Contacts of the helix formed by residues 225 - 240 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223A ASN 3.8 1.8 + - - +
224A PHE* 1.3 73.8 - - - +
226A PRO* 1.3 74.1 - - + +
227A GLU* 3.0 30.7 + - - +
228A GLU* 3.0 30.4 + - - +
229A LEU* 2.9 17.3 + - - +
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Residues in contact with PRO 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE 3.7 0.2 - - - -
225A LYS* 1.3 83.6 - - + +
227A GLU* 1.3 77.9 + - + +
229A LEU* 3.1 18.2 + - + -
230A HIS* 3.1 24.3 + - + +
258A GLN* 3.7 40.2 - - + +
259A PHE* 3.7 35.2 - - + -
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Residues in contact with GLU 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A LYS* 3.3 35.3 - - - +
226A PRO* 1.3 94.1 - - + +
228A GLU* 1.3 61.8 + - + +
230A HIS* 5.4 0.4 - - - -
231A PRO* 3.1 22.2 - - - +
258A GLN* 5.5 0.3 - - - +
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Residues in contact with GLU 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.7 20.2 - - + -
225A LYS* 3.0 35.8 + - + +
227A GLU* 1.3 81.9 - - + +
229A LEU* 1.3 62.2 + - - +
230A HIS 3.4 0.7 - - - -
231A PRO* 3.8 5.1 - - - +
232A THR* 2.8 32.5 + - - +
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Residues in contact with LEU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 3.7 33.7 - - + +
224A PHE* 3.9 16.4 - - + -
225A LYS 2.9 13.5 + - - +
226A PRO* 3.1 12.5 + - + +
228A GLU* 1.3 79.2 - - - +
230A HIS* 1.3 63.7 + - + +
232A THR* 3.7 2.6 - - - -
233A ALA* 3.1 24.4 + - - +
245A VAL* 5.6 0.7 - - + -
247A ALA* 3.7 18.8 - - + -
259A PHE* 3.5 33.4 - - + +
264A ILE* 3.7 29.4 - - + -
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Residues in contact with HIS 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A PRO* 3.1 24.2 + - + -
229A LEU* 1.3 77.4 - - + +
231A PRO* 1.3 72.1 - - + +
233A ALA* 3.2 5.4 + - - +
234A THR* 2.7 31.2 + - - +
258A GLN 2.9 23.5 + - - -
259A PHE* 3.5 7.3 - - - -
260A CYS 3.5 22.7 + - - -
261A GLY* 3.7 8.1 - - - -
262A PRO* 5.0 5.5 - - + +
263A HIS* 4.9 0.9 + - - +
264A ILE* 3.2 32.1 - - + +
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Residues in contact with PRO 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A GLU* 3.1 26.7 - - - +
228A GLU* 3.8 7.4 - - - +
230A HIS* 1.3 94.1 - - + +
232A THR* 1.3 61.9 + - - +
234A THR* 3.2 8.1 + - - +
235A VAL* 3.1 27.6 + - - +
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.9 41.1 - - + +
221A LEU* 3.7 21.3 - - + -
224A PHE* 3.7 16.6 - - + -
228A GLU* 2.8 24.0 + - - +
229A LEU 3.7 3.6 - - - -
230A HIS 3.2 0.8 - - - -
231A PRO* 1.3 77.8 - - - +
233A ALA* 1.3 62.4 + - - +
235A VAL* 3.5 4.6 + - - +
236A LEU* 3.1 28.7 + - + +
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Residues in contact with ALA 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.2 4.7 - - + +
229A LEU 3.1 17.6 + - - +
230A HIS* 3.2 5.1 + - - +
232A THR* 1.3 74.1 - - - +
234A THR* 1.3 60.6 + - - +
236A LEU* 3.5 7.3 - - - +
237A LYS* 2.9 33.8 + - - +
245A VAL* 4.0 16.8 - - + +
263A HIS* 3.6 31.0 - - + +
264A ILE* 4.5 7.0 - - + -
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Residues in contact with THR 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A HIS* 2.7 23.7 + - - +
231A PRO* 3.2 8.7 + - - +
233A ALA* 1.3 73.7 - - - +
235A VAL* 1.3 66.9 + - + +
236A LEU 3.2 0.2 + - - -
237A LYS* 3.3 2.4 + - - +
238A ALA* 3.0 25.6 + - + +
263A HIS* 3.1 36.5 + - + +
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 3.9 32.5 - - + -
209A VAL* 5.1 0.7 - - + -
231A PRO* 3.1 13.9 + - + +
232A THR 3.8 6.7 - - - +
234A THR* 1.3 77.2 - - + +
236A LEU* 1.3 64.2 + - - +
238A ALA* 3.4 5.1 + - - +
239A GLN* 3.0 47.8 + - + +
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Residues in contact with LEU 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A LEU* 4.8 5.4 - - + -
208A ALA* 3.6 45.5 - - + +
209A VAL* 4.3 5.6 - - + +
212A ALA* 4.5 3.8 - - + -
219A VAL* 4.1 11.7 - - + -
221A LEU* 4.0 20.0 - - + -
232A THR* 3.1 23.7 + - + +
233A ALA* 3.5 9.2 - - - +
234A THR 3.1 0.2 - - - -
235A VAL* 1.3 77.3 - - - +
237A LYS* 1.3 55.3 + - - +
239A GLN* 3.1 0.9 + - - -
240A PHE* 2.6 64.5 + - + +
243A VAL* 5.8 3.6 - - + -
245A VAL* 4.5 13.0 - - + -
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Residues in contact with LYS 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ALA 2.9 21.7 + - - +
234A THR 3.9 2.7 - - - +
236A LEU* 1.3 74.0 - - - +
238A ALA* 1.3 61.5 + - - +
240A PHE 4.3 2.2 - - - -
241A PRO* 3.2 41.3 + - + +
242A SER 5.4 0.2 - - - -
243A VAL 2.8 29.0 + - - +
244A ALA* 3.8 1.2 - - - +
245A VAL* 4.2 6.3 - - + -
262A PRO 5.8 0.4 - - - -
263A HIS* 3.8 44.9 - - + +
265A ASP* 2.7 37.3 + - - -
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Residues in contact with ALA 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR* 3.0 18.8 + - + +
235A VAL* 3.8 6.3 - - - +
237A LYS* 1.3 80.4 - - - +
239A GLN* 1.3 60.7 + - + +
241A PRO* 4.0 6.2 - - - +
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 4.4 13.5 - - - +
213A GLU* 5.5 0.3 - - - +
235A VAL* 3.0 39.0 + - + +
238A ALA* 1.3 80.9 - - + +
240A PHE* 1.3 97.3 + - + +
241A PRO* 3.5 5.6 - - - +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A VAL* 4.0 30.5 - - + -
212A ALA* 3.5 33.7 - - + -
213A GLU* 4.1 22.4 - - + -
236A LEU* 2.6 30.4 + - + +
237A LYS* 4.2 2.1 - - - +
239A GLN* 1.3 110.8 - - + +
241A PRO* 1.3 65.6 - - - +
242A SER* 3.2 3.8 - - - -
243A VAL* 3.0 38.4 + - + +
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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