Contacts of the helix formed by residues 259 - 264 (chain E) in PDB entry 1TYE
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 259 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PHE 4.8 1.6 - - - +
232E ASP* 2.6 28.5 + - - +
233E GLY* 2.9 16.1 + - - -
234E TYR* 3.4 9.8 - - + -
257E ALA 2.8 2.6 + - - -
258E PRO* 1.3 80.7 - - - +
260E TRP* 1.3 69.2 + - - +
261E SER 3.7 0.2 + - - -
262E TRP* 3.9 2.6 + - - -
263E THR* 3.1 25.5 + - + +
265E GLY 4.1 0.2 - - - -
288E TYR* 3.7 16.8 - - + +
256F ILE* 4.3 11.2 - - + -
259F ASP* 3.6 25.8 - - - +
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Residues in contact with TRP 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E GLU* 3.4 44.9 + - + -
230E TYR* 3.4 43.2 - + - -
233E GLY* 3.6 11.3 + - - -
235E TRP* 5.4 0.4 - + + -
257E ALA* 2.9 28.0 + - + +
258E PRO 3.6 0.4 - - - -
259E THR* 1.3 78.7 - - - +
261E SER* 1.3 91.1 + - - +
264E LEU* 2.8 22.3 + - + -
265E GLY 2.9 10.3 + - - +
266E ALA* 3.5 27.6 - - + +
268E GLU* 4.7 1.7 + - - -
279E ARG* 3.4 48.9 - - - -
281E ARG* 3.8 24.0 - - + -
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Residues in contact with SER 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229E GLU* 2.6 36.6 + - - -
259E THR 3.7 0.2 + - - -
260E TRP* 1.3 102.6 - - - +
262E TRP* 1.3 89.6 + - - +
264E LEU* 3.2 16.8 - - - +
281E ARG* 4.5 4.7 + - - -
1I NAG 4.9 2.6 - - - +
2I NAG 5.6 1.0 + - - -
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Residues in contact with TRP 262 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228E PRO* 3.8 33.4 + - + -
229E GLU* 4.1 20.8 + - + -
231E PHE 5.3 1.2 + - - -
259E THR 3.9 2.3 + - - -
260E TRP 3.4 0.6 - - - -
261E SER* 1.3 102.4 - - - +
263E THR* 1.3 69.8 + - - +
264E LEU* 2.8 9.9 + - - -
285E MET* 4.0 10.6 - - - +
253F LYS* 3.8 44.7 - - + +
314F VAL* 6.1 0.8 - - + +
317F LEU* 3.8 34.3 - - + -
1I NAG 4.2 19.5 - - + +
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Residues in contact with THR 263 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258E PRO 4.5 3.9 - - - +
259E THR* 3.1 29.9 + - + +
262E TRP* 1.3 81.9 + - - +
264E LEU* 1.3 62.6 + - - +
265E GLY* 3.2 2.4 + - - -
284E GLN 4.3 0.5 - - - +
285E MET* 3.4 9.9 - - - +
286E ALA* 2.9 30.2 + - - -
287E SER 4.6 0.7 + - - -
288E TYR 5.3 0.7 + - - -
253F LYS* 6.5 1.6 - - + -
254F THR 4.7 7.2 - - - +
256F ILE* 3.8 27.1 - - + -
259F ASP* 6.0 0.4 - - - +
317F LEU* 5.9 0.2 - - + -
321F TYR* 2.9 32.9 + - - +
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Residues in contact with LEU 264 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260E TRP* 2.8 12.4 + - + +
261E SER* 3.2 21.5 - - - +
262E TRP 2.8 3.9 + - - +
263E THR* 1.3 75.8 - - - +
265E GLY* 1.3 72.1 + - - +
281E ARG* 3.5 33.0 - - + +
282E ALA* 2.7 62.6 - - - +
283E GLU 4.6 6.1 - - - +
284E GLN 4.4 3.6 - - - +
285E MET* 4.3 25.1 - - + +
289E PHE* 4.4 1.1 + - - +
1I NAG 6.2 0.2 - - - +
2I NAG 5.2 3.1 - - - +
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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