Contacts of the helix formed by residues 283 - 288 (chain A) in PDB entry 1T8U
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 TRP 283 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A TYR* 4.0 13.2 - + + -
266A PHE* 3.6 31.4 - + - -
269A LEU* 3.6 51.3 - - + +
270A THR* 3.6 26.7 - - - -
280A ASP* 3.0 26.3 + - - +
282A SER* 1.3 80.8 + - - +
284A SER* 1.3 82.8 + - - +
285A ALA* 3.4 24.8 - - + +
286A ILE* 2.9 36.8 + - + +
287A GLN* 2.9 11.5 + - - +
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Residues in contact with SER 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LYS* 5.8 1.9 + - - -
252A ASP* 5.1 2.3 + - - -
282A SER 3.4 5.6 + - - -
283A TRP* 1.3 80.4 + - - +
285A ALA* 1.3 66.0 + - - +
287A GLN* 4.2 7.9 - - - -
288A ILE* 2.9 43.4 + - - +
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Residues in contact with ALA 285 (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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248A ARG* 2.7 33.5 + - - +
249A ALA* 3.6 25.2 - - + +
252A ASP* 3.9 11.0 - - + +
253A TYR 5.1 0.9 - - - +
283A TRP* 3.2 41.3 - - + +
284A SER* 1.3 82.1 + - - +
286A ILE* 1.3 60.3 + - - +
289A GLY 4.2 1.0 + - - -
387A TYR* 3.7 1.9 + - - -
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Residues in contact with ILE 286 (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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249A ALA* 5.5 3.4 - - + -
266A PHE* 6.2 0.2 - - + -
270A THR* 3.8 14.8 - - + +
279A ILE* 3.3 24.9 - - + -
280A ASP 3.2 21.5 - - - +
281A THR* 4.1 13.9 - - - -
283A TRP* 2.9 33.7 + - + +
285A ALA* 1.3 78.7 - - - +
287A GLN* 1.3 65.7 + - - +
289A GLY* 3.1 5.9 + - - -
290A ILE* 3.9 3.0 + - + +
383A LEU* 4.6 7.9 - - + -
386A PHE* 3.9 24.7 - - + -
387A TYR* 2.7 33.7 + - + +
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Residues in contact with GLN 287 (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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281A THR* 2.7 34.8 + - - +
282A SER 5.3 1.1 - - - -
283A TRP 2.9 13.9 + - - +
284A SER* 3.8 8.5 - - - +
286A ILE* 1.3 74.2 - - - +
288A ILE* 1.3 64.8 + - + +
290A ILE* 3.1 27.4 + - - +
293A LYS* 2.6 41.1 + - - +
294A HIS* 2.9 29.3 + - + -
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Residues in contact with ILE 288 (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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160A VAL* 4.6 14.4 - - + -
161A LYS* 4.3 21.1 - - + +
220A PHE* 4.9 0.7 - - - -
221A VAL* 4.2 29.6 - - + +
248A ARG* 3.7 28.7 - - - +
252A ASP* 3.7 20.0 - - - +
284A SER* 2.9 35.1 + - - +
287A GLN* 1.3 73.3 - - + +
289A GLY* 1.3 61.4 + - - +
290A ILE 3.3 1.2 + - - -
291A TYR* 3.3 14.6 - - - -
294A HIS* 3.7 14.1 - - - -
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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