Contacts of the helix formed by residues 234 - 241 (chain A) in PDB entry 3Q8B
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 SER 234 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU 4.9 1.1 + - - -
181A ASP* 3.8 5.5 + - - +
226A TRP* 3.1 52.2 - - - -
233A TYR* 1.3 75.7 - - - +
235A ASP* 1.3 65.0 + - - +
236A PHE* 3.1 11.6 + - - +
237A GLU* 3.0 34.3 + - - +
238A LYS* 2.9 24.2 + - - +
464A PHE* 5.5 0.2 - - - -
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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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181A ASP* 3.8 8.0 + - - +
183A ILE* 3.9 12.4 - - + +
188A GLU* 3.1 2.9 - - - +
221A SER* 3.9 8.7 - - - +
225A LYS 3.2 1.4 - - - +
226A TRP 2.9 13.2 + - - -
227A SER* 3.5 1.9 + - - -
228A THR* 2.7 42.1 + - - -
234A SER* 1.3 72.7 + - - +
236A PHE* 1.3 61.6 + - - +
238A LYS* 3.8 4.8 - - - +
239A VAL* 3.3 30.1 + - - +
254A PRO* 3.7 21.5 - - + +
736A CA 2.3 29.0 - - - -
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Residues in contact with PHE 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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20A LEU* 4.0 26.7 - - + -
35A VAL* 4.5 13.5 - - + -
36A THR* 6.3 1.8 - - - -
37A SER* 6.2 0.4 - - - -
153A LEU* 6.1 1.8 - - + -
156A LEU* 4.0 17.3 - - + -
181A ASP* 2.9 31.3 - - - +
182A GLY 4.4 5.2 - - - -
183A ILE* 3.7 27.1 - - + +
203A LEU* 4.4 7.4 - - + -
234A SER* 3.0 2.1 + - - +
235A ASP* 1.3 78.6 - - - +
237A GLU* 1.3 64.8 + - - +
239A VAL* 3.4 1.5 + - - -
240A THR* 2.8 48.4 + - + +
242A ARG* 3.7 37.0 - - - -
464A PHE* 4.4 10.3 - + - -
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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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157A LYS* 2.7 31.9 + - - -
226A TRP* 3.7 5.1 - - - -
232A PRO 4.4 0.9 - - - +
233A TYR* 3.6 14.2 - - + +
234A SER* 3.0 39.6 + - - +
236A PHE* 1.3 75.0 - - - +
238A LYS* 1.3 63.9 + - - +
240A THR* 4.0 4.7 - - - -
241A GLY* 3.0 20.1 + - - -
242A ARG* 3.0 36.4 + - + +
243A ILE* 4.0 4.9 - - + +
462A TYR* 4.1 8.8 + - + +
464A PHE* 3.3 29.8 - - + -
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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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227A SER* 4.7 1.5 + - - -
229A ALA* 4.4 6.1 - - - +
231A ASP* 2.8 39.2 + - - -
233A TYR* 3.6 17.7 - - + -
234A SER 2.9 17.5 + - - +
235A ASP* 3.8 6.3 - - - +
237A GLU* 1.3 80.2 - - - +
239A VAL* 1.3 62.9 + - + +
241A GLY* 3.4 8.5 + - - -
243A ILE* 3.9 22.5 - - + +
251A ALA 3.3 19.7 + - - +
252A ARG* 3.4 26.5 + - - +
253A HIS 3.6 14.1 + - - +
254A PRO* 4.0 11.4 + - + +
256A VAL 3.0 23.4 + - - -
258A ALA 4.3 0.2 - - - +
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Residues in contact with VAL 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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183A ILE* 4.4 0.2 - - + -
192A TYR* 4.1 7.2 - - + -
194A VAL* 3.6 45.1 - - + +
201A THR* 4.5 2.1 + - - +
203A LEU* 4.0 18.4 - - + -
219A TYR* 4.1 21.8 - - + -
235A ASP 3.3 19.0 + - - +
236A PHE* 3.8 7.9 - - - +
238A LYS* 1.3 77.7 - - - +
240A THR* 1.3 62.6 + - + +
241A GLY 3.4 0.2 - - - -
252A ARG 4.1 5.2 - - - +
254A PRO* 3.6 31.0 - - + -
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Residues in contact with THR 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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16A SER* 6.0 0.7 - - - -
194A VAL* 5.0 0.2 - - + -
201A THR* 4.5 32.1 + - + +
203A LEU* 5.0 5.6 - - + -
236A PHE* 2.8 49.1 + - + +
237A GLU 3.7 0.7 + - - -
239A VAL* 1.3 85.9 - - + +
241A GLY* 1.3 61.2 + - - +
242A ARG* 2.9 40.5 + - - +
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Residues in contact with GLY 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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16A SER* 6.3 0.4 - - - -
237A GLU 3.0 6.0 + - - -
238A LYS 3.4 7.4 + - - -
239A VAL 3.4 1.0 + - - -
240A THR* 1.3 77.8 - - - +
242A ARG* 1.3 56.1 + - - +
243A ILE* 2.9 27.3 + - - +
245A LYS* 5.8 3.6 - - - +
252A ARG* 5.0 6.7 + - - -
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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