Contacts of the helix formed by residues 82 - 86 (chain c) in PDB entry 5XTD
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 SER 82 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80c ASP 3.6 1.0 + - - -
81c ARG* 1.3 77.4 - - - +
83c GLN* 1.3 65.7 + - - +
84c HIS* 2.9 19.5 + - - +
85c GLU* 3.1 18.4 + - - +
86c ARG* 4.3 3.0 + - - +
112c TYR* 3.8 25.4 - - - -
117c VAL 3.9 1.1 - - - -
118c ASP* 3.3 15.0 - - - +
119c THR* 2.7 39.7 + - - -
120c SER 4.1 1.9 + - - -
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Residues in contact with GLN 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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81c ARG 4.3 5.9 - - - +
82c SER* 1.3 76.0 - - - +
84c HIS* 1.3 63.4 + - - +
85c GLU 3.0 1.4 + - - -
86c ARG* 3.2 43.9 + - - +
97c LEU* 3.1 24.4 + - + +
98c ARG* 2.9 39.1 + - + -
99c LEU* 3.8 10.2 - - - +
106c HIS* 5.9 2.9 - - - +
109c LEU* 4.8 13.0 - - + +
112c TYR* 3.0 28.1 + - + +
114c ARG* 4.1 18.3 - - + -
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Residues in contact with HIS 84 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82c SER* 2.9 16.7 + - - +
83c GLN* 1.3 78.6 - - - +
85c GLU* 1.3 59.4 + - - +
86c ARG 4.0 0.3 - - - +
88c PRO* 5.8 0.2 - - - +
98c ARG* 3.6 15.8 + - - +
114c ARG* 3.2 48.4 + - + +
115c ASN* 3.7 7.5 + - - -
116c ARG 4.1 5.3 + - - -
117c VAL 3.9 7.6 + - - -
118c ASP* 3.1 37.6 + - + +
120c SER* 4.8 11.6 - - - +
702l PEE 4.6 16.6 + - - -
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Residues in contact with GLU 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 ARG* 3.0 41.1 + - + +
82c SER* 3.1 10.3 + - - +
83c GLN 3.0 1.0 - - - -
84c HIS* 1.3 76.9 - - - +
86c ARG* 1.3 66.6 + - + +
87c ASP* 3.7 4.9 + - - +
88c PRO* 5.4 0.3 - - - +
119c THR* 2.7 19.5 - - - +
120c SER* 3.2 22.9 - - - +
121c PRO* 3.5 8.4 - - + +
13o THR* 2.7 25.3 + - - -
14o LEU 5.9 0.4 - - - -
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Residues in contact with ARG 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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78c LEU* 6.3 1.2 - - - +
82c SER 5.0 1.6 - - - +
83c GLN* 3.2 40.8 + - - +
84c HIS 4.0 0.7 - - - +
85c GLU* 1.3 81.0 - - + +
87c ASP* 1.3 65.8 + - - +
88c PRO* 3.1 4.2 - - - +
92c TRP* 3.2 43.0 - - + -
98c ARG* 3.1 44.7 + - - -
99c LEU* 4.1 9.2 - - - +
103c GLU* 3.5 21.1 + - - -
104c PRO 5.6 3.2 + - - -
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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