Contacts of the helix formed by residues 228 - 233 (chain A) in PDB entry 2W6U
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 ASN 228 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204A ARG* 5.8 0.2 - - - -
215A ASN* 5.1 4.5 - - - +
226A ALA 3.9 5.0 - - - +
227A ARG* 1.3 82.1 + - - +
229A VAL* 1.3 67.8 + - + +
230A GLY* 2.4 36.6 + - - -
231A TYR* 3.5 19.2 + - - -
232A SER* 3.1 19.6 + - - -
485A TRP* 3.6 21.9 - - - -
524A ASP* 4.6 3.0 + - - -
597A ASP* 4.7 10.5 + - - +
599A TRP* 5.3 14.8 - - + -
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Residues in contact with VAL 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200A TYR* 6.2 1.8 - - + -
204A ARG* 3.4 38.1 - - - +
228A ASN* 1.3 76.0 - - + +
230A GLY* 1.3 70.0 + - - +
232A SER* 3.2 12.8 + - - -
233A ALA* 3.5 12.1 + - - +
391A TRP* 4.8 21.2 - - + -
423A TYR* 5.0 3.7 - - - -
485A TRP* 6.4 0.2 - - + -
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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
----------------------------------------------------------
228A ASN* 2.4 22.5 + - - -
229A VAL* 1.3 78.7 - - - +
231A TYR* 1.3 57.0 + - - -
232A SER 3.2 2.6 + - - -
233A ALA 4.2 2.8 + - - -
421A ASN 4.6 2.6 - - - +
423A TYR* 4.0 18.2 - - - -
452A THR* 3.4 13.1 + - - -
485A TRP* 3.7 31.1 - - - -
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Residues in contact with TYR 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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225A THR* 3.6 33.5 - - + +
226A ALA* 4.2 0.9 - - - -
227A ARG* 3.7 28.3 - - + -
228A ASN* 3.5 18.8 + - - +
229A VAL 3.4 0.4 - - - -
230A GLY* 1.3 73.7 - - - +
232A SER* 1.3 56.4 - - - +
233A ALA 3.8 0.7 - - - -
421A ASN* 3.2 28.5 - - - +
452A THR* 3.7 21.0 + - + +
483A SER* 3.4 33.0 - - - -
485A TRP* 4.0 17.5 - + + -
524A ASP* 2.5 49.9 + - + +
526A THR* 3.1 21.3 + - - -
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Residues in contact with SER 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 3.3 24.0 + - - -
215A ASN* 4.6 3.9 + - - -
217A PHE* 5.0 2.8 - - - -
225A THR 4.7 1.6 - - - -
226A ALA* 3.4 24.1 + - - +
228A ASN 3.1 21.1 - - - -
229A VAL* 3.9 3.4 - - - -
230A GLY 3.1 1.6 - - - -
231A TYR* 1.3 76.4 - - - +
233A ALA* 1.3 66.6 + - - +
235A ASN* 3.2 35.8 + - - +
421A ASN* 3.9 2.9 - - - +
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Residues in contact with ALA 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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204A ARG* 4.8 2.2 - - - +
229A VAL 3.5 7.9 + - - +
230A GLY 4.7 0.4 - - - +
231A TYR 3.8 1.2 - - - -
232A SER* 1.3 73.9 - - - +
234A GLY* 1.3 58.7 + - - +
391A TRP* 5.9 2.0 - - - +
393A GLN* 4.0 11.2 - - + -
395A THR* 3.2 9.1 - - - +
421A ASN* 2.8 28.6 + - + +
422A GLY 3.2 39.7 - - - +
423A TYR* 4.2 15.3 - - + +
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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