Contacts of the helix formed by residues 234 - 246 (chain B) in PDB entry 3M0V
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 234 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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220B HIS* 3.4 21.2 - - + +
232B VAL 3.6 0.4 - - - -
233B GLN* 1.3 105.5 + - + +
235B TRP* 1.3 65.4 + - + +
236B GLY 3.1 3.5 + - - -
237B THR* 3.0 21.0 + - - -
238B ASN 2.9 22.2 + - - -
258B HIS* 6.2 1.1 - - - +
235D TRP* 2.8 30.1 + - - -
262D THR* 6.1 0.5 - - - +
267D ILE* 4.9 2.1 - - - +
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Residues in contact with TRP 235 (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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220B HIS* 3.7 18.2 - - + +
234B ASP* 1.3 80.9 - - + +
236B GLY* 1.3 60.2 + - - +
238B ASN* 3.5 8.8 - - - +
239B TYR* 2.7 44.1 + + + +
258B HIS* 5.8 0.2 + - - -
267B ILE* 3.4 48.7 - - + +
270B ARG* 3.6 30.5 - - + -
271B LEU* 3.9 29.4 - - + +
233D GLN* 4.3 4.7 - - - -
234D ASP* 2.8 27.1 + - - -
236D GLY* 3.7 10.4 - - - -
237D THR* 3.5 36.3 - - - -
240D LEU* 3.9 17.0 - - + -
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Residues in contact with GLY 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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234B ASP* 3.1 7.9 + - - -
235B TRP* 1.3 83.6 - - - +
237B THR* 1.3 64.5 + - - +
239B TYR* 3.2 6.6 + - - +
240B LEU* 3.1 24.8 + - - +
235D TRP* 3.7 17.5 - - - -
236D GLY* 4.1 22.0 - - - -
239D TYR* 6.0 0.3 - - - -
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Residues in contact with THR 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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196B PHE* 3.5 27.6 - - + -
231B VAL 3.5 21.1 - - - +
232B VAL* 4.2 2.5 - - - -
233B GLN* 2.6 30.9 + - - -
234B ASP* 3.0 7.8 + - - -
236B GLY* 1.3 75.3 - - - +
238B ASN* 1.3 63.0 + - - +
240B LEU* 3.1 9.1 + - - +
241B ILE* 3.0 27.6 + - + +
235D TRP* 3.5 7.6 - - - -
270D ARG* 3.1 20.5 + - - +
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Residues in contact with ASN 238 (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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218B SER* 2.5 51.4 + - - -
220B HIS* 2.9 35.8 + - + +
232B VAL* 4.4 3.1 - - - +
234B ASP 2.9 18.4 + - - +
235B TRP* 3.5 6.1 - - - +
236B GLY 3.1 0.2 - - - -
237B THR* 1.3 77.9 - - - +
239B TYR* 1.3 63.0 + - - +
241B ILE* 3.1 9.5 + - - +
242B ALA 3.0 19.1 + - - -
251B CYS* 3.3 26.0 - - + +
252B LEU 3.8 1.6 + - - -
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Residues in contact with TYR 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B TRP* 2.7 35.0 + + + +
236B GLY* 3.2 6.0 + - - +
238B ASN* 1.3 72.6 - - - +
240B LEU* 1.3 68.8 + - + +
242B ALA* 3.2 1.3 + - - -
243B GLN* 2.9 60.1 + - + +
251B CYS* 3.9 7.6 - - - -
271B LEU* 4.6 8.5 - - + -
274B PHE* 3.9 26.9 + - + +
276B LYS* 3.9 30.5 - - + -
239D TYR* 4.4 21.8 - + - -
240D LEU* 3.6 31.8 - - + +
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Residues in contact with LEU 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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196B PHE* 4.3 11.2 - - + -
200B LEU* 5.2 0.2 - - - -
236B GLY 3.1 12.7 + - - +
237B THR* 3.1 11.0 + - - +
239B TYR* 1.3 78.5 - - + +
241B ILE* 1.3 59.5 + - - +
243B GLN* 4.2 2.8 - - + +
244B THR* 2.6 34.4 + - - -
235D TRP* 3.8 31.4 - - + -
239D TYR* 3.4 43.1 - - + +
270D ARG* 4.6 4.3 - - + -
274D PHE* 3.7 46.4 - - + -
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Residues in contact with ILE 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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196B PHE* 3.5 24.5 - - + -
199B TYR* 3.3 39.7 - - + +
200B LEU* 4.1 10.1 - - + -
203B MET* 4.7 0.4 - - + -
218B SER* 3.9 13.2 - - - +
232B VAL* 3.7 26.9 - - + -
237B THR* 3.0 20.6 + - + +
238B ASN* 3.4 10.8 - - - +
239B TYR 3.1 0.2 - - - -
240B LEU* 1.3 77.2 - - - +
242B ALA* 1.3 58.8 + - - +
244B THR* 3.3 1.6 + - - -
245B LEU* 3.0 56.1 + - + +
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Residues in contact with ALA 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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218B SER* 5.2 1.1 - - - +
238B ASN 3.0 15.9 + - - +
239B TYR 3.8 2.7 - - - +
241B ILE* 1.3 78.9 - - - +
243B GLN* 1.3 63.4 + - - +
246B GLY 3.2 20.8 + - - +
249B ALA* 3.5 26.8 - - - +
250B GLN* 4.0 7.6 - - - -
251B CYS* 3.8 14.8 - - - -
276B LYS* 3.2 27.6 + - + -
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Residues in contact with GLN 243 (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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239B TYR* 2.9 53.0 + - + +
240B LEU* 4.2 3.8 - - + +
242B ALA* 1.3 77.9 - - - +
244B THR* 1.3 62.9 + - - +
246B GLY* 3.9 6.8 + - - -
274B PHE 5.0 2.8 - - - +
276B LYS* 3.6 19.8 + - - +
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Residues in contact with THR 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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200B LEU* 4.4 26.6 - - + +
240B LEU 2.6 22.6 + - - -
241B ILE 3.7 4.0 - - - -
243B GLN* 1.3 79.2 - - - +
245B LEU* 1.3 66.1 + - + +
246B GLY 3.7 0.2 + - - -
274D PHE* 4.3 17.8 - - - -
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Residues in contact with LEU 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200B LEU* 4.1 9.2 - - + +
203B MET* 3.9 29.2 - - + +
204B ALA* 3.8 35.9 - - + +
207B TYR* 3.5 27.5 - - + -
216B LEU* 4.1 9.0 - - + -
218B SER* 5.8 0.2 - - - +
241B ILE* 3.0 40.4 + - + +
242B ALA 3.4 0.2 + - - -
244B THR* 1.3 83.8 - - + +
246B GLY* 1.3 58.1 + - - +
249B ALA* 3.5 24.5 - - + -
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Residues in contact with GLY 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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207B TYR* 3.4 4.7 - - - -
242B ALA 3.2 6.8 + - - +
243B GLN 3.9 5.3 + - - -
244B THR 3.5 2.0 - - - -
245B LEU* 1.3 80.2 - - - +
247B PRO* 1.3 69.6 - - - +
248B LYS 3.2 2.9 - - - -
249B ALA 3.0 15.1 + - - -
276B LYS* 3.0 20.3 + - - -
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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