Contacts of the helix formed by residues 82 - 89 (chain F) in PDB entry 2YW7
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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33C LEU* 4.8 0.4 - - - -
34C THR* 4.8 5.4 - - - -
37C HIS* 3.5 41.1 - - + +
94C ASP* 3.1 27.7 + - - -
95C TYR* 4.1 21.6 + - + +
80F LYS* 3.6 3.7 - - + -
81F GLY* 1.3 76.4 - - - +
83F PRO* 1.4 66.4 - - - +
84F GLY 2.7 13.0 + - - -
85F ALA* 3.0 15.4 + - - +
86F ILE* 3.0 17.6 + - - +
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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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30C ASP* 2.9 37.9 - - + +
33C LEU* 3.4 28.3 - - + -
34C THR* 4.7 0.7 - - - +
83C PRO* 5.5 0.9 - - + -
86C ILE* 4.1 11.0 - - + +
87C ILE* 3.6 17.3 - - + +
90C ARG* 3.2 18.2 - - - +
94C ASP* 4.2 0.2 - - - -
82F THR* 1.4 84.2 - - - +
84F GLY* 1.3 59.2 + - - +
86F ILE* 3.5 14.5 - - + +
87F ILE* 3.6 24.1 - - - +
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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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87C ILE* 5.6 0.2 - - - -
90C ARG* 4.1 4.2 - - - +
94C ASP* 3.0 27.3 + - - -
82F THR 2.7 5.9 + - - -
83F PRO* 1.3 70.9 - - - +
85F ALA* 1.3 67.1 + - - -
86F ILE 2.7 3.8 + - - -
87F ILE* 2.8 22.1 + - - +
88F LYS* 2.8 18.7 + - - -
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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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94C ASP* 3.9 2.2 + - - -
22F GLN* 4.1 4.7 - - - +
26F SER* 3.1 2.4 + - - -
80F LYS* 3.0 48.7 - - + +
82F THR* 3.0 18.7 + - - +
84F GLY* 1.3 69.4 - - - +
86F ILE* 1.3 58.9 + - - +
88F LYS* 3.7 11.9 - - - +
89F ASP* 2.8 32.4 + - - +
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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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33C LEU* 3.8 19.1 - - + -
83C PRO* 4.5 14.1 - - + -
26F SER* 3.1 43.7 - - - +
29F ASN* 3.5 22.4 - - + +
30F ASP* 4.0 6.4 - - + +
33F LEU* 4.4 9.6 - - + -
81F GLY* 5.6 0.9 - - - -
82F THR* 3.0 23.6 - - - +
83F PRO* 3.5 22.7 - - + +
84F GLY 2.7 4.6 + - - -
85F ALA* 1.3 74.4 - - + +
87F ILE* 1.3 56.9 + - - +
89F ASP* 3.6 2.1 - - - +
90F ARG* 3.0 28.8 + - - +
92F TRP* 5.2 1.4 - - - -
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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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83C PRO* 3.9 19.7 - - + -
84C GLY* 4.2 7.9 - - - +
87C ILE* 4.6 14.6 - - + -
83F PRO 3.6 17.5 - - - +
84F GLY* 2.8 17.5 + - - +
86F ILE* 1.3 71.0 - - - +
88F LYS* 1.3 75.6 + - + +
90F ARG* 3.5 47.0 + - - +
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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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94C ASP* 5.6 3.2 + - - -
84F GLY* 2.8 20.2 + - - +
85F ALA* 3.7 10.9 - - - +
87F ILE* 1.3 89.0 - - + +
89F ASP* 1.3 60.8 + - + +
90F ARG 3.6 3.8 + - - +
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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* 2.8 39.7 + - - +
23F LYS* 4.5 23.9 - - + +
26F SER* 2.8 31.7 + - - -
85F ALA* 2.8 12.1 + - - +
86F ILE 3.6 0.2 - - - +
88F LYS* 1.3 77.4 - - + +
90F ARG* 1.3 63.0 + - - +
91F THR* 4.0 2.4 + - - +
92F TRP* 4.9 5.5 - - - -
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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