Contacts of the helix formed by residues 227 - 239 (chain B) in PDB entry 2W93
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 VAL 227 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B CYS* 2.9 30.3 + - - +
225B HIS 3.5 9.4 - - - +
226B ASP* 1.3 76.9 - - - +
228B LYS* 1.3 54.4 + - - +
229B ALA 3.3 1.8 - - - -
230B GLU* 3.2 14.5 + - - +
231B THR* 2.7 39.7 + - + +
285B VAL* 3.8 18.8 - - + -
326B MET* 4.0 17.7 - - + -
327B LYS* 3.9 28.5 - - + -
330B LEU* 3.9 21.1 - - + -
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Residues in contact with LYS 228 (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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222B CYS* 3.8 17.9 - - - +
223B SER* 4.1 19.6 + - - +
226B ASP* 3.0 22.0 + - - +
227B VAL* 1.3 76.9 - - - +
229B ALA* 1.3 58.3 + - - +
231B THR* 3.3 1.4 + - - -
232B LYS* 2.9 31.2 + - - +
250B GLY 4.2 11.0 + - - -
251B SER* 3.7 38.8 - - - +
404B THR 5.1 1.6 + - - -
405B TYR* 3.5 34.4 - - + -
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Residues in contact with ALA 229 (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 ASP* 4.3 1.8 + - - -
227B VAL 3.3 0.2 - - - -
228B LYS* 1.3 79.2 - - - +
230B GLU* 1.3 69.6 + - - +
232B LYS* 3.4 5.8 + - - +
233B LYS* 3.0 29.8 + - + +
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Residues in contact with GLU 230 (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 VAL* 3.2 30.0 - - + +
229B ALA* 1.3 81.1 + - - +
231B THR* 1.3 58.9 + - - +
233B LYS* 3.3 3.2 + - - +
234B LEU* 2.8 29.3 + - - +
327B LYS* 2.5 37.6 + - - +
330B LEU* 4.0 26.6 - - + +
331B GLN* 3.2 28.4 + - + -
334B LEU* 3.9 21.7 - - + +
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Residues in contact with THR 231 (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 ILE* 4.5 11.8 - - - +
218B ALA* 4.7 1.4 - - - +
222B CYS* 3.5 24.1 - - - -
227B VAL* 2.7 26.5 + - + +
228B LYS 3.7 3.4 - - - -
230B GLU* 1.3 78.5 - - - +
232B LYS* 1.3 62.3 + - - +
234B LEU* 3.1 9.5 + - - +
235B ILE* 3.0 26.9 + - - +
252B ILE* 4.0 17.3 - - - +
285B VAL* 3.7 25.8 - - + +
330B LEU* 4.8 5.2 - - + -
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Residues in contact with LYS 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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228B LYS 2.9 17.1 + - - +
229B ALA* 3.8 6.7 - - - +
231B THR* 1.3 76.1 - - - +
233B LYS* 1.3 65.1 + - + +
235B ILE* 3.2 13.9 + - + +
236B ASP* 2.8 51.6 + - - +
252B ILE* 5.5 4.1 - - + +
253B ASP* 4.1 21.8 + - + +
256B HIS* 4.7 12.4 - - + -
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Residues in contact with LYS 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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229B ALA* 3.0 21.7 + - + +
230B GLU 3.6 4.7 - - - +
232B LYS* 1.3 77.9 - - + +
234B LEU* 1.3 54.3 + - - +
236B ASP* 3.1 9.9 + - + +
237B LEU* 2.8 67.5 + - - +
334B LEU* 3.9 23.1 - - + -
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Residues in contact with LEU 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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216B ILE* 3.9 32.1 - - + -
230B GLU 2.8 14.4 + - - +
231B THR* 3.1 13.0 + - - +
233B LYS* 1.3 75.7 - - - +
235B ILE* 1.3 58.7 + - - +
237B LEU* 4.1 1.9 - - - +
238B THR* 2.9 35.9 + - - +
283B LEU* 4.3 17.5 - - + -
285B VAL* 4.7 10.3 - - + -
309B PHE* 5.3 3.8 - - + -
330B LEU* 4.3 22.4 - - + -
333B LEU* 5.5 6.7 - - + -
334B LEU* 3.7 15.4 - - + +
337B ILE* 4.2 29.6 - - + -
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Residues in contact with ILE 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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216B ILE* 3.8 21.8 - - + -
231B THR* 3.0 16.0 + - - +
232B LYS* 3.2 11.9 + - + +
234B LEU* 1.3 75.5 - - - +
236B ASP* 1.3 57.2 + - - +
238B THR* 4.0 0.2 - - - -
239B GLN* 2.8 31.4 + - - -
240B PHE 4.1 13.5 - - - +
242B ALA* 3.5 31.0 - - + -
252B ILE* 3.9 29.2 - - + -
253B ASP 5.9 0.4 - - - +
256B HIS* 3.8 32.1 - - + +
258B ARG* 4.3 2.9 - - + -
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Residues in contact with ASP 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 LYS* 2.8 46.0 + - - +
233B LYS* 3.7 12.6 - - + +
235B ILE* 1.3 78.1 - - - +
237B LEU* 1.3 63.5 + - + +
239B GLN* 2.9 25.8 + - - +
256B HIS* 2.7 30.7 + - - -
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Residues in contact with LEU 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 LYS* 2.8 51.7 + - - +
234B LEU 4.3 0.9 - - - +
236B ASP* 1.3 75.0 - - + +
238B THR* 1.3 59.7 + - - +
239B GLN* 5.3 1.2 - - - +
334B LEU* 3.5 35.2 - - + +
337B ILE* 3.9 21.5 - - + -
338B ALA* 3.8 33.5 - - + +
341B ALA* 4.9 1.4 - - - +
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Residues in contact with THR 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216B ILE* 3.8 9.4 - - + -
234B LEU* 2.9 27.1 + - - +
235B ILE 3.6 2.7 - - - +
237B LEU* 1.3 81.5 - - - +
239B GLN* 1.3 72.2 + - - +
240B PHE* 3.1 62.6 + - + +
337B ILE* 3.8 21.3 - - - +
341B ALA* 4.3 9.8 - - - +
344B TYR* 3.8 5.9 - - - +
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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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235B ILE 2.8 15.2 + - - -
236B ASP* 2.9 34.3 + - - +
237B LEU 5.3 0.7 - - - -
238B THR* 1.3 79.5 - - - +
240B PHE* 1.3 61.4 + - - +
256B HIS* 4.8 3.1 - - - -
258B ARG* 2.8 55.7 + - - +
344B TYR* 3.4 12.6 - - + -
346B PRO* 4.8 12.2 - - + +
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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