Contacts of the helix formed by residues 222 - 230 (chain A) in PDB entry 4U6Q
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 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203A TYR* 3.6 8.5 - - - -
220A VAL* 3.5 7.8 - - - +
221A SER* 1.3 89.9 - - - +
223A LEU* 1.3 64.2 + - - +
224A GLN* 3.7 9.6 + - - +
225A ASP* 2.7 38.8 + - - +
226A LEU 3.2 14.7 + - - -
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Residues in contact with LEU 223 (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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180A ILE* 3.7 32.8 - - + -
203A TYR* 3.7 31.0 + - + +
222A THR* 1.3 70.4 - - - +
224A GLN* 1.3 60.4 + - - +
226A LEU* 3.1 5.9 + - + +
227A LEU* 2.9 51.5 + - + +
246A LEU* 3.4 32.5 - - + +
251A THR* 3.9 25.1 - - + -
254A GLN* 4.9 0.2 - - - +
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Residues in contact with GLN 224 (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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222A THR* 3.2 8.0 - - - +
223A LEU* 1.3 80.3 - - - +
225A ASP* 1.3 58.3 + - - +
227A LEU* 3.4 3.4 + - - +
228A PHE* 2.9 37.7 + - + +
254A GLN* 3.6 46.3 + - + +
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Residues in contact with ASP 225 (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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220A VAL* 3.8 22.2 - - + -
221A SER* 4.5 4.9 + - - -
222A THR* 2.7 37.1 + - - +
224A GLN* 1.3 77.6 - - - +
226A LEU* 1.3 64.3 + - - +
228A PHE* 3.2 6.6 + - - -
229A HIS* 3.0 45.1 + - - +
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Residues in contact with LEU 226 (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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178A GLY* 3.8 28.9 - - - +
179A ILE 4.0 0.7 - - - +
180A ILE* 3.8 28.9 - - + -
201A LEU* 4.0 14.6 - - + -
202A PHE* 4.0 24.7 - - - -
203A TYR* 3.9 14.6 - - + +
220A VAL* 3.8 10.4 - - + +
222A THR 3.2 8.8 + - - +
223A LEU* 3.1 10.7 + - - +
225A ASP* 1.3 82.0 - - - +
227A LEU* 1.3 70.0 + - + +
229A HIS* 3.3 0.7 + - - +
230A SER* 2.5 38.2 + - - +
233A VAL* 4.4 4.0 - - + -
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Residues in contact with LEU 227 (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 LEU* 2.9 50.4 + - + +
224A GLN 3.9 2.7 - - - +
226A LEU* 1.3 74.9 - - + +
228A PHE* 1.3 60.5 + - - +
229A HIS 3.6 0.3 + - - -
230A SER* 3.8 12.2 + - - +
233A VAL* 3.9 29.4 - - + +
247A ILE* 4.3 10.8 - - + -
251A THR* 3.5 30.7 - - - +
254A GLN* 3.6 26.5 - - + +
255A MET* 3.7 19.4 - - + +
256A ARG 3.5 19.9 + - - -
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Residues in contact with PHE 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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224A GLN* 2.9 24.4 + - + +
225A ASP* 3.6 6.7 - - - +
226A LEU 3.1 0.2 - - - -
227A LEU* 1.3 78.7 - - - +
229A HIS* 1.3 92.0 + + - +
254A GLN 3.8 12.1 - - - +
256A ARG* 2.9 25.5 + - + +
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Residues in contact with HIS 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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176A THR* 3.2 21.9 + - + +
201A LEU* 3.9 23.1 - - + +
220A VAL* 5.2 3.0 - - + +
225A ASP* 3.0 40.4 + - + +
228A PHE* 1.3 105.4 - + - +
230A SER* 1.3 60.1 + - - +
256A ARG* 3.4 28.2 + - - +
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Residues in contact with SER 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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176A THR* 3.7 8.7 - - - +
178A GLY* 3.3 35.2 + - - -
201A LEU* 4.8 1.7 - - - +
226A LEU* 2.5 26.3 + - - +
227A LEU 3.8 4.7 + - - +
228A PHE 3.5 1.2 - - - -
229A HIS* 1.3 80.1 - - - +
231A ASP* 1.3 63.0 + - - +
232A CYS 4.0 0.9 - - - -
233A VAL* 3.9 19.7 - - - +
256A ARG* 3.6 21.0 + - - +
259A ALA* 4.2 4.5 - - - +
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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