Contacts of the helix formed by residues 281 - 286 (chain D) 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 TYR 281 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D GLY* 5.6 0.7 + - - -
190D TYR* 3.0 40.1 + - + +
224D ASP* 3.3 39.1 + - + -
228D GLN* 3.4 43.7 + - + -
269D ASN* 3.5 23.7 + - - -
274D HIS* 3.6 20.0 - + + -
275D VAL* 4.2 5.3 - - - +
279D ASN 4.3 0.2 + - - -
280D HIS* 1.3 71.5 - - - +
282D SER* 1.3 63.1 + - - +
283D ALA* 3.8 10.8 + - + +
284D SER* 3.4 38.7 - - - -
287D MET* 3.9 15.1 + - - +
288D ASP 5.0 0.2 + - - -
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Residues in contact with SER 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D HIS* 2.9 29.4 + - - +
276D GLY 5.4 1.5 + - - -
278D ASP* 5.7 4.0 - - - -
280D HIS* 3.2 5.8 + - - -
281D TYR* 1.3 68.6 - - - +
283D ALA* 1.3 57.2 + - - +
284D SER* 3.1 8.5 + - - -
285D THR* 4.4 9.9 + - - +
286D THR* 4.6 3.1 + - - +
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Residues in contact with ALA 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D HIS* 4.1 12.5 - - + +
281D TYR* 3.6 20.8 + - + -
282D SER* 1.3 75.3 + - - +
284D SER* 1.3 58.4 + - - +
285D THR 3.1 3.4 - - - -
286D THR* 2.9 19.8 + - - +
287D MET* 2.9 55.8 + - + +
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Residues in contact with SER 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D LYS* 2.8 42.2 + - - +
160D PRO* 3.5 23.9 - - - +
189D GLY* 3.7 14.6 - - - -
224D ASP* 4.1 4.5 + - - -
281D TYR* 3.4 41.7 + - - -
282D SER 3.1 2.4 - - - -
283D ALA* 1.3 76.3 - - - +
285D THR* 1.3 58.0 + - - +
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Residues in contact with THR 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C ARG* 5.8 1.6 + - - -
160D PRO* 3.8 28.0 - - + +
161D VAL* 3.7 30.8 - - + +
265D ILE* 3.6 22.7 - - - +
282D SER 4.4 6.0 + - - +
283D ALA 3.1 0.2 - - - -
284D SER* 1.3 80.8 - - - +
286D THR* 1.3 70.2 + - - +
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Residues in contact with THR 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ILE* 3.7 8.8 - - - +
267D GLN* 2.9 26.5 + - - +
282D SER 4.6 2.6 + - - +
283D ALA* 2.9 25.6 + - - +
285D THR* 1.3 95.6 - - - +
287D MET* 1.3 58.3 + - - +
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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