Contacts of the helix formed by residues 258 - 264 (chain F) 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 LEU 258 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237E TYR* 2.8 28.4 + - - +
288E TYR* 3.0 31.2 + - + -
291E HIS* 3.7 31.6 - - + +
311E PRO* 3.9 14.4 - - + -
312E LEU* 3.8 19.3 - - + -
355E ARG* 3.9 25.6 - - - +
358E SER* 6.3 0.2 - - - -
419E PHE* 6.1 4.9 - - + -
257F ALA* 1.3 75.4 - - - +
259F ASP* 1.3 61.3 + - - +
260F GLY 3.3 1.6 - - - -
261F ARG* 3.9 5.3 + - + +
266F VAL 5.8 3.1 - - - +
288F ASP* 2.9 23.3 + - - +
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Residues in contact with ASP 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234E TYR* 3.6 19.6 - - + -
259E THR* 3.6 7.0 - - - +
263E THR* 6.0 0.3 - - - +
288E TYR* 2.7 34.2 + - - -
164F TYR* 3.3 8.2 + - - -
254F THR 4.6 1.4 - - - +
255F HIS* 2.8 34.6 + - + +
256F ILE* 3.3 31.2 + - - +
257F ALA 3.2 2.8 - - - -
258F LEU* 1.3 73.6 - - - +
260F GLY* 1.3 54.0 + - - +
261F ARG 2.7 18.3 + - - -
262F LEU* 3.0 20.2 + - - +
289F TYR* 3.8 4.9 - - + -
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Residues in contact with GLY 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159F LYS* 5.1 0.7 - - - -
164F TYR* 3.8 9.4 - - - -
259F ASP* 1.3 77.4 - - - +
261F ARG* 1.3 59.3 + - - +
262F LEU 3.1 1.3 - - - -
263F ALA* 3.1 8.1 + - - +
265F ILE* 2.8 43.4 + - - +
288F ASP* 3.1 21.5 + - - -
289F TYR* 3.7 8.6 - - - -
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Residues in contact with ARG 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21E PHE* 3.9 21.5 - - - -
95E ALA 4.5 3.4 + - - -
110E TRP* 3.2 25.3 + - + -
171E PHE* 3.5 45.2 + - + -
172E SER* 6.1 0.2 - - - -
237E TYR* 3.4 39.1 + - + +
291E HIS* 4.3 11.7 + - - -
419E PHE* 3.5 27.9 - - - -
258F LEU* 3.9 4.7 + - + +
259F ASP 2.7 4.9 + - - -
260F GLY* 1.3 70.9 - - - +
262F LEU* 1.3 60.7 + - - +
263F ALA 3.0 6.7 + - - -
264F GLY 3.2 8.6 + - - -
265F ILE 3.3 11.1 + - - +
266F VAL* 3.9 22.2 - - + -
288F ASP* 5.8 0.2 - - - +
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Residues in contact with LEU 262 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TRP* 3.7 4.4 + - - -
168E GLU* 2.5 42.8 - - - +
171E PHE* 4.3 6.5 - - + -
186E PRO* 4.7 14.1 - - + -
187E GLY* 4.8 2.7 - - - +
191E PHE* 4.2 17.3 - - + -
234E TYR* 3.5 52.9 - - + +
237E TYR* 4.1 20.2 - - + -
163F PRO* 3.3 12.4 - - + +
164F TYR* 4.0 10.8 - - + +
259F ASP 3.0 20.0 + - - +
261F ARG* 1.3 77.9 - - - +
263F ALA* 1.3 56.9 + - - +
264F GLY 3.5 0.7 - - - -
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Residues in contact with ALA 263 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TRP* 4.6 4.3 - - - +
161F VAL* 4.3 14.8 - - + +
162F SER 3.7 18.6 - - - +
164F TYR* 3.6 29.6 - - + -
260F GLY 3.1 8.1 + - - +
261F ARG 3.0 0.8 - - - -
262F LEU* 1.3 81.0 - - - +
264F GLY* 1.3 58.1 + - - +
265F ILE* 3.1 22.4 + - + +
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Residues in contact with GLY 264 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E ARG* 2.7 37.2 + - - -
110E TRP* 3.7 39.0 - - - -
261F ARG* 3.2 7.5 + - - -
262F LEU 3.5 1.0 - - - -
263F ALA* 1.3 79.0 - - - +
265F ILE* 1.3 55.2 + - - +
266F VAL* 3.7 4.1 + - - +
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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