Contacts of the helix formed by residues 223 - 230 (chain A) in PDB entry 3R2W
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 GLY 223 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A PHE 3.8 0.2 + - - -
220A TYR 3.4 10.7 + - - -
221A ASN 3.4 2.4 - - - -
222A SER* 1.3 81.5 + - - +
224A LEU* 1.3 53.4 + - - +
225A LEU 3.2 3.3 + - - -
226A ASP* 3.7 11.1 + - - +
227A THR* 2.8 28.7 + - - -
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Residues in contact with LEU 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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149A VAL* 4.4 10.1 - - + -
175A TYR* 4.0 33.7 - - + -
176A THR 4.1 8.7 - - - +
177A PHE* 3.8 37.0 - - + -
219A PHE* 4.5 8.7 - - + -
222A SER* 2.7 19.9 + - - +
223A GLY* 1.3 77.0 - - - +
225A LEU* 1.3 66.9 + - - +
227A THR* 3.2 16.5 + - + +
228A PHE* 3.0 38.3 + - + -
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Residues in contact with LEU 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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219A PHE* 3.5 37.0 + - + +
220A TYR* 3.3 43.5 - - + +
223A GLY 3.2 0.2 - - - -
224A LEU* 1.3 81.8 - - - +
226A ASP* 1.3 67.2 + - - +
227A THR 3.1 0.3 + - - -
228A PHE* 3.2 8.5 + - - -
229A ILE* 3.3 16.8 + - + +
325A LEU* 3.3 43.5 - - + +
328A VAL* 4.5 14.4 - - + +
329A LYS* 4.1 24.5 - - + +
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Residues in contact with ASP 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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220A TYR* 4.7 17.4 - - - +
223A GLY* 3.7 10.2 + - - +
224A LEU 3.4 0.2 - - - -
225A LEU* 1.3 89.7 - - - +
227A THR* 1.3 61.0 + - - +
228A PHE 3.5 0.2 - - - -
229A ILE* 3.9 12.0 - - - +
230A GLY* 3.3 17.5 + - - -
329A LYS* 5.7 4.5 - - - +
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Residues in contact with THR 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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175A TYR* 5.8 5.8 - - + +
223A GLY 2.8 21.0 + - - -
224A LEU* 3.4 18.7 - - + +
225A LEU 3.1 1.0 - - - -
226A ASP* 1.3 78.3 - - - +
228A PHE* 1.3 72.5 + - + +
230A GLY* 3.3 3.2 + - - -
231A GLU* 3.0 33.1 + - + +
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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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98A VAL* 3.7 28.7 - - + -
147A PRO* 3.7 22.4 - - + -
149A VAL* 4.0 22.2 - - + -
175A TYR* 3.7 37.7 - + - -
219A PHE* 4.6 10.3 - + - -
224A LEU* 3.0 39.7 + - + +
225A LEU* 3.2 4.8 + - - +
227A THR* 1.3 83.1 - - + +
229A ILE* 1.3 67.7 + - - +
230A GLY 2.9 1.1 - - - -
231A GLU* 2.9 31.8 + - - -
232A GLY 3.3 0.2 + - - -
233A LYS* 3.1 25.9 + - + +
236A ILE* 5.3 0.7 - - + -
325A LEU* 4.2 7.4 - - + -
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Residues in contact with ILE 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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225A LEU* 3.3 22.1 + - + +
226A ASP* 3.9 15.0 - - - +
228A PHE* 1.3 78.0 - - - +
230A GLY* 1.3 64.3 + - - +
232A GLY* 3.1 12.0 + - - -
233A LYS 3.3 23.1 - - - +
234A GLU* 4.8 6.5 - - + -
325A LEU* 4.2 18.2 - - + +
326A ALA* 4.6 23.3 - - + +
329A LYS* 5.8 6.3 - - + -
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Residues in contact with GLY 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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226A ASP 3.3 13.1 + - - -
227A THR 3.3 8.1 - - - -
228A PHE 2.9 1.0 - - - -
229A ILE* 1.3 84.4 - - - +
231A GLU* 1.3 56.8 + - - +
232A GLY 3.5 0.6 + - - -
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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