 - - + -
893N GLU* 2.9 20.0 + - + +
894N LYS* 3.4 5.4 - - - +
895N VAL 3.1 0.2 - - - -
896N ALA* 1.3 74.5 - - - +
898N GLU* 1.3 69.8 + - + +
900N ILE* 4.0 18.9 - - + +
902N LEU* 3.5 36.6 - - + -
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Residues in contact with GLU 898 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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894N LYS* 3.0 23.3 + - - +
895N VAL* 2.9 12.5 + - - +
897N TRP* 1.3 84.0 - - + +
899N LEU* 1.3 63.4 + - - +
900N ILE 3.8 4.3 - - - +
921N ARG* 3.4 33.4 + - - +
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Residues in contact with LEU 899 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886N VAL* 5.2 3.8 - - + -
890N VAL* 5.7 0.4 - - + -
895N VAL* 2.9 18.3 + - + +
896N ALA* 3.8 10.8 - - - +
897N TRP 3.3 0.2 - - - -
898N GLU* 1.3 79.7 - - - +
900N ILE* 1.3 65.1 + - - +
901N GLN* 3.8 5.7 + - - +
914N LEU* 3.8 21.6 - - + +
917N GLN* 3.6 31.2 - - + +
918N ALA* 4.0 28.5 - - + +
921N ARG* 4.0 32.3 - - + +
922N LEU* 4.0 18.8 - - + -
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Residues in contact with ILE 900 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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882N PHE* 4.1 17.5 - - + -
883N ALA* 3.6 35.7 - - + +
886N VAL* 3.8 27.8 - - + -
896N ALA 3.4 19.3 - - - +
897N TRP* 4.0 19.5 - - + +
898N GLU 3.8 6.6 - - - +
899N LEU* 1.3 78.9 - - - +
901N GLN* 1.3 63.4 + - - +
902N LEU* 3.9 21.7 + - + +
914N LEU* 3.8 18.4 - - + -
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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