Contacts of the helix formed by residues 83 - 88 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79G LEU* 3.9 14.8 - - - +
80G HIS* 2.6 32.7 + - - -
81G PRO 3.3 1.0 - - - -
82G GLY* 1.3 74.6 - - - +
84G SER* 1.3 59.7 + - - +
85G ALA* 4.4 0.9 - - - -
86G LEU* 2.9 33.8 + - - +
87G HIS* 3.2 10.6 - - - -
166G GLY 3.9 12.6 - - - -
167G THR* 3.8 15.3 + - - +
168G GLU 3.2 9.8 + - - -
169G PRO* 4.4 1.0 - - - +
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Residues in contact with SER 84 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G GLY 3.2 6.3 + - - -
83G SER* 1.3 70.0 - - - +
85G ALA* 1.3 58.0 + - - +
86G LEU 3.1 1.1 - - - -
87G HIS* 3.8 3.4 - - - +
88G TYR* 2.9 43.0 + - - +
89G ALA 3.3 4.7 + - - -
90G VAL* 3.5 22.4 + - - +
166G GLY* 3.5 22.3 + - - -
168G GLU* 3.3 21.8 + - - +
170G SER 5.1 3.4 - - - -
172G GLY 5.9 1.3 - - - -
174G LYS 5.6 5.2 - - - -
176G PRO* 4.3 3.5 - - - +
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Residues in contact with ALA 85 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G SER* 3.1 2.2 + - - +
84G SER* 1.3 75.9 + - - +
86G LEU* 1.3 52.6 - - + +
89G ALA* 3.8 1.3 - - - -
90G VAL 3.6 24.0 + - - +
91G GLU* 3.0 20.7 - - - +
165G ILE* 3.7 20.2 - - + -
166G GLY 3.1 20.4 + - - +
85J ALA 3.5 1.9 - - - +
86J LEU* 4.2 12.3 - - + -
91J GLU* 2.7 26.5 - - - +
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Residues in contact with LEU 86 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79G LEU* 4.8 5.2 - - + -
80G HIS 4.1 16.4 - - - +
81G PRO 4.1 7.0 - - - +
83G SER* 2.9 18.9 + - - +
85G ALA* 1.3 76.7 - - - +
87G HIS* 1.3 66.7 + - + +
77J LEU* 3.9 28.0 - - + -
79J LEU* 4.1 10.8 - - + -
85J ALA* 4.3 7.2 - - + -
86J LEU* 3.7 28.5 - - + -
91J GLU* 3.3 27.0 - - - +
92J LEU 5.1 4.3 + - - +
163J ALA* 5.3 2.8 - - - +
165J ILE* 3.7 34.4 - - + +
182J PHE* 4.5 3.8 - - + -
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Residues in contact with HIS 87 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81G PRO 2.8 25.4 + - - -
82G GLY* 3.5 15.6 - - - -
83G SER 3.2 24.2 - - - -
84G SER* 3.3 2.2 + - - +
86G LEU* 1.3 81.1 - - + +
88G TYR* 1.3 81.1 + + + +
171G LEU* 4.0 8.7 - - + -
91J GLU* 3.4 6.6 - - - +
92J LEU 5.6 0.8 - - - -
93J PHE* 3.3 18.0 - - + +
161J ARG* 3.1 54.8 + - + +
163J ALA* 4.0 18.4 - - + +
182J PHE* 4.3 4.5 - + - -
184J LEU* 4.4 1.8 - - + -
222J GLY* 3.3 17.0 - - - -
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Residues in contact with TYR 88 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82G GLY 6.1 0.4 - - - -
84G SER* 2.9 22.2 + - - +
87G HIS* 1.3 91.4 - - + +
89G ALA* 1.3 62.2 + - - +
90G VAL* 3.2 11.0 + - + +
170G SER 4.8 2.5 - - - -
171G LEU* 2.4 41.3 + - - -
172G GLY 3.9 8.3 - - - -
173G VAL* 3.7 27.6 - - + -
174G LYS 5.5 0.4 - - - -
93J PHE* 3.7 24.9 - + - -
161J ARG* 3.0 33.5 + - - -
222J GLY 3.3 9.0 - - - -
225J TYR* 3.8 23.8 - - + +
226J GLY* 2.7 34.3 + - - +
229J LEU* 5.8 1.3 - - + -
4401J CBC 3.9 5.3 - + - -
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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