Contacts of the helix formed by residues 249 - 264 (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 SER 249 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248M ARG* 1.3 73.1 - - - +
250M PRO* 1.3 75.1 - - - +
251M ILE* 3.3 13.6 + - - +
252M SER* 3.2 8.5 + - - -
253M VAL* 3.1 24.3 + - - +
285P PRO* 3.6 23.3 + - - -
286P GLU* 3.7 13.9 - - - +
84Y G 4.5 2.7 + - - -
85Y G 3.2 26.8 + - - -
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Residues in contact with PRO 250 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209M ILE* 3.6 34.5 - - + +
210M THR* 4.8 0.9 - - - -
211M THR* 3.8 28.2 - - + +
240M VAL* 6.1 1.8 - - + -
248M ARG 4.0 4.7 - - - +
249M SER* 1.3 91.4 - - - +
251M ILE* 1.3 56.6 + - + +
253M VAL* 3.6 9.4 + - + +
254M ALA* 2.9 28.2 + - - +
285P PRO* 4.3 17.9 - - + -
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Residues in contact with ILE 251 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176M THR* 4.3 14.1 - - + -
209M ILE* 4.7 10.8 - - + -
210M THR 5.5 0.4 - - - +
211M THR* 6.5 0.2 - - - -
214M PHE* 3.6 49.1 - - + -
218M PHE* 4.8 15.8 - - + -
249M SER* 3.3 6.2 - - - +
250M PRO* 1.3 78.8 - - + +
252M SER* 1.3 57.7 + - - +
254M ALA* 3.1 6.7 + - + +
255M ALA* 2.9 27.2 + - - +
278M ALA* 5.2 7.6 - - + +
280M VAL* 4.5 17.7 - - + -
286P GLU* 4.1 27.8 - - + +
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Residues in contact with SER 252 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248M ARG* 5.5 1.8 - - - -
249M SER* 3.2 11.8 + - - -
251M ILE* 1.3 75.9 - - - +
253M VAL* 1.3 61.8 + - - +
255M ALA* 3.3 9.0 + - - +
256M ALA* 2.9 28.1 + - - +
280M VAL* 4.4 14.6 - - - +
284M THR* 3.9 23.2 - - - +
285M ILE* 5.2 2.8 - - - -
288M SER* 4.1 12.3 - - - -
85Y G 2.9 26.9 + - - -
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Residues in contact with VAL 253 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211M THR* 4.8 10.8 - - + -
236M ALA* 5.2 4.7 - - - +
239M ALA* 4.5 18.4 - - + -
240M VAL* 5.1 3.6 - - + -
245M VAL* 3.7 45.1 - - + -
248M ARG* 3.9 10.5 - - + -
249M SER 3.1 16.8 + - - +
250M PRO* 3.8 10.3 - - + +
252M SER* 1.3 72.1 - - - +
254M ALA* 1.3 66.7 + - - +
256M ALA* 3.3 6.9 + - + +
257M ALA* 3.0 23.0 + - + +
288M SER* 5.1 3.6 - - - +
292M ILE* 5.5 5.4 - - + -
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Residues in contact with ALA 254 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211M THR* 4.7 15.5 - - + +
214M PHE* 5.2 6.7 - - + -
215M MET* 3.7 27.8 - - + +
218M PHE* 5.3 4.0 - - + -
236M ALA* 5.2 0.7 - - - -
250M PRO 2.9 16.4 + - - +
251M ILE* 3.1 13.0 + - + +
253M VAL* 1.3 75.9 - - - +
255M ALA* 1.3 58.2 + - - +
257M ALA* 3.2 5.2 + - - +
258M ILE* 3.0 35.9 + - + +
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Residues in contact with ALA 255 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218M PHE* 6.0 0.6 - - - -
251M ILE 2.9 12.7 + - - +
252M SER* 3.4 11.4 - - - +
254M ALA* 1.3 75.7 - - - +
256M ALA* 1.3 57.3 + - - +
258M ILE* 3.4 14.7 + - - +
259M TYR* 3.1 27.2 + - - +
274M ILE* 4.2 11.5 - - + +
278M ALA* 4.5 8.3 - - + -
280M VAL* 4.5 9.0 - - + -
285M ILE* 4.0 27.8 - - + +
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Residues in contact with ALA 256 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252M SER 2.9 16.1 + - - +
253M VAL* 3.3 6.2 + - - +
255M ALA* 1.3 73.6 - - - +
257M ALA* 1.3 61.1 + - - +
259M TYR* 3.4 3.3 + - - +
260M MET* 3.0 27.9 + - - +
285M ILE* 4.1 12.7 - - + +
288M SER* 3.7 24.2 - - - +
289M TYR* 4.0 15.4 - - - +
292M ILE* 4.0 16.4 - - + +
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Residues in contact with ALA 257 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215M MET* 4.1 8.1 - - + -
232M ALA* 4.0 15.7 - - - +
235M ILE* 3.5 32.5 - - + +
236M ALA* 4.2 6.5 - - + +
253M VAL* 3.0 13.5 + - + +
254M ALA 3.5 8.3 - - - +
256M ALA* 1.3 74.5 - - - +
258M ILE* 1.3 65.8 + - - +
260M MET* 3.4 3.6 + - - +
261M ALA* 3.0 25.6 + - - +
292M ILE* 4.5 3.5 - - + +
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Residues in contact with ILE 258 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215M MET* 3.5 23.8 - - - -
218M PHE* 3.6 36.1 - - + -
219M CYS* 3.6 7.9 - - - -
222M LEU* 4.3 15.3 - - + -
224M LEU* 4.0 24.0 - - + -
232M ALA* 4.5 2.9 - - - +
254M ALA* 3.0 25.9 + - + +
255M ALA* 3.5 11.9 - - - +
256M ALA 3.4 0.2 - - - -
257M ALA* 1.3 76.2 - - - +
259M TYR* 1.3 56.8 + - - +
261M ALA* 3.5 5.5 + - - +
262M SER* 2.9 36.7 + - - +
274M ILE* 4.3 13.0 - - + -
278M ALA* 6.3 1.1 - - + -
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Residues in contact with TYR 259 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255M ALA 3.1 13.8 + - - +
256M ALA* 3.6 8.1 - - - +
257M ALA 3.3 0.2 - - - -
258M ILE* 1.3 76.1 - - - +
260M MET* 1.3 57.7 + - - +
262M SER* 3.2 2.1 + - - -
263M GLN* 2.9 74.1 + - + +
269M ARG 4.0 4.3 - - - -
270M THR* 5.0 0.2 - - - -
271M GLN* 3.4 47.4 + - + +
274M ILE* 3.6 26.0 - - + +
285M ILE* 4.4 11.4 - - + -
289M TYR* 3.9 39.5 - + + -
314M PRO* 5.9 2.4 - - - +
316M LEU* 4.0 15.0 - - + +
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Residues in contact with MET 260 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235M ILE* 4.8 9.6 - - + -
256M ALA 3.0 15.6 + - - +
257M ALA* 3.4 7.2 + - - +
259M TYR* 1.3 76.9 - - - +
261M ALA* 1.3 62.2 + - - +
263M GLN* 3.5 4.7 + - - +
264M ALA* 3.1 22.5 + - - +
289M TYR* 3.4 33.7 - - + +
292M ILE* 3.5 29.4 - - + -
293M TYR* 4.3 8.1 - - - -
296M ALA* 4.0 28.5 - - + -
299M LEU* 4.8 3.8 - - - -
300M PHE* 3.6 31.6 - - + -
313M LEU* 4.4 9.2 - - + +
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Residues in contact with ALA 261 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224M LEU* 6.5 0.2 - - + -
228M VAL* 3.7 23.9 - - + +
231M ALA* 5.2 3.4 - - + -
232M ALA* 4.1 18.2 - - + +
235M ILE* 4.2 13.1 - - + +
257M ALA 3.0 17.9 + - - +
258M ILE 3.6 3.6 - - - +
260M MET* 1.3 77.3 - - - +
262M SER* 1.3 59.1 + - - +
264M ALA* 2.9 24.0 + - - +
265M SER* 3.1 13.7 + - - -
300M PHE* 5.2 0.9 - - - -
304M PHE* 5.2 2.7 - - + -
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Residues in contact with SER 262 (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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224M LEU* 3.7 28.1 - - - +
228M VAL* 4.7 2.6 - - - +
258M ILE* 2.9 28.0 + - - +
259M TYR* 3.7 5.6 - - - -
261M ALA* 1.3 72.5 - - - +
263M GLN* 1.3 57.3 + - - +
265M SER* 3.0 22.6 + - - +
267M GLU* 5.3 0.4 - - - -
268M LYS* 3.0 23.8 + - - -
269M ARG* 3.9 29.5 - - - +
274M ILE* 4.8 0.4 - - - +
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Residues in contact with GLN 263 (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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259M TYR* 2.9 56.0 + - + +
260M MET* 3.8 4.9 - - - +
262M SER* 1.3 76.1 - - - +
264M ALA* 1.3 57.7 + - - +
265M SER 3.2 2.4 + - - -
268M LYS* 3.4 51.2 + - - +
269M ARG 3.2 26.3 + - - -
270M THR* 4.8 2.2 - - - +
289M TYR* 5.4 1.1 - - - +
308M THR* 4.5 6.8 - - - -
313M LEU* 4.2 19.9 - - + +
314M PRO* 4.8 17.3 - - + +
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Residues in contact with ALA 264 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260M MET 3.1 16.8 + - - +
261M ALA* 2.9 9.4 + - - +
263M GLN* 1.3 77.0 - - - +
265M SER* 1.3 57.7 + - - +
268M LYS* 5.1 0.2 - - - -
300M PHE* 4.1 25.6 - - + -
304M PHE* 4.1 17.5 - - + -
306M PHE* 4.8 1.7 - - + -
307M ASP* 3.7 23.1 + - - +
308M THR 3.9 18.1 + - - +
313M LEU* 4.7 7.0 - - + -
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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
------------------------------------------------------------
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