Contacts of the helix formed by residues 229 - 237 (chain A) in PDB entry 1MRA
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 229 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A GLN* 3.4 24.3 + - - -
227A HIS* 2.9 20.9 + - + +
228A ASP* 1.3 71.4 + - - +
230A GLU* 1.3 63.3 + - - +
232A HIS* 3.1 8.5 + - - +
233A GLN* 3.0 18.5 + - - +
245A MET* 4.3 5.2 - - + -
249A TRP* 4.0 16.7 - + - -
254A GLU* 3.5 37.0 + - - +
257A LYS* 3.7 29.8 - - + +
258A ALA* 3.8 22.0 - - + -
261A ILE* 3.3 21.5 - - + -
263A ALA* 3.5 13.4 - - + +
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Residues in contact with GLU 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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228A ASP* 3.4 7.0 + - - +
229A TYR* 1.3 77.7 - - - +
231A GLY* 1.3 61.0 + - - +
233A GLN* 2.9 26.0 + - + +
234A ARG* 3.0 56.0 + - + +
261A ILE* 3.7 13.8 - - + +
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Residues in contact with GLY 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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202A VAL* 3.8 19.0 - - - +
224A THR* 4.5 0.2 - - - -
228A ASP* 3.0 29.5 + - - -
230A GLU* 1.3 83.2 + - - +
232A HIS* 1.3 56.9 + - - +
234A ARG* 2.9 24.4 + - - +
235A ILE* 3.0 16.7 + - - +
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Residues in contact with HIS 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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222A GLU* 4.2 9.2 - - + -
223A PRO* 3.8 30.1 - - + +
224A THR* 3.4 24.2 + - + +
225A LEU 3.0 21.4 + - - -
226A GLN* 4.1 0.6 - - - -
228A ASP 2.8 32.9 + - - -
229A TYR 3.1 8.9 + - - +
231A GLY* 1.3 74.3 - - - +
233A GLN* 1.3 58.7 + - - +
234A ARG 3.2 0.2 - - - -
235A ILE* 3.8 10.8 - - + +
236A GLN* 3.0 23.4 + - - +
243A VAL* 4.2 10.1 - - + +
245A MET* 3.7 33.8 - - + +
263A ALA* 3.2 24.3 - - + +
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Residues in contact with GLN 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 TYR 3.0 10.9 + - - +
230A GLU* 2.9 18.7 + - + +
232A HIS* 1.3 76.1 - - - +
234A ARG* 1.3 70.0 + - - +
236A GLN* 3.9 1.8 - - - +
237A SER* 3.0 35.9 + - - +
261A ILE* 3.3 27.6 - - + +
262A GLY 3.4 18.5 + - - +
263A ALA* 3.9 3.1 + - - -
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Residues in contact with ARG 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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202A VAL* 3.8 43.7 - - + +
203A PRO* 5.9 0.8 - - - +
206A ILE* 4.3 4.2 - - + +
228A ASP* 5.0 2.8 + - - -
230A GLU* 3.0 46.0 + - - +
231A GLY* 2.9 9.0 + - - +
233A GLN* 1.3 84.7 - - - +
235A ILE* 1.3 64.0 + - - +
237A SER* 2.6 24.5 + - - -
238A LYS* 3.3 10.4 - - - +
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Residues in contact with ILE 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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202A VAL* 3.9 29.4 - - + +
205A ALA* 3.8 33.7 - - + +
206A ILE* 4.1 8.7 - - + -
209A SER* 4.6 2.7 - - - +
223A PRO* 4.3 13.5 - - + -
224A THR* 3.6 28.0 - - + -
231A GLY 3.0 15.7 + - - +
232A HIS* 3.9 8.5 - - - +
234A ARG* 1.3 76.5 - - - +
236A GLN* 1.3 65.0 + - - +
238A LYS* 3.0 14.7 + - - +
239A LEU* 3.5 27.9 - - + +
243A VAL* 4.3 7.6 - - + -
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Residues in contact with GLN 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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232A HIS 3.0 19.1 + - - +
233A GLN* 3.9 5.2 - - - +
234A ARG 3.3 0.2 - - - -
235A ILE* 1.3 77.0 - - - +
237A SER* 1.3 62.7 + - - +
239A LEU* 3.0 15.8 + - - +
241A VAL 3.0 24.2 + - - -
243A VAL* 2.9 38.4 + - + +
262A GLY 4.9 5.6 - - - +
263A ALA 4.2 9.0 - - - +
264A CYS* 5.1 1.6 - - - -
265A ARG* 3.0 55.8 + - + +
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Residues in contact with SER 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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233A GLN* 3.0 33.3 + - - +
234A ARG* 2.6 20.8 + - - -
236A GLN* 1.3 79.6 - - - +
238A LYS* 1.3 68.3 + - - +
239A LEU 3.7 2.1 + - - +
265A ARG* 6.0 0.2 - - - +
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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