Contacts of the helix formed by residues 821 - 824 (chain A) in PDB entry 2VJ0
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 THR 821 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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705A PHE* 3.5 33.7 - - + -
709A VAL* 4.6 7.7 - - + -
795A PHE* 3.6 11.0 - - - -
819A PRO* 3.7 5.6 - - + -
820A ILE* 1.3 77.6 - - - +
822A LEU* 1.3 67.0 + - - +
823A ASN* 2.7 25.1 + - - -
824A LYS* 2.9 37.6 + - - +
825A PHE* 3.9 2.1 - - - -
929A ARG* 4.1 7.0 - - - +
933A LEU* 3.9 20.2 - - + -
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Residues in contact with LEU 822 (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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791A CYS* 4.9 1.6 - - - -
794A ASP* 3.9 23.3 - - + -
795A PHE* 3.7 42.3 + - + +
821A THR* 1.3 73.3 - - - +
823A ASN* 1.3 57.4 + - - +
825A PHE* 3.1 20.2 + - + +
893A ILE* 3.6 34.0 - - + +
895A THR* 4.9 2.7 - - + -
926A VAL* 3.9 41.3 - - + -
929A ARG* 4.3 16.6 - - + +
930A LEU* 4.3 11.2 - - + -
933A LEU* 4.3 3.2 - - + +
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Residues in contact with ASN 823 (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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709A VAL* 2.8 31.7 + - - +
821A THR* 2.7 27.5 + - - -
822A LEU* 1.3 73.9 - - - +
824A LYS* 1.3 61.2 + - - +
825A PHE 3.0 6.3 - - - -
826A PHE* 3.0 31.1 + - + +
871A GLY 4.7 0.8 + - - -
872A PHE* 3.2 64.6 + - + +
873A GLY* 4.8 0.2 - - - -
930A LEU* 4.1 8.1 - - + +
933A LEU* 3.7 8.7 - - - +
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Residues in contact with LYS 824 (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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708A PHE 3.0 28.1 + - - -
709A VAL 3.2 19.7 + - - +
710A CYS 4.6 0.8 - - - -
711A LYS* 3.0 12.1 + - - +
712A ASN* 2.8 23.3 + - - +
730A PHE* 3.3 63.7 - - + +
732A GLN 4.8 0.5 - - - +
819A PRO 4.0 10.1 - - - +
821A THR* 2.9 34.2 + - - +
823A ASN* 1.3 78.6 - - - +
825A PHE* 1.3 60.7 + - + +
826A PHE 3.4 1.6 + - - +
827A GLN* 4.5 7.8 + - - -
871A GLY 5.6 0.8 + - - -
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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