Contacts of the helix formed by residues 227 - 234 (chain A) in PDB entry 4QYJ
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 THR 227 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A ASP* 5.5 1.4 + - - -
49A GLY 4.0 7.1 + - - -
50A ASP* 3.5 26.0 + - - +
51A VAL* 4.6 3.8 - - - +
224A ARG* 3.5 11.8 + - + +
225A GLY 3.2 0.6 - - - -
226A GLU* 1.3 89.2 - - + +
228A ALA* 1.3 77.8 + - - +
229A GLY 3.3 1.1 - - - -
230A ASP* 3.2 4.4 + - - +
231A ALA* 3.0 22.2 + - - +
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Residues in contact with ALA 228 (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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49A GLY 3.9 18.1 + - - +
50A ASP* 5.2 0.9 - - - +
54A VAL* 3.7 19.1 - - + +
192A LYS* 4.1 20.2 - - + -
221A VAL* 4.9 2.9 - - + -
222A THR 4.4 4.9 - - - +
223A GLY* 4.3 9.4 - - - -
224A ARG 3.3 13.2 + - - +
227A THR* 1.3 82.4 + - - +
229A GLY* 1.3 64.5 + - - +
231A ALA* 3.2 3.7 + - - +
232A LEU* 3.1 19.8 + - - +
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Residues in contact with GLY 229 (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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165A ILE* 4.7 11.3 - - - +
192A LYS* 3.9 15.9 - - - +
225A GLY 3.3 15.9 + - - -
227A THR 3.3 0.4 - - - -
228A ALA* 1.3 78.1 - - - +
230A ASP* 1.3 60.9 + - - +
232A LEU* 3.0 8.8 + - - +
233A VAL* 3.0 27.7 + - - +
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Residues in contact with ASP 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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225A GLY 4.0 1.6 + - - +
226A GLU* 2.7 28.3 + - - +
227A THR* 3.2 6.8 + - - +
229A GLY* 1.3 75.2 - - - +
231A ALA* 1.3 63.2 + - - +
233A VAL* 3.4 6.3 + - - +
234A ARG* 3.1 27.7 + - - +
252A ILE* 5.4 7.6 - - - +
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Residues in contact with ALA 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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51A VAL* 3.4 39.2 - - + +
54A VAL* 3.8 23.5 - - + +
227A THR 3.0 5.1 + - - +
228A ALA* 3.5 8.5 - - - +
230A ASP* 1.3 79.0 - - - +
232A LEU* 1.3 63.2 + - - +
234A ARG* 3.4 3.9 + - - -
235A HIS* 3.3 25.3 + - - +
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Residues in contact with LEU 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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54A VAL* 3.6 15.7 - - + +
58A VAL* 3.8 19.1 - - + -
163A ALA* 3.9 23.3 - - + +
164A ALA 4.8 1.8 - - - +
165A ILE* 4.9 7.6 - - + -
190A VAL* 3.8 42.2 - - + +
192A LYS* 4.0 28.7 - - + +
221A VAL* 5.6 2.5 - - + -
228A ALA 3.1 11.5 + - - +
229A GLY* 3.0 11.1 + - - +
231A ALA* 1.3 78.4 - - - +
233A VAL* 1.3 62.5 + - + +
235A HIS* 3.6 2.7 + - - +
238A VAL* 3.4 29.4 - - + +
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Residues in contact with VAL 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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163A ALA* 5.4 3.1 - - - -
165A ILE* 4.3 15.9 - - + -
229A GLY 3.0 19.3 + - - +
230A ASP* 3.8 7.4 - - - +
231A ALA 3.3 0.2 - - - -
232A LEU* 1.3 77.0 - - + +
234A ARG* 1.3 61.8 + - + +
235A HIS 3.2 0.2 - - - -
238A VAL* 5.0 0.6 - - - +
241A VAL* 5.1 8.5 - - + -
253A ILE* 3.9 39.3 - - + -
256A ALA* 3.8 29.5 - - + +
257A CYS* 4.7 7.2 - - - -
260A SER* 5.4 0.3 + - - -
262A LYS* 2.8 29.3 + - - +
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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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230A ASP 3.1 16.7 + - - +
231A ALA* 3.7 5.4 - - - +
232A LEU 3.4 0.2 - - - -
233A VAL* 1.3 79.8 - - + +
235A HIS* 1.3 60.7 + - - +
236A PRO* 3.4 8.7 - - - +
256A ALA* 5.9 3.4 - - + -
260A SER* 5.5 3.6 - - - -
262A LYS* 4.2 2.9 - - - +
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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