Contacts of the helix formed by residues 235 - 249 (chain B) in PDB entry 3MY0
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 ASP 235 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212B ARG 4.5 1.8 - - - +
213B TYR* 3.7 32.2 - - - +
229B LYS* 5.0 1.0 + - - -
231B PHE* 3.6 11.6 - - + -
232B SER* 3.0 21.6 + - - +
234B ARG* 1.3 78.4 - - - +
236B GLU* 1.3 65.0 + - - +
237B GLN 3.1 4.0 - - - +
238B SER* 2.6 44.8 + - - -
239B TRP 3.5 4.0 + - - -
367B ASN* 4.2 6.2 + - - +
369B ARG* 3.8 20.5 + - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 5.2 0.4 - - - -
232B SER 3.5 7.5 + - - +
233B SER* 3.4 29.8 + - - +
234B ARG 3.7 0.6 - - - -
235B ASP* 1.3 78.0 - - - +
237B GLN* 1.3 66.2 + - - +
239B TRP* 3.2 10.9 + - - +
240B PHE* 3.2 20.1 + - - +
273B LEU* 3.6 30.9 - - + +
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Residues in contact with GLN 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B ASP 3.1 1.2 - - - -
236B GLU* 1.3 81.1 - - - +
238B SER* 1.3 64.5 + - - +
240B PHE* 3.4 21.8 + - + +
241B ARG* 3.1 24.3 + - - +
366B ASN* 4.1 21.8 - - + +
367B ASN* 3.8 42.1 + - + +
368B PRO* 4.6 5.2 - - + -
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Residues in contact with SER 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B PHE* 3.9 10.1 - - - -
235B ASP* 2.6 35.6 + - - -
237B GLN* 1.3 75.9 - - - +
239B TRP* 1.3 60.0 + - - +
241B ARG 3.3 0.7 + - - -
242B GLU* 2.9 32.1 + - - +
350B GLY* 3.7 11.4 - - - -
367B ASN* 2.8 18.0 + - - +
369B ARG* 2.7 30.5 + - - -
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Residues in contact with TRP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B PHE* 3.5 42.5 - + + -
235B ASP 3.5 2.0 + - - -
236B GLU 3.2 10.4 + - - +
238B SER* 1.3 80.0 - - - +
240B PHE* 1.3 89.6 + + + +
242B GLU* 3.9 2.2 - - - +
243B THR* 2.9 46.6 + - + -
262B SER* 3.1 19.8 + - - -
263B ASP 4.0 17.0 - - - -
264B MET* 4.4 15.3 - - + -
273B LEU* 3.7 44.6 - - + -
274B TRP 3.1 30.3 + - - +
275B LEU* 4.5 3.1 - - + -
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Residues in contact with PHE 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B GLU 3.2 9.1 + - - +
237B GLN* 3.6 30.1 - - + +
238B SER 3.2 0.2 - - - -
239B TRP* 1.3 99.4 - + + +
241B ARG* 1.3 62.8 + - + +
243B THR* 3.2 7.2 + - + -
244B GLU* 2.8 46.7 + - + +
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Residues in contact with ARG 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B GLN 3.1 10.9 + - - +
238B SER 3.8 0.4 - - - +
240B PHE* 1.3 81.8 - - + +
242B GLU* 1.3 58.1 + - - +
244B GLU* 2.8 40.8 + - - +
245B ILE* 3.0 35.6 + - + +
349B LEU 3.8 10.8 - - - +
350B GLY 3.4 26.9 - - - +
351B LEU 5.0 0.4 - - - -
352B ALA 2.8 27.9 + - - +
353B VAL* 3.6 0.2 - - - +
354B MET* 3.1 33.2 - - - +
363B ASP* 2.9 36.5 + - - -
365B GLY* 5.0 18.3 - - - +
367B ASN* 5.7 0.9 - - + +
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Residues in contact with GLU 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B LYS* 4.7 3.0 + - - +
231B PHE* 3.7 21.1 - - - -
238B SER 2.9 15.6 + - - +
239B TRP* 4.0 3.6 - - - +
241B ARG* 1.3 76.9 - - - +
243B THR* 1.3 58.3 + - - +
245B ILE* 4.1 3.0 - - - +
246B TYR* 3.1 60.8 + - + -
257B LEU* 5.9 2.1 - - - +
275B LEU* 3.5 23.9 - - + +
348B ASP* 3.3 19.9 + - - +
349B LEU* 3.2 36.0 + - + +
350B GLY* 4.0 7.8 + - - +
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TRP* 2.9 39.4 + - + -
240B PHE* 3.5 8.3 - - + +
242B GLU* 1.3 74.5 - - - +
244B GLU* 1.3 67.2 + - - +
246B TYR* 4.0 2.8 - - - +
247B ASN* 2.8 45.5 + - - +
259B PHE* 5.4 1.8 - - - -
262B SER* 2.5 35.1 + - - +
275B LEU* 5.2 2.4 - - - +
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Residues in contact with GLU 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240B PHE* 2.8 39.6 + - + +
241B ARG* 2.8 40.7 + - - +
243B THR* 1.3 77.6 - - - +
245B ILE* 1.3 60.9 + - - +
247B ASN* 3.2 2.6 + - - +
248B THR* 3.0 45.8 + - + +
354B MET* 3.8 8.2 - - + +
363B ASP* 3.9 6.9 - - - +
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Residues in contact with ILE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B ARG* 3.0 34.1 + - - +
242B GLU* 4.1 3.4 - - - +
244B GLU* 1.3 79.7 - - + +
246B TYR* 1.3 58.3 + - - +
248B THR* 4.5 0.4 - - - -
249B VAL* 2.9 43.8 + - + +
251B LEU* 3.9 12.9 - - + +
326B ILE* 5.1 2.9 - - + -
349B LEU* 3.6 37.2 - - + +
352B ALA* 3.5 32.5 - - + -
354B MET* 3.8 26.7 - - + -
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Residues in contact with TYR 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B GLU* 3.1 55.4 + - + +
243B THR 4.2 0.9 - - - +
245B ILE* 1.3 77.9 - - - +
247B ASN* 1.3 61.4 + - - +
248B THR 3.7 0.2 + - - -
249B VAL 4.1 4.3 - - - +
251B LEU* 5.0 11.4 - - + -
256B ILE* 4.6 7.5 - - + +
257B LEU* 3.2 41.8 + - - +
258B GLY 5.3 0.2 - - - -
259B PHE* 3.4 60.1 - + + -
275B LEU* 4.3 6.7 - - + -
277B THR* 5.4 3.4 - - + -
347B ALA* 5.1 0.7 - - - -
349B LEU* 3.9 31.4 - - + +
321C GLN* 3.7 14.9 - - - +
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Residues in contact with ASN 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195B GLN* 6.2 2.2 - - - +
243B THR* 2.8 41.8 + - - +
244B GLU* 3.9 3.4 - - - +
246B TYR* 1.3 76.0 + - - +
248B THR* 1.3 59.2 + - - +
259B PHE* 3.9 23.7 - - - -
262B SER* 4.9 1.6 - - - -
319C GLY* 5.8 0.4 - - - -
320C THR* 3.2 43.0 + - + +
321C GLN* 3.1 22.1 + - - +
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Residues in contact with THR 248 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244B GLU* 3.0 31.7 + - + +
245B ILE 4.2 0.4 - - - -
247B ASN* 1.3 80.5 - - - +
249B VAL* 1.3 70.0 + - + +
250B LEU 4.2 0.3 + - - -
354B MET* 5.6 3.6 - - + -
321C GLN* 2.6 19.0 + - - +
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Residues in contact with VAL 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B ILE* 2.9 24.2 + - + +
246B TYR 4.1 4.2 - - - +
248B THR* 1.3 91.4 - - + +
250B LEU* 1.3 60.3 + - - +
251B LEU* 3.0 42.3 + - + +
323B LYS* 4.0 8.3 - - + -
324B PRO* 3.9 28.5 - - + -
326B ILE* 4.1 3.8 - - + -
354B MET* 4.0 26.7 - - + -
321C GLN* 3.5 11.8 - - - +
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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