Contacts of the helix formed by residues 221 - 232 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B PHE* 3.9 11.1 - - - +
157B VAL 3.2 8.1 + - - -
158B ASP* 3.4 19.0 + - - -
189B GLY 4.9 2.8 - - - +
220B GLU* 1.3 75.5 - - - +
222B GLY* 1.3 61.3 + - - -
223B PHE 3.2 3.1 - - - -
224B ASP* 3.2 21.5 + - - +
225B ALA* 3.5 4.7 + - - +
289B TYR* 3.9 18.4 - - - -
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Residues in contact with GLY 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B PHE* 3.4 27.9 - - - -
220B GLU* 3.4 6.7 + - - +
221B GLY* 1.3 78.2 - - - +
223B PHE* 1.3 57.7 + - - +
225B ALA* 3.1 6.8 + - - +
226B ILE* 2.9 28.2 + - - +
248B PHE* 3.5 22.7 - - - -
254B THR* 4.4 2.7 + - - -
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Residues in contact with PHE 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLY* 3.2 0.8 - - - -
222B GLY* 1.3 75.5 - - - +
224B ASP* 1.3 65.5 + - - +
226B ILE* 3.5 27.4 - - + +
227B MET* 3.0 24.3 + - - +
248B PHE* 4.6 3.4 - + - -
254B THR* 3.6 32.1 + - + -
255B HIS 3.5 22.9 - - - +
256B ILE* 4.2 15.5 - - + -
289B TYR* 5.5 1.1 - - + -
290B PRO* 3.5 13.9 - - + +
292B LEU* 4.2 11.4 - - + -
295B MET* 3.3 38.1 - - + +
306B LEU* 6.0 0.2 - - + -
308B PHE* 4.5 16.8 - + - -
318B TYR* 4.5 7.9 - + - -
321B TYR* 4.2 15.5 - + + -
325B ILE* 5.7 1.1 - - + -
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Residues in contact with ASP 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159B LYS* 2.7 36.0 + - - +
189B GLY* 5.9 3.1 - - - +
190B TYR* 5.1 2.9 - - + -
221B GLY* 3.2 14.4 + - - +
223B PHE* 1.3 78.7 - - - +
225B ALA* 1.3 57.3 + - - +
227B MET* 3.6 3.3 - - - +
228B GLN* 3.1 35.2 + - - +
269B ASN* 4.1 2.9 + - - -
281B TYR* 3.5 30.8 - - + -
284B SER* 4.4 2.4 + - - -
288B ASP 4.0 3.3 - - - +
289B TYR* 3.7 16.3 - - - -
290B PRO* 3.4 20.1 - - - +
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Residues in contact with ALA 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.7 14.6 - - + +
156B PHE* 3.8 23.6 - - + -
190B TYR* 3.6 34.4 - - + +
221B GLY 3.5 0.8 + - - -
222B GLY 3.1 9.9 + - - +
224B ASP* 1.3 79.2 - - - +
226B ILE* 1.3 59.1 + - - +
228B GLN* 4.1 0.7 - - - +
229B ALA* 2.9 31.9 + - - +
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Residues in contact with ILE 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.7 9.9 - - + -
222B GLY 2.9 12.5 + - - +
223B PHE* 3.3 38.1 + - + +
225B ALA* 1.3 73.6 - - - +
227B MET* 1.3 61.9 + - - +
229B ALA* 4.0 1.6 - - - +
230B THR* 2.7 36.1 + - - +
246B LEU* 4.1 16.8 - - + +
248B PHE* 3.5 36.1 - - + -
295B MET* 4.7 13.2 - - + -
299B LEU* 4.5 8.1 - - + -
306B LEU* 4.1 26.5 - - + -
308B PHE* 4.3 4.0 - - + -
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Residues in contact with MET 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE 3.0 17.1 + - - +
224B ASP* 3.6 6.1 - - - +
226B ILE* 1.3 77.8 - - - +
228B GLN* 1.3 70.6 + - - +
230B THR* 3.0 8.6 + - - -
231B VAL* 3.0 38.2 + - + +
269B ASN* 4.3 15.7 - - - +
271B GLY* 4.1 8.7 - - - -
290B PRO* 3.6 27.4 - - + -
294B LEU* 3.8 40.4 - - + +
295B MET* 3.8 11.9 - - + +
298B LYS* 3.8 21.8 - - + -
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Residues in contact with GLN 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190B TYR* 3.8 22.4 - - + -
224B ASP 3.1 16.6 + - - +
225B ALA 4.1 0.7 - - - +
227B MET* 1.3 87.9 - - - +
229B ALA* 1.3 60.6 + - - +
230B THR 3.0 5.8 + - - -
231B VAL* 4.1 2.4 - - - +
232B CYS* 3.2 38.8 + - - +
236B ILE* 4.4 0.6 - - - +
269B ASN* 5.2 2.0 + - - -
272B GLN 3.3 17.9 + - - -
273B CYS* 3.6 0.7 - - - -
274B HIS* 3.0 25.3 + - - -
275B VAL* 3.8 4.5 - - + +
281B TYR* 3.1 52.5 + - + -
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Residues in contact with ALA 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B TYR* 3.7 33.9 - - + -
117B LEU* 4.3 4.9 - - + -
190B TYR* 4.2 4.6 + - - +
225B ALA 2.9 19.9 + - - +
226B ILE 4.1 3.4 - - - +
228B GLN* 1.3 76.7 - - - +
230B THR* 1.3 57.2 + - - +
236B ILE* 3.3 19.7 - - - +
238B TRP* 2.9 28.1 + - - -
246B LEU* 4.7 10.3 - - + -
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Residues in contact with THR 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ILE 2.7 17.2 + - - -
227B MET* 3.0 11.4 + - - -
228B GLN 3.0 0.4 - - - -
229B ALA* 1.3 80.4 - - - +
231B VAL* 1.3 61.1 + - - +
232B CYS 3.5 0.9 + - - -
233B ASP* 4.3 2.8 - - - +
238B TRP* 4.1 5.0 + - - -
246B LEU* 3.8 8.3 - - - +
298B LYS* 3.6 39.9 - - + +
299B LEU* 3.4 23.3 - - + +
302B LYS* 3.5 18.1 - - + +
304B ILE* 3.6 23.7 - - + +
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Residues in contact with VAL 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B MET* 3.0 24.4 + - + +
228B GLN* 4.1 6.3 - - - +
230B THR* 1.3 77.1 - - + +
232B CYS* 1.3 58.8 + - - +
233B ASP* 3.4 10.3 + - - +
271B GLY 3.4 21.5 - - - +
272B GLN* 3.7 27.4 - - - +
273B CYS* 3.6 16.1 + - - +
298B LYS* 3.8 31.4 - - + +
302B LYS* 4.4 16.2 + - - +
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Residues in contact with CYS 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B GLN* 3.2 37.1 + - - +
229B ALA 4.6 0.2 - - - -
230B THR 3.5 2.5 - - - -
231B VAL* 1.3 75.5 - - - +
233B ASP* 1.3 66.4 + - - +
234B GLU 3.6 1.6 - - - -
235B LYS* 3.3 16.4 + - + -
236B ILE* 3.1 26.2 + - + +
238B TRP* 5.2 0.9 - - - -
273B CYS* 2.0 50.3 - - - -
275B VAL* 3.8 13.7 - - + -
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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