Contacts of the helix formed by residues 227 - 234 (chain A) in PDB entry 2OT7
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 PHE 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A LEU* 4.0 33.7 - - + -
82A PHE* 4.0 18.6 - - - -
83A THR* 4.1 19.7 - - - -
223A ALA 3.0 19.2 + - - +
224A LYS 3.4 5.8 - - - +
226A PHE* 1.3 92.8 - - + +
228A PRO* 1.3 65.1 - - - +
229A GLY 3.3 3.0 + - - -
230A SER* 3.4 16.7 + - - +
231A ALA* 3.2 18.7 + - - +
237A PHE* 4.1 13.6 - + + -
243A THR* 3.6 27.4 - - + -
244A LEU 4.6 0.4 - - - -
245A ILE* 4.5 5.6 - - + -
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Residues in contact with PRO 228 (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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224A LYS 3.2 13.6 - - - +
225A GLY* 3.6 11.4 - - - +
226A PHE 3.4 9.2 - - - +
227A PHE* 1.3 89.4 - - - +
229A GLY* 1.3 58.5 + - - +
231A ALA* 3.8 3.3 - - + +
232A GLN* 2.9 31.0 + - - +
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Residues in contact with GLY 229 (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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227A PHE 3.3 1.0 - - - -
228A PRO* 1.3 79.7 - - - +
230A SER* 1.3 65.1 + - - +
232A GLN* 3.3 6.4 + - - +
233A SER* 3.3 24.3 + - - -
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Residues in contact with SER 230 (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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227A PHE* 3.4 17.5 + - - +
229A GLY* 1.3 74.7 - - - +
231A ALA* 1.3 56.8 + - - +
233A SER* 3.5 6.5 + - - -
234A CYS* 3.1 27.2 + - - +
237A PHE* 3.7 34.5 - - - +
240A HIS* 5.6 1.5 - - - -
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Residues in contact with ALA 231 (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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224A LYS* 4.0 23.6 - - + +
227A PHE 3.2 16.3 + - - +
228A PRO* 3.8 4.3 - - + +
230A SER* 1.3 75.6 - - - +
232A GLN* 1.3 63.6 + - - +
233A SER 3.1 1.6 + - - -
234A CYS 3.3 17.7 + - - +
235A GLU* 3.9 5.2 + - - +
237A PHE* 3.7 24.2 - - + -
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Residues in contact with GLN 232 (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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228A PRO 2.9 18.9 + - - +
229A GLY* 3.3 6.5 + - - +
231A ALA* 1.3 75.1 - - - +
233A SER* 1.3 58.5 + - - +
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Residues in contact with SER 233 (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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229A GLY 3.3 13.3 + - - -
230A SER* 3.7 9.0 + - - -
231A ALA 3.1 0.4 - - - -
232A GLN* 1.3 78.8 - - - +
234A CYS* 1.3 63.1 + - - +
308A CYS* 4.2 12.5 - - - +
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Residues in contact with CYS 234 (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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230A SER 3.1 12.6 + - - +
231A ALA* 3.3 11.9 + - - +
233A SER* 1.3 82.8 - - - +
235A GLU* 1.3 69.9 + - - +
236A ALA* 3.6 19.3 - - - -
237A PHE* 3.2 9.0 + - - +
240A HIS* 3.6 11.4 - - + -
306A CYS* 4.0 9.9 - - - -
307A SER* 4.4 9.0 - - - -
308A CYS* 3.7 10.1 - - + -
502A ZN 2.3 37.7 - - - -
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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