Contacts of the helix formed by residues 226 - 242 (chain A) in PDB entry 2WTB
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 GLU 226 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A PRO* 4.1 9.3 - - + +
223A PRO* 2.9 34.8 + - + +
225A GLY* 1.3 73.9 - - - +
227A ALA* 1.3 62.3 + - - +
229A GLU* 2.9 20.6 + - - +
230A ILE* 2.9 42.7 + - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.9 21.3 - - + +
222A PRO* 4.1 16.7 - - + +
223A PRO 2.9 15.3 + - - +
224A LEU 3.7 5.6 - - - +
226A GLU* 1.3 76.8 - - - +
228A ARG* 1.3 57.1 + - + +
230A ILE* 3.2 3.6 + - - +
231A LEU* 2.8 36.3 + - + +
259A ILE* 4.2 25.6 - - + -
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Residues in contact with ARG 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A LEU* 3.1 35.3 + - + +
225A GLY* 3.3 12.3 + - - +
226A GLU 3.1 0.6 - - - -
227A ALA* 1.3 75.8 - - + +
229A GLU* 1.3 61.5 + - - +
231A LEU* 3.9 7.3 - - + +
232A THR* 2.8 37.0 + - - +
256A GLU* 3.7 23.9 + - + +
260A VAL* 3.4 40.7 - - + +
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Residues in contact with GLU 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A GLY 3.3 6.7 + - - +
226A GLU* 2.9 26.9 + - + +
228A ARG* 1.3 80.5 - - - +
230A ILE* 1.3 58.3 + - + +
232A THR* 4.0 5.0 - - - +
233A PHE* 3.1 28.2 + - - +
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Residues in contact with ILE 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.8 14.1 - - + -
161A THR* 4.3 21.3 - - + +
164A LEU* 3.6 24.4 - - + +
222A PRO* 4.0 25.6 - - + -
226A GLU* 2.9 31.6 + - + +
227A ALA 3.2 6.3 + - - +
229A GLU* 1.3 77.0 - - + +
231A LEU* 1.3 64.6 + - - +
233A PHE* 3.6 6.8 + - - +
234A ALA* 3.1 22.5 + - - +
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Residues in contact with LEU 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 4.3 7.9 - - + -
164A LEU* 4.6 7.4 - - + -
227A ALA* 2.8 25.3 + - + +
228A ARG* 3.9 6.3 - - + +
230A ILE* 1.3 74.8 - - - +
232A THR* 1.3 64.9 + - - +
234A ALA* 3.4 5.7 + - - +
235A LYS* 3.0 32.4 + - - +
252A LEU* 4.1 28.7 - - + +
255A ILE* 3.9 24.9 - - + -
256A GLU* 3.5 44.0 - - + +
259A ILE* 4.0 17.7 - - + -
260A VAL* 6.0 0.7 - - + -
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Residues in contact with THR 232 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ARG* 2.8 25.6 + - - +
229A GLU* 4.0 5.2 - - - +
231A LEU* 1.3 74.5 - - - +
233A PHE* 1.3 66.7 + - - +
235A LYS* 3.2 13.1 + - - +
236A ALA* 2.9 24.0 + - + +
256A GLU* 5.8 0.2 + - - -
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Residues in contact with PHE 233 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A GLU 3.1 17.7 + - - +
230A ILE* 3.7 7.4 - - - +
232A THR* 1.3 81.0 - - - +
234A ALA* 1.3 69.4 + - + +
236A ALA* 3.0 19.0 + - + +
237A GLN* 3.0 46.4 + - + +
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Residues in contact with ALA 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LEU* 4.1 19.5 - - + -
168A LEU* 4.5 11.4 - - + -
230A ILE 3.1 15.5 + - - +
231A LEU 3.6 4.5 - - - +
232A THR 3.3 0.2 - - - -
233A PHE* 1.3 85.4 - - + +
235A LYS* 1.3 64.6 + - - +
236A ALA 3.1 0.3 + - - -
237A GLN* 3.2 9.8 + - - +
238A THR* 2.9 28.3 + - - -
252A LEU* 4.1 15.7 - - + -
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A LEU* 3.0 22.9 + - - +
232A THR* 3.4 11.4 - - - +
234A ALA* 1.3 78.6 - - - +
236A ALA* 1.3 62.9 + - - +
238A THR 3.3 0.3 + - - -
239A LEU* 3.2 25.0 + - + +
249A LEU* 3.6 23.2 + - + +
252A LEU* 3.7 39.9 - - + +
253A ASP* 2.8 31.1 + - - +
256A GLU* 3.4 24.0 + - - -
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Residues in contact with ALA 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A THR* 2.9 16.5 + - + +
233A PHE* 3.0 14.6 + - + +
235A LYS* 1.3 77.9 - - - +
237A GLN* 1.3 61.4 + - - +
239A LEU* 3.2 18.6 + - - +
240A LYS* 3.3 8.8 + - - -
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Residues in contact with GLN 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 5.4 8.5 - - - +
233A PHE* 3.0 42.4 + - + +
234A ALA* 3.5 14.1 - - - +
236A ALA* 1.3 75.1 - - - +
238A THR* 1.3 63.7 + - - +
239A LEU 3.2 0.2 - - - -
240A LYS* 3.6 4.2 - - - +
241A ARG* 3.3 40.0 + - + +
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Residues in contact with THR 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A LEU* 4.0 20.1 - - + +
234A ALA 2.9 20.4 + - - -
235A LYS 3.7 4.9 - - - -
236A ALA 3.2 0.2 - - - -
237A GLN* 1.3 79.7 + - - +
239A LEU* 1.3 58.1 + - - +
240A LYS 3.3 0.4 - - - -
241A ARG* 5.2 1.6 - - - -
242A ALA* 3.2 35.6 + - + +
245A MET 5.6 0.7 - - - +
248A PRO* 3.6 33.2 - - + -
249A LEU* 3.8 17.0 - - + -
252A LEU* 4.4 3.0 - - + +
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Residues in contact with LEU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235A LYS* 3.2 16.7 + - + +
236A ALA* 3.2 11.2 + - - +
238A THR* 1.3 78.4 - - - +
240A LYS* 1.3 59.7 + - - +
242A ALA 4.5 3.1 - - - +
243A PRO* 3.5 38.6 - - + +
245A MET 5.5 0.9 - - - +
249A LEU* 3.4 34.8 - - + -
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Residues in contact with LYS 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236A ALA 3.3 10.0 + - - -
237A GLN* 3.5 5.8 + - - +
238A THR 3.3 0.6 - - - -
239A LEU* 1.3 80.7 - - - +
241A ARG* 1.3 71.9 + - - +
243A PRO* 4.1 6.6 - - - +
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Residues in contact with ARG 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A GLN* 3.3 24.9 + - + +
238A THR* 4.8 1.6 - - - +
240A LYS* 1.3 85.2 + - - +
242A ALA* 1.3 60.6 + - + +
243A PRO* 3.1 11.0 - - - +
244A ASN* 4.7 2.8 + - - -
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Residues in contact with ALA 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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238A THR* 3.2 28.0 + - + +
239A LEU* 4.5 1.6 - - - +
241A ARG* 1.3 81.6 - - + +
243A PRO* 1.3 60.8 - - - +
244A ASN* 3.0 22.0 + - - +
245A MET* 3.4 32.8 + - + +
248A PRO* 5.6 3.4 - - + -
249A LEU* 6.0 0.2 - - - +
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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