Contacts of the helix formed by residues 221 - 235 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C LYS* 5.5 0.7 - - - +
218C LYS* 3.2 47.3 + - + +
219C ASN 3.6 0.4 - - - -
220C ASP* 1.3 77.7 + - - +
222C THR* 1.3 62.9 + - - +
223C GLU* 3.3 10.3 + - - +
224C ALA* 2.9 37.2 + - + +
225C PHE* 3.5 19.6 + - - -
251C LEU* 4.2 1.1 - - - -
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Residues in contact with THR 222 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220C ASP 3.3 5.3 + - - -
221C ASN* 1.3 72.4 + - - +
223C GLU* 1.3 68.6 + - + +
225C PHE* 3.3 7.8 + - - +
226C TYR* 3.2 15.6 + - - +
248C CYS* 3.1 38.5 + - - -
251C LEU* 4.2 13.5 - - - -
252C ASP* 4.0 15.6 - - + +
255C HIS* 3.6 27.5 + - + +
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Residues in contact with GLU 223 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221C ASN* 3.3 7.9 + - - +
222C THR* 1.3 83.3 - - + +
224C ALA* 1.3 57.8 + - - +
226C TYR* 3.0 20.4 + - - +
227C LYS* 2.9 32.3 + - + +
255C HIS* 4.3 9.0 - - - -
257C ARG* 3.1 29.4 + - - -
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Residues in contact with ALA 224 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLU* 4.4 17.5 - - - +
211C LEU* 4.4 3.3 - - - +
214C ALA* 4.5 3.1 - - + -
215C SER* 3.6 30.7 - - - +
218C LYS* 4.6 3.4 - - - +
221C ASN* 2.9 25.9 + - + +
222C THR 3.4 0.2 - - - -
223C GLU* 1.3 76.0 - - - +
225C PHE* 1.3 58.1 + - - +
227C LYS* 3.7 7.7 + - - +
228C ILE* 3.3 25.6 + - - +
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Residues in contact with PHE 225 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215C SER* 3.7 34.5 - - - -
216C LYS* 5.0 3.1 - - - -
219C ASN* 3.6 25.1 - - - -
221C ASN 3.5 19.1 + - - -
222C THR 3.3 9.1 + - - +
223C GLU 3.1 0.4 - - - -
224C ALA* 1.3 77.0 - - - +
226C TYR* 1.3 64.2 + - - +
228C ILE* 3.3 5.6 - - - +
229C SER* 3.1 24.0 + - - -
244C GLU* 3.5 35.5 - - + +
247C GLU* 3.6 33.4 - - + -
248C CYS* 3.9 15.3 - - + -
251C LEU* 3.7 15.9 - - + -
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Residues in contact with TYR 226 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222C THR 3.2 6.8 + - - +
223C GLU* 3.0 29.2 + - - +
225C PHE* 1.3 78.3 - - - +
227C LYS* 1.3 62.3 + - + +
229C SER* 3.0 6.4 + - - -
230C THR* 2.8 54.8 + - + +
245C VAL* 5.1 2.9 - - + +
248C CYS* 4.5 1.6 - - - +
255C HIS* 4.7 0.9 - - - +
257C ARG* 3.4 56.4 + - + +
258C CYS* 3.6 32.8 - - - -
261C HIS* 4.1 18.2 - + + +
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Residues in contact with LYS 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C GLU* 6.5 0.4 - - - -
196C GLU* 4.4 14.6 + - - -
199C ILE* 6.1 4.8 - - - +
211C LEU* 3.6 32.2 - - + +
223C GLU* 2.9 19.7 + - + +
224C ALA* 3.9 9.4 - - - +
225C PHE 3.3 0.2 - - - -
226C TYR* 1.3 82.2 - - + +
228C ILE* 1.3 55.8 + - - +
230C THR* 3.4 8.8 + - + -
231C LEU* 3.0 34.1 + - - +
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Residues in contact with ILE 228 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE* 3.4 35.2 - - + +
211C LEU* 3.6 28.1 - - + +
212C LYS* 3.6 9.2 - - + +
215C SER* 4.2 13.5 - - - +
224C ALA 3.3 17.3 + - - +
225C PHE* 3.3 15.3 - - - +
227C LYS* 1.3 76.5 - - - +
229C SER* 1.3 50.4 + - - +
231C LEU* 3.3 6.5 + - + -
232C TYR* 2.8 63.1 + - + -
244C GLU* 3.6 15.7 - - + -
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Residues in contact with SER 229 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C PHE 3.1 18.7 + - - -
226C TYR* 3.0 6.8 + - - -
228C ILE* 1.3 75.5 - - - +
230C THR* 1.3 58.9 + - - +
232C TYR* 3.3 3.7 + - - -
233C TYR* 2.9 16.5 + - - +
241C SER* 2.7 45.9 + - - -
244C GLU* 3.9 8.5 - - - -
245C VAL* 3.4 16.9 - - - +
261C HIS* 3.0 21.6 + - - -
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Residues in contact with THR 230 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226C TYR* 2.8 52.2 + - + +
227C LYS* 3.6 12.6 - - + -
229C SER* 1.3 72.0 - - - +
231C LEU* 1.3 63.8 + - - +
233C TYR* 3.2 10.3 + - + +
234C GLN* 3.1 40.1 + - + +
261C HIS* 4.4 8.8 + - - -
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Residues in contact with LEU 231 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199C ILE* 4.2 15.7 - - + -
204C PRO* 3.7 44.0 - - + +
207C ALA* 3.9 4.3 - - + -
208C ILE* 3.8 30.3 - - + +
211C LEU* 3.9 22.9 - - + -
227C LYS* 3.0 22.0 + - - +
228C ILE* 3.6 6.3 - - + +
230C THR* 1.3 75.4 - - - +
232C TYR* 1.3 66.4 + - - +
233C TYR 3.3 0.2 + - - -
234C GLN* 3.4 12.5 + - + +
235C LEU* 3.4 25.2 + - + +
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Residues in contact with TYR 232 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208C ILE* 4.5 27.1 - - + +
212C LYS* 3.2 26.8 - - - +
228C ILE* 2.8 51.7 + - + +
229C SER* 3.4 10.5 - - - +
231C LEU* 1.3 73.9 - - - +
233C TYR* 1.3 65.1 + - - +
235C LEU* 3.3 8.0 + - + -
237C ASP* 3.0 42.8 + - + +
240C LEU* 3.5 43.6 - - + +
241C SER* 3.5 19.3 - - - +
244C GLU* 3.6 17.7 - - + -
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Residues in contact with TYR 233 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C SER 2.9 13.7 + - - +
230C THR* 3.2 11.9 + - + +
232C TYR* 1.3 74.3 - - - +
234C GLN* 1.3 55.6 + - + +
236C GLY 2.8 15.9 + - - -
237C ASP 4.6 0.4 - - - -
241C SER* 3.5 7.6 - - - +
261C HIS* 3.5 24.5 - + + -
264C GLN* 2.9 25.7 + - + +
265C VAL* 3.9 30.1 - - + -
268C LEU* 3.2 24.5 - - + +
298C GLU* 2.7 25.2 + - + -
301C ILE* 3.5 29.2 - - + -
304C TYR* 2.6 35.6 + + - -
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Residues in contact with GLN 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PRO* 5.9 4.4 - - + +
230C THR* 3.1 27.8 + - + +
231C LEU* 3.4 16.0 + - + +
233C TYR* 1.3 80.1 - - + +
235C LEU* 1.3 59.7 + - + +
236C GLY 3.1 3.0 + - - -
301C ILE* 3.4 45.5 - - + +
303C GLU* 4.1 6.1 - - - +
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Residues in contact with LEU 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C PRO* 3.8 26.9 - - + -
205C ARG* 3.7 59.5 + - + +
208C ILE* 4.1 18.8 - - + -
231C LEU* 3.4 24.7 + - + +
232C TYR* 3.3 7.9 + - + +
233C TYR 3.2 1.0 + - - -
234C GLN* 1.3 77.8 - - + +
236C GLY* 1.3 58.7 + - - +
237C ASP* 3.2 11.3 + - - +
303C GLU* 4.0 14.5 - - - +
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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