Contacts of the helix formed by residues 235 - 249 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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212E ARG 4.5 2.0 - - - +
213E TYR* 3.8 31.0 - - - +
229E LYS* 5.0 1.4 + - - -
231E PHE* 3.7 11.8 - - + -
232E SER* 3.0 22.5 + - - +
234E ARG* 1.3 80.2 - - - +
236E GLU* 1.3 63.4 + - - +
237E GLN 3.1 3.4 - - - -
238E SER* 2.8 44.3 + - - -
239E TRP 3.5 3.5 + - - -
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Residues in contact with GLU 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PHE* 5.2 0.9 - - - -
232E SER 3.5 8.7 + - - +
233E SER* 3.4 30.3 + - - +
234E ARG 3.7 0.6 - - - -
235E ASP* 1.3 77.8 - - - +
237E GLN* 1.3 62.2 + - - +
239E TRP* 3.2 10.5 + - - +
240E PHE* 3.2 20.6 + - - +
273E LEU* 3.7 29.6 - - + +
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Residues in contact with GLN 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235E ASP* 3.1 1.4 - - - +
236E GLU* 1.3 76.8 - - - +
238E SER* 1.3 60.0 + - - +
239E TRP 3.4 0.2 - - - -
240E PHE* 3.5 14.9 + - + +
241E ARG* 3.1 27.9 + - + +
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Residues in contact with SER 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E LYS* 5.9 0.4 - - - -
231E PHE* 3.9 10.1 - - - -
235E ASP* 2.8 39.2 + - - -
237E GLN* 1.3 75.6 - - - +
239E TRP* 1.3 65.0 + - - +
241E ARG* 3.5 5.6 + - - +
242E GLU* 3.0 28.1 + - - +
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Residues in contact with TRP 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231E PHE* 3.5 42.5 - + + -
235E ASP 3.5 1.0 + - - -
236E GLU 3.2 10.4 + - - +
238E SER* 1.3 79.0 - - - +
240E PHE* 1.3 89.4 + + + +
242E GLU* 3.7 1.8 - - - +
243E THR* 2.8 52.0 + - + -
262E SER* 3.1 19.6 + - - -
263E ASP* 3.9 16.8 - - - -
264E MET* 5.1 4.9 - - + -
273E LEU* 3.5 47.1 - - + -
274E TRP 2.9 30.8 + - - +
275E LEU* 4.4 2.9 - - + -
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Residues in contact with PHE 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236E GLU 3.2 10.2 + - - +
237E GLN* 3.7 21.1 - - + +
238E SER 3.3 0.4 - - - -
239E TRP* 1.3 102.8 - + + +
241E ARG* 1.3 56.9 + - + +
243E THR* 3.3 6.4 + - + -
244E GLU* 2.8 41.7 + - + +
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Residues in contact with ARG 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237E GLN* 3.1 14.9 + - + +
238E SER* 3.9 5.6 - - - +
239E TRP 3.4 0.2 - - - -
240E PHE* 1.3 83.1 - - + +
242E GLU* 1.3 57.9 + - - +
244E GLU* 3.4 10.5 + - - +
245E ILE* 3.0 63.2 + - + +
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Residues in contact with GLU 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E LYS* 4.5 6.1 + - - -
231E PHE* 3.7 15.1 - - - -
238E SER* 3.0 18.4 + - - +
239E TRP* 3.9 4.3 - - - +
241E ARG* 1.3 77.3 - - - +
243E THR* 1.3 61.2 + - - +
245E ILE* 4.1 5.7 - - + +
246E TYR* 3.1 60.0 + - + -
257E LEU* 5.9 2.4 - - - +
275E LEU* 3.4 31.5 - - + +
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Residues in contact with THR 243 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239E TRP* 2.8 40.2 + - + -
240E PHE* 3.6 8.3 - - + +
242E GLU* 1.3 76.0 - - - +
244E GLU* 1.3 66.4 + - - +
246E TYR* 4.1 3.2 - - - +
247E ASN* 3.2 38.1 + - - +
259E PHE* 5.4 2.0 - - - -
262E SER* 2.5 36.4 + - - +
275E LEU* 5.1 2.6 - - - +
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Residues in contact with GLU 244 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240E PHE* 2.8 29.9 + - + +
241E ARG* 3.6 14.8 - - - +
243E THR* 1.3 77.3 - - - +
245E ILE* 1.3 62.9 + - + +
247E ASN* 3.7 2.2 - - - +
248E THR* 3.0 36.2 + - - +
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Residues in contact with ILE 245 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241E ARG* 3.0 58.6 + - + +
242E GLU* 4.1 5.6 - - + +
244E GLU* 1.3 76.4 - - + +
246E TYR* 1.3 60.2 + - + +
248E THR* 4.5 1.1 - - - -
249E VAL* 2.9 46.0 + - + +
251E LEU* 3.9 26.5 - - + -
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Residues in contact with TYR 246 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242E GLU* 3.1 52.8 + - + +
243E THR 4.2 0.9 - - - +
245E ILE* 1.3 80.2 - - + +
247E ASN* 1.3 61.2 + - - +
248E THR 3.7 0.3 + - - -
249E VAL 4.1 9.6 - - - +
251E LEU* 4.9 18.6 - - + -
256E ILE* 4.7 11.7 - - + +
257E LEU* 3.1 42.6 + - - +
258E GLY 5.3 0.2 - - - -
259E PHE* 3.4 60.0 - + + -
275E LEU* 4.1 8.3 - - + -
277E THR* 5.4 2.9 - - + -
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Residues in contact with ASN 247 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E GLN* 4.2 15.4 + - - +
243E THR* 3.2 36.0 + - - +
244E GLU* 3.8 4.3 - - - +
246E TYR* 1.3 76.3 - - - +
248E THR* 1.3 60.3 + - - +
249E VAL 3.9 0.4 - - - -
259E PHE* 4.1 22.0 - - - -
262E SER* 5.1 1.6 - - - -
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Residues in contact with THR 248 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244E GLU* 3.0 23.6 + - - +
245E ILE* 4.1 0.7 - - - -
247E ASN* 1.3 80.8 + - - +
249E VAL* 1.4 73.8 + - + +
250E LEU 4.3 0.7 + - - -
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Residues in contact with VAL 249 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E ILE* 2.9 33.6 + - + +
246E TYR 4.1 8.7 - - - +
247E ASN 3.9 0.2 - - - -
248E THR* 1.4 92.6 - - + +
250E LEU* 1.3 69.6 + - - +
251E LEU* 2.9 32.0 + - + +
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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
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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