Contacts of the helix formed by residues 82 - 86 (chain L) in PDB entry 6D2P
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 GLN 82 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15L PRO* 5.5 1.6 - - - -
64L ARG* 3.3 34.1 + - - +
80L GLY* 3.5 11.6 + - - +
81L LEU* 1.3 76.7 - - - +
83L ALA* 1.3 66.6 + - - +
84L GLU* 2.9 33.6 - - + +
85L ASP* 2.9 26.5 + - - +
108L VAL* 3.3 14.9 - - - +
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Residues in contact with ALA 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15L PRO* 6.1 0.4 - - - +
82L GLN* 1.3 76.0 - - - +
84L GLU* 1.3 60.3 + - - +
85L ASP 3.1 0.2 - - - -
86L GLU* 3.2 25.6 + - - +
108L VAL* 4.2 15.8 - - + +
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Residues in contact with GLU 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L GLN* 4.0 2.6 + - - -
42L HIS* 2.9 31.3 + - + +
64L ARG* 5.2 2.7 - - - -
82L GLN* 2.9 31.5 - - + +
83L ALA* 1.3 75.0 - - - +
85L ASP* 1.3 64.0 + - - +
86L GLU 3.1 6.0 + - - -
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Residues in contact with ASP 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L GLN* 3.9 4.6 + - - +
64L ARG* 2.6 34.6 + - - -
65L PHE* 3.9 13.5 - - + -
78L ILE* 3.7 8.7 - - + +
80L GLY 3.6 0.3 - - - +
81L LEU* 3.6 21.7 - - + -
82L GLN 2.9 29.0 + - - +
84L GLU* 1.3 82.7 - - - +
86L GLU* 1.3 58.8 + - - +
87L ALA 2.9 8.3 + - - -
89L TYR* 2.6 34.9 + - - +
106L LEU* 3.5 4.9 - - + +
108L VAL* 4.5 0.2 - - - -
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Residues in contact with GLU 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42L HIS* 3.4 13.0 - - - -
43L PRO* 4.7 5.5 - - - +
83L ALA* 3.2 18.9 + - - +
84L GLU 3.1 1.8 - - - +
85L ASP* 1.3 73.9 - - - +
87L ALA* 1.3 61.4 + - - +
106L LEU 3.4 19.7 - - - +
107L THR* 3.6 8.7 - - - +
108L VAL* 3.6 40.1 + - + +
143L TYR* 5.3 0.9 + - - -
169L LYS* 3.7 22.8 + - - -
175L TYR* 3.1 25.3 + - - -
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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