Contacts of the helix formed by residues 84 - 93 (chain B) in PDB entry 2OUX
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 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55B ASN* 5.9 3.0 - - - +
82B GLU 4.2 0.2 + - - -
83B MSE 1.3 71.3 - - - +
85B PRO* 1.3 68.0 - - + -
86B SER* 3.1 26.4 + - - +
87B TYR* 2.7 54.2 + - + +
88B ALA 2.8 11.8 + - - -
90B ASP* 5.8 1.0 + - - -
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Residues in contact with PRO 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B MSE 3.2 8.4 - - - +
84B ARG* 1.3 88.4 - - + +
86B SER* 1.3 57.6 + - - +
88B ALA* 3.2 1.8 + - + +
89B ALA* 2.8 31.4 + - - +
114B LYS* 4.3 24.5 - - - +
115B TYR* 4.2 12.0 - - + -
118B LEU* 3.7 24.0 - - + +
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B ARG* 3.1 30.3 + - - +
85B PRO* 1.3 78.8 - - - +
87B TYR* 1.3 64.3 + - - +
89B ALA* 3.4 6.9 + - - +
90B ASP* 2.8 36.3 + - - +
118B LEU* 4.4 8.9 - - - +
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Residues in contact with TYR 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B TYR* 3.1 41.4 + + + -
57B LEU* 2.7 31.0 + - - +
59B PRO* 3.8 29.3 - - + +
62B LEU* 3.6 34.5 - - + +
83B MSE 4.0 17.9 - - + -
84B ARG* 2.7 43.5 + - + +
86B SER* 1.3 76.7 + - - +
88B ALA* 1.3 63.5 + - - +
90B ASP* 3.2 9.7 + - - +
91B MSE 3.0 21.2 + - + +
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Residues in contact with ALA 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.7 20.1 - - + +
83B MSE 3.7 33.9 - - + -
84B ARG 2.8 11.6 + - - +
85B PRO* 3.6 7.4 - - + +
87B TYR* 1.3 73.4 - - - +
89B ALA* 1.3 62.0 + - - +
91B MSE 3.1 5.8 + - - +
92B LEU* 3.0 29.3 + - - +
115B TYR* 4.0 13.9 - - + -
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Residues in contact with ALA 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B PRO 2.8 20.8 + - - +
86B SER* 3.6 5.4 - - - +
88B ALA* 1.3 73.1 - - - +
90B ASP* 1.3 65.0 + - - +
92B LEU* 3.2 21.3 + - - +
93B ALA 3.2 4.0 + - - -
115B TYR* 4.2 7.5 - - - +
118B LEU* 3.9 31.0 - - + +
119B LEU* 3.2 30.9 - - + +
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PRO* 3.8 19.8 - - + +
84B ARG* 5.8 0.9 + - - -
86B SER* 2.8 28.4 + - - +
87B TYR* 3.2 7.2 + - - +
89B ALA* 1.3 79.3 - - - +
91B MSE 1.3 62.8 + - - +
93B ALA* 3.4 8.6 + - - +
94B GLU* 3.3 27.8 + - + +
118B LEU 5.7 0.5 - - - +
119B LEU* 5.0 1.0 - - - +
123B GLU* 3.9 16.1 - - - +
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Residues in contact with MSE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B PRO* 3.5 28.9 - - + +
62B LEU* 3.8 18.8 - - + -
63B ALA* 3.5 15.8 - - - +
66B PHE* 3.3 46.4 - - + -
80B LEU* 4.6 12.1 - - + -
83B MSE 4.3 11.9 - - + -
87B TYR* 3.0 14.2 + - + +
88B ALA* 3.4 10.5 - - - +
89B ALA 3.1 0.2 - - - -
90B ASP* 1.3 76.0 - - - +
92B LEU* 1.3 64.3 + - - +
94B GLU 3.4 0.7 + - - -
95B MSE 3.0 51.3 + - - +
103B LEU* 4.8 0.4 - - + -
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B LEU* 3.9 20.2 - - + -
88B ALA 3.0 20.3 + - - +
89B ALA* 3.2 8.7 + - - +
91B MSE 1.3 77.9 - - - +
93B ALA* 1.3 62.3 + - - +
94B GLU 3.1 2.1 + - - -
95B MSE 3.2 43.8 + - + +
100B ALA* 3.7 12.7 - - + +
103B LEU* 4.2 13.0 - - + -
104B LEU* 3.9 22.9 - - + -
115B TYR* 3.4 39.5 - - + +
116B LEU* 6.2 0.2 - - + -
119B LEU* 5.0 10.5 - - + -
127B ILE* 4.7 4.1 - - + +
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Residues in contact with ALA 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA 3.2 9.7 + - - +
90B ASP* 3.7 10.1 - - - +
91B MSE 3.3 0.2 - - - -
92B LEU* 1.3 79.4 - - - +
94B GLU* 1.3 63.9 + - + +
95B MSE 4.3 3.1 - - - +
119B LEU* 3.9 17.4 - - + +
123B GLU* 4.0 35.6 - - + +
127B ILE* 5.8 3.1 - - - -
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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