Contacts of the helix formed by residues 235 - 249 (chain Y) in PDB entry 5G04
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 TRP 235 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56X LEU* 4.1 9.9 - - + -
59X LEU* 4.1 15.9 - - + -
60X LEU* 5.5 1.1 - - + -
63X MET* 3.1 42.0 - - + -
203Y LEU* 3.7 27.8 - - + -
232Y ASN 3.5 13.3 + - - -
233Y LEU* 3.5 27.5 - - + +
234Y ASP* 1.3 79.8 - - + +
236Y LEU* 1.3 107.6 + - + +
237Y SER* 3.1 4.5 + - - -
238Y VAL* 3.1 21.3 + - - +
239Y TRP* 3.3 39.3 + + + +
261Y LEU* 4.6 3.7 - - + +
264Y LYS* 6.1 2.7 - - + -
266Y LEU* 5.8 0.4 - - + -
267Y LEU* 4.1 23.6 - - + -
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Residues in contact with LEU 236 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Y LEU* 5.6 2.7 - - - +
203Y LEU* 3.9 17.5 - - + -
206Y ILE* 4.4 7.2 - - + -
222Y MET* 4.0 15.9 - - + -
226Y VAL* 3.7 31.8 - - + +
229Y THR* 5.0 4.9 - - - +
233Y LEU* 3.9 36.6 - - + +
234Y ASP 3.4 2.0 - - - -
235Y TRP* 1.3 105.2 - - + +
237Y SER* 1.3 62.0 + - - +
239Y TRP* 3.4 2.0 + - + +
240Y ILE* 3.2 45.6 + - + +
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Residues in contact with SER 237 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y VAL* 4.9 3.6 - - - +
223Y THR* 5.1 15.3 - - - -
226Y VAL* 5.1 8.4 - - - +
234Y ASP 4.4 8.5 + - - -
235Y TRP 4.3 0.7 + - - -
236Y LEU* 1.3 77.4 - - - +
238Y VAL* 1.3 74.5 + - - +
240Y ILE* 3.5 11.2 + - - +
241Y LYS* 3.3 35.4 + - - +
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Residues in contact with VAL 238 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234Y ASP 5.8 0.7 - - - +
235Y TRP* 3.1 8.6 + - - +
237Y SER* 1.3 81.2 - - - +
239Y TRP* 1.3 55.8 + - - +
241Y LYS* 3.3 12.8 + - + +
242Y ALA* 2.8 34.4 + - - +
257Y THR* 3.7 21.3 - - - +
260Y SER* 4.7 9.4 - - - +
261Y LEU* 3.8 24.9 - - + -
264Y LYS* 5.6 7.4 - - - -
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Residues in contact with TRP 239 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X LEU* 4.5 16.2 - - + -
59X LEU* 3.6 30.5 - - + +
203Y LEU* 4.2 39.0 - - + -
206Y ILE* 4.7 4.7 - - + -
207Y LEU* 4.2 21.5 - - + -
210Y LEU* 4.2 14.1 - - + -
235Y TRP* 3.3 24.1 + + + +
236Y LEU 3.4 9.9 - - - +
237Y SER 3.3 0.2 - - - -
238Y VAL* 1.3 78.4 - - - +
240Y ILE* 1.3 72.0 + - + +
242Y ALA* 3.4 1.7 + - - +
243Y TYR* 3.1 77.1 + + - -
261Y LEU* 4.1 23.6 - - + +
267Y LEU* 5.0 2.0 - - + -
272Y ASP* 6.0 0.2 - - - -
273Y LEU* 4.3 5.0 - - + +
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Residues in contact with ILE 240 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206Y ILE* 4.1 17.3 - - + -
210Y LEU* 3.6 24.6 - - + +
218Y GLU 4.7 0.4 - - - -
219Y VAL* 3.8 35.2 - - + +
222Y MET* 3.6 33.0 - - + -
223Y THR* 5.4 1.3 - - + +
226Y VAL* 5.4 1.3 - - + -
236Y LEU* 3.2 37.6 + - + +
237Y SER* 3.8 9.6 - - - +
238Y VAL 3.3 0.2 - - - -
239Y TRP* 1.3 79.0 - - + +
241Y LYS* 1.3 67.1 + - - +
243Y TYR 3.3 1.6 + - - -
244Y ALA* 2.9 24.9 + - - +
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Residues in contact with LYS 241 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219Y VAL* 4.7 24.5 - - + -
237Y SER* 3.3 21.0 + - - +
238Y VAL* 3.5 16.8 - - + +
240Y ILE* 1.3 77.0 - - - +
242Y ALA* 1.3 63.2 + - - +
244Y ALA* 3.2 9.0 - - - +
245Y PHE* 3.0 43.8 + - + -
257Y THR* 5.1 4.0 - - - +
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Residues in contact with ALA 242 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238Y VAL 2.8 20.5 + - - +
239Y TRP* 3.4 8.5 - - - +
240Y ILE 3.3 0.2 - - - -
241Y LYS* 1.3 74.0 - - - +
243Y TYR* 1.3 59.2 + - + +
245Y PHE* 3.3 5.4 + - - +
246Y VAL* 3.0 28.6 + - - +
254Y ALA* 4.1 3.1 - - - +
257Y THR* 3.7 22.6 - - + +
258Y ILE* 3.7 28.5 - - + +
261Y LEU* 4.4 7.0 - - + -
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Residues in contact with TYR 243 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55X LEU* 6.3 0.9 - - + -
207Y LEU* 4.0 23.6 - - + -
210Y LEU* 3.6 22.2 - - + -
239Y TRP* 3.1 62.5 + + + +
242Y ALA* 1.3 78.6 - - + +
244Y ALA* 1.3 66.1 + - - +
246Y VAL* 3.0 22.5 + - + +
247Y HIS* 3.0 31.9 + - + -
258Y ILE* 4.1 6.1 - - + -
272Y ASP* 3.8 9.9 + - - -
273Y LEU* 3.5 20.2 - - + +
276Y SER* 2.6 38.8 + - - -
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Residues in contact with ALA 244 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210Y LEU* 3.9 15.3 - - + +
215Y LYS* 3.4 30.0 - - + +
219Y VAL* 5.4 2.7 - - + -
240Y ILE* 2.9 15.4 + - + +
241Y LYS* 3.2 14.6 - - - +
243Y TYR* 1.3 74.7 - - - +
245Y PHE* 1.3 60.3 + - + +
247Y HIS* 3.2 7.3 + - - +
248Y THR* 2.9 31.5 + - + +
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Residues in contact with PHE 245 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241Y LYS* 3.0 36.0 + - + -
242Y ALA 3.6 6.3 - - - +
244Y ALA* 1.3 77.0 - - + +
246Y VAL* 1.3 65.6 + - - +
248Y THR* 2.5 35.9 + - + +
249Y GLY 3.5 2.9 + - - -
250Y ASP* 3.5 10.2 - - + +
253Y ARG* 3.7 40.8 - - + -
254Y ALA* 3.6 20.0 - - - +
257Y THR* 4.1 14.6 - - + -
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Residues in contact with VAL 246 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242Y ALA 3.0 23.1 + - - +
243Y TYR* 3.0 32.5 + - + +
245Y PHE* 1.3 78.0 - - - +
247Y HIS* 1.3 72.0 + - + +
249Y GLY* 3.5 10.7 + - - -
250Y ASP 5.7 0.3 - - - -
254Y ALA* 3.5 15.9 - - + +
258Y ILE* 4.7 7.0 - - + -
276Y SER* 5.8 3.6 - - - +
280Y LEU* 3.8 22.5 - - + +
283Y ARG* 3.6 37.6 + - - +
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Residues in contact with HIS 247 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207Y LEU* 4.0 21.4 - - + +
210Y LEU* 3.2 27.8 - - + +
211Y SER* 3.4 43.9 + - - +
213Y SER* 5.6 5.2 - - - -
243Y TYR* 3.0 26.3 + - + -
244Y ALA 3.5 4.3 - - - +
246Y VAL* 1.3 85.8 + - + +
248Y THR* 1.3 64.0 + - - +
249Y GLY* 3.1 2.3 + - - -
283Y ARG* 5.8 1.7 + - - -
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Residues in contact with THR 248 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215Y LYS* 5.8 4.0 - - + -
244Y ALA* 2.9 22.3 + - + +
245Y PHE* 2.5 41.0 + - + +
247Y HIS* 1.3 77.8 - - - +
249Y GLY* 1.3 58.0 + - - +
250Y ASP* 3.3 22.2 + - - +
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Residues in contact with GLY 249 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245Y PHE 3.5 3.2 + - - -
246Y VAL 3.5 8.9 + - - -
247Y HIS 3.1 3.8 - - - -
248Y THR* 1.3 78.6 + - - +
250Y ASP* 1.3 62.5 + - - +
251Y ASN* 3.2 21.3 + - - -
283Y ARG* 6.1 0.2 - - - -
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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