Contacts of the helix formed by residues 78 - 83 (chain B) in PDB entry 2OT3
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 GLN 78 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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254A CYS* 5.3 2.9 - - - +
313A ASP* 3.2 45.6 + - + +
27B GLU* 4.0 14.6 - - + +
76B ALA 3.5 2.3 - - - +
77B GLY* 1.3 79.6 - - - +
79B GLU* 1.3 66.5 + - - +
80B ARG* 2.7 44.6 + - + +
81B PHE* 2.9 36.5 + - + +
82B HIS* 3.8 2.9 + - - -
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Residues in contact with GLU 79 (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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27B GLU* 4.6 4.2 + - - +
77B GLY 3.6 2.0 + - - -
78B GLN* 1.3 72.2 - - - +
80B ARG* 1.3 58.5 + - - +
82B HIS* 2.9 42.2 + - - +
109B LYS* 5.6 11.9 - - - +
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Residues in contact with ARG 80 (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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252A MET 4.7 1.6 + - - -
253A LEU* 2.7 49.9 + - - +
254A CYS* 4.0 14.9 + - - +
313A ASP 4.6 0.2 + - - -
317A PRO* 3.6 14.5 - - - +
365A PHE* 3.5 24.8 - - + -
372A GLN 5.6 0.4 - - - +
373A SER* 3.9 32.3 + - - +
375A ASN* 6.1 2.0 - - - +
78B GLN* 2.7 44.4 + - + +
79B GLU* 1.3 77.5 - - - +
81B PHE* 1.3 88.0 + - + +
82B HIS 3.4 1.5 + - - -
83B ALA 5.2 0.5 + - - -
84B LEU* 5.5 0.2 - - - +
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Residues in contact with PHE 81 (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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316A LEU* 3.7 7.0 - - + -
317A PRO* 4.0 24.7 - - + -
320A ILE* 3.7 16.6 - - + -
365A PHE* 3.7 27.4 - + - -
76B ALA* 3.5 34.7 - - + +
78B GLN* 2.9 37.4 + - + +
80B ARG* 1.3 111.5 - - + +
82B HIS* 1.3 64.1 + - - +
83B ALA 3.3 2.5 - - - -
84B LEU* 3.1 43.6 + - + +
85B GLY 4.1 2.3 + - - -
88B TYR* 5.9 0.6 - - + -
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Residues in contact with HIS 82 (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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78B GLN 3.8 1.8 + - - -
79B GLU* 2.9 38.3 + - - +
80B ARG 3.4 2.0 - - - -
81B PHE* 1.3 77.1 - - - +
83B ALA* 1.3 63.5 + - + +
84B LEU 3.2 1.4 + - - -
85B GLY* 3.8 7.3 + - - -
112B ASN* 5.5 9.9 - - + -
113B TRP* 4.7 12.3 + + - -
116B GLU* 2.9 41.3 + - + +
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Residues in contact with ALA 83 (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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368A LYS* 6.4 2.5 - - + -
80B ARG 5.2 0.6 + - - -
81B PHE 3.2 1.0 + - - -
82B HIS* 1.3 80.0 - - - +
84B LEU* 1.3 67.4 + - + +
85B GLY 3.5 0.6 + - - -
86B PRO* 3.8 13.6 - - - +
87B ILE* 5.2 2.9 - - - +
116B GLU* 5.7 0.4 - - - -
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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