Contacts of the helix formed by residues 229 - 246 (chain D) in PDB entry 1WLZ
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 ALA 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230D THR* 1.3 69.4 + - - +
231D ALA* 3.3 6.3 - - - +
232D ASP* 3.4 22.7 + - - +
233D ARG* 3.2 25.7 + - - +
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Residues in contact with THR 230 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ALA* 1.3 75.0 - - - +
231D ALA* 1.3 68.2 + - - +
233D ARG* 3.1 10.2 + - + +
234D ASP* 3.0 23.2 + - + +
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Residues in contact with ALA 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ALA 4.3 3.5 - - - +
230D THR* 1.3 78.1 - - - +
232D ASP* 1.3 63.8 + - - +
234D ASP* 3.2 8.5 + - - +
235D ILE* 3.0 30.2 + - + +
285D GLN* 5.4 9.6 - - + +
288D ARG* 4.7 14.4 - - - +
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Residues in contact with ASP 232 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ALA* 3.4 22.2 + - - +
230D THR 3.2 0.6 - - - -
231D ALA* 1.3 79.5 - - - +
233D ARG* 1.3 61.8 + - + +
235D ILE* 3.5 8.0 + - - +
236D LEU* 3.1 29.6 + - + +
285D GLN* 5.1 1.7 - - - +
288D ARG* 2.7 55.2 + - - +
292D GLU* 3.9 19.4 - - - +
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Residues in contact with ARG 233 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229D ALA 3.2 14.6 + - - +
230D THR* 3.1 12.3 + - - +
232D ASP* 1.3 73.9 - - + +
234D ASP* 1.3 61.2 + - - +
236D LEU* 3.4 14.1 + - + +
237D ALA* 2.9 29.8 + - - +
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Residues in contact with ASP 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D THR* 3.0 14.6 + - + +
231D ALA* 3.2 12.8 + - - +
233D ARG* 1.3 78.3 - - - +
235D ILE* 1.3 65.3 - - + +
237D ALA* 3.3 7.2 + - - +
238D ARG* 3.0 22.7 + - - +
279D GLN* 5.7 0.2 - - - -
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Residues in contact with ILE 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ALA* 3.0 17.7 + - + +
232D ASP* 3.7 9.4 - - - +
233D ARG 3.3 0.2 - - - -
234D ASP* 1.3 80.4 - - + +
236D LEU* 1.3 57.0 + - - +
238D ARG* 3.1 6.7 + - - +
239D LEU* 2.8 27.2 + - - +
278D VAL* 4.1 7.7 - - + +
279D GLN* 2.8 41.3 - - - +
281D LEU* 3.6 23.6 - - + -
285D GLN* 4.9 16.4 - - + +
289D LEU* 4.1 31.6 - - + -
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Residues in contact with LEU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D ASP* 3.1 16.4 + - + +
233D ARG* 3.7 14.6 - - + +
235D ILE* 1.3 78.8 - - - +
237D ALA* 1.3 57.8 + - - +
239D LEU* 3.2 5.5 + - - +
240D HIS* 2.9 41.6 + - + +
289D LEU* 3.9 13.0 - - + -
292D GLU* 3.5 41.5 - - + +
293D MET* 4.0 3.4 - - + -
310D PHE* 3.6 31.2 - - + -
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233D ARG 2.9 17.7 + - - +
234D ASP* 3.5 7.4 - - - +
236D LEU* 1.3 72.5 - - - +
238D ARG* 1.3 67.4 + - - +
240D HIS* 3.2 12.0 + - - +
241D LYS* 3.0 22.7 + - - +
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Residues in contact with ARG 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ASP 3.0 13.4 + - - +
235D ILE* 3.4 10.8 - - - +
237D ALA* 1.3 76.6 - - - +
239D LEU* 1.3 58.3 + - - +
241D LYS* 3.3 7.8 + - - +
242D ALA* 2.9 30.0 + - - +
278D VAL* 3.6 23.2 - - + +
279D GLN* 4.9 6.1 - - - +
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235D ILE* 2.8 13.9 + - + +
236D LEU* 3.4 9.4 - - + +
237D ALA 3.2 0.2 - - - -
238D ARG* 1.3 78.2 - - - +
240D HIS* 1.3 56.4 + - - +
242D ALA* 3.2 3.0 + - + +
243D VAL* 2.9 37.5 + - + +
250D ILE* 6.1 1.1 - - + -
270D PHE* 4.4 10.8 - - + -
274D CYS* 4.6 3.4 - - - -
278D VAL* 3.5 28.2 - - + +
289D LEU* 3.9 14.8 - - + -
293D MET* 3.9 16.6 - - + -
306D PHE* 3.7 31.6 - - + -
310D PHE* 3.5 28.9 - - + -
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Residues in contact with HIS 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236D LEU* 2.9 33.3 + - + +
237D ALA* 3.4 12.1 - - - +
239D LEU* 1.3 76.8 - - - +
241D LYS* 1.3 61.6 + - - +
243D VAL 3.4 0.3 + - - -
244D THR* 3.0 33.0 + - + +
309D ARG 3.7 22.4 - - - -
310D PHE* 3.6 40.8 + + - +
311D SER 5.7 0.4 + - - -
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Residues in contact with LYS 241 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237D ALA 3.0 13.0 + - - +
238D ARG* 3.3 10.5 + - - +
240D HIS* 1.3 77.4 - - - +
242D ALA* 1.3 57.2 + - - +
244D THR* 3.0 8.0 + - - -
245D SER* 2.8 36.0 + - - +
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Residues in contact with ALA 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238D ARG 2.9 16.5 + - - +
239D LEU* 3.6 5.2 - - + +
241D LYS* 1.3 77.5 - - - +
243D VAL* 1.3 58.0 + - + +
245D SER* 3.9 4.9 - - - -
246D HIS* 2.8 40.5 + - + +
250D ILE* 3.6 4.5 - - + +
277D ARG* 3.3 41.5 - - + +
278D VAL* 4.3 5.8 - - + -
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Residues in contact with VAL 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D LEU* 2.9 21.9 + - + +
242D ALA* 1.3 76.6 - - - +
244D THR* 1.3 58.9 + - - +
247D TYR* 3.1 46.2 + - + +
250D ILE* 3.8 15.7 - - + -
306D PHE* 3.6 33.0 - - + -
307D LEU* 4.3 13.0 - - + +
310D PHE* 3.3 36.8 - - + +
311D SER* 3.9 3.8 - - - -
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Residues in contact with THR 244 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240D HIS* 3.0 18.2 + - + +
241D LYS* 3.0 17.5 + - - -
243D VAL* 1.3 78.1 - - - +
245D SER* 1.3 58.1 + - - +
246D HIS 3.9 0.2 + - - -
247D TYR* 4.4 6.5 + - - +
310D PHE 3.7 13.7 - - - +
311D SER* 4.0 19.5 - - - +
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Residues in contact with SER 245 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241D LYS* 2.8 24.7 + - - -
242D ALA* 3.9 0.5 - - - -
244D THR* 1.3 77.9 + - - +
246D HIS* 1.3 92.1 + - - +
247D TYR 3.7 0.9 - - - -
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Residues in contact with HIS 246 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242D ALA* 2.8 24.8 + - + +
245D SER* 1.3 106.6 + - - +
247D TYR* 1.3 66.0 + - - +
248D HIS* 3.3 2.9 - - - -
249D ALA* 3.2 15.6 + - + +
250D ILE* 3.0 22.6 + - + +
277D ARG* 4.3 31.4 + - - +
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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