Contacts of the helix formed by residues 221 - 232 (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 GLY 221 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156F PHE* 4.0 10.5 - - - +
157F VAL 3.2 10.8 + - - -
158F ASP* 3.4 11.8 + - - -
159F LYS 5.2 0.2 - - - -
189F GLY 4.7 3.0 - - - +
220F GLU* 1.3 73.8 - - - +
222F GLY* 1.3 62.4 + - - +
223F PHE 3.4 2.7 - - - -
224F ASP* 3.1 21.7 + - - +
225F ALA* 3.4 4.9 + - - +
255F HIS 5.6 0.2 - - - -
289F TYR* 3.8 24.5 - - - -
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Residues in contact with GLY 222 (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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156F PHE* 3.5 26.6 - - - -
220F GLU* 3.3 8.3 + - - +
221F GLY* 1.3 75.8 - - - +
223F PHE* 1.3 56.6 + - - +
225F ALA* 2.9 19.2 + - - +
226F ILE* 2.9 16.5 + - - +
248F PHE* 3.6 23.1 - - - -
254F THR* 4.2 3.4 + - - -
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Residues in contact with PHE 223 (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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221F GLY 3.4 0.4 - - - -
222F GLY* 1.3 76.4 - - - +
224F ASP* 1.3 61.9 + - - +
226F ILE* 3.7 27.1 - - + +
227F MET* 3.1 18.7 + - - +
248F PHE* 4.6 3.8 - + - -
254F THR* 3.4 35.8 + - + -
255F HIS 3.7 18.4 + - - +
256F ILE* 4.3 11.2 - - + -
289F TYR* 5.5 0.7 - - + -
290F PRO* 3.3 33.6 - - + +
292F LEU* 3.9 15.0 - - + -
295F MET* 3.3 32.8 - - + +
308F PHE* 4.8 10.8 - + - -
318F TYR* 4.6 11.0 - + - -
321F TYR* 4.7 14.1 - + + -
325F ILE* 5.5 1.1 - - + -
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Residues in contact with ASP 224 (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* 3.0 28.0 + - - +
189F GLY* 5.8 2.9 - - - +
190F TYR* 4.9 3.6 - - + -
221F GLY* 3.1 15.8 + - - +
222F GLY 3.1 0.6 - - - -
223F PHE* 1.3 78.1 - - - +
225F ALA* 1.3 62.0 + - - +
227F MET* 3.7 2.9 + - - +
228F GLN* 3.3 28.9 + - - +
269F ASN* 4.0 2.6 + - - +
281F TYR* 3.2 29.1 - - + -
284F SER* 3.9 6.2 + - - -
288F ASP 3.8 4.2 - - - +
289F TYR* 3.5 17.5 - - + -
290F PRO* 3.2 22.6 - - - +
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Residues in contact with ALA 225 (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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117F LEU* 3.9 10.3 - - + -
156F PHE* 3.9 28.9 - - + -
190F TYR* 3.4 36.0 - - + +
221F GLY 3.4 1.6 + - - +
222F GLY 2.9 10.2 + - - +
224F ASP* 1.3 76.9 - - - +
226F ILE* 1.3 66.4 + - - +
228F GLN* 3.2 3.5 + - - +
229F ALA* 2.9 23.6 + - - +
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Residues in contact with ILE 226 (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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117F LEU* 3.8 10.5 - - + -
222F GLY 2.9 14.2 + - - +
223F PHE* 3.7 36.3 - - + +
225F ALA* 1.3 73.3 - - - +
227F MET* 1.3 65.7 + - - +
229F ALA* 3.0 5.2 + - - +
230F THR* 2.9 35.4 + - - +
246F LEU* 4.0 12.1 - - + -
248F PHE* 3.7 31.6 - - + -
295F MET* 4.7 13.0 - - + -
299F LEU* 4.7 7.4 - - + -
306F LEU* 4.2 30.3 - - + -
308F PHE* 4.3 1.8 - - + -
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Residues in contact with MET 227 (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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223F PHE 3.1 15.4 + - - +
224F ASP* 3.8 5.2 - - - +
226F ILE* 1.3 80.9 - - - +
228F GLN* 1.3 74.5 + - - +
230F THR* 3.3 6.8 + - - -
231F VAL* 3.1 28.7 + - + +
269F ASN* 4.1 15.7 - - - +
271F GLY* 4.2 17.7 - - - +
290F PRO* 3.7 16.8 - - + -
294F LEU* 3.8 10.8 - - + +
295F MET* 3.6 45.1 - - + +
298F LYS* 3.9 24.5 - - + -
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Residues in contact with GLN 228 (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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190F TYR* 3.8 22.4 - - + -
224F ASP 3.3 15.7 + - - +
225F ALA 3.2 2.4 + - - +
227F MET* 1.3 87.2 - - - +
229F ALA* 1.3 66.3 + - - +
231F VAL* 4.3 2.1 - - - +
232F CYS* 3.0 35.0 + - - +
236F ILE* 5.2 0.2 - - - -
269F ASN* 5.3 2.0 + - - -
272F GLN 3.2 22.0 + - - -
274F HIS* 2.8 28.1 + - - -
275F VAL* 3.6 11.1 - - + +
281F TYR* 3.5 44.8 + - + -
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Residues in contact with ALA 229 (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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115F TYR* 4.0 31.6 - - + -
117F LEU* 4.5 3.8 - - + -
190F TYR* 4.1 4.4 + - - +
225F ALA 2.9 13.4 + - - +
226F ILE 3.5 7.9 - - - +
228F GLN* 1.3 76.2 - - - +
230F THR* 1.3 59.2 + - - +
232F CYS 4.3 0.7 + - - -
236F ILE* 3.3 18.8 - - - +
238F TRP* 2.8 28.8 + - + -
246F LEU* 4.4 14.1 - - + -
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Residues in contact with THR 230 (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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226F ILE* 2.9 21.3 + - - +
227F MET* 3.6 8.1 - - - -
228F GLN 3.1 0.2 - - - -
229F ALA* 1.3 79.0 - - - +
231F VAL* 1.3 57.8 + - - +
232F CYS 3.7 0.2 - - - -
233F ASP* 4.1 4.5 - - - +
238F TRP* 4.6 0.9 + - - -
246F LEU* 3.9 6.6 - - - +
298F LYS* 3.5 34.3 - - + +
299F LEU* 3.5 31.5 - - + +
302F LYS* 3.2 20.3 - - + +
304F ILE* 3.9 20.8 - - + +
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Residues in contact with VAL 231 (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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227F MET* 3.1 23.2 + - - +
228F GLN* 4.2 4.7 - - - +
230F THR* 1.3 80.7 - - + +
232F CYS* 1.3 57.2 + - - +
233F ASP* 3.3 16.6 + - - +
271F GLY 3.6 28.3 - - - +
272F GLN* 3.8 19.7 - - - +
273F CYS* 3.7 13.9 + - - +
298F LYS* 3.9 31.4 - - + +
302F LYS* 4.1 17.7 + - - +
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Residues in contact with CYS 232 (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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228F GLN* 3.0 37.8 + - - +
229F ALA 4.3 0.4 + - - -
230F THR 3.7 1.2 - - - -
231F VAL* 1.3 75.4 - - - +
233F ASP* 1.3 64.3 + - - +
234F GLU 3.3 1.8 - - - -
235F LYS* 2.8 28.5 + - + -
236F ILE* 3.1 17.3 + - + -
273F CYS* 2.0 50.3 - - - -
275F VAL* 3.9 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