Contacts of the helix formed by residues 82 - 89 (chain A) in PDB entry 3APO
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 ARG 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.7 15.2 - - + -
81A ASN* 1.3 80.8 + - - +
83A ALA* 1.3 66.2 + - - +
84A TYR 3.1 0.4 - - - -
85A GLU* 3.0 18.8 + - - +
86A VAL* 3.2 34.0 + - + +
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 3.7 51.1 - - + +
39A LEU* 4.8 11.7 - - + -
40A LEU* 4.1 14.4 - - + -
81A ASN 2.5 8.1 + - - +
82A ARG* 1.3 76.4 - - - +
84A TYR* 1.3 55.6 + - - +
86A VAL* 3.3 1.6 + - - +
87A LEU* 2.8 35.6 + - + +
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Residues in contact with TYR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.4 9.7 - - + +
51A ILE* 3.7 17.5 - - + -
52A ARG* 3.3 29.3 + - + +
55A PHE* 3.3 65.5 - + + -
81A ASN* 2.7 14.9 + - - +
83A ALA* 1.3 70.3 - - - +
85A GLU* 1.3 70.6 + - - +
87A LEU* 4.5 1.1 - - - +
88A LYS* 2.7 76.1 + - + +
122A PHE* 3.3 26.9 - + - -
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A ASN* 4.0 13.1 + - - +
82A ARG* 3.0 13.6 + - - +
84A TYR* 1.3 92.6 - - - +
86A VAL* 1.3 62.7 + - + +
88A LYS* 3.2 30.9 - - - +
89A ASP* 3.6 22.7 + - - +
92A LEU* 4.8 5.1 - - + +
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Residues in contact with VAL 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.0 24.7 - - + -
82A ARG* 3.2 38.7 + - - +
83A ALA 3.5 6.3 - - - +
85A GLU* 1.3 79.9 - - + +
87A LEU* 1.3 60.1 + - + +
89A ASP 3.1 22.5 - - - +
92A LEU* 3.6 37.2 - - + +
93A ARG* 3.4 7.1 + - - +
96A TYR* 4.2 14.1 - - + -
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Residues in contact with LEU 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A PHE* 4.0 19.5 - - + +
37A TYR* 3.6 52.7 - - + +
40A LEU* 3.8 25.1 - - + -
48A SER* 6.1 0.5 - - - -
51A ILE* 4.2 21.6 - - + +
83A ALA 2.8 19.7 + - - +
84A TYR 4.2 0.9 - - - +
86A VAL* 1.3 74.7 - - + +
88A LYS* 1.3 65.3 + - - +
89A ASP 3.4 0.7 + - - +
90A GLU* 5.1 0.3 - - - -
93A ARG* 3.6 38.1 + - + +
96A TYR* 4.3 14.8 - - + -
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Residues in contact with LYS 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A SER* 5.0 13.9 + - - +
51A ILE* 4.7 5.3 - - - +
52A ARG* 5.9 5.2 - - - +
84A TYR* 2.7 61.0 + - + +
85A GLU* 3.2 31.4 - - - +
87A LEU* 1.3 72.7 - - - +
89A ASP* 1.3 67.0 + - - +
90A GLU* 3.3 5.4 + - - +
188A ASP* 4.6 18.4 + - - -
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Residues in contact with ASP 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A GLU* 3.6 16.3 + - - +
86A VAL 3.1 5.6 + - - +
87A LEU 3.3 0.9 - - - -
88A LYS* 1.3 83.4 - - + +
90A GLU* 1.3 68.2 + - - +
91A ASP* 3.0 14.3 + - - +
92A LEU* 3.0 38.4 + - + +
93A ARG* 3.1 11.3 + - - +
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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