Contacts of the helix formed by residues 226 - 233 (chain A) in PDB entry 1W3U
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 ARG 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A MET* 3.6 2.2 - - - -
87A ASN* 3.6 4.0 - - - -
216A GLU* 5.6 0.4 - - - +
217A SER* 3.7 22.5 + - - -
218A PRO 3.6 10.7 + - - +
219A LYS* 3.7 31.7 + - - +
221A LEU* 3.7 28.0 + - + -
222A PRO 3.6 10.1 - - - +
223A THR* 3.3 10.9 + - - +
225A LEU* 1.3 79.1 - - - +
227A TYR* 1.3 64.2 + - - +
228A ASP* 2.9 45.8 + - - +
229A THR* 3.3 14.9 + - - +
230A TYR* 3.2 18.2 - - - -
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Residues in contact with TYR 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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71A LEU* 4.0 19.2 - - + +
73A ILE* 3.9 9.2 - - + -
80A GLN* 2.5 30.4 + - - -
83A MET* 3.4 25.9 - - + +
84A ILE* 3.2 23.8 + - - +
87A ASN* 3.0 50.6 + - + +
88A PHE* 3.8 26.0 - + - -
190A LEU* 3.7 8.0 - - + +
207A VAL* 4.0 9.0 - - + -
209A VAL* 5.3 1.6 - - + -
214A VAL* 3.6 24.9 - - + -
217A SER* 4.2 0.4 - - - +
226A ARG* 1.3 71.1 - - - +
228A ASP* 1.3 58.5 + - - +
230A TYR* 3.0 7.8 + - - +
231A VAL* 2.9 27.1 + - - +
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Residues in contact with ASP 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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214A VAL 3.7 17.2 + - - +
215A ALA 4.2 1.3 - - - +
216A GLU* 3.7 5.2 - - - -
217A SER* 2.8 44.2 + - - +
226A ARG* 2.9 38.8 + - - +
227A TYR* 1.3 74.5 - - - +
229A THR* 1.3 72.8 + - - +
231A VAL* 4.1 6.5 - - - +
232A LYS* 2.8 48.3 + - - +
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Residues in contact with THR 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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223A THR* 2.7 40.1 + - + +
224A MET* 4.8 3.1 - - - -
226A ARG* 3.3 16.6 + - - +
227A TYR 3.2 0.4 - - - -
228A ASP* 1.3 82.2 + - - +
230A TYR* 1.3 69.4 + - + +
233A ASN* 2.8 36.1 + - - +
237A TYR* 3.6 37.6 - - + +
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Residues in contact with TYR 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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71A LEU* 3.8 23.3 - - + +
72A PHE 3.8 13.2 - - - -
73A ILE* 3.8 40.7 - - + +
74A GLN 5.2 1.5 + - - -
83A MET* 3.7 14.4 - - + -
224A MET* 2.7 59.5 + - + +
226A ARG 3.2 18.8 - - - -
227A TYR* 3.0 6.5 + - - +
229A THR* 1.3 82.7 - - + +
231A VAL* 1.3 67.9 + - - +
234A ASN* 2.9 4.3 + - - -
235A SER* 2.8 40.8 + - - +
237A TYR* 6.2 2.7 - - + -
238A ASN* 5.3 4.0 - - - -
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Residues in contact with VAL 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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69A LYS* 4.3 19.7 + - + +
71A LEU* 3.9 23.3 - - + -
209A VAL* 4.4 5.2 - - + -
211A GLU* 4.4 20.4 - - + +
214A VAL* 3.8 28.3 - - + +
227A TYR 2.9 20.2 + - - +
228A ASP* 4.0 6.3 - - + +
230A TYR* 1.3 81.9 - - - +
232A LYS* 1.3 74.7 + - + +
233A ASN 3.2 0.3 + - - -
234A ASN* 3.2 8.5 + - - +
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Residues in contact with LYS 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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214A VAL 4.8 0.6 + - - -
215A ALA* 3.2 35.8 + - - +
228A ASP* 2.8 35.5 + - + +
231A VAL* 1.3 84.8 - - + +
233A ASN* 1.3 67.1 + - - +
234A ASN* 3.4 0.8 - - - +
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Residues in contact with ASN 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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43A ARG* 5.3 2.8 + - - +
229A THR* 2.8 30.1 + - - +
231A VAL 3.2 0.4 - - - -
232A LYS* 1.3 85.5 + - - +
234A ASN* 1.3 73.4 + - - +
235A SER 3.1 1.6 - - - -
236A LEU* 2.8 17.7 + - - +
237A TYR* 3.5 40.7 - - - +
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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