Contacts of the helix formed by residues 232 - 239 (chain A) in PDB entry 1B4V
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 TYR 232 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ALA* 3.6 23.3 - - + +
24A VAL* 3.8 23.6 - - + -
27A LEU* 3.6 26.9 - - + +
28A ARG* 4.3 0.2 - - - -
151A ALA* 3.8 5.9 - - - -
154A MET* 3.2 36.7 - - + +
155A LEU* 3.8 13.7 - - + -
228A LEU* 3.4 19.7 + - + -
231A THR* 1.3 83.1 + - - +
233A LEU* 1.3 59.0 + - - +
235A ALA* 3.2 7.4 + - - +
236A ALA* 2.8 28.9 + - - +
491A THR* 3.3 34.4 - - + +
495A GLU* 2.6 30.0 + - - -
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Residues in contact with LEU 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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18A THR* 3.7 21.3 - - - +
23A ALA* 3.7 26.9 - - + +
38A MET* 3.7 35.0 - - + -
112A VAL* 3.6 28.5 - - + -
113A GLY* 3.7 11.7 - - - +
228A LEU* 2.9 15.9 + - + +
229A ASP* 3.8 14.4 - - + +
232A TYR* 1.3 69.3 - - - +
234A ALA* 1.3 61.3 + - - +
236A ALA* 3.2 6.4 + - + +
237A LEU* 2.9 37.3 + - + +
244A ILE* 4.4 9.9 - - + -
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Residues in contact with ALA 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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156A ARG* 5.6 0.9 - - - +
229A ASP 3.3 21.5 + - - +
230A LYS* 3.4 21.5 - - - +
231A THR 3.3 1.5 + - - +
232A TYR 3.3 0.2 - - - -
233A LEU* 1.3 78.2 - - - +
235A ALA* 1.3 58.0 + - - +
237A LEU* 3.4 9.8 + - - +
238A GLY* 3.0 23.2 + - - -
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Residues in contact with ALA 235 (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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27A LEU* 3.6 23.2 - - + +
154A MET* 4.6 8.7 - - + -
231A THR 3.1 12.9 + - - +
232A TYR* 3.5 8.1 - - - +
234A ALA* 1.3 75.6 - - - +
236A ALA* 1.3 65.8 + - - +
238A GLY* 3.0 12.8 + - - +
239A THR* 3.2 15.2 + - - +
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Residues in contact with ALA 236 (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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23A ALA 4.8 0.9 - - - +
26A ALA* 4.1 9.4 - - + -
27A LEU* 3.6 33.5 - - - +
232A TYR 2.8 17.1 + - - +
233A LEU* 3.2 12.8 + - + +
235A ALA* 1.3 76.6 - - - +
237A LEU* 1.3 58.0 + - + +
239A THR* 2.7 27.9 + - - -
242A VAL* 3.4 23.2 + - + +
244A ILE* 6.4 0.2 - - + -
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Residues in contact with LEU 237 (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 ASP 6.0 0.2 - - - +
233A LEU* 2.9 23.7 + - + +
234A ALA* 3.8 7.9 - - - +
236A ALA* 1.3 75.5 - - + +
238A GLY* 1.3 62.4 + - - +
240A GLY* 3.2 14.6 + - - -
242A VAL* 3.4 28.6 - - + +
243A THR* 4.4 2.7 - - - -
244A ILE* 4.0 36.8 - - + +
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Residues in contact with GLY 238 (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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234A ALA 3.0 11.9 + - - -
235A ALA* 3.0 12.0 + - - -
237A LEU* 1.3 78.2 - - - +
239A THR* 1.3 59.8 + - - +
240A GLY* 3.2 1.3 + - - -
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Residues in contact with THR 239 (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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27A LEU* 4.1 8.7 - - + +
30A GLY* 3.7 22.7 - - - +
31A GLU* 3.8 34.5 - - + +
235A ALA 3.2 14.3 + - - +
236A ALA* 2.7 18.1 + - - +
238A GLY* 1.3 77.3 - - - +
240A GLY* 1.3 60.7 + - - +
241A LYS* 3.1 18.0 + - - +
242A VAL* 3.8 0.7 - - - +
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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