Contacts of the helix formed by residues 85 - 90 (chain r) in PDB entry 3J7Y
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 ASP 85 (chain r).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K TYR* 4.7 4.9 - - - -
166K PHE* 6.1 1.1 - - + -
53S LYS 5.3 0.9 - - - +
54S THR* 3.5 28.5 - - + -
55S SER* 2.7 43.3 + - - +
56S LEU 4.4 0.2 + - - -
81r TYR* 3.4 5.7 - - - +
82r ASN 2.5 40.7 + - - +
83r TYR 3.2 1.5 + - - -
84r ASP* 1.3 72.3 - - - +
86r VAL* 1.3 61.3 + - - +
87r LEU* 3.5 2.9 - - + +
88r LEU* 4.0 7.3 + - + +
89r LEU* 3.5 28.2 + - - +
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Residues in contact with VAL 86 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153K LYS 4.0 15.5 - - - +
154K ARG* 4.9 0.2 - - - -
155K LEU* 3.7 16.6 - - + +
158K TYR* 4.3 6.3 - - + -
83r TYR 4.0 2.2 - - - +
84r ASP 3.3 15.9 - - - +
85r ASP* 1.3 71.1 - - - +
87r LEU* 1.3 62.7 + - - +
88r LEU 3.2 1.8 - - - -
89r LEU* 3.8 10.1 - - + -
90r SER* 2.9 29.1 + - - -
122r ALA* 4.8 3.4 - - + -
127r LEU* 3.5 35.0 - - + +
128r LEU* 3.3 35.9 - - + -
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Residues in contact with LEU 87 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K LEU* 3.8 10.1 - - + -
158K TYR* 3.6 35.9 - - + -
162K GLU* 4.2 21.5 - - + +
163K ILE* 3.8 28.3 - - + -
166K PHE* 3.8 41.7 - - + -
53S LYS* 5.3 9.0 - - + +
85r ASP* 3.5 1.8 - - + -
86r VAL* 1.3 79.2 - - - +
88r LEU* 1.3 56.6 + - - +
90r SER* 3.3 9.6 + - - -
91r GLN* 3.3 25.3 + - - +
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Residues in contact with LEU 88 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166K PHE* 3.7 24.5 - - + -
169K LEU* 3.4 28.5 - - + -
54S THR* 5.2 3.6 - - + -
72r ILE* 5.1 2.7 - - + -
77r LEU* 3.9 19.1 - - + -
81r TYR* 3.4 43.7 - - + -
85r ASP* 4.0 14.3 + - + +
86r VAL 3.2 0.2 - - - -
87r LEU* 1.3 78.4 - - - +
89r LEU* 1.3 69.5 + - + +
91r GLN* 3.1 17.8 + - - +
92r PHE* 3.5 19.8 - - + -
115r ILE* 6.1 1.6 - - + -
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Residues in contact with LEU 89 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81r TYR* 4.8 3.8 - - + -
82r ASN 3.5 21.1 - - - +
83r TYR 3.9 11.7 - - - +
85r ASP 3.5 14.7 + - - +
86r VAL* 3.4 13.1 + - + +
88r LEU* 1.3 91.9 - - + +
90r SER* 1.3 62.3 + - - +
91r GLN 3.1 1.7 + - - -
92r PHE* 3.1 17.4 + - - +
93r ILE* 3.2 19.4 - - + +
115r ILE* 4.8 7.9 - - + +
118r CYS* 3.6 40.8 - - + +
119r VAL* 3.8 20.6 - - + +
122r ALA* 3.9 11.7 - - + -
128r LEU* 5.5 0.2 - - + -
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Residues in contact with SER 90 (chain r).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K LEU* 3.9 24.1 - - - +
86r VAL* 2.9 19.4 + - - +
87r LEU* 3.3 14.2 + - - -
89r LEU* 1.3 74.5 - - - +
91r GLN* 1.3 61.8 + - - +
92r PHE 3.3 0.6 + - - -
93r ILE* 3.5 28.6 + - - +
128r LEU* 4.7 1.3 - - - -
131r HIS* 4.4 13.3 - - - -
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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