Contacts of the helix formed by residues 231 - 250 (chain B) in PDB entry 3MYV
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 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194B ILE* 3.8 3.5 - - - +
226B TYR* 2.9 26.6 + - + +
229B HIS* 2.6 41.9 + - - +
230B ASP* 1.3 73.5 - - - +
232B ASN* 1.3 59.6 + - - +
233B ARG 3.4 2.2 - - - -
234B LYS* 3.3 35.5 + - + +
235B ALA* 2.9 27.5 + - - +
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Residues in contact with ASN 232 (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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227B LEU* 3.6 22.4 + - - +
230B ASP* 3.0 37.0 + - - +
231B ASP* 1.3 73.9 - - - +
233B ARG* 1.3 57.3 + - - +
235B ALA* 4.2 2.5 - - - -
236B PHE 2.9 25.1 + - - -
370B ALA* 3.4 14.1 - - + +
373B LYS* 3.4 37.4 - - + +
374B LEU* 3.5 23.2 - - + +
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Residues in contact with ARG 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B ASP 3.4 0.6 - - - -
232B ASN* 1.3 77.5 - - - +
234B LYS* 1.3 61.7 + - + +
236B PHE* 3.9 15.8 - - - +
237B ASP* 2.9 71.3 + - - +
374B LEU* 3.7 36.6 + - + +
375B GLY 5.1 1.4 + - - -
378B ALA* 3.9 21.0 - - - +
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Residues in contact with LYS 234 (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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194B ILE* 5.8 2.2 - - - +
198B GLU* 4.7 8.0 + - - -
226B TYR* 3.7 41.1 - - + +
231B ASP* 3.3 29.1 + - + +
233B ARG* 1.3 78.8 - - + +
235B ALA* 1.3 63.5 + - - +
237B ASP* 4.0 4.5 - - - +
238B LEU* 3.1 26.3 + - - +
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Residues in contact with ALA 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ALA* 3.7 21.0 - - - +
226B TYR* 3.8 14.1 - - + +
227B LEU* 3.8 16.8 - - + +
231B ASP 2.9 18.0 + - - +
232B ASN* 3.7 5.2 - - - +
234B LYS* 1.3 77.1 - - - +
236B PHE* 1.3 58.5 + - - +
238B LEU* 4.0 0.9 - - - +
239B ALA* 3.0 32.1 + - - +
366B ILE* 4.2 6.6 - - + +
370B ALA* 4.2 10.1 - - + -
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Residues in contact with PHE 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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232B ASN 2.9 17.2 + - - +
233B ARG* 3.9 11.9 - - - +
235B ALA* 1.3 74.7 - - - +
237B ASP* 1.3 76.4 + - - +
239B ALA* 4.0 3.1 - - - +
240B ASP* 2.9 44.8 + - + +
367B ALA* 3.5 32.8 - - + +
370B ALA* 3.7 7.7 - - + +
371B GLY 4.2 6.1 - - - -
374B LEU* 3.7 11.7 - - + -
378B ALA* 3.5 26.9 - - + -
381B GLN* 3.5 49.1 - - + -
382B GLY 4.0 3.4 - - - -
385B TYR* 4.7 2.0 - + - -
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Residues in contact with ASP 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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233B ARG* 2.9 58.5 + - - +
234B LYS* 4.1 4.3 - - - +
236B PHE* 1.3 83.4 - - - +
238B LEU* 1.3 58.9 + - - +
240B ASP* 3.7 4.3 - - - +
241B GLN* 3.0 29.5 + - - +
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Residues in contact with LEU 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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219B ARG* 3.4 62.6 - - + +
222B LEU* 3.8 26.5 - - + -
223B ALA* 3.6 16.8 - - + +
226B TYR* 3.8 8.5 - - + -
234B LYS 3.1 18.1 + - - +
235B ALA 4.1 2.0 - - - +
237B ASP* 1.3 74.4 - - - +
239B ALA* 1.3 59.9 + - - +
241B GLN* 3.2 5.0 + - + -
242B LEU* 2.8 31.7 + - + +
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Residues in contact with ALA 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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223B ALA* 4.3 6.4 - - + +
235B ALA 3.0 19.3 + - - +
236B PHE 4.0 0.7 - - - +
238B LEU* 1.3 76.3 - - - +
240B ASP* 1.3 64.0 + - - +
242B LEU* 3.2 3.0 + - - +
243B ILE* 2.9 31.1 + - - +
363B VAL* 3.7 34.5 - - + +
366B ILE* 4.1 7.6 - - + -
367B ALA* 3.9 17.3 - - + +
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Residues in contact with ASP 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B PHE* 2.9 36.8 + - + +
237B ASP* 3.7 5.4 - - - +
239B ALA* 1.3 73.5 - - - +
241B GLN* 1.3 64.0 + - - +
243B ILE* 3.5 0.5 + - - +
244B LYS* 2.6 55.5 + - - +
367B ALA* 4.6 1.4 - - - +
381B GLN* 3.8 17.2 + - - -
385B TYR* 2.6 43.4 + - + -
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Residues in contact with GLN 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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219B ARG* 3.7 16.6 - - - +
237B ASP 3.0 16.0 + - - +
238B LEU* 3.2 5.8 + - + +
240B ASP* 1.3 83.3 + - - +
242B LEU* 1.3 57.5 + - - +
244B LYS* 3.2 21.0 + - - +
245B ASP* 2.8 57.8 + - - +
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Residues in contact with LEU 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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216B TYR* 3.6 37.5 - - + +
219B ARG* 3.8 30.7 - - + +
220B ALA* 3.4 44.2 - - + +
223B ALA* 5.4 1.1 - - + -
238B LEU* 2.8 18.2 + - + +
239B ALA* 3.6 5.8 - - - +
241B GLN* 1.3 76.9 - - - +
243B ILE* 1.3 58.0 + - - +
245B ASP* 3.1 2.0 + - - +
246B ALA* 2.9 28.8 + - - +
275B PHE* 4.5 10.5 - - + -
363B VAL* 3.9 17.3 - - + -
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Residues in contact with ILE 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B ALA 2.9 20.8 + - - +
240B ASP 3.8 4.0 - - - +
242B LEU* 1.3 73.9 - - - +
244B LYS* 1.3 65.5 + - + +
246B ALA* 3.4 8.2 + - - +
247B ASP* 3.0 30.3 + - - +
360B LEU* 4.5 4.3 - - + -
363B VAL* 3.7 16.2 - - + +
364B TYR* 3.5 70.4 - - + +
367B ALA* 4.5 0.7 - - + -
385B TYR* 3.7 36.3 - - + +
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Residues in contact with LYS 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B ASP* 2.6 52.2 + - - +
241B GLN* 3.2 24.0 + - - +
243B ILE* 1.3 76.4 - - + +
245B ASP* 1.3 57.9 + - - +
247B ASP* 3.3 8.5 + - - +
248B THR* 2.9 35.6 + - - +
381B GLN* 4.2 9.8 - - - +
385B TYR* 4.1 8.5 - - - +
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Residues in contact with ASP 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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206B GLU* 5.4 2.6 - - - +
216B TYR* 4.1 12.1 - - + +
219B ARG* 2.8 41.2 + - - +
241B GLN* 2.8 40.8 + - - +
242B LEU 3.1 4.7 + - - +
244B LYS* 1.3 71.5 - - - +
246B ALA* 1.3 59.5 + - - +
248B THR* 4.0 6.1 + - - +
249B SER* 2.8 35.8 + - - -
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Residues in contact with ALA 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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216B TYR* 4.1 9.2 - - + -
242B LEU 2.9 13.1 + - - +
243B ILE 3.6 8.5 - - - +
245B ASP* 1.3 75.7 - - - +
247B ASP* 1.3 60.4 + - - +
249B SER* 3.8 4.9 - - - -
250B GLY* 3.0 27.4 + - - -
251B SER 3.4 4.2 + - - -
252B TYR* 3.4 38.4 - - + +
275B PHE* 5.2 1.1 - - + -
360B LEU* 4.2 17.5 - - + -
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Residues in contact with ASP 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ILE* 3.0 30.2 + - - +
244B LYS* 3.5 10.9 - - - +
246B ALA* 1.3 79.4 - - - +
248B THR* 1.3 65.4 + - - +
250B GLY* 3.3 10.3 + - - -
252B TYR 4.7 4.7 - - - +
253B ALA* 5.6 2.1 - - - +
360B LEU* 5.6 2.9 - - - +
364B TYR* 4.3 10.5 + - - -
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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 LYS* 2.9 23.6 + - - +
245B ASP* 4.0 7.4 + - - -
247B ASP* 1.3 73.8 - - - +
249B SER* 1.3 63.2 + - - +
250B GLY 3.5 0.2 + - - -
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Residues in contact with SER 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B TYR* 3.1 21.6 + - - -
245B ASP 2.8 23.1 + - - -
246B ALA* 3.4 2.6 + - - -
248B THR* 1.3 79.6 - - - +
250B GLY* 1.3 59.9 + - - +
251B SER* 3.1 27.3 + - - -
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Residues in contact with GLY 250 (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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208B LYS* 5.2 0.5 + - - -
246B ALA 3.0 11.3 + - - -
247B ASP* 3.3 7.4 + - - -
248B THR 3.3 3.8 + - - -
249B SER* 1.3 76.7 - - - +
251B SER* 1.3 61.5 + - - +
252B TYR 3.4 6.8 + - - +
253B ALA* 5.8 1.6 - - - +
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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
------------------------------------------------------------
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