Contacts of the helix formed by residues 82 - 90 (chain F) in PDB entry 1VEQ
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 82 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80F LYS* 3.8 2.5 - - - +
81F GLY* 1.3 78.0 + - - +
83F PRO* 1.3 76.8 - - + +
84F GLY 2.8 2.4 + - - -
85F ALA* 3.2 23.9 + - - +
86F ILE* 3.0 16.3 + - - +
33L LEU* 5.2 1.8 - - - -
34L THR* 4.6 4.9 - - - +
37L HIS* 3.8 26.7 - - + +
94L ASP* 3.6 16.5 + - - -
95L TYR* 3.8 37.8 + - + +
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Residues in contact with PRO 83 (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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82F THR* 1.3 86.7 - - - +
84F GLY* 1.3 59.8 + - - +
86F ILE* 2.7 25.4 - - + +
87F ILE* 3.4 11.8 + - - +
30L ASP* 2.9 33.7 - - - +
33L LEU* 4.6 13.8 - - + -
34L THR* 4.3 7.6 - - - +
83L PRO* 5.6 4.1 - - + +
86L ILE* 3.5 31.9 - - + -
87L ILE* 5.4 7.9 - - + +
90L ARG* 3.6 13.9 - - - +
94L ASP* 3.9 4.7 - - + -
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Residues in contact with GLY 84 (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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82F THR 2.8 2.6 + - - -
83F PRO* 1.3 73.2 - - - +
85F ALA* 1.3 66.0 + - - -
86F ILE 2.8 3.4 + - - -
87F ILE* 2.8 29.9 + - - +
88F LYS* 3.3 5.3 + - - +
87L ILE* 5.8 1.8 - - - -
90L ARG* 4.7 2.0 - - - +
94L ASP* 3.0 28.5 + - - -
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Residues in contact with ALA 85 (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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26F SER* 4.2 0.2 - - - -
80F LYS* 3.5 53.2 - - + +
82F THR* 3.2 19.4 + - - +
84F GLY* 1.3 71.3 - - - +
86F ILE* 1.3 61.5 + - - +
88F LYS* 3.4 10.9 + - - +
89F ASP* 3.1 33.5 + - - +
94L ASP* 5.2 0.2 + - - -
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Residues in contact with ILE 86 (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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26F SER* 3.8 26.2 + - - +
29F ASN* 4.0 13.5 - - + +
30F ASP* 3.5 32.8 - - + +
33F LEU* 5.2 4.0 - - + -
80F LYS 5.4 0.2 + - - -
81F GLY* 5.5 2.4 - - - -
82F THR 3.0 13.0 + - - +
83F PRO* 2.7 34.1 - - + +
84F GLY 2.8 1.2 + - - -
85F ALA* 1.3 72.0 - - - +
87F ILE* 1.3 59.2 + - - +
88F LYS 2.9 10.1 + - - -
89F ASP* 3.3 0.7 + - - +
90F ARG* 3.2 26.1 + - + +
33L LEU* 5.3 5.6 - - + -
83L PRO* 3.5 31.4 - - + -
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Residues in contact with ILE 87 (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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83F PRO 3.4 11.2 - - - +
84F GLY* 2.8 33.1 + - - +
86F ILE* 1.3 79.4 - - + +
88F LYS* 1.3 61.3 + - + +
90F ARG* 3.2 53.3 - - - +
83L PRO* 5.5 9.2 - - + +
84L GLY* 5.8 2.0 - - - -
87L ILE* 5.5 21.1 - - + -
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Residues in contact with LYS 88 (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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80F LYS* 4.9 13.4 - - - +
84F GLY 3.3 8.3 + - - +
85F ALA* 3.5 14.1 - - - +
86F ILE 2.9 2.0 + - - -
87F ILE* 1.3 78.5 - - + +
89F ASP* 1.3 71.4 + - - +
90F ARG 3.1 11.3 + - - +
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Residues in contact with ASP 89 (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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22F GLN* 3.3 29.1 + - - +
23F LYS* 4.6 24.4 - - + +
26F SER* 3.1 33.0 + - - +
80F LYS* 5.5 0.9 - - - +
85F ALA* 3.1 15.7 + - - +
88F LYS* 1.3 84.9 - - - +
90F ARG* 1.3 59.8 - - - +
91F THR* 3.9 9.1 + - - +
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Residues in contact with ARG 90 (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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26F SER* 5.0 5.1 - - - +
27F THR* 6.2 0.2 - - - -
30F ASP* 3.3 17.3 + - + -
86F ILE* 3.2 19.8 + - + +
87F ILE* 3.2 46.4 - - - +
88F LYS 3.1 12.0 - - - +
89F ASP* 1.3 78.5 - - - +
91F THR* 1.3 64.2 + - - +
92F TRP* 3.4 47.1 + - + +
93F ASP* 4.2 1.6 - - - +
94F ASP* 3.1 57.9 + - - +
83L PRO* 3.7 11.1 - - - +
84L GLY* 4.9 0.4 - - - +
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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