Contacts of the helix formed by residues 156 - 158 (chain C) in PDB entry 6O81
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 LEU 156 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ALA 3.6 19.3 - - - +
153C ALA* 3.9 11.0 - - - +
154C GLN 3.2 2.2 - - - -
155C ALA* 1.3 78.6 - - - +
157C GLU* 1.3 64.9 + - - +
158C HIS 3.3 3.5 + - - -
159C ILE* 3.9 14.5 - - - +
180C GLU* 3.9 15.5 - - - +
181C ALA* 5.3 11.4 - - - -
184C LYS* 4.9 21.8 - - + +
185C ARG* 3.9 34.2 + - + +
453E VAL* 5.2 2.8 - - - +
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Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153C ALA 4.1 2.6 - - - +
154C GLN* 3.2 36.1 - - - +
156C LEU* 1.3 88.1 + - - +
158C HIS* 1.3 74.8 + - + +
446E ARG* 4.4 35.2 - - + +
447E VAL 4.2 6.4 - - - +
448E GLN* 4.4 1.4 - - + +
453E VAL* 3.4 27.1 - - + +
454E SER* 5.6 4.9 - - - -
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Residues in contact with HIS 158 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C GLN* 3.5 27.2 + - + -
155C ALA* 3.4 9.3 + - - +
156C LEU 3.3 0.8 - - - -
157C GLU* 1.3 83.8 + - + +
159C ILE* 1.3 70.5 + - + +
163C GLU* 4.1 0.3 - - - +
177C PHE* 4.5 14.8 - + + -
231C LYS* 2.9 29.9 + - - +
233C ILE* 5.5 4.3 - - + -
266C ILE* 4.7 11.1 - - + +
323C LEU* 3.5 29.3 - - + +
325C ILE* 3.5 22.4 - - + +
447E VAL* 3.2 31.1 + - + +
448E GLN* 4.5 5.4 - - - -
449E THR* 5.1 2.4 + - - -
453E VAL* 3.6 10.4 - - - +
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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
------------------------------------------------------------
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