Contacts of the helix formed by residues 84 - 90 (chain C) in PDB entry 1XBT
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 VAL 84 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51C LEU* 3.9 13.7 - - + -
53C ILE* 3.7 34.1 - - + -
76C LEU* 4.2 23.6 - - + -
77C PRO 4.5 6.3 - - - +
78C ALA* 3.9 27.6 - - + -
81C LEU* 3.0 9.8 + - - +
83C ASP* 1.3 82.6 - - + +
85C ALA* 1.3 66.1 + - - +
86C GLN 3.2 3.8 + - - -
87C GLU* 3.2 11.1 + - + +
88C ALA* 3.1 14.6 + - + +
108C PHE* 4.9 0.2 - - - -
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Residues in contact with ALA 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 LEU 3.2 4.8 + - - -
82C ARG* 3.3 25.3 + - + +
83C ASP 3.6 0.2 - - - -
84C VAL* 1.3 77.5 - - - +
86C GLN* 1.3 56.4 + - - +
88C ALA* 3.3 2.9 + - - +
89C LEU* 3.1 38.4 + - + +
108C PHE* 4.0 22.2 - - + -
112C MET* 3.8 6.9 - - + +
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Residues in contact with GLN 86 (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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82C ARG 5.0 0.2 + - - -
83C ASP 5.5 0.6 - - - +
84C VAL 3.2 1.0 + - - -
85C ALA* 1.3 75.7 - - - +
87C GLU* 1.3 72.4 + - + +
89C LEU* 3.3 25.0 + - - +
90C GLY* 3.8 4.3 + - - -
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Residues in contact with GLU 87 (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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51C LEU* 4.1 10.8 - - + +
76C LEU* 3.4 34.4 - - + +
83C ASP 4.3 4.9 - - - +
84C VAL* 3.2 22.7 + - - +
86C GLN* 1.3 82.2 - - + +
88C ALA* 1.3 62.2 + - - +
89C LEU 3.3 0.5 + - - -
90C GLY* 3.4 12.3 + - - -
91C VAL* 4.1 10.7 + - - +
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Residues in contact with ALA 88 (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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51C LEU* 3.8 16.9 - - + +
84C VAL* 3.1 13.2 + - + +
85C ALA 3.6 8.5 - - - +
86C GLN 3.3 0.2 - - - -
87C GLU* 1.3 76.7 - - - +
89C LEU* 1.3 61.6 + - - +
91C VAL* 3.4 13.6 + - - +
94C ILE* 3.7 29.0 - - + +
108C PHE* 3.8 12.1 - - + -
112C MET* 3.7 12.6 - - + -
117C LYS* 3.4 12.3 - - - -
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Residues in contact with LEU 89 (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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85C ALA* 3.1 25.9 + - + +
86C GLN* 3.6 19.5 - - - +
87C GLU 3.2 0.8 - - - -
88C ALA* 1.3 77.6 - - - +
90C GLY* 1.3 55.6 + - - +
91C VAL 3.3 1.5 + - - -
112C MET* 3.7 28.5 - - + -
115C ALA* 5.1 8.5 - - + -
117C LYS* 3.3 26.4 + - + +
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Residues in contact with GLY 90 (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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49C LYS* 4.1 19.4 + - - +
86C GLN 3.8 4.2 + - - -
87C GLU 3.4 8.0 + - - -
88C ALA 3.3 0.8 - - - -
89C LEU* 1.3 77.2 - - - +
91C VAL* 1.3 63.3 + - - +
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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