Contacts of the helix formed by residues 226 - 237 (chain Z) in PDB entry 5L4K
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 TYR 226 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222Z ASP* 2.9 49.8 + - + +
223Z GLU* 3.1 9.3 + - - +
225Z ALA* 1.3 82.5 - - + +
227Z ALA* 1.3 63.6 + - - +
228Z LYS 3.2 3.1 + - - -
229Z VAL* 3.6 11.1 + - - +
230Z CYS* 3.7 4.7 + - - -
256Z PHE* 4.8 1.0 - - - -
259Z PHE* 3.7 22.6 - + + +
260Z SER* 3.8 26.5 + - - -
261Z ARG* 3.4 70.5 + - + +
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Residues in contact with ALA 227 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Z LEU* 5.9 4.3 - - + -
223Z GLU 3.2 11.6 + - - +
224Z ASN* 4.1 10.9 - - - +
225Z ALA 3.7 0.2 - - - -
226Z TYR* 1.3 77.3 - - - +
228Z LYS* 1.3 58.3 + - - +
229Z VAL 3.6 0.2 - - - -
230Z CYS* 3.6 13.9 - - - -
231Z LEU* 3.0 35.6 - - + +
261Z ARG* 5.3 0.2 - - - +
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Residues in contact with LYS 228 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179Z VAL* 4.6 10.9 - - - +
184Z LEU* 3.3 47.9 - - + +
188Z VAL* 3.7 14.9 - - - +
189Z LYS* 3.7 27.3 - - + +
208Z LEU* 6.4 0.4 - - + -
211Z ILE* 5.5 3.6 - - - -
212Z GLU* 3.6 30.3 - - - +
215Z ASP* 4.2 8.1 - - - +
220Z ASP* 4.4 4.5 - - - +
224Z ASN 3.5 20.0 + - - +
225Z ALA 4.8 0.2 - - - +
226Z TYR 3.2 1.0 - - - -
227Z ALA* 1.3 77.9 - - - +
229Z VAL* 1.3 61.6 + - + +
230Z CYS 3.4 0.2 - - - -
231Z LEU* 3.5 8.8 + - - +
232Z TYR* 3.0 26.2 + - - +
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Residues in contact with VAL 229 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208Z LEU* 4.7 7.0 - - + -
212Z GLU* 4.0 22.0 - - + +
225Z ALA 3.9 16.6 - - - +
226Z TYR 3.6 3.2 + - - +
228Z LYS* 1.3 76.3 - - - +
230Z CYS* 1.3 60.2 + - - +
231Z LEU 3.4 0.2 - - - -
232Z TYR* 3.4 9.6 - - + +
233Z LEU* 2.9 25.1 + - - +
252Z ALA* 3.7 26.0 - - + +
255Z VAL* 3.9 23.8 - - + -
256Z PHE* 3.7 29.6 - - + -
259Z PHE* 4.5 3.1 - - + -
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Residues in contact with CYS 230 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226Z TYR 3.7 12.1 + - - -
227Z ALA* 3.6 19.1 - - - -
229Z VAL* 1.3 75.5 - - - +
231Z LEU* 1.3 67.8 + - - +
233Z LEU* 3.6 11.6 - - + +
234Z THR* 2.9 33.6 + - - -
256Z PHE* 4.4 7.7 - - + -
261Z ARG* 4.0 18.8 - - - +
264Z GLU* 5.8 0.7 - - + -
267Z ARG* 5.5 9.6 + - - +
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Residues in contact with LEU 231 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184Z LEU* 4.5 20.0 - - + -
189Z LYS* 3.5 17.7 - - + -
227Z ALA* 3.0 29.6 - - + +
228Z LYS* 3.5 8.4 + - - +
230Z CYS* 1.3 78.9 - - - +
232Z TYR* 1.3 57.3 + - - +
234Z THR* 4.1 4.1 - - - +
235Z SER* 2.6 38.3 + - - -
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Residues in contact with TYR 232 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189Z LYS* 3.5 17.6 - - + +
192Z VAL* 3.9 30.5 - - + +
193Z PRO* 3.9 26.1 - - + -
196Z MET* 5.3 2.6 - - - +
204Z ALA 4.5 1.9 + - - -
208Z LEU* 3.6 41.0 - - + +
228Z LYS 3.0 16.0 + - - +
229Z VAL* 3.4 13.9 - - + +
231Z LEU* 1.3 75.3 - - - +
233Z LEU* 1.3 60.1 + - + +
235Z SER* 3.5 2.1 + - - -
236Z CYS* 3.0 47.6 + - + +
248Z LEU* 3.6 43.2 - - + +
249Z LEU* 6.5 0.2 - - + -
251Z CYS* 5.7 0.2 - - - +
252Z ALA* 4.5 7.9 - - + -
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Residues in contact with LEU 233 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229Z VAL 2.9 17.9 + - - +
230Z CYS* 3.6 9.2 - - + +
231Z LEU 3.2 0.6 - - - -
232Z TYR* 1.3 78.6 - - + +
234Z THR* 1.3 61.4 + - - +
236Z CYS* 5.0 1.1 - - - -
237Z VAL* 2.9 45.2 + - + +
249Z LEU* 3.8 24.2 - - + -
252Z ALA* 5.4 5.8 - - + -
256Z PHE* 4.9 9.4 - - + -
267Z ARG* 3.4 35.7 - - - +
268Z LEU* 3.7 40.2 - - + -
271Z MET* 4.9 4.7 - - + -
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Residues in contact with THR 234 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230Z CYS* 2.9 17.4 + - - +
231Z LEU* 4.3 4.7 - - - -
233Z LEU* 1.3 77.1 - - - +
235Z SER* 1.3 61.3 + - - +
237Z VAL* 4.3 7.3 + - + +
238Z ASN* 4.2 16.0 - - - +
239Z TYR* 4.7 9.2 - - - -
267Z ARG* 5.1 7.6 + - - -
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Residues in contact with SER 235 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189Z LYS* 3.1 26.3 + - - -
190Z GLU* 5.2 6.4 + - - -
193Z PRO* 5.6 3.4 - - - -
231Z LEU 2.6 24.7 + - - -
232Z TYR* 3.7 5.6 - - - -
233Z LEU 3.2 0.2 - - - -
234Z THR* 1.3 79.5 - - - +
236Z CYS* 1.3 65.0 + - - +
239Z TYR* 3.7 23.9 - - - +
240Z VAL* 5.1 1.0 - - - +
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Residues in contact with CYS 236 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193Z PRO* 3.9 33.0 - - - -
196Z MET* 4.9 3.4 - - - -
232Z TYR* 3.0 40.5 + - + +
233Z LEU* 4.5 1.3 - - - +
235Z SER* 1.3 82.4 - - - +
237Z VAL* 1.3 64.3 + - - +
238Z ASN 3.3 3.6 + - - -
239Z TYR 4.4 0.2 - - - -
240Z VAL* 3.2 22.3 - - + +
245Z ASN* 3.0 22.9 - - - +
248Z LEU* 4.3 16.2 - - + -
249Z LEU* 5.6 2.2 - - + -
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Residues in contact with VAL 237 (chain Z).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233Z LEU* 2.9 33.3 + - + +
234Z THR* 4.3 8.1 - - + +
235Z SER 3.7 0.2 - - - -
236Z CYS* 1.3 77.5 - - - +
238Z ASN* 1.3 86.7 + - - +
240Z VAL 4.9 0.3 + - - -
242Z GLU* 4.3 7.3 - - - +
245Z ASN* 3.0 24.9 + - - +
249Z LEU* 4.1 25.1 - - + -
271Z MET* 4.6 13.7 - - + -
771Z LEU* 5.9 1.2 - - - +
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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
------------------------------------------------------------
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