Contacts of the helix formed by residues 233 - 238 (chain A) in PDB entry 3LEZ
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A THR 4.2 12.6 - - - +
230A GLY* 3.1 11.0 + - - +
231A ASP 3.4 0.8 - - - -
232A ALA* 1.3 93.9 - - + +
234A ILE* 1.3 70.1 + - - +
235A ARG 3.2 0.9 - - - -
236A ALA* 2.9 15.4 + - - +
237A GLY 3.6 2.9 + - - -
248A THR* 4.0 5.6 - - + -
256A ARG* 3.7 42.2 - - - +
257A ASN 3.9 8.7 - - - +
258A ASP* 3.2 28.5 - - + +
288A ASP* 4.0 11.2 - - - +
291A ILE* 3.7 31.4 - - + -
292A GLU* 3.6 8.2 - - - +
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Residues in contact with ILE 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 GLY 4.4 0.2 + - - -
233A LEU* 1.3 78.9 - - - +
235A ARG* 1.3 63.6 + - - +
237A GLY* 2.9 13.9 + - - -
238A VAL* 3.4 13.5 + - + +
244A VAL* 4.2 15.9 - - + -
246A ASP* 4.8 2.9 - - + -
258A ASP* 3.0 48.6 + - + +
259A ILE 4.1 9.4 - - - +
260A GLY* 4.2 2.0 - - - +
262A ILE* 4.0 28.3 - - + -
273A ILE* 3.9 24.0 - - + -
275A ILE* 4.1 8.5 - - + -
291A ILE* 3.9 1.4 - - + +
295A THR* 3.5 23.5 - - + +
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Residues in contact with ARG 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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224A LEU 3.0 25.5 + - - -
225A ILE* 3.2 14.8 + - - +
227A ASN* 3.8 13.2 + - - +
230A GLY* 3.6 18.7 + - - +
231A ASP* 3.7 29.7 + - - +
233A LEU 3.2 0.4 - - - -
234A ILE* 1.3 79.0 - - - +
236A ALA* 1.3 60.4 + - - +
238A VAL* 3.2 28.1 + - - +
244A VAL* 3.0 43.9 + - + +
246A ASP* 2.9 30.5 + - - +
258A ASP* 4.8 0.2 + - - -
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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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231A ASP 3.5 18.0 + - - +
232A ALA* 3.7 11.7 - - - -
233A LEU 2.9 11.3 + - - +
235A ARG* 1.3 78.4 - - - +
237A GLY* 1.3 57.5 + - - +
238A VAL 3.5 3.1 + - - +
292A GLU* 3.4 33.9 - - - +
296A GLU* 4.1 2.4 - - - +
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Residues in contact with GLY 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 LEU 3.6 3.4 + - - -
234A ILE 2.9 7.7 + - - -
236A ALA* 1.3 79.7 - - - +
238A VAL* 1.3 62.2 + - - +
239A PRO* 4.3 1.2 - - - +
292A GLU* 3.8 11.4 - - - +
295A THR* 3.8 6.7 - - - +
296A GLU* 3.7 32.5 - - - +
299A LEU* 3.6 14.4 - - - +
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Residues in contact with VAL 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 ILE* 3.4 14.4 - - + +
235A ARG* 3.2 20.5 - - + +
236A ALA 3.5 2.6 - - - +
237A GLY* 1.3 82.3 - - - +
239A PRO* 1.3 77.1 - - + +
240A ASP* 3.7 2.9 + - - +
242A TRP* 4.7 12.3 - - + +
244A VAL* 3.6 27.4 - - + -
262A ILE* 3.9 28.9 - - + -
295A THR* 3.9 5.8 - - + -
299A LEU* 4.0 5.2 - - + -
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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