Contacts of the helix formed by residues 816 - 820 (chain B) in PDB entry 4YZ9
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 816 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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814B ALA* 3.1 7.8 - - + +
815B MET* 1.3 77.4 - - - +
817B PRO* 1.3 75.1 - - - +
818B GLN* 3.0 34.2 + - - +
819B LYS* 3.0 40.8 + - + +
820B ARG* 3.8 3.8 + - - +
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Residues in contact with PRO 817 (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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741B GLU* 3.5 45.3 - - + +
752B THR* 5.9 0.7 - - + -
754B THR* 3.5 30.7 - - - +
815B MET 3.3 9.8 - - - +
816B ASP* 1.3 90.9 - - - +
818B GLN* 1.3 61.5 + - + +
819B LYS 3.5 0.5 + - - -
820B ARG* 3.5 20.6 + - - +
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Residues in contact with GLN 818 (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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816B ASP* 3.0 25.1 + - - +
817B PRO* 1.3 81.3 - - + +
819B LYS* 1.3 61.3 + - + +
820B ARG 3.4 4.0 + - - +
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Residues in contact with LYS 819 (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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811B LYS* 3.6 25.3 - - + +
814B ALA* 4.5 10.8 - - + -
816B ASP* 3.0 31.0 + - + +
818B GLN* 1.3 76.7 - - - +
820B ARG* 1.3 62.7 + - - +
821B PRO* 3.7 4.3 - - - +
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Residues in contact with ARG 820 (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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739B ALA* 3.9 2.0 - - - +
740B PRO* 3.8 18.0 - - - +
741B GLU* 2.6 34.8 + - - -
753B TYR* 4.9 3.5 + - - -
754B THR* 3.2 36.6 + - + +
757B ILE* 4.0 13.0 - - + -
758B PHE* 3.5 19.9 - - - +
811B LYS 3.4 8.5 - - - +
812B MET 3.4 21.8 + - - +
814B ALA* 2.8 25.7 + - + +
815B MET* 3.6 15.0 + - - +
816B ASP 3.9 7.4 - - - +
817B PRO* 3.7 22.6 - - - +
818B GLN 3.4 5.0 - - - +
819B LYS* 1.3 77.5 - - - +
821B PRO* 1.3 68.9 - - + +
822B SER 3.8 0.9 + - - -
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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