Contacts of the helix formed by residues 229 - 240 (chain A) in PDB entry 1RI4
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 ASP 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A PHE* 3.5 17.0 - - + -
177A ARG* 5.3 5.2 - - - +
227A PHE 3.6 4.4 + - - +
228A VAL* 1.3 69.7 - - - +
230A PHE* 1.3 62.4 + - - +
231A THR* 3.4 9.5 + - - -
232A ARG* 2.8 40.5 + - + +
233A MET* 3.0 19.1 + - - +
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Residues in contact with PHE 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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174A VAL* 6.1 0.4 - - + -
228A VAL* 2.9 19.1 + - + +
229A ASP* 1.3 70.2 + - - +
231A THR* 1.3 55.2 + - - +
233A MET* 3.0 26.7 + - + +
234A VAL* 2.7 67.5 + - + +
244A LEU* 4.0 19.1 - - + -
247A ARG* 3.3 64.4 - - + +
285A GLU* 4.4 3.4 - - - -
287A VAL* 3.8 26.7 - - + -
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Residues in contact with THR 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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229A ASP* 3.4 6.9 + - - -
230A PHE* 1.3 77.7 - - - +
232A ARG* 1.3 62.7 + - - +
234A VAL* 3.8 5.8 - - - +
235A ASP* 3.0 48.6 + - - +
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Residues in contact with ARG 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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150A SER* 3.1 40.0 - - - +
153A LEU* 3.6 24.2 - - + -
157A GLN* 4.3 2.1 - - - +
229A ASP* 2.8 37.8 + - + +
231A THR* 1.3 76.1 - - - +
233A MET* 1.3 57.7 + - - +
235A ASP* 4.2 4.1 - - - +
236A GLY* 2.9 26.0 + - - -
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Residues in contact with MET 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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143A PHE* 3.6 28.3 - - + -
147A PHE* 3.9 18.6 - - + -
153A LEU* 4.7 3.8 - - + +
157A GLN* 2.9 15.4 + - - +
172A MET* 3.7 18.2 - - + +
174A VAL* 5.9 0.4 - - + -
228A VAL* 4.6 6.7 - - + -
229A ASP 3.0 11.2 + - - +
230A PHE* 3.0 41.1 + - + +
232A ARG* 1.3 76.2 - - - +
234A VAL* 1.3 67.4 + - - +
236A GLY 3.1 0.5 + - - -
237A PHE* 2.8 39.6 + - + +
287A VAL* 3.9 1.3 - - + -
289A PHE* 3.6 25.8 - - + -
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Residues in contact with VAL 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 PHE* 2.7 56.6 + - + +
231A THR* 3.8 5.8 - - - +
233A MET* 1.3 73.3 - - + +
235A ASP* 1.3 66.0 + - - +
237A PHE* 3.7 1.6 - - - +
238A LYS* 2.8 40.4 + - + +
242A LEU 4.7 0.7 - - - +
243A SER* 6.5 0.2 - - - -
244A LEU* 4.9 13.7 - - + +
289A PHE* 4.1 23.7 - - + -
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Residues in contact with ASP 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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231A THR* 3.0 35.3 + - - +
232A ARG* 4.2 4.4 - - - +
234A VAL* 1.3 82.7 - - - +
236A GLY* 1.3 63.3 + - - +
238A LYS* 3.4 8.1 + - - +
239A ARG* 3.2 22.7 + - - +
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Residues in contact with GLY 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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157A GLN* 3.5 19.2 - - - +
232A ARG 2.9 19.9 + - - -
233A MET 3.1 0.2 + - - -
235A ASP* 1.3 78.6 - - - +
237A PHE* 1.3 60.1 + - - +
239A ARG* 3.3 20.9 - - - +
240A LEU* 3.6 13.3 + - - +
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Residues in contact with PHE 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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143A PHE* 3.9 3.1 - + - -
157A GLN* 3.2 52.2 - - + +
160A ILE* 3.9 13.0 - - + -
170A PHE* 3.6 36.1 - + - -
233A MET* 2.8 33.2 + - + +
234A VAL 3.8 2.7 - - - +
236A GLY* 1.3 67.9 - - - +
238A LYS* 1.3 55.9 + - - +
239A ARG 2.9 5.2 - - - -
240A LEU* 2.7 31.1 + - + +
241A GLY 3.0 0.2 + - - -
242A LEU* 3.0 49.2 + - + +
289A PHE* 3.6 28.0 - + + -
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Residues in contact with LYS 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 VAL* 2.8 25.5 + - + +
235A ASP* 3.7 9.9 - - - +
236A GLY 3.4 0.2 - - - -
237A PHE* 1.3 76.0 - - - +
239A ARG* 1.3 59.1 + - - +
241A GLY* 3.5 9.8 + - - -
242A LEU 3.2 15.7 + - - +
243A SER* 3.1 28.8 - - - +
244A LEU 5.0 1.7 - - - +
292A LEU* 5.3 2.6 - - - +
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Residues in contact with ARG 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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154A ASP* 4.9 1.4 + - - -
158A ARG* 3.4 37.0 - - - +
235A ASP 3.2 11.9 + - - +
236A GLY* 3.3 15.7 - - - +
237A PHE 2.9 0.4 - - - -
238A LYS* 1.3 80.0 - - - +
240A LEU* 1.3 65.7 + - + +
241A GLY 3.4 0.4 + - - -
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Residues in contact with LEU 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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157A GLN* 3.2 46.7 - - + +
158A ARG* 3.8 37.9 - - + +
161A ALA* 3.9 20.4 - - + +
236A GLY 3.6 12.6 - - - +
237A PHE* 2.7 11.0 + - + +
239A ARG* 1.3 86.8 - - + +
241A GLY* 1.3 59.5 + - - +
242A LEU* 3.6 9.9 - - + +
291A LYS* 4.7 8.3 - - - -
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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