Contacts of the helix formed by residues 225 - 240 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223D ASN 3.9 6.6 + - - +
224D PHE* 1.3 73.4 - - - +
226D PRO* 1.3 74.1 - - + +
227D GLU* 3.0 21.6 + - + +
228D GLU* 3.1 32.2 + - - +
229D LEU* 2.9 19.6 + - - +
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Residues in contact with PRO 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224D PHE 3.7 0.4 - - - -
225D LYS* 1.3 86.1 - - + +
227D GLU* 1.3 72.7 + - + +
229D LEU* 3.3 15.0 + - + -
230D HIS* 3.1 26.1 + - + +
258D GLN* 3.3 50.3 - - + +
259D PHE* 3.8 29.8 - - + -
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Residues in contact with GLU 227 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225D LYS* 3.0 14.4 + - + +
226D PRO* 1.3 93.8 - - + +
228D GLU* 1.3 58.9 + - + +
231D PRO* 3.0 23.9 - - - +
258D GLN* 5.6 0.3 - - - +
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Residues in contact with GLU 228 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223D ASN 4.8 1.6 - - - +
224D PHE* 3.5 24.3 - - + -
225D LYS* 3.1 43.9 + - - +
227D GLU* 1.3 79.2 - - - +
229D LEU* 1.3 66.1 + - - +
230D HIS 3.4 0.7 - - - -
231D PRO* 3.5 6.0 - - - +
232D THR* 2.9 31.1 + - - +
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Residues in contact with LEU 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 3.6 41.5 - - + +
224D PHE* 3.7 19.7 - - + -
225D LYS 2.9 17.3 + - - +
226D PRO* 3.3 6.0 + - + +
228D GLU* 1.3 79.0 - - - +
230D HIS* 1.3 76.1 + - + +
232D THR* 3.3 4.2 + - - -
233D ALA* 2.8 24.8 + - - +
247D ALA* 4.1 12.3 - - + -
259D PHE* 3.8 31.0 - - + +
264D ILE* 3.9 24.9 - - + -
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Residues in contact with HIS 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226D PRO* 3.1 23.6 + - + -
229D LEU* 1.3 84.3 - - + +
231D PRO* 1.3 73.6 - - + +
233D ALA* 3.2 5.9 + - - +
234D THR* 2.9 29.4 + - - +
258D GLN 3.1 23.9 + - - -
259D PHE* 3.3 18.0 + - - -
260D CYS 3.2 26.6 + - - -
261D GLY* 3.6 12.7 - - - -
262D PRO* 5.0 4.9 - - + +
263D HIS* 5.5 0.4 + - - +
264D ILE* 4.1 8.9 - - + +
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Residues in contact with PRO 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D GLU 3.0 28.9 - - - +
228D GLU* 3.5 8.7 - - - +
230D HIS* 1.3 89.2 - - + +
232D THR* 1.3 62.9 + - - +
234D THR* 3.2 9.0 + - - +
235D VAL* 3.1 28.2 + - + +
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Residues in contact with THR 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 3.0 46.7 - - + +
221D LEU* 3.8 29.2 - - + -
224D PHE* 3.8 15.7 - - + -
228D GLU* 2.9 20.0 + - - +
229D LEU 3.3 4.0 + - - -
230D HIS 3.2 0.2 - - - -
231D PRO* 1.3 76.2 - - - +
233D ALA* 1.3 65.9 + - - +
235D VAL 3.4 0.3 + - - -
236D LEU* 3.2 22.7 + - + +
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Residues in contact with ALA 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221D LEU* 4.2 6.9 - - + +
229D LEU 2.8 20.2 + - - +
230D HIS* 3.2 7.4 + - - +
232D THR* 1.3 72.7 - - - +
234D THR* 1.3 57.2 + - - +
236D LEU* 3.5 5.4 + - - +
237D LYS* 3.0 33.6 + - - +
245D VAL* 4.3 6.9 - - + +
263D HIS* 3.6 28.9 - - + +
264D ILE* 3.7 19.1 - - + -
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Residues in contact with THR 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D HIS* 2.9 15.7 + - - +
231D PRO* 3.5 10.9 - - - +
232D THR 3.1 0.2 - - - -
233D ALA* 1.3 74.1 - - - +
235D VAL* 1.3 66.3 + - + +
237D LYS* 3.5 2.1 + - - +
238D ALA* 3.0 25.5 + - + +
263D HIS* 3.4 33.0 + - + +
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Residues in contact with VAL 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 3.9 28.5 - - + -
209D VAL* 5.2 3.6 - - + -
231D PRO* 3.1 16.2 + - + +
232D THR 3.4 6.0 + - - +
234D THR* 1.3 75.0 - - + +
236D LEU* 1.3 59.7 + - - +
238D ALA* 3.2 6.7 + - - +
239D GLN* 2.9 50.5 + - + +
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D LEU* 4.5 4.7 - - + -
208D ALA* 3.5 47.8 - - + +
209D VAL* 4.0 12.6 - - + +
212D ALA* 4.6 3.1 - - + -
219D VAL* 3.9 17.3 - - + -
221D LEU* 4.1 15.9 - - + -
232D THR* 3.2 19.0 + - + +
233D ALA* 3.8 4.0 - - - +
235D VAL* 1.3 79.1 - - - +
237D LYS* 1.3 54.8 + - - +
239D GLN 3.3 0.2 + - - -
240D PHE* 2.7 60.3 + - + +
243D VAL* 6.2 4.0 - - + -
245D VAL* 4.5 14.1 - - + -
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Residues in contact with LYS 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ALA 3.0 21.4 + - - +
234D THR 3.9 2.0 - - - +
236D LEU* 1.3 75.8 - - - +
238D ALA* 1.3 63.2 + - - +
240D PHE 4.2 2.2 - - - +
241D PRO* 3.3 40.1 + - + +
243D VAL 3.1 25.2 + - - +
244D ALA* 4.1 1.8 - - - +
245D VAL* 4.0 7.9 - - + -
263D HIS* 3.5 47.6 - - + +
265D ASP* 2.8 36.6 + - - -
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Residues in contact with ALA 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D THR* 3.0 20.5 + - + +
235D VAL* 3.5 6.5 - - - +
237D LYS* 1.3 79.5 - - - +
239D GLN* 1.3 62.6 + - + +
241D PRO* 4.2 8.5 - - - +
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Residues in contact with GLN 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D VAL* 4.8 12.9 - - - +
213D GLU* 5.3 4.0 + - - -
235D VAL* 2.9 35.4 + - + +
238D ALA* 1.3 80.4 - - + +
240D PHE* 1.3 95.5 + - + +
241D PRO* 3.5 7.1 - - - +
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Residues in contact with PHE 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209D VAL* 4.0 22.2 - - + -
212D ALA* 3.5 31.9 - - + -
213D GLU* 3.5 38.6 - - + -
236D LEU* 2.7 35.1 + - + +
237D LYS* 4.0 2.1 - - - +
239D GLN* 1.3 102.5 - - + +
241D PRO* 1.3 66.7 - - - +
242D SER* 3.0 5.1 + - - -
243D VAL* 3.0 37.2 + - + +
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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