Contacts of the helix formed by residues 225 - 242 (chain M) in PDB entry 5IY8
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 PRO 225 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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223M CYS 3.8 4.2 - - - +
224M LEU* 1.3 92.5 - - + +
226M LYS* 1.3 63.9 + - - +
227M GLN* 3.3 7.0 - - + +
228M VAL* 3.3 26.1 + - + +
229M GLN* 3.0 20.6 + - - +
265M SER* 5.9 1.1 - - - +
267M GLU* 4.5 20.4 - - + +
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Residues in contact with LYS 226 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38L GLU* 2.9 40.8 + - - +
39L CYS* 4.3 0.6 - - - +
40L GLY* 4.0 14.5 - - - +
224M LEU 3.7 1.2 + - - -
225M PRO* 1.3 72.0 - - - +
227M GLN* 1.3 58.0 + - - +
229M GLN* 3.3 19.8 + - - +
230M MET* 3.0 27.8 + - + +
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Residues in contact with GLN 227 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225M PRO* 3.3 4.6 - - + +
226M LYS* 1.3 77.5 - - - +
228M VAL* 1.3 60.7 + - + +
230M MET* 3.2 14.2 + - + +
231M ALA* 3.0 26.6 + - - +
303M ASP 4.1 3.3 - - - +
304M PHE* 4.0 18.1 - - + -
305M LYS* 3.2 45.4 + - - +
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Residues in contact with VAL 228 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219M CYS* 6.1 0.9 - - - -
224M LEU* 4.9 12.8 - - + -
225M PRO* 3.3 35.8 + - + +
227M GLN* 1.3 72.9 - - + +
229M GLN* 1.3 66.2 + - - +
231M ALA* 3.2 6.3 + - - +
232M ALA* 2.9 23.4 + - + +
261M ALA* 3.7 34.5 - - + +
262M SER* 4.4 5.4 - - - +
265M SER* 4.0 23.3 - - - +
304M PHE* 4.6 12.8 - - + -
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Residues in contact with GLN 229 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215M MET* 4.3 5.0 - - + +
216M SER* 3.3 36.6 + - - +
219M CYS* 3.8 33.9 - - + +
220M SER* 4.3 7.7 + - - +
224M LEU* 5.3 4.1 + - - +
225M PRO 3.0 12.6 + - - +
226M LYS* 3.4 23.3 + - - +
228M VAL* 1.3 76.7 - - - +
230M MET* 1.3 61.2 + - - +
232M ALA* 3.4 2.1 + - - +
233M THR* 2.9 33.6 + - - +
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Residues in contact with MET 230 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226M LYS* 3.0 14.7 + - + +
227M GLN* 3.3 15.9 - - - +
228M VAL 3.2 0.4 - - - -
229M GLN* 1.3 77.7 - - - +
231M ALA* 1.3 62.1 + - - +
233M THR* 3.3 9.9 - - - -
234M HIS* 3.1 21.4 + - + +
301M PRO* 5.9 6.1 - - + -
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Residues in contact with ALA 231 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227M GLN 3.0 13.0 + - - +
228M VAL* 3.6 7.6 - - - +
230M MET* 1.3 73.8 - - - +
232M ALA* 1.3 53.9 + - - +
234M HIS* 3.0 3.8 + - - +
235M ILE* 2.6 46.7 + - + +
261M ALA* 5.2 3.8 - - + -
300M PHE* 5.8 1.3 - - + -
301M PRO* 3.8 24.1 - - + +
304M PHE* 3.9 26.7 - - + -
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Residues in contact with ALA 232 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215M MET* 3.7 24.0 - - + +
219M CYS* 4.4 9.9 - - - -
228M VAL 2.9 15.7 + - - +
229M GLN 3.6 5.6 - - - +
231M ALA* 1.3 76.0 - - - +
233M THR* 1.3 52.8 + - - +
235M ILE* 3.1 14.2 + - - +
236M ALA* 2.6 37.1 + - - +
257M ALA* 4.0 8.8 - - - +
258M ILE* 4.5 0.4 - - - -
261M ALA* 4.1 14.8 - - + +
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Residues in contact with THR 233 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212M GLY* 5.3 10.8 - - - -
215M MET* 3.6 22.6 - - + +
229M GLN* 2.9 20.5 + - - +
230M MET* 3.3 12.3 - - - -
231M ALA 3.3 0.2 - - - -
232M ALA* 1.3 74.2 - - - +
234M HIS* 1.3 58.5 + - - +
236M ALA* 3.3 3.9 + - - +
237M ARG* 2.8 35.2 + - + +
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Residues in contact with HIS 234 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230M MET* 3.1 12.4 + - + +
231M ALA 3.0 9.0 + - - +
233M THR* 1.3 73.2 - - - +
235M ILE* 1.3 66.1 + - - +
237M ARG* 3.8 10.9 - - - +
238M LYS* 2.9 53.7 + - + +
299M LEU 3.1 25.6 - - - -
300M PHE 4.5 1.8 + - - -
301M PRO* 3.8 32.1 - - + +
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Residues in contact with ILE 235 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231M ALA* 2.6 28.7 + - + +
232M ALA* 3.3 15.0 - - - +
234M HIS* 1.3 73.1 - - - +
236M ALA* 1.3 63.3 + - - +
238M LYS* 4.1 1.3 - - - +
239M ALA* 3.0 25.1 + - + +
257M ALA* 3.5 25.8 - - + +
260M MET* 4.8 7.6 - - + -
261M ALA* 4.2 18.2 - - + +
292M ILE* 5.4 3.4 - - + -
299M LEU* 3.9 29.9 - - + +
300M PHE* 3.3 42.4 - - + -
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Residues in contact with ALA 236 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M THR* 3.8 23.5 - - + +
215M MET* 3.6 24.0 - - + -
232M ALA 2.6 19.0 + - - +
233M THR* 3.5 5.8 - - - +
235M ILE* 1.3 73.9 - - - +
237M ARG* 1.3 64.8 + - - +
239M ALA* 3.2 8.3 + - - +
240M VAL* 3.1 25.3 + - - +
253M VAL* 5.2 3.5 - - + +
254M ALA* 5.2 1.8 - - - -
257M ALA* 4.4 7.6 - - + -
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Residues in contact with ARG 237 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M THR* 4.2 7.5 + - - +
233M THR* 2.8 26.2 + - + +
234M HIS* 3.8 11.0 - - - +
236M ALA* 1.3 72.3 - - - +
238M LYS* 1.3 57.4 + - - +
240M VAL* 3.4 5.5 + - - +
241M GLU* 3.0 28.1 + - + +
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Residues in contact with LYS 238 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234M HIS* 2.9 50.6 + - + +
235M ILE 4.1 1.8 - - - +
237M ARG* 1.3 71.2 - - - +
239M ALA* 1.3 56.7 + - - +
241M GLU* 2.8 26.0 + - - +
242M LEU* 2.7 49.3 + - + +
298M ASP* 3.1 28.3 - - + +
299M LEU* 3.6 22.4 - - + +
300M PHE 5.5 0.4 - - - -
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Residues in contact with ALA 239 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235M ILE* 3.0 22.2 + - + +
236M ALA* 3.4 7.9 - - - +
238M LYS* 1.3 74.2 - - - +
240M VAL* 1.3 60.8 + - - +
242M LEU 3.7 0.7 + - - -
243M ASP 3.4 2.3 + - - -
244M LEU* 3.3 41.0 + - + +
245M VAL* 4.3 6.0 - - + +
253M VAL* 4.5 16.8 - - + -
257M ALA* 6.4 0.2 - - + -
292M ILE* 5.2 9.4 - - + -
299M LEU* 4.4 12.7 - - + +
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Residues in contact with VAL 240 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M THR* 3.8 27.6 - - + +
236M ALA 3.1 14.3 + - - +
237M ARG* 3.7 7.6 - - - +
239M ALA* 1.3 75.8 - - + +
241M GLU* 1.3 64.5 + - - +
243M ASP* 3.2 14.4 + - - +
245M VAL* 5.0 9.0 - - + -
250M PRO* 6.1 1.3 - - + -
253M VAL* 5.1 6.1 - - + -
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Residues in contact with GLU 241 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237M ARG* 3.0 15.7 + - + +
238M LYS* 2.8 34.4 + - - +
240M VAL* 1.3 78.1 - - - +
242M LEU* 1.3 65.3 + - + +
243M ASP* 3.1 3.7 + - - +
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Residues in contact with LEU 242 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238M LYS* 2.7 32.0 + - + +
241M GLU* 1.3 78.0 - - + +
243M ASP* 1.3 70.5 + - - +
244M LEU* 3.2 28.6 + - + +
295M ARG* 4.0 29.2 - - - +
298M ASP* 5.1 2.7 - - + -
299M LEU* 3.7 29.6 - - + -
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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