Contacts of the helix formed by residues 57 - 61 (chain F) in PDB entry 1VHA
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 57 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107D ARG* 2.7 41.4 + - - -
130D VAL 4.7 0.7 - - - +
131D LYS* 3.5 22.8 - - + +
132D ALA 4.8 2.2 - - - -
47F ASP* 3.2 15.9 - - - +
50F LEU* 3.4 17.6 - - - +
55F LEU 3.3 5.1 + - - +
56F GLY* 1.3 76.1 - - - +
58F ILE* 1.3 55.9 + - + +
59F GLY* 2.9 30.5 + - - -
60F LYS* 2.8 39.6 + - - +
61F LEU 3.8 0.5 + - - -
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Residues in contact with ILE 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASP* 5.5 2.7 - - - +
43F HIS* 3.7 33.9 - - + +
46F THR* 4.0 17.5 - - + +
47F ASP* 2.8 27.6 + - - +
50F LEU* 3.4 12.2 - - - +
57F ASP* 1.3 72.6 - - - +
59F GLY* 1.3 65.8 + - - +
60F LYS 3.1 1.8 + - - -
61F LEU* 3.3 27.2 + - + +
62F PHE 4.8 0.3 + - - -
77F LEU* 3.6 34.5 - - + +
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Residues in contact with GLY 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ARG* 5.1 8.8 - - - -
57F ASP* 2.9 13.0 + - - -
58F ILE* 1.3 82.5 - - - +
60F LYS* 1.3 62.3 + - - +
61F LEU 3.5 0.2 - - - -
62F PHE 4.8 7.2 + - - +
63F PRO* 5.5 1.0 - - - +
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Residues in contact with LYS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ARG* 4.5 32.1 + - - +
110D ILE* 4.8 16.5 - - - +
111D ASP* 4.8 12.9 + - - -
114D ARG* 6.1 0.8 - - - +
130D VAL 5.6 0.6 + - - -
55F LEU 4.5 8.7 - - - +
56F GLY* 4.3 22.5 - - - -
57F ASP* 2.8 19.3 + - - +
59F GLY* 1.3 78.5 - - - +
61F LEU* 1.3 67.8 + - - +
62F PHE 3.2 2.7 - - - -
63F PRO* 3.1 23.0 - - + +
84F GLN* 5.3 0.5 + - - +
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Residues in contact with LEU 61 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F THR* 4.0 7.2 - - + -
50F LEU* 3.5 35.2 - - + -
57F ASP 3.8 1.4 + - - -
58F ILE* 3.3 23.6 + - + +
60F LYS* 1.3 75.8 - - - +
62F PHE* 1.3 74.9 + - + +
63F PRO* 3.0 10.0 - - - +
77F LEU* 3.4 48.0 - - + +
80F GLU* 4.1 8.9 - - + +
81F ALA* 3.9 11.7 - - - +
84F GLN* 3.7 34.0 + - - +
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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