Contacts of the helix formed by residues 83 - 91 (chain A) in PDB entry 1O9R
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81A LEU 3.8 0.8 - - - -
82A GLY* 1.3 80.1 - - - +
84A LEU* 1.3 67.4 + - - +
85A GLN* 3.6 15.1 + - - +
86A ALA* 3.0 20.6 + - - +
87A VAL* 2.9 22.8 + - - +
34B LEU* 4.6 6.1 - - - -
35B VAL* 5.5 2.9 - - - +
38B GLN* 3.3 24.1 - - - +
96B TYR* 4.6 15.8 + - - -
98B THR* 4.3 10.3 - - - +
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Residues in contact with LEU 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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34A LEU* 5.7 0.2 - - + -
82A GLY 3.9 0.2 + - - -
83A SER* 1.3 73.2 - - - +
85A GLN* 1.3 77.6 - - + +
87A VAL* 3.5 3.4 + - - +
88A SER* 2.9 32.1 + - - -
31B ASP* 3.7 35.1 + - - +
34B LEU* 3.9 21.8 - - + +
35B VAL* 6.1 0.4 - - - +
84B LEU* 3.7 20.4 - - + -
87B VAL* 3.8 23.3 - - + -
88B SER* 3.4 31.0 - - - +
91B THR* 3.8 18.2 - - + -
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Residues in contact with GLN 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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83A SER* 3.1 11.2 + - - +
84A LEU* 1.3 102.6 - - + +
86A ALA* 1.3 65.3 + - - +
88A SER* 3.7 6.5 - - - -
89A SER* 3.0 25.6 + - - -
31B ASP* 5.1 3.0 + - - +
91B THR* 5.5 0.9 - - - +
93B LEU 5.1 3.3 - - - +
94B LYS 5.0 0.2 - - - -
95B ALA* 3.5 42.9 + - + +
96B TYR 3.9 7.7 + - - +
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Residues in contact with ALA 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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27A ALA* 4.9 1.3 - - - -
81A LEU* 3.9 41.5 - - + +
83A SER* 3.0 20.7 + - - +
85A GLN* 1.3 78.0 - - - +
87A VAL* 1.4 62.6 + - - +
89A SER* 3.3 6.4 + - - -
90A THR* 2.9 32.9 + - - +
98B THR* 5.5 2.2 - - + -
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Residues in contact with VAL 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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27A ALA* 3.4 31.4 - - - +
30A ILE* 3.8 28.0 - - + -
31A ASP* 4.1 13.2 - - + +
81A LEU 4.9 0.2 - - - +
82A GLY* 3.7 17.0 - - - +
83A SER 2.9 17.5 + - - +
84A LEU* 3.8 5.6 - - - +
86A ALA* 1.4 75.6 - - - +
88A SER* 1.4 57.4 + - - +
91A THR* 2.9 34.5 + - - +
34B LEU* 5.4 1.3 - - + -
84B LEU* 3.9 24.9 - - + -
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Residues in contact with SER 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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84A LEU* 2.9 20.6 + - - +
85A GLN* 3.7 7.4 - - - -
86A ALA 3.3 0.2 - - - -
87A VAL* 1.4 78.4 - - - +
89A SER* 1.3 60.6 + - - +
90A THR 3.5 0.2 + - - -
91A THR* 4.0 10.0 - - - +
84B LEU* 3.7 19.3 - - - +
88B SER* 3.2 22.7 + - - -
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Residues in contact with SER 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 GLN 3.0 15.7 + - - -
86A ALA* 3.3 9.2 + - - -
87A VAL 3.3 0.2 - - - -
88A SER* 1.3 76.7 - - - +
90A THR* 1.3 68.5 + - - +
91A THR 5.1 1.0 - - - +
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Residues in contact with THR 90 (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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23A ASN* 4.2 3.8 - - + +
24A GLU* 4.0 28.0 - - + +
27A ALA* 3.5 18.4 - - + +
28A SER* 4.6 1.2 + - - -
86A ALA* 2.9 21.2 + - - +
89A SER* 1.3 85.3 + - - +
91A THR* 1.3 69.6 + - - +
92A LYS* 3.5 14.7 + - - +
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Residues in contact with THR 91 (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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27A ALA* 3.8 8.4 - - - +
28A SER* 3.8 6.7 + - - -
31A ASP* 2.6 42.1 + - - +
87A VAL 2.9 21.0 + - - +
88A SER 4.0 10.3 - - - +
89A SER 5.1 0.9 - - - +
90A THR* 1.3 81.8 + - - +
92A LYS* 1.3 68.5 + - - +
93A LEU* 3.1 18.4 + - - +
84B LEU* 3.8 12.3 - - + -
85B GLN* 5.5 1.3 - - - +
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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