Contacts of the helix formed by residues 82 - 90 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H THR* 3.4 27.1 - - - +
37H HIS* 4.1 18.5 - - + -
94H ASP* 3.5 19.6 + - - +
95H TYR* 3.6 31.8 + - + +
80J LYS* 5.1 0.2 - - - +
81J GLY* 1.3 77.0 - - - +
83J PRO* 1.4 66.6 - - + +
84J GLY 3.3 0.2 - - - -
85J ALA* 2.7 31.0 + - - +
86J ILE* 2.9 16.2 + - - +
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Residues in contact with PRO 83 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30H ASP* 3.1 36.8 - - + +
33H LEU* 4.3 23.1 - - + -
34H THR* 4.9 0.4 - - - +
83H PRO* 5.8 2.9 - - + +
86H ILE* 4.1 23.8 - - + -
87H ILE* 4.9 9.9 - - + -
90H ARG* 5.5 2.9 - - - -
94H ASP* 3.7 4.5 - - - +
82J THR* 1.4 90.3 - - + +
84J GLY* 1.3 56.4 + - - +
86J ILE* 2.8 31.9 + - + +
87J ILE* 3.2 17.4 + - - +
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Residues in contact with GLY 84 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87H ILE* 5.0 0.4 - - - +
90H ARG* 4.9 8.6 - - - +
94H ASP* 2.9 29.1 + - - -
83J PRO* 1.3 76.4 - - - +
85J ALA* 1.3 56.5 + - - +
87J ILE* 3.6 15.2 - - - +
88J LYS* 3.1 27.0 + - - +
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Residues in contact with ALA 85 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94H ASP* 3.4 4.8 + - - +
22J GLN* 5.0 0.6 + - - +
26J SER* 3.5 4.6 + - - -
80J LYS* 3.7 33.9 - - + +
81J GLY* 4.6 0.2 - - - -
82J THR* 2.7 35.5 + - - +
84J GLY* 1.3 71.6 - - - +
86J ILE* 1.3 51.8 + - - +
88J LYS* 3.7 8.8 - - - +
89J ASP* 2.4 33.8 - - - +
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Residues in contact with ILE 86 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33H LEU* 3.9 20.0 - - + -
83H PRO* 4.1 25.8 - - + -
26J SER* 4.1 21.4 - - - +
29J ASN* 3.8 32.5 - - + +
30J ASP* 4.4 8.3 - - + +
33J LEU* 4.1 11.9 - - + -
81J GLY* 5.7 0.2 - - - -
82J THR 2.9 13.2 + - - +
83J PRO* 2.8 23.2 + - + +
85J ALA* 1.3 74.1 - - + +
87J ILE* 1.3 55.7 + - + +
88J LYS 3.0 3.4 - - - -
89J ASP* 2.9 10.0 - - - +
90J ARG* 2.8 36.7 + - + +
92J TRP* 6.0 0.2 - - + -
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Residues in contact with ILE 87 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83H PRO* 4.1 15.9 - - + -
87H ILE* 3.6 48.5 - - + -
90H ARG* 4.8 4.0 - - - +
83J PRO* 3.2 13.0 + - + +
84J GLY* 3.6 12.3 - - - +
86J ILE* 1.3 76.0 - - - +
88J LYS* 1.3 66.4 + - - +
89J ASP 3.5 0.2 + - - -
90J ARG* 3.7 52.2 + - - +
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Residues in contact with LYS 88 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84J GLY 3.1 22.0 + - - +
85J ALA* 3.7 11.9 - - - +
86J ILE 2.9 1.0 + - - -
87J ILE* 1.3 79.5 - - - +
89J ASP* 1.3 64.6 + - + +
90J ARG 4.4 2.3 - - - +
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Residues in contact with ASP 89 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22J GLN* 3.8 25.8 + - - +
23J LYS* 4.3 25.8 - - + +
26J SER* 3.0 21.7 + - - -
85J ALA 2.4 28.6 - - - +
86J ILE 2.9 6.8 - - - +
88J LYS* 1.3 78.0 - - + +
90J ARG* 1.3 67.9 + - - +
91J THR* 3.3 15.1 + - - +
92J TRP* 5.3 0.9 - - - -
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Residues in contact with ARG 90 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83H PRO* 3.2 23.1 - - - +
84H GLY* 3.8 19.6 - - - +
87H ILE* 5.2 2.8 - - - +
26J SER* 5.4 1.7 - - - -
30J ASP* 3.7 10.3 + - - -
86J ILE* 2.8 20.4 + - + +
87J ILE* 3.7 33.9 - - - +
88J LYS 3.6 2.3 - - - +
89J ASP* 1.3 79.9 + - - +
91J THR* 1.3 60.2 + - - +
92J TRP* 3.4 39.7 + - + +
93J ASP* 4.4 0.8 - - - +
94J ASP* 3.0 50.3 + - - +
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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