Contacts of the helix formed by residues 259 - 264 (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 ASP 259 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234C TYR* 3.3 22.1 + - + -
259C THR* 3.5 9.4 - - - +
288C TYR* 2.6 29.1 + - - -
164D TYR* 3.1 11.5 + - - -
254D THR 4.6 1.2 - - - +
255D HIS* 2.8 35.1 + - + +
256D ILE* 3.2 32.9 + - - +
258D LEU* 1.3 75.0 - - - +
260D GLY* 1.3 61.9 + - - +
261D ARG 3.0 6.6 + - - -
262D LEU* 3.0 19.4 + - - +
289D TYR* 3.8 6.5 - - + -
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Residues in contact with GLY 260 (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* 5.0 1.1 - - - -
164D TYR* 3.8 8.7 - - - -
258D LEU 3.3 0.2 - - - -
259D ASP* 1.3 76.0 - - - +
261D ARG* 1.3 60.4 + - - +
262D LEU 3.0 0.4 - - - -
263D ALA* 2.8 19.0 + - - +
265D ILE* 2.9 36.8 + - - +
288D ASP* 3.1 20.6 + - - -
289D TYR* 3.9 7.2 - - - -
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Residues in contact with ARG 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C PHE* 3.5 27.8 - - - -
95C ALA 4.4 6.3 + - - -
110C TRP* 3.4 23.9 + - + -
171C PHE* 3.6 39.0 + - + -
237C TYR* 3.3 39.8 + - + +
291C HIS* 4.3 11.3 + - - -
419C PHE* 3.7 25.9 - - - -
258D LEU* 3.9 5.4 + - + +
259D ASP 3.0 0.8 + - - -
260D GLY* 1.3 76.3 - - - +
262D LEU* 1.3 56.2 + - - +
264D GLY 2.7 21.5 + - - -
265D ILE 3.2 12.8 + - - +
266D VAL* 3.9 17.9 - - + -
288D ASP* 5.0 0.6 + - - -
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Residues in contact with LEU 262 (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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110C TRP* 3.7 4.6 + - - -
168C GLU* 2.6 44.4 - - - +
171C PHE* 4.0 19.5 - - + -
186C PRO* 4.5 7.6 - - + -
187C GLY* 4.7 8.5 - - - +
191C PHE* 4.1 22.0 - - + -
234C TYR* 3.5 52.0 - - + +
237C TYR* 4.3 8.3 - - + -
163D PRO* 3.4 9.4 - - + +
164D TYR* 4.0 11.2 - - + +
259D ASP 3.0 17.7 + - - +
261D ARG* 1.3 77.8 - - - +
263D ALA* 1.3 55.8 + - - +
264D GLY 3.4 0.4 - - - -
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Residues in contact with ALA 263 (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 1.2 + - - -
110C TRP* 4.7 4.9 - - - -
161D VAL* 3.9 16.1 - - + +
162D SER 3.6 21.3 - - - +
163D PRO* 4.6 0.2 - - + -
164D TYR* 3.7 26.9 + - + +
260D GLY 2.8 8.7 + - - +
262D LEU* 1.3 78.6 - - - +
264D GLY* 1.3 62.1 + - - +
265D ILE* 3.2 14.5 + - + +
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Residues in contact with GLY 264 (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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41C ARG* 2.9 28.6 + - - -
90C ARG* 4.8 5.3 + - - -
110C TRP* 3.6 35.0 - - - -
261D ARG* 2.7 15.1 + - - -
262D LEU 3.4 0.6 - - - -
263D ALA* 1.3 78.2 - - - +
265D ILE* 1.3 56.4 + - - -
266D VAL* 3.8 4.0 + - - +
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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