Contacts of the helix formed by residues 221 - 235 (chain B) in PDB entry 2Y4T
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 ASN 221 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B LYS* 2.8 45.9 + - + +
219B ASN 3.2 0.4 - - - -
220B ASP* 1.3 76.4 - - + +
222B THR* 1.3 68.4 + - - +
223B GLU* 3.4 16.6 + - - +
224B ALA* 3.4 32.1 + - + +
225B PHE* 3.2 21.7 - - - -
251B LEU* 4.2 1.3 - - - -
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Residues in contact with THR 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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220B ASP 3.4 5.7 + - - +
221B ASN* 1.3 71.6 + - - +
223B GLU* 1.3 71.0 + - + +
225B PHE* 3.1 16.3 + - - +
226B TYR* 3.3 8.7 + - - +
248B CYS* 3.1 32.1 + - - -
251B LEU* 4.3 16.2 - - - -
252B ASP* 4.2 19.5 - - + +
255B HIS* 3.5 14.8 + - + +
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Residues in contact with GLU 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 ASN* 3.4 14.5 + - - +
222B THR* 1.3 83.5 - - + +
224B ALA* 1.3 62.9 + - - +
226B TYR* 3.1 26.8 + - - +
227B LYS* 3.1 41.0 + - - +
255B HIS* 4.7 3.8 - - - -
257B ARG* 3.1 38.2 + - - -
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Residues in contact with ALA 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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192B GLU* 5.5 2.7 - - - +
211B LEU* 4.7 2.4 - - - +
214B ALA* 5.0 1.3 - - + -
215B SER* 3.7 29.5 - - - +
218B LYS* 4.3 6.7 - - + -
221B ASN* 3.4 35.5 - - + +
222B THR 3.2 0.2 - - - -
223B GLU* 1.3 78.7 - - - +
225B PHE* 1.3 58.4 + - - +
227B LYS* 3.9 6.7 + - - +
228B ILE* 3.2 24.6 + - - +
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Residues in contact with PHE 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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215B SER* 3.6 34.1 - - - -
216B LYS* 4.9 2.5 - - - -
219B ASN* 3.5 30.5 - - + -
221B ASN 3.2 20.6 - - - -
222B THR 3.1 7.6 + - - +
224B ALA* 1.3 75.2 - - - +
226B TYR* 1.3 66.0 + - - +
228B ILE* 3.2 4.8 - - - +
229B SER* 3.0 26.7 + - - -
244B GLU* 3.5 41.1 - - + +
247B GLU* 3.7 29.2 - - + -
248B CYS* 4.0 12.8 - - + -
251B LEU* 4.0 13.9 - - + -
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Residues in contact with TYR 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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222B THR 3.3 7.1 + - - +
223B GLU* 3.1 21.8 + - - +
225B PHE* 1.3 73.3 - - - +
227B LYS* 1.3 70.8 + - + +
229B SER* 3.2 5.4 + - - -
230B THR* 2.9 47.0 + - + +
245B VAL* 5.2 0.9 - - + -
255B HIS* 4.9 2.5 - + + -
257B ARG* 3.7 59.4 + - + +
258B CYS* 4.0 31.9 - - - -
261B HIS* 4.0 18.8 - + + +
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Residues in contact with LYS 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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192B GLU* 6.0 4.0 - - + -
211B LEU* 4.8 26.9 - - + +
223B GLU* 3.1 42.2 + - - +
224B ALA* 4.2 6.5 - - - +
225B PHE 3.5 0.2 - - - -
226B TYR* 1.3 80.3 - - + +
228B ILE* 1.3 63.1 + - - +
230B THR* 3.3 6.1 + - - -
231B LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 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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208B ILE* 3.6 38.1 - - + +
211B LEU* 3.8 21.3 - - + +
212B LYS* 3.7 15.9 - - + +
215B SER* 4.2 11.9 - - - +
224B ALA 3.2 20.3 + - - +
225B PHE* 3.2 15.0 - - - +
227B LYS* 1.3 77.7 - - - +
229B SER* 1.3 63.4 + - - +
231B LEU* 3.4 4.2 + - + +
232B TYR* 3.1 47.6 + - + +
244B GLU* 3.6 17.0 - - + -
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Residues in contact with SER 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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225B PHE 3.0 19.7 + - - -
226B TYR* 3.7 4.5 - - - -
228B ILE* 1.3 77.6 - - - +
230B THR* 1.3 56.2 + - - +
232B TYR* 3.6 0.6 - - - +
233B TYR* 3.0 14.9 + - - +
241B SER* 2.7 51.6 + - - +
244B GLU* 3.9 8.7 - - - -
245B VAL* 3.4 18.3 - - - +
261B HIS* 2.9 21.4 + - - -
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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
----------------------------------------------------------
226B TYR* 2.9 47.8 + - + +
227B LYS* 3.6 6.3 - - - -
228B ILE 3.3 0.2 - - - -
229B SER* 1.3 73.4 - - - +
231B LEU* 1.3 55.1 + - - +
233B TYR* 3.1 10.3 + - + +
234B GLN* 2.7 61.1 + - + +
261B HIS* 4.3 9.4 + - + -
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Residues in contact with LEU 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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199B ILE* 4.3 16.6 - - + -
204B PRO* 3.7 42.4 - - + +
207B ALA* 3.9 11.0 - - + -
208B ILE* 3.8 17.7 - - + +
211B LEU* 3.8 25.1 - - + -
227B LYS 3.1 16.0 + - - +
228B ILE* 3.9 5.6 - - + +
230B THR* 1.3 71.9 - - - +
232B TYR* 1.3 67.7 + - - +
234B GLN* 3.2 20.5 + - + +
235B LEU* 2.9 37.1 + - + +
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Residues in contact with TYR 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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205B ARG* 4.8 0.4 - - - -
208B ILE* 4.0 37.1 - - + +
212B LYS* 2.9 40.7 + - - -
228B ILE* 3.1 42.2 + - + +
229B SER* 3.6 5.4 - - - +
231B LEU* 1.3 74.6 - - - +
233B TYR* 1.3 63.6 + - - +
235B LEU* 3.0 10.5 + - - -
237B ASP* 3.0 59.8 + - + +
240B LEU* 3.7 43.2 - - + +
241B SER* 3.7 4.5 - - - -
244B GLU* 4.3 3.8 - - + -
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Residues in contact with TYR 233 (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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229B SER 3.0 8.4 + - - +
230B THR* 3.1 9.6 + - + +
232B TYR* 1.3 74.1 - - - +
234B GLN* 1.3 59.3 + - + +
236B GLY 2.9 10.9 + - - -
237B ASP 4.4 0.9 - - - -
238B HIS* 5.1 0.2 - - - -
241B SER* 3.3 16.9 - - - +
261B HIS* 3.7 14.4 - + + -
264B GLN* 2.8 29.1 + - + -
265B VAL* 3.8 35.2 - - + -
268B LEU* 3.5 26.9 - - + +
298B GLU* 2.7 30.1 + - + +
301B ILE* 3.5 26.7 - - + -
304B TYR* 2.6 36.6 + + - -
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Residues in contact with GLN 234 (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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199B ILE* 6.0 0.5 - - - +
204B PRO* 6.5 0.2 - - + -
230B THR* 2.7 43.5 + - + +
231B LEU* 3.6 23.7 - - + +
233B TYR* 1.3 73.6 - - + +
235B LEU* 1.3 61.5 + - + +
236B GLY 3.3 0.4 - - - -
301B ILE* 3.5 41.6 - - + +
303B GLU* 4.6 2.8 - - - +
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Residues in contact with LEU 235 (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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204B PRO* 3.8 16.8 - - + -
205B ARG* 3.6 76.4 + - + +
208B ILE* 3.6 23.6 - - + -
231B LEU* 2.9 30.0 + - + +
232B TYR* 3.0 5.3 + - - +
234B GLN* 1.3 78.5 - - + +
236B GLY* 1.3 60.4 + - - +
237B ASP* 3.3 2.8 + - - +
303B GLU* 3.8 15.2 - - - +
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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