Contacts of the helix formed by residues 231 - 239 (chain A) in PDB entry 3H8E
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 MET 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226A ILE* 3.0 41.3 + - + +
227A LYS* 4.0 1.7 + - - -
229A LEU* 4.0 11.0 - - + -
230A GLY* 1.3 75.1 - - - +
232A GLY* 1.3 54.6 + - - +
234A PHE* 4.0 6.1 - - + -
235A TYR* 2.9 29.8 + - - +
247A LEU* 3.6 20.6 - - + -
338A MET* 3.7 21.1 - - + -
358A ASP* 3.0 40.2 - - + +
359A THR* 5.5 0.7 - - - -
362A TYR* 3.6 44.4 - - + -
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Residues in contact with GLY 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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230A GLY 2.9 13.0 + - - -
231A MET* 1.3 72.1 - - - +
233A ALA* 1.3 58.0 + - - +
235A TYR* 4.0 6.4 - - - +
236A ALA* 3.1 27.4 + - - +
335A VAL* 3.7 16.4 - - - +
336A THR 3.1 17.6 + - - -
337A THR* 4.2 0.2 - - - +
358A ASP* 3.4 0.8 + - - -
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Residues in contact with ALA 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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232A GLY* 1.3 76.1 - - - +
234A PHE* 1.4 66.7 + - - +
236A ALA* 3.2 5.4 + - - +
237A VAL* 3.2 25.8 + - - +
335A VAL* 3.8 12.5 - - + +
336A THR 4.2 1.4 + - - -
337A THR* 4.1 10.7 - - + +
345A ILE* 5.3 0.2 - - - -
354A LEU* 3.4 37.1 - - + +
357A CYS* 3.8 15.9 - - - -
358A ASP* 3.0 8.2 + - - +
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Residues in contact with PHE 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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226A ILE* 2.2 62.8 - - + -
231A MET* 3.8 12.6 - - + +
233A ALA* 1.4 72.5 - - - +
235A TYR* 1.4 64.7 + - - +
237A VAL* 3.1 13.9 + - - +
238A GLY* 3.3 9.2 + - - -
245A PRO* 3.9 9.1 - - + +
246A ARG 3.6 19.7 - - - -
247A LEU* 4.0 6.3 - - + -
318A ALA* 3.9 8.3 - - + -
319A CYS 3.7 24.0 - - - -
320A ALA* 5.2 1.2 - - - +
354A LEU 3.6 1.2 + - - -
355A VAL* 3.2 50.6 - - + +
358A ASP* 2.9 21.7 + - + +
359A THR* 4.5 4.0 - - - -
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Residues in contact with TYR 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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223A GLU* 3.7 41.4 + - + +
224A LYS* 6.1 0.2 - - - -
226A ILE* 4.4 8.3 - - + -
227A LYS* 3.8 49.2 + - + +
231A MET 2.9 19.4 + - - +
232A GLY* 4.0 5.8 - - - +
234A PHE* 1.4 77.7 - - - +
236A ALA* 1.3 66.3 + - - +
238A GLY* 3.2 3.0 + - - +
239A GLN* 3.2 52.6 + - + +
245A PRO* 5.5 3.1 - - + -
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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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232A GLY 3.1 21.1 + - - +
233A ALA 3.2 6.7 + - - +
235A TYR* 1.3 80.4 - - - +
237A VAL* 1.3 65.2 + - + +
239A GLN* 3.5 13.3 - - - +
240A GLY 4.8 0.2 + - - -
329A THR* 2.7 35.5 + - + +
335A VAL* 4.0 8.3 - - + -
345A ILE* 3.7 25.8 - - + -
354A LEU* 5.9 0.2 - - - -
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Residues in contact with VAL 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 ALA 3.2 14.0 + - - +
234A PHE 3.1 7.4 + - - +
236A ALA* 1.3 80.6 - - - +
238A GLY* 1.4 61.6 + - - +
239A GLN 3.5 0.3 + - - -
240A GLY* 4.3 4.3 + - - -
269A ILE* 3.9 22.9 - - + -
320A ALA* 4.1 5.4 - - + -
321A GLU 4.0 6.1 - - - +
322A ASN* 3.9 22.1 - - + +
323A MET 5.1 0.5 + - - +
329A THR* 5.6 0.7 - - - -
351A GLU* 3.5 43.1 - - + +
354A LEU* 3.5 21.3 - - + -
355A VAL* 3.8 8.7 - - + -
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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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223A GLU* 4.4 6.9 - - - +
234A PHE 3.3 5.6 + - - -
235A TYR 3.2 6.0 + - - -
237A VAL* 1.4 77.7 - - - +
239A GLN* 1.3 65.0 + - - +
240A GLY 3.2 4.3 + - - -
241A SER* 3.3 20.8 + - - +
243A GLN 4.3 5.4 - - - +
244A PRO* 5.1 1.0 - - - +
245A PRO* 4.4 13.4 - - - +
320A ALA* 4.1 18.8 - - - +
321A GLU 4.2 5.4 - - - -
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Residues in contact with GLN 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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223A GLU* 4.2 9.9 - - - +
235A TYR* 3.2 44.2 + - + +
236A ALA* 3.5 16.7 - - - +
237A VAL 3.3 0.8 - - - -
238A GLY* 1.3 78.7 - - - +
240A GLY* 1.3 64.5 + - - +
241A SER 3.3 6.1 + - - +
325A SER* 5.0 0.2 + - - -
327A GLY* 3.4 25.5 + - - +
328A ALA 3.9 2.0 + - - -
329A THR* 3.3 26.3 + - - +
330A ARG* 4.7 10.3 - - - +
333A ASP* 4.9 1.2 + - - -
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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