Contacts of the helix formed by residues 226 - 239 (chain B) in PDB entry 5TQB
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 ARG 226 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B GLU* 3.6 15.0 + - - -
221B ARG* 2.9 42.4 + - - +
222B ILE* 4.4 0.6 + - - -
224B GLN* 3.1 37.7 + - + +
225B GLU* 1.3 77.6 - - - +
227B THR* 1.3 63.4 + - - +
228B GLU 3.5 2.5 - - - -
229B GLU* 3.0 44.0 + - + +
230B ALA* 3.1 20.8 + - - +
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Residues in contact with THR 227 (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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77A ARG* 4.1 31.0 + - - +
78A VAL* 5.9 2.6 - - - +
222B ILE* 5.5 3.8 + - - +
225B GLU* 3.6 9.9 + - - -
226B ARG* 1.3 70.6 - - - +
228B GLU* 1.3 60.8 + - - +
230B ALA* 3.1 8.3 + - - +
231B ARG* 2.9 63.7 + - - +
267B VAL* 4.2 12.8 - - + +
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Residues in contact with GLU 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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226B ARG 3.5 0.2 - - - -
227B THR* 1.3 78.9 - - - +
229B GLU* 1.3 59.9 - - + +
231B ARG* 3.2 28.5 + - - +
232B GLU* 3.0 26.0 + - + +
235B ARG* 3.5 25.5 + - - -
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Residues in contact with GLU 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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217B VAL* 5.6 0.2 - - - +
221B ARG* 3.4 26.0 + - - +
226B ARG* 3.0 50.4 + - + +
228B GLU* 1.3 77.5 - - + +
230B ALA* 1.3 60.1 + - - +
232B GLU* 3.5 19.8 - - - +
233B ALA* 3.0 29.1 + - - +
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Residues in contact with ALA 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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218B ALA* 3.6 18.0 - - + +
221B ARG* 3.9 6.7 - - + +
222B ILE* 3.7 29.4 - - + -
226B ARG 3.1 14.6 + - - +
227B THR* 3.1 12.2 + - - +
229B GLU* 1.3 75.2 - - - +
231B ARG* 1.3 63.9 + - - +
233B ALA 3.3 1.0 + - - -
234B LEU* 3.0 30.5 + - + +
267B VAL* 4.0 7.9 - - + -
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Residues in contact with ARG 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 4.5 3.8 - - - +
227B THR* 2.9 44.9 + - - +
228B GLU* 3.2 34.8 + - - +
230B ALA* 1.3 75.6 - - - +
232B GLU* 1.3 57.1 + - - +
234B LEU* 3.2 1.9 + - - +
235B ARG* 2.9 54.1 + - - +
267B VAL* 2.8 25.0 + - + +
268B ASP* 3.5 26.4 + - - +
269B MSE 3.6 25.7 - - + +
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Residues in contact with GLU 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 GLU* 3.0 16.7 + - + +
229B GLU* 3.5 22.1 - - - +
231B ARG* 1.3 77.0 - - - +
233B ALA* 1.3 62.9 + - - +
235B ARG* 3.6 21.5 + - - +
236B ARG* 3.2 21.1 + - - +
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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
----------------------------------------------------------
214B TRP* 3.5 37.2 - - + +
217B VAL* 4.0 14.6 - - + -
218B ALA* 3.9 12.1 - - + +
229B GLU 3.0 17.7 + - - +
230B ALA 3.6 4.3 - - - +
232B GLU* 1.3 77.2 - - - +
234B LEU* 1.3 58.4 + - - +
236B ARG* 3.1 8.8 + - - +
237B SER* 3.0 22.2 + - - -
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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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214B TRP 5.1 0.2 - - - -
215B GLN* 4.4 5.4 - - - -
218B ALA* 3.6 19.1 - - + -
222B ILE* 5.3 0.9 - - + -
230B ALA 3.0 17.7 + - - +
233B ALA* 1.3 72.5 - - - +
235B ARG* 1.3 66.0 + - - +
237B SER* 2.8 22.5 + - - +
238B LEU* 3.0 17.0 + - - +
260B LEU* 3.6 29.2 - - + -
263B LEU* 3.8 32.8 - - + +
264B LEU* 4.1 7.4 - - + -
267B VAL* 3.6 16.4 - - + -
269B MSE 3.3 31.6 - - + -
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Residues in contact with ARG 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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228B GLU* 3.5 20.2 + - - -
231B ARG* 2.9 42.4 + - - +
232B GLU* 3.7 22.7 - - - +
234B LEU* 1.3 76.2 - - - +
236B ARG* 1.3 61.2 + - - +
238B LEU* 3.9 11.7 - - + +
239B GLY* 3.3 17.7 + - - -
269B MSE 4.4 15.8 - - - +
272B GLU* 5.0 9.2 - - + +
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Residues in contact with ARG 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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208B PRO* 3.8 21.0 + - - +
214B TRP* 3.3 57.4 - - + +
232B GLU 3.2 13.2 + - - +
233B ALA* 3.1 12.0 + - - +
234B LEU 3.1 0.4 - - - -
235B ARG* 1.3 77.1 - - - +
237B SER* 1.3 65.1 + - - +
239B GLY* 3.3 10.2 + - - -
240B LEU* 3.4 18.8 + - + +
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Residues in contact with SER 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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211B PRO* 3.3 36.5 - - - +
214B TRP* 3.9 7.6 - - - +
215B GLN* 4.1 6.9 + - - -
233B ALA 3.0 11.7 + - - -
234B LEU* 2.8 31.0 + - - +
236B ARG* 1.3 75.8 - - - +
238B LEU* 1.3 64.9 + - - +
240B LEU* 3.3 15.0 + - - +
241B TRP* 3.0 20.9 + - - -
260B LEU* 4.4 6.9 - - - +
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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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234B LEU* 3.0 18.5 + - + +
235B ARG* 3.9 10.1 - - + +
237B SER* 1.3 79.9 + - - +
239B GLY* 1.3 56.6 + - - +
240B LEU 3.0 10.3 + - - -
241B TRP* 3.1 22.1 + - + +
242B THR* 3.0 53.7 + - + +
260B LEU* 3.9 18.2 - - + -
264B LEU* 4.2 14.6 - - + -
269B MSE 5.5 1.6 - - - -
272B GLU* 4.1 30.5 - - + -
276B VAL* 4.2 10.8 - - + -
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Residues in contact with GLY 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 ARG 3.3 12.8 + - - -
236B ARG* 3.3 6.1 + - - -
238B LEU* 1.3 77.2 - - - +
240B LEU* 1.3 61.2 + - - +
241B TRP 3.5 0.4 - - - -
242B THR* 4.5 3.8 - - - -
243B HIS* 2.8 24.2 + - - -
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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