Contacts of the helix formed by residues 83 - 88 (chain J) in PDB entry 2ABJ
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 83 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79J LEU* 3.9 12.5 - - - +
80J HIS* 2.7 30.9 + - - +
81J PRO 3.3 1.4 - - - -
82J GLY* 1.3 73.7 - - - +
84J SER* 1.3 61.1 + - - +
85J ALA* 3.1 1.8 - - - -
86J LEU* 2.8 34.9 + - - +
87J HIS* 3.2 12.0 - - - -
165J ILE* 6.3 0.2 - - - -
166J GLY 3.9 11.7 - - - -
167J THR* 3.7 20.1 + - - -
168J GLU 3.3 8.0 + - - -
169J PRO* 4.4 0.4 - - - +
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Residues in contact with SER 84 (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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82J GLY 3.2 5.7 + - - -
83J SER* 1.3 71.4 - - - +
85J ALA* 1.3 57.7 + - - +
86J LEU 3.1 0.2 - - - -
87J HIS* 3.8 3.1 - - - +
88J TYR* 2.8 45.6 + - - +
89J ALA 3.3 4.3 + - - -
90J VAL* 3.5 23.0 + - - +
166J GLY* 3.6 21.1 + - - -
168J GLU* 3.3 25.5 + - - +
170J SER 5.4 2.5 - - - -
174J LYS 5.5 4.3 - - - -
176J PRO* 4.3 2.9 - - - +
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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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85G ALA 3.5 1.3 - - - +
86G LEU* 4.3 10.3 - - + -
91G GLU* 2.6 27.5 - - - +
83J SER* 4.7 1.8 - - - +
84J SER* 1.3 77.6 + - - +
86J LEU* 1.3 54.3 + - + +
87J HIS 3.5 0.2 - - - -
89J ALA* 3.8 1.4 - - - -
90J VAL 3.4 25.5 + - - +
91J GLU* 3.0 19.8 - - - +
165J ILE* 3.7 20.9 - - + -
166J GLY 3.0 19.7 + - - +
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Residues in contact with LEU 86 (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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77G LEU* 3.6 31.0 - - + -
79G LEU* 4.0 16.8 - - + -
85G ALA* 4.2 16.2 - - + -
86G LEU* 3.7 29.8 - - + -
91G GLU* 3.4 26.4 - - - +
92G LEU 5.0 4.7 + - - +
163G ALA* 5.3 2.4 - - - +
165G ILE* 3.9 18.5 - - + +
182G PHE* 4.3 4.5 - - + -
79J LEU* 5.1 4.0 - - + -
80J HIS 4.4 3.1 - - - +
81J PRO 4.1 12.3 - - - +
83J SER* 2.8 25.5 + - - +
85J ALA* 1.3 77.9 - - + +
87J HIS* 1.3 66.9 + - + +
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Residues in contact with HIS 87 (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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91G GLU* 3.5 3.5 - - - +
92G LEU 5.6 0.2 - - - -
93G PHE* 3.4 21.3 - - + +
161G ARG* 2.9 57.6 + - + +
163G ALA* 3.9 19.7 - - + +
182G PHE* 4.3 5.1 - + - -
184G LEU* 4.5 1.8 - - + -
222G GLY* 3.3 18.9 - - - -
81J PRO 2.7 25.8 + - - -
82J GLY* 3.5 16.3 - - - -
83J SER 3.2 16.6 - - - +
84J SER* 3.3 2.6 + - - +
86J LEU* 1.3 83.8 - - + +
88J TYR* 1.3 71.6 + + + +
171J LEU* 4.0 8.5 - - + -
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Residues in contact with TYR 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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93G PHE* 3.7 21.1 - + - -
161G ARG* 2.4 40.1 + - - -
222G GLY 3.3 7.6 - - - -
225G TYR* 3.8 24.0 - + + -
226G GLY* 2.7 32.4 + - - -
229G LEU* 5.2 1.1 - - + -
3401G CBC 3.7 15.0 - + - -
82J GLY 6.1 0.9 - - - -
84J SER* 2.8 25.5 + - - +
87J HIS* 1.3 82.9 - - + +
89J ALA* 1.3 61.5 + - - +
90J VAL* 3.1 12.1 + - + +
170J SER 5.1 1.3 - - - -
171J LEU* 2.4 32.1 + - - -
172J GLY 3.8 11.2 - - - -
173J VAL* 3.6 25.4 - - + -
174J LYS 5.4 0.7 - - - -
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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