Contacts of the helix formed by residues 233 - 243 (chain A) in PDB entry 1YAA
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 233 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A ILE* 4.7 16.2 - - + +
226A GLN* 2.8 67.9 + - - +
227A GLY* 4.0 1.8 - - - -
231A GLY 4.2 0.8 + - - -
232A ASP* 1.3 75.3 + - - +
234A ASP* 1.3 66.5 + - - +
236A ASP* 3.4 1.7 + - - -
237A ALA 3.2 11.3 + - - -
259A ASN* 4.8 0.2 - - - +
319A TRP* 3.7 24.2 - - + -
320A HIS* 3.4 35.7 - - + +
323A MET* 3.7 19.9 - - + +
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Residues in contact with ASP 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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86A ILE 4.6 1.2 - - - +
232A ASP* 3.3 11.6 + - - +
233A LEU* 1.3 75.6 - - - +
235A LYS* 1.3 67.1 + - - +
237A ALA* 3.1 13.2 + - - +
238A TYR* 3.6 8.5 + - - +
241A ARG* 3.0 40.7 + - - +
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Residues in contact with LYS 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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230A THR* 3.3 40.3 + - + +
232A ASP* 3.4 25.0 + - - +
233A LEU 3.4 0.4 - - - -
234A ASP* 1.3 78.8 - - - +
236A ASP* 1.3 61.4 + - - +
238A TYR* 3.5 18.9 - - - +
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Residues in contact with ASP 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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190A SER* 4.1 11.8 - - - +
191A CYS* 3.8 27.9 - - - +
223A THR* 5.9 0.2 - - - +
225A TYR 4.0 0.5 - - - +
226A GLN* 4.0 5.4 - - + +
227A GLY* 2.8 34.3 + - - +
228A PHE 3.3 0.2 + - - -
229A ALA* 3.1 32.4 + - - +
230A THR* 2.9 31.8 + - - +
232A ASP 3.0 16.5 + - - +
233A LEU 3.9 3.8 - - - +
234A ASP 3.2 0.2 - - - -
235A LYS* 1.3 74.5 - - - +
237A ALA* 1.3 56.6 + - - +
238A TYR 3.3 6.3 + - - -
239A ALA 4.9 0.3 + - - -
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Residues in contact with ALA 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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87A ILE* 3.4 25.8 - - + +
190A SER* 6.0 0.2 - - - -
223A THR* 6.5 0.7 - - - -
226A GLN* 3.5 24.2 - - - +
233A LEU 3.2 5.5 + - - +
234A ASP 3.1 6.4 + - - +
236A ASP* 1.3 76.2 - - - +
238A TYR* 1.3 64.0 + - - +
239A ALA 3.5 1.8 - - - -
240A VAL* 3.3 12.4 + - + +
241A ARG* 3.0 36.8 + - - +
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Residues in contact with TYR 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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202A SER* 3.5 53.1 + - - -
205A TRP* 4.0 12.6 - + + -
206A VAL* 3.5 16.8 - - - +
234A ASP 3.6 4.9 + - - +
235A LYS* 3.5 18.2 + - - +
236A ASP 3.3 2.0 - - - -
237A ALA* 1.3 77.1 - - - +
239A ALA* 1.3 61.3 + - - +
241A ARG* 3.3 6.3 + - + +
242A LEU* 2.9 54.9 + - + +
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Residues in contact with ALA 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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190A SER* 3.9 11.8 + - - +
205A TRP* 3.4 49.1 - - + +
209A VAL* 4.7 2.6 - - - +
221A PHE* 3.3 19.7 - - + -
236A ASP 4.9 1.6 + - - -
237A ALA 3.5 0.4 - - - -
238A TYR* 1.3 84.5 - - - +
240A VAL* 1.3 56.9 + - - +
242A LEU* 2.9 29.2 + - - +
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Residues in contact with VAL 240 (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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87A ILE* 4.8 16.4 - - + +
88A PHE* 4.8 6.3 - - + -
190A SER* 3.3 32.3 - - - +
221A PHE* 3.8 22.3 - - + -
223A THR* 4.1 8.7 - - + +
237A ALA* 3.3 14.9 + - + +
239A ALA* 1.3 75.6 - - - +
241A ARG* 1.3 58.6 + - - +
242A VAL* 2.9 43.8 + - - +
252A VAL* 4.0 28.0 - - + -
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Residues in contact with ARG 241 (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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85A LYS 4.3 0.8 + - - -
86A ILE* 3.0 24.5 + - - +
87A ILE 2.9 20.6 + - - +
88A PHE* 3.5 15.4 + - - +
89A GLY* 3.5 23.4 - - - -
234A ASP* 3.0 41.9 + - - +
237A ALA* 3.0 31.9 + - - +
238A TYR* 3.8 5.6 - - + +
240A VAL* 1.3 72.3 - - - +
242A LEU* 1.3 100.4 + - - +
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Residues in contact with LEU 242 (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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205A TRP* 4.1 9.4 - - + +
206A VAL* 3.9 29.4 - - + +
209A VAL* 4.2 13.5 - - + -
238A TYR* 2.9 53.4 + - + +
239A ALA* 3.6 5.2 - - - +
241A ARG* 1.3 76.0 - - - +
242A GLY* 1.3 74.4 + - - +
243A LYS* 3.0 56.3 + - + +
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Residues in contact with GLY 242 (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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209A VAL* 4.4 11.0 - - - +
221A PHE* 4.2 14.4 - - - -
239A ALA 2.9 15.5 + - - -
240A VAL 3.2 3.5 + - - -
242A LEU* 1.3 133.8 - - - +
244A LEU* 3.0 47.0 + - - +
250A VAL* 4.4 2.5 - - - -
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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