Contacts of the helix formed by residues 80 - 85 (chain C) in PDB entry 3STJ
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 ASN 80 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79C THR* 1.3 83.2 + - - +
81C ASN* 1.3 66.0 + - - +
82C HIS* 3.3 24.5 - - + -
83C VAL* 3.0 32.9 + - + +
84C ILE 3.6 3.3 + - - -
112C ASP* 2.9 22.4 + - - +
114C ALA* 4.0 2.4 - - - +
187C SER* 3.4 0.2 - - - -
188C GLY* 3.0 23.2 + - - -
201C ILE* 3.8 8.5 - - - +
202C ASN 3.2 7.8 - - - +
203C THR* 3.1 25.1 + - - +
219C ILE* 3.8 5.5 - - - +
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ASN* 1.3 70.5 - - - +
82C HIS* 1.3 53.0 + - - +
84C ILE* 3.0 10.0 + - - +
85C ASN* 2.8 55.3 + - - +
107C SER* 3.3 25.7 + - - -
108C ASP 3.9 17.9 - - - +
109C ASP* 3.8 28.1 + - - +
112C ASP* 2.8 20.7 + - - +
113C ILE 4.1 5.8 - - - +
114C ALA* 3.8 11.3 - - - +
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Residues in contact with HIS 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80C ASN* 3.3 24.2 + - - -
81C ASN* 1.3 75.7 - - - +
83C VAL* 1.3 68.7 + - + +
85C ASN* 3.9 24.3 + - - +
86C GLN* 4.9 3.3 - - - +
112C ASP* 2.7 33.3 + - - +
187C SER* 3.2 22.0 + - - -
203C THR* 3.4 20.4 + - + -
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Residues in contact with VAL 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 4.0 25.1 - - + +
31C VAL* 3.8 20.7 - - + +
63C GLY* 5.9 1.6 - - - -
64C LEU* 4.8 2.5 - - - +
65C GLY* 3.9 25.1 - - - +
79C THR* 4.1 9.4 - - - +
80C ASN* 3.0 25.1 + - + +
82C HIS* 1.3 90.9 - - + +
84C ILE* 1.3 60.8 + - + +
86C GLN 5.5 0.3 + - - -
187C SER* 3.7 26.2 - - - +
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Residues in contact with ILE 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C VAL* 3.7 30.3 - - + -
31C VAL* 3.9 9.2 - - + -
79C THR* 3.9 10.8 - - + -
80C ASN 4.1 3.4 - - - +
81C ASN* 3.0 15.0 + - - +
83C VAL* 1.3 80.0 - - + +
85C ASN* 1.3 66.5 + - - +
86C GLN 3.4 2.2 - - - -
87C ALA* 3.0 24.3 + - - +
90C ILE* 3.7 15.2 - - + +
104C LEU* 3.9 22.0 - - + +
114C ALA* 3.9 20.2 - - + -
116C LEU* 3.7 32.1 - - + -
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Residues in contact with ASN 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81C ASN* 2.8 36.5 + - - +
82C HIS* 3.9 24.9 + - - +
83C VAL 3.7 0.4 - - - -
84C ILE* 1.3 72.9 - - - +
86C GLN* 1.4 75.9 + - - +
87C ALA 5.3 0.5 - - - +
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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