Contacts of the helix formed by residues 89 - 94 (chain J) in PDB entry 3BBX
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 PHE 89 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70J THR* 3.4 23.6 - - - +
71J ASP* 3.1 17.0 - - - +
72J LYS 3.9 3.1 - - - -
73J VAL* 5.3 4.0 - - - -
74J TYR* 4.3 0.2 - - - -
87J ALA* 6.2 4.3 - - + -
88J THR* 1.3 79.7 - - - +
90J GLU* 1.3 67.3 + - - +
91J GLU* 3.4 7.9 - - + +
92J MET* 3.0 30.7 + - + +
93J ILE* 3.0 10.0 + - - +
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Residues in contact with GLU 90 (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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62J VAL* 4.7 8.8 - - - +
63J ALA* 5.6 0.2 - - - -
64J VAL* 3.9 20.5 - - + +
68J LYS 3.5 23.6 - - - +
69J ARG* 4.0 8.3 - - - +
71J ASP 2.6 13.4 + - - +
72J LYS* 3.7 19.1 + - + -
74J TYR* 3.7 26.5 - - + +
88J THR 3.8 0.4 + - - -
89J PHE* 1.3 70.8 - - - +
91J GLU* 1.3 56.0 + - - +
93J ILE* 2.8 6.6 + - + +
94J ALA* 2.6 47.3 + - - +
101J ILE* 4.0 21.1 - - + +
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Residues in contact with GLU 91 (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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69J ARG* 3.0 27.9 + - + +
70J THR* 3.1 29.7 + - - -
89J PHE* 4.7 8.3 - - + -
90J GLU* 1.3 84.3 + - - +
92J MET* 1.3 66.9 + - + +
93J ILE 3.3 0.3 + - - -
94J ALA* 3.4 10.3 + - - +
95J ARG* 3.3 19.8 + - - +
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Residues in contact with MET 92 (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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87J ALA 4.6 2.2 - - - +
88J THR* 3.3 39.7 - - + -
89J PHE* 3.0 30.0 + - + +
91J GLU* 1.3 84.6 - - + +
93J ILE* 1.3 56.3 + - - +
95J ARG* 3.0 22.4 - - - +
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Residues in contact with ILE 93 (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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74J TYR* 3.6 27.6 - - + -
76J HIS* 4.1 19.5 - - + -
88J THR* 4.2 15.5 - - - +
89J PHE 3.0 6.2 + - - +
90J GLU* 2.8 20.9 + - + +
92J MET* 1.3 77.3 - - - +
94J ALA* 1.3 58.6 + - - +
95J ARG 2.8 12.4 + - - -
96J ARG* 3.0 21.5 + - - +
97J PRO* 4.0 1.0 - - - +
98J GLU* 5.2 6.1 - - + -
100J VAL* 3.4 42.0 - - + -
101J ILE* 5.0 4.9 - - + -
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Residues in contact with ALA 94 (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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60J ASP* 4.4 6.4 - - - +
62J VAL* 6.0 2.5 - - + -
90J GLU* 2.6 35.2 + - - +
91J GLU* 3.4 10.3 + - - +
93J ILE* 1.3 73.6 - - - +
95J ARG* 1.3 62.0 + - - +
96J ARG 3.1 1.6 + - - -
97J PRO* 3.3 21.6 - - + +
101J ILE* 4.6 10.5 - - + -
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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