Contacts of the helix formed by residues 3947 - 3954 (chain A) in PDB entry 5NUG
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 LEU3947 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3935A VAL* 3.5 40.2 - - + +
3938A LEU* 3.6 37.9 - - + +
3939A SER* 3.8 9.2 - - - +
3944A PHE* 4.3 16.4 - - + +
3945A LYS 2.9 11.5 + - - +
3946A ASP* 1.3 73.6 - - - +
3948A ILE* 1.3 67.6 + - - +
3949A ALA 3.3 1.3 - - - -
3950A LYS* 3.3 19.5 + - + +
3951A VAL* 3.8 11.7 + - + +
3992A LEU* 4.4 13.5 - - + -
3996A PHE* 4.2 21.3 - - + -
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Residues in contact with ILE3948 (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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3922A PRO* 4.9 24.9 - - + -
3923A ARG* 5.2 11.9 - - + +
3935A VAL* 3.8 25.4 - - + -
3936A VAL* 5.6 3.1 - - + -
3939A SER* 4.6 17.9 - - - +
3945A LYS 4.7 1.9 + - - +
3947A LEU* 1.3 76.6 - - + +
3949A ALA* 1.3 62.0 + - - +
3951A VAL* 3.4 23.3 - - + +
3952A GLN* 4.1 10.9 + - - +
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Residues in contact with ALA3949 (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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3946A ASP* 5.0 15.3 - - + -
3947A LEU 3.3 1.2 - - - +
3948A ILE* 1.3 77.8 - - - +
3950A LYS* 1.3 63.5 + - - +
3952A GLN* 3.6 9.6 + - - +
3953A ALA* 3.2 23.6 + - - +
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Residues in contact with LYS3950 (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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3946A ASP* 3.7 26.5 + - + +
3947A LEU* 3.3 15.4 + - + +
3948A ILE 3.2 0.6 - - - -
3949A ALA* 1.3 77.4 - - - +
3951A VAL* 1.3 58.0 + - + +
3953A ALA* 3.8 5.7 - - + +
3954A ASP* 2.7 50.8 + - + +
3972A TYR* 4.3 33.6 - - + +
3973A LEU 5.0 4.8 + - - +
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Residues in contact with VAL3951 (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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3923A ARG* 5.4 9.2 - - + -
3927A LEU* 4.8 18.4 - - + -
3935A VAL* 6.5 0.9 - - + -
3947A LEU 3.8 11.4 + - - +
3948A ILE* 3.4 19.3 - - + +
3950A LYS* 1.3 77.7 - - + +
3952A GLN* 1.3 69.4 - - + +
3954A ASP* 3.2 21.3 - - - +
3955A GLU* 3.3 8.8 - - - +
3996A PHE* 4.3 27.6 - - + -
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Residues in contact with GLN3952 (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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3923A ARG* 4.4 19.0 - - + +
3948A ILE* 4.2 16.1 - - - +
3949A ALA* 3.6 9.4 + - - +
3950A LYS 3.3 0.2 - - - -
3951A VAL* 1.3 82.5 - - + +
3953A ALA* 1.3 65.0 + - - +
3955A GLU* 3.6 15.5 - - - +
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Residues in contact with ALA3953 (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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3949A ALA 3.2 15.3 + - - +
3950A LYS* 3.8 9.0 - - + +
3952A GLN* 1.3 81.4 - - - +
3954A ASP* 1.3 57.4 + - + +
3955A GLU* 3.3 5.2 + - - +
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Residues in contact with ASP3954 (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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3950A LYS* 2.7 32.5 + - + +
3951A VAL* 3.2 13.2 - - - +
3953A ALA* 1.3 70.9 - - + +
3955A GLU* 1.3 60.5 + - - +
3956A GLN 3.6 2.2 - - - +
3957A PHE* 3.5 28.2 - - + +
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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