Contacts of the helix formed by residues 231 - 239 (chain B) in PDB entry 3H8E
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 MET 231 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B ILE* 3.1 37.4 + - + +
227B LYS* 4.0 1.7 + - - -
229B LEU* 3.9 14.6 - - + -
230B GLY* 1.4 73.1 - - - +
232B GLY* 1.3 56.4 + - - +
234B PHE* 4.0 5.6 - - + -
235B TYR* 2.9 29.8 + - - +
247B LEU* 3.7 20.4 - - + -
338B MET* 3.6 32.3 - - - -
358B ASP* 3.0 41.5 - - + +
359B THR* 5.2 0.7 - - - -
362B TYR* 3.6 32.8 - - + -
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Residues in contact with GLY 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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230B GLY 2.9 11.0 + - - -
231B MET* 1.3 72.3 - - - +
233B ALA* 1.3 58.9 + - - +
235B TYR* 4.0 6.8 - - - +
236B ALA* 3.1 27.2 + - - +
335B VAL* 3.8 15.1 - - - +
336B THR 3.1 19.0 + - - -
337B THR* 4.2 0.6 - - - +
358B ASP* 3.3 1.0 + - - -
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Residues in contact with ALA 233 (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 GLY* 1.3 75.1 - - - +
234B PHE* 1.4 66.5 + - - +
236B ALA* 3.2 12.4 + - - +
237B VAL* 3.2 18.7 + - - +
335B VAL* 3.9 13.2 - - + +
336B THR 4.3 1.6 + - - -
337B THR* 4.1 11.8 - - + +
343B VAL* 5.5 0.2 - - + -
345B ILE* 5.3 0.2 - - - -
354B LEU* 3.5 33.9 - - + +
357B CYS* 3.8 15.7 - - - -
358B ASP* 2.9 9.8 + - - +
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Residues in contact with PHE 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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226B ILE* 2.0 70.4 - - + -
231B MET* 3.8 11.4 - - + +
233B ALA* 1.4 74.7 - - - +
235B TYR* 1.3 62.8 + - - +
237B VAL* 3.1 14.4 + - - +
238B GLY* 3.3 8.8 + - - -
245B PRO* 3.8 8.8 - - + +
246B ARG 3.6 19.5 - - - -
247B LEU* 3.9 6.7 - - + -
318B ALA* 4.0 7.6 - - + -
319B CYS 3.8 26.7 - - - -
320B ALA* 5.2 1.7 - - + +
354B LEU 3.6 1.4 + - - -
355B VAL* 3.3 46.1 - - + +
358B ASP* 2.9 22.2 + - + +
359B THR* 4.6 4.5 - - - -
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Residues in contact with TYR 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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223B GLU* 3.3 44.1 + - + +
224B LYS* 6.0 0.2 - - - -
226B ILE* 4.4 8.1 - - + -
227B LYS* 3.8 48.4 + - + +
231B MET 2.9 19.3 + - - +
232B GLY* 4.0 6.5 - - - +
234B PHE* 1.3 77.7 - - - +
236B ALA* 1.4 67.7 + - - +
238B GLY* 3.2 2.7 + - - +
239B GLN* 3.1 50.9 + - + +
245B PRO* 5.5 3.1 - - + -
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Residues in contact with ALA 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 GLY 3.1 20.9 + - - +
233B ALA 3.5 5.6 - - - +
234B PHE 3.2 0.6 - - - -
235B TYR* 1.4 82.7 - - - +
237B VAL* 1.3 64.3 + - + +
239B GLN* 3.5 13.0 - - - +
240B GLY 4.8 0.2 + - - -
329B THR* 2.7 36.1 + - + +
335B VAL* 4.1 8.3 - - + -
345B ILE* 3.7 25.6 - - + -
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Residues in contact with VAL 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 ALA 3.2 13.4 + - - +
234B PHE 3.1 7.2 + - - +
236B ALA* 1.3 77.6 - - - +
238B GLY* 1.3 62.8 + - - +
239B GLN 3.4 0.2 + - - -
240B GLY* 4.3 4.0 + - - -
269B ILE* 4.0 13.5 - - + -
320B ALA* 4.1 5.2 - - + -
321B GLU 4.0 7.3 - - - +
322B ASN* 4.0 21.0 - - + +
323B MET 5.1 0.7 + - - -
329B THR* 5.6 0.7 - - - -
351B GLU* 3.5 44.4 - - + +
354B LEU* 3.6 20.6 - - + -
355B VAL* 3.8 18.8 - - + -
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Residues in contact with GLY 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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223B GLU* 4.9 2.1 - - - +
234B PHE 3.3 5.7 + - - -
235B TYR 3.2 5.3 + - - -
237B VAL* 1.3 80.6 - - - +
239B GLN* 1.3 64.4 + - - +
240B GLY 3.2 1.8 + - - -
241B SER* 3.3 20.8 + - - +
243B GLN 4.3 5.2 - - - +
244B PRO* 5.1 1.6 - - - +
245B PRO* 4.5 16.7 - - - +
320B ALA* 4.1 18.6 - - - +
321B GLU 4.2 5.4 - - - -
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Residues in contact with GLN 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 GLU* 4.2 10.5 - - - +
235B TYR* 3.1 44.7 + - + +
236B ALA* 3.5 17.7 - - - +
237B VAL 3.3 0.8 - - - -
238B GLY* 1.3 78.8 - - - +
240B GLY* 1.3 62.4 + - - +
241B SER 3.2 6.5 + - - +
325B SER* 5.0 0.2 + - - -
327B GLY* 3.2 25.5 + - - +
328B ALA 3.9 2.2 + - - -
329B THR* 3.4 23.3 + - - +
330B ARG* 4.8 10.7 - - - +
333B ASP* 5.0 0.6 + - - -
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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
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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