Contacts of the helix formed by residues 225 - 240 (chain C) in PDB entry 5AYZ
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 LYS 225 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223C ASN 3.9 0.8 + - - -
224C PHE* 1.3 71.8 - - - +
226C PRO* 1.3 65.0 - - + +
227C GLU* 3.3 27.1 - - + +
228C GLU* 2.9 40.9 + - + +
229C LEU* 2.7 25.9 + - - +
223I ASN* 3.1 37.1 + - - +
224I PHE 4.7 2.2 - - - -
225I LYS* 4.0 44.9 - - + +
228I GLU* 4.5 1.0 + - - -
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Residues in contact with PRO 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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224C PHE 3.6 5.6 - - - +
225C LYS* 1.3 82.1 - - + +
227C GLU* 1.3 74.2 + - - +
229C LEU* 3.3 16.6 + - + -
230C HIS* 3.2 27.7 + - + +
258C GLN* 3.6 40.4 - - + +
259C PHE* 3.8 29.8 - - + -
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Residues in contact with GLU 227 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225C LYS* 3.3 25.3 - - + +
226C PRO* 1.3 95.1 - - - +
228C GLU* 1.3 57.3 + - + +
231C PRO* 3.0 24.8 - - - +
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Residues in contact with GLU 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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223C ASN 4.5 1.9 - - - +
224C PHE* 3.6 23.6 - - + -
225C LYS* 2.9 64.9 + - + +
227C GLU* 1.3 74.8 - - - +
229C LEU* 1.3 58.7 + - - +
230C HIS 3.4 0.4 - - - -
231C PRO* 3.8 4.4 - - - +
232C THR* 2.4 36.3 + - - +
223I ASN* 5.9 0.9 + - - -
225I LYS* 4.5 0.5 + - - -
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Residues in contact with LEU 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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221C LEU* 3.5 37.5 - - + +
224C PHE* 3.7 18.8 - - + -
225C LYS 2.7 15.8 + - - +
226C PRO* 3.3 6.9 + - + +
228C GLU* 1.3 78.4 - - - +
230C HIS* 1.3 71.0 + - + +
232C THR* 3.1 4.7 + - - -
233C ALA* 3.0 25.1 + - - +
247C ALA* 4.0 18.2 - - + -
259C PHE* 3.6 43.7 - - + +
264C ILE* 4.1 12.8 - - + -
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Residues in contact with HIS 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 PRO* 3.2 24.3 + - + +
229C LEU* 1.3 79.0 - - + +
231C PRO* 1.3 72.1 - - + +
233C ALA* 3.4 4.6 + - - +
234C THR* 2.8 30.4 + - - +
258C GLN 2.9 25.7 + - - -
259C PHE* 3.3 24.4 + - - -
260C CYS 3.3 21.0 + - - -
261C GLY* 3.5 11.8 - - - -
262C PRO* 5.1 2.9 - - + +
263C HIS* 4.9 1.1 + - - +
264C ILE* 3.9 12.7 - - + +
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Residues in contact with PRO 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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227C GLU 3.0 28.7 - - - +
228C GLU* 3.8 7.0 - - - +
230C HIS* 1.3 89.9 - - + +
232C THR* 1.3 60.3 + - - +
234C THR* 3.4 7.6 + - - +
235C VAL* 3.1 29.1 + - - +
83J PRO 5.2 2.5 - - - +
84J VAL* 4.0 30.4 + - + +
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Residues in contact with THR 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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205C LEU* 3.8 43.8 - - + +
208C ALA* 4.9 0.2 - - + -
221C LEU* 3.9 22.0 - - + -
224C PHE* 3.5 17.1 - - + -
228C GLU* 2.4 23.7 + - - +
229C LEU 3.1 9.7 + - - -
231C PRO* 1.3 75.3 - - - +
233C ALA* 1.3 65.0 + - - +
235C VAL* 3.2 6.6 + - - +
236C LEU* 3.0 25.5 + - + +
84J VAL* 6.2 0.2 - - - -
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Residues in contact with ALA 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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221C LEU* 4.1 6.9 - - + +
229C LEU 3.0 10.9 + - - +
230C HIS* 3.9 4.5 - - - +
232C THR* 1.3 75.1 - - - +
234C THR* 1.3 56.9 + - - +
236C LEU* 3.1 7.6 + - - +
237C LYS* 2.8 33.6 + - - +
245C VAL* 4.0 9.0 - - + -
263C HIS* 3.4 30.3 - - + +
264C ILE* 3.6 22.4 - - + -
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Residues in contact with THR 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230C HIS* 2.8 22.2 + - - +
231C PRO* 3.6 9.3 - - - +
232C THR 3.2 0.2 - - - -
233C ALA* 1.3 75.8 - - - +
235C VAL* 1.3 63.3 + - + +
237C LYS* 4.0 1.4 - - - +
238C ALA* 3.1 25.3 + - + +
263C HIS* 2.9 37.5 + - + +
84J VAL 6.3 1.1 - - - +
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Residues in contact with VAL 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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205C LEU* 3.9 22.9 - - + -
209C VAL* 4.8 2.5 - - + -
231C PRO 3.1 15.0 + - - +
232C THR 3.5 7.4 - - - +
234C THR* 1.3 78.6 - - + +
236C LEU* 1.3 57.8 + - - +
238C ALA* 3.3 4.3 + - - +
239C GLN* 3.0 57.3 + - - +
47J TRP* 4.0 10.1 - - + -
84J VAL* 3.1 44.4 - - + +
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Residues in contact with LEU 236 (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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205C LEU* 4.8 2.5 - - + -
208C ALA* 3.7 45.5 - - + +
209C VAL* 4.0 19.5 - - + +
212C ALA* 4.4 4.0 - - + -
219C VAL* 3.9 17.3 - - + -
221C LEU* 4.1 13.2 - - + -
232C THR* 3.0 22.5 + - + +
233C ALA* 3.1 6.3 + - - +
235C VAL* 1.3 74.8 - - - +
237C LYS* 1.3 54.9 + - - +
240C PHE* 2.6 56.0 + - + +
243C VAL* 6.1 3.6 - - + -
245C VAL* 4.3 19.7 - - + -
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Residues in contact with LYS 237 (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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233C ALA 2.8 22.2 + - - +
234C THR 4.1 1.6 - - - +
236C LEU* 1.3 72.1 - - - +
238C ALA* 1.3 62.6 + - - +
240C PHE 4.1 1.8 - - - +
241C PRO* 3.2 39.3 + - + +
243C VAL 3.0 25.6 + - - +
244C ALA* 3.9 1.6 - - - +
245C VAL* 3.9 7.6 - - + -
263C HIS* 3.7 48.0 - - + +
265C ASP* 2.5 38.2 + - - -
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Residues in contact with ALA 238 (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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234C THR* 3.1 20.3 + - + +
235C VAL* 3.8 5.2 - - - +
236C LEU 3.2 0.2 - - - -
237C LYS* 1.3 79.5 - - - +
239C GLN* 1.3 65.2 + - + +
241C PRO* 3.8 7.3 - - - +
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Residues in contact with GLN 239 (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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209C VAL* 4.8 5.2 - - - +
213C GLU* 4.9 1.8 + - - -
235C VAL* 3.0 39.9 + - - +
238C ALA* 1.3 80.1 - - + +
240C PHE* 1.3 91.8 + - + +
241C PRO* 3.6 5.0 - - - +
47J TRP* 4.1 11.1 - - - -
86J ARG* 3.6 34.8 + - - +
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Residues in contact with PHE 240 (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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209C VAL* 4.0 14.1 - - + -
212C ALA* 3.7 27.8 - - + -
213C GLU* 3.6 48.5 - - + -
236C LEU* 2.6 35.9 + - + +
237C LYS* 3.9 1.9 - - - +
239C GLN* 1.3 101.6 - - + +
241C PRO* 1.3 66.9 - - - +
242C SER* 3.1 5.0 + - - +
243C VAL* 3.2 34.7 + - + +
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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