Contacts of the strand formed by residues 228 - 233 (chain A) in PDB entry 1TYG
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 ILE 228 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ILE* 3.8 13.9 - - + +
107A GLY* 4.1 18.8 - - - +
195A ASP* 3.3 20.8 + - + +
196A MET* 3.2 28.1 - - + -
197A ILE* 2.6 34.8 + - - +
226A GLY 4.3 4.0 + - - +
227A PHE* 1.3 76.9 - - - +
229A VAL* 1.3 53.0 + - - +
230A LEU* 3.6 1.8 - - + +
249A HIS* 3.5 39.7 - - + +
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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
----------------------------------------------------------
197A ILE* 3.7 4.0 - - + -
199A VAL* 3.8 18.8 - - + -
219A SER* 3.7 28.9 - - - +
222A LEU* 3.7 15.5 - - + -
223A LEU* 3.5 30.1 - - + +
227A PHE* 3.6 25.1 - - + -
228A ILE* 1.3 70.1 - - - +
230A LEU* 1.3 65.3 + - - +
231A PRO* 3.5 5.6 - - + +
248A VAL* 3.7 9.1 - - + +
249A HIS* 2.9 32.7 + - - -
250A ALA 3.7 1.0 + - - -
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Residues in contact with LEU 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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106A ILE* 4.1 16.8 - - + -
116A LEU* 5.7 0.2 - - + -
169A LEU* 4.1 10.3 - - + -
196A MET* 3.5 34.3 - - + -
197A ILE 2.8 16.6 + - - +
198A LYS* 3.2 7.6 - - - +
199A VAL 2.9 19.4 + - - -
228A ILE* 3.6 14.4 - - + +
229A VAL* 1.3 80.1 - - - +
231A PRO* 1.3 65.4 - - - +
232A TYR 3.7 0.2 + - - -
249A HIS* 5.1 0.2 - - + -
250A ALA* 3.7 28.3 - - + +
252A MET* 3.9 31.0 - - + +
282A ILE* 4.3 5.4 - - + -
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Residues in contact with PRO 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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199A VAL* 3.7 13.0 - - + +
215A THR* 5.3 3.4 - - - +
219A SER* 3.7 13.0 - - - +
229A VAL* 3.8 0.7 - - + -
230A LEU* 1.3 83.1 - - - +
232A TYR* 1.3 61.9 + - - +
233A THR* 3.5 0.5 + - - -
243A LEU* 3.7 31.9 - - + -
248A VAL* 3.4 34.5 - - + -
250A ALA 3.0 19.3 - - - +
251A ILE* 4.5 1.8 - - + -
252A MET* 3.1 27.6 + - - +
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Residues in contact with TYR 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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198A LYS* 4.0 21.9 - - - +
199A VAL 2.8 22.0 + - - +
200A GLU* 4.3 22.0 - - + -
202A ILE* 4.8 4.3 - - + -
208A LEU 3.7 11.8 + - - -
209A LEU* 3.9 9.5 - - - +
210A PRO* 3.4 41.3 - - + +
215A THR* 3.8 16.8 - - - +
230A LEU 3.7 2.2 + - - -
231A PRO* 1.3 68.4 - - - +
233A THR* 1.3 76.1 + - - +
234A SER* 5.8 0.2 - - - -
252A MET* 3.5 14.1 - - - -
254A GLY* 4.0 8.5 - - - -
256A SER 4.9 1.7 + - - -
258A ILE* 4.0 24.6 + - + +
284A ASP* 3.7 13.0 - - - +
285A ALA* 3.8 23.6 - - + +
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Residues in contact with THR 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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210A PRO* 3.8 8.5 - - - -
215A THR* 5.7 2.4 + - - -
231A PRO 3.5 0.8 + - - -
232A TYR* 1.3 82.6 - - - +
234A SER* 1.3 65.6 + - - +
235A ASP 3.9 7.5 + - - +
239A LEU* 3.3 25.1 - - - +
240A ALA* 4.9 8.6 + - + -
243A LEU* 3.6 25.3 - - + +
251A ILE* 4.5 7.6 - - + -
252A MET 3.0 16.0 + - - +
253A PRO* 3.6 25.6 - - + -
254A GLY 3.0 22.9 + - - -
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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