Contacts of the helix formed by residues 231 - 242 (chain A) in PDB entry 3R29
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 PRO 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228A GLU* 3.2 18.6 - - + +
229A ASP* 3.6 10.3 - - - +
230A MET* 1.3 89.2 - - - +
232A VAL* 1.3 66.2 + - - +
233A GLU* 4.1 11.2 - - + +
234A ARG* 3.0 40.5 + - + +
235A ILE* 3.5 7.7 + - - +
287A PRO* 4.4 13.9 - - + -
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Residues in contact with VAL 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 GLU* 3.5 18.9 + - - +
230A MET 3.3 1.9 + - - +
231A PRO* 1.3 72.8 - - - +
233A GLU* 1.3 81.4 + - - +
235A ILE* 3.1 9.6 + - - +
236A LEU* 3.0 22.2 + - - +
365A THR* 3.4 26.1 - - + +
369A CYS* 4.1 17.9 - - - -
399A SER* 4.4 10.8 - - - +
403A TYR* 3.7 38.4 - - + -
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Residues in contact with GLU 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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228A GLU* 4.0 7.4 - - - +
231A PRO* 3.1 9.0 - - + +
232A VAL* 1.3 99.3 + - - +
234A ARG* 1.3 57.6 + - + +
236A LEU* 3.4 13.1 - - + +
237A GLU* 2.9 39.0 + - - +
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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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231A PRO* 3.0 33.3 + - + +
233A GLU* 1.3 78.6 - - + +
235A ILE* 1.3 60.9 + - - +
237A GLU* 3.0 21.8 + - - +
238A ALA* 2.8 28.8 + - - +
285A ARG* 4.2 15.3 + - - +
286A ILE 5.1 0.4 - - - -
287A PRO* 3.9 43.8 - - + +
288A HIS 5.2 0.2 - - - +
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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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230A MET* 4.5 20.9 - - + +
231A PRO 3.8 12.8 - - - +
232A VAL* 3.1 7.3 + - - +
234A ARG* 1.3 75.7 - - - +
236A LEU* 1.3 57.7 + - - +
238A ALA* 3.4 5.3 + - - +
239A GLU* 2.9 28.7 + - - +
282A TRP* 5.1 1.6 - - - +
285A ARG 5.3 0.4 - - - -
286A ILE* 4.1 19.7 - - + -
287A PRO* 4.7 13.9 - - + -
364A LYS 5.5 0.4 - - - -
365A THR* 5.0 2.0 - - + +
368A GLY* 3.5 35.0 - - - +
369A CYS* 3.7 25.6 - - - +
372A ALA* 4.8 4.9 - - + -
396A VAL* 4.4 14.8 - - + -
399A SER* 6.2 0.4 - - - -
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Residues in contact with LEU 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 VAL 3.0 11.7 + - - +
233A GLU* 3.4 17.3 - - + +
235A ILE* 1.3 72.5 - - - +
237A GLU* 1.3 70.5 + - + +
239A GLU* 3.2 6.6 + - - +
240A LEU* 2.9 60.2 + - + +
364A LYS* 4.7 9.9 - - + -
365A THR* 3.1 36.0 - - + +
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Residues in contact with GLU 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 GLU* 2.9 27.7 + - + +
234A ARG* 3.0 24.8 + - - +
236A LEU* 1.3 79.1 - - + +
238A ALA* 1.3 51.4 + - - +
240A LEU* 3.3 6.2 + - - +
241A ALA* 2.7 36.8 + - - +
285A ARG* 4.7 5.4 - - + -
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Residues in contact with ALA 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 ARG 2.8 11.0 + - - +
235A ILE* 3.6 10.5 - - - +
237A GLU* 1.3 72.9 - - - +
239A GLU* 1.3 67.6 + - - +
241A ALA* 3.1 11.6 + - - +
242A VAL* 3.3 16.8 + - - +
282A TRP* 3.8 21.7 - - + +
285A ARG* 3.4 43.3 - - + +
286A ILE* 4.3 2.0 - - + -
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Residues in contact with GLU 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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235A ILE 2.9 16.3 + - - +
236A LEU* 3.5 8.5 - - - +
238A ALA* 1.3 72.6 - - - +
240A LEU* 1.3 66.2 + - + +
242A VAL* 3.2 19.6 + - - +
243A GLU* 3.5 9.6 + - - +
282A TRP* 3.0 11.4 + - - +
312A SER* 5.0 2.8 + - - -
364A LYS* 3.6 24.2 - - + +
367A LEU* 3.7 17.8 - - - +
368A GLY* 3.5 29.5 - - - -
371A ARG* 2.6 41.4 + - - -
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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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236A LEU* 2.9 44.4 + - + +
237A GLU* 3.6 6.1 - - - +
239A GLU* 1.3 72.9 - - - +
241A ALA* 1.3 64.0 + - - +
242A VAL 3.0 0.7 + - - -
243A GLU* 3.0 48.4 + - - +
245A LYS* 5.7 3.5 - - - -
364A LYS* 3.5 24.7 - - + +
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Residues in contact with ALA 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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237A GLU 2.7 21.4 + - - +
238A ALA 3.1 6.7 + - - +
240A LEU* 1.3 75.4 - - - +
242A VAL* 1.3 62.7 + - + +
243A GLU 3.7 2.3 + - - +
245A LYS* 5.9 1.6 - - - +
285A ARG* 3.8 36.3 - - - +
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Residues in contact with VAL 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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238A ALA 3.7 8.1 - - - +
239A GLU* 3.2 20.2 + - - +
241A ALA* 1.3 81.0 - - + +
243A GLU* 1.3 68.2 + - - +
244A PRO* 3.2 6.8 - - - +
277A PHE* 6.2 3.6 - - + -
278A THR* 3.8 33.2 + - + +
281A GLU* 4.4 9.2 - - + -
282A TRP* 3.6 42.2 - - + +
312A SER* 6.1 0.9 - - - +
371A ARG* 5.3 3.4 - - - +
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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