Contacts of the helix formed by residues 82 - 89 (chain C) in PDB entry 2O1S
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 ALA 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C TRP* 4.1 16.4 - - + -
79C GLY 3.2 16.2 + - - +
80C HIS 3.4 0.6 - - - -
81C GLN* 1.3 78.0 + - - +
83C TYR* 1.3 66.7 + - - +
84C PRO* 3.4 2.2 - - - -
85C HIS* 3.4 18.1 - - + +
86C LYS* 3.1 25.7 + - + +
108C PRO* 3.7 25.4 - - + -
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Residues in contact with TYR 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C LEU* 4.1 20.0 - - + -
43C VAL* 4.0 17.9 - - + -
47C SER* 3.7 5.7 - - - -
49C HIS* 3.5 32.1 - - + +
50C PHE* 3.8 27.8 - - - -
53C GLY* 5.1 0.4 - - - -
79C GLY 5.2 1.3 - - - -
80C HIS 4.7 5.2 - - - -
81C GLN 3.5 0.8 - - - -
82C ALA* 1.3 76.1 - - - +
84C PRO* 1.4 76.7 - - + +
86C LYS* 3.1 8.5 + - + +
87C ILE* 2.9 28.1 + - + +
95C ILE* 4.0 5.6 - - + +
98C ILE* 3.3 41.5 - - + -
99C ARG* 3.5 29.5 - - - +
106C PRO 3.9 15.3 - - - -
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Residues in contact with PRO 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 4.0 19.7 - - + -
39C LEU* 3.8 14.6 - - + -
53C GLY* 3.3 28.5 - - - +
56C THR* 3.8 2.9 - - - +
57C VAL* 4.2 10.1 - - + -
60C THR* 3.9 18.4 - - - +
81C GLN 3.8 10.8 - - - +
82C ALA 3.6 2.5 - - - -
83C TYR* 1.4 95.0 - - + +
85C HIS* 1.3 61.8 + - - +
87C ILE* 3.2 12.0 + - + +
88C LEU* 3.0 28.4 + - - +
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Residues in contact with HIS 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C THR* 3.5 14.3 + - + +
64C HIS* 2.9 37.5 + + - -
74C LEU* 4.2 4.9 - - + -
76C TRP* 3.3 41.1 + + + +
82C ALA* 3.4 19.9 + - + +
84C PRO* 1.3 81.4 - - - +
86C LYS* 1.3 58.1 + - + +
88C LEU* 3.4 0.9 + - - +
89C THR* 2.6 44.8 + - + +
91C ARG* 3.8 7.4 + - - -
108C PRO* 4.8 2.4 - - + +
115C TYR 3.4 17.6 + - - -
116C ASP* 2.9 29.1 + - - -
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Residues in contact with LYS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ALA* 3.1 21.9 + - + +
83C TYR* 3.1 8.9 + - + +
85C HIS* 1.3 81.0 - - + +
87C ILE* 1.3 63.8 - - - +
89C THR* 3.3 11.9 + - - -
91C ARG* 3.0 51.5 + - + +
95C ILE* 4.3 8.7 - - + -
98C ILE* 3.7 22.2 - - + -
104C LEU* 4.2 8.3 - - - -
105C HIS 3.1 18.4 + - - -
106C PRO 5.6 0.7 - - - +
107C PHE* 3.0 32.9 + - - -
108C PRO* 3.9 4.6 - - + +
112C GLU* 2.9 29.5 + - - -
116C ASP* 4.1 0.6 + - - +
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Residues in contact with ILE 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 4.6 5.8 - - + +
14C VAL 4.9 4.0 - - - +
15C ASP 5.6 0.7 - - - +
35C LEU* 3.7 28.0 - - + -
38C TYR* 3.9 22.0 - - + -
39C LEU* 4.2 23.3 - - + -
83C TYR 2.9 20.8 + - - +
84C PRO* 3.2 6.7 + - + +
86C LYS* 1.3 77.7 - - - +
88C LEU* 1.3 59.5 + - + +
89C THR 3.5 0.3 + - - -
90C GLY 4.1 1.0 + - - -
91C ARG 4.0 1.8 + - - -
92C ARG* 3.4 48.0 + - + +
95C ILE* 3.8 31.0 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C LEU* 5.0 5.4 - - + -
14C VAL* 3.7 33.4 - - + +
15C ASP 5.4 0.9 - - - -
16C SER* 4.1 4.7 + - - -
17C THR* 3.8 25.5 + - - +
20C LEU* 4.6 11.4 - - + -
31C LEU* 4.7 13.7 - - + -
35C LEU* 4.0 21.8 - - + -
60C THR* 4.0 23.6 - - + +
61C VAL* 4.0 29.4 - - + -
64C HIS* 4.8 7.0 - - + -
84C PRO 3.0 16.0 + - - +
85C HIS 4.1 2.9 - - - +
87C ILE* 1.3 77.4 - - - +
89C THR* 1.3 62.2 + - + +
90C GLY 3.5 3.1 + - - -
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Residues in contact with THR 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C THR* 4.1 4.7 - - - +
64C HIS* 3.7 22.9 - - + +
85C HIS* 2.6 25.4 + - + +
86C LYS 3.4 2.3 + - - -
87C ILE 3.3 1.0 - - - -
88C LEU* 1.3 82.3 - - - +
90C GLY* 1.3 59.1 + - - +
91C ARG* 2.9 35.8 + - - +
113C SER* 4.3 2.6 + - - -
115C TYR* 3.5 54.9 - - + -
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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