Contacts of the helix formed by residues 239 - 257 (chain B) in PDB entry 1T0H
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 TYR 239 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B LEU* 3.6 45.9 - - + +
237B LYS 3.3 7.7 - - - -
238B GLY* 1.3 82.0 - - - +
240B GLU* 1.3 65.2 + - - +
241B VAL 3.3 1.3 + - - -
242B THR* 3.4 5.0 + - - +
243B ASP* 3.0 23.5 + - - -
363B HIS* 3.5 37.7 - + + -
366B VAL* 4.0 17.0 - - + +
367B GLN* 3.4 36.6 - - + +
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Residues in contact with GLU 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B TYR* 1.3 74.0 - - - +
241B VAL* 1.3 59.3 + - + +
243B ASP* 4.4 4.9 - - - -
244B MSE 2.8 41.0 + - + +
356B ARG* 3.3 59.4 + - + +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PRO* 4.2 11.0 - - + -
235B SER* 5.8 0.7 - - - -
239B TYR* 3.3 2.0 + - - +
240B GLU* 1.3 77.7 - - - +
242B THR* 1.3 63.9 + - - +
244B MSE 4.1 10.1 - - + +
245B MSE 3.2 27.1 + - - +
349B LEU* 3.9 25.6 - - + -
352B LEU* 3.7 29.6 - - + +
353B ILE* 3.6 43.1 - - + +
356B ARG* 4.1 12.1 - - + -
367B GLN* 4.8 4.6 + - - +
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Residues in contact with THR 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLY 3.5 21.1 - - - +
234B PRO* 3.7 8.5 - - - +
235B SER* 2.9 47.4 + - - +
236B LEU 3.3 22.3 + - - +
237B LYS* 4.0 6.7 - - + +
239B TYR* 3.4 2.9 + - - +
240B GLU 3.3 0.2 - - - -
241B VAL* 1.3 79.9 - - - +
243B ASP* 1.3 57.7 + - - +
245B MSE 3.2 1.4 + - - +
246B GLN* 2.9 45.9 + - - +
367B GLN* 5.4 0.9 + - - -
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Residues in contact with ASP 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237B LYS* 3.8 2.8 - - - -
238B GLY* 3.0 37.5 + - - +
239B TYR 3.0 18.2 + - - +
240B GLU* 3.9 4.9 - - - +
242B THR* 1.3 76.0 - - - +
244B MSE 1.3 59.1 + - + +
247B LYS* 3.0 29.3 + - - +
424B ARG* 2.7 47.6 + - + +
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Residues in contact with MSE 244 (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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240B GLU* 2.8 30.8 + - + +
241B VAL* 4.2 16.4 - - + +
243B ASP* 1.3 73.5 - - + +
245B MSE 1.3 67.7 + - + +
247B LYS* 3.3 6.4 + - - +
248B ALA* 3.1 23.4 + - - +
352B LEU* 6.1 4.0 - - + -
356B ARG* 3.6 49.6 - - - +
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Residues in contact with MSE 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B PRO* 3.7 28.0 - - + -
241B VAL* 3.2 16.5 + - + +
242B THR 3.9 1.8 - - - +
244B MSE 1.3 84.9 - - + +
246B GLN* 1.3 62.2 + - - +
248B ALA* 3.6 7.2 + - - +
249B LEU* 3.5 27.8 + - + +
341B VAL* 3.6 26.2 - - + -
342B LYS 5.2 4.0 - - - +
343B ILE* 3.8 24.0 - - + -
352B LEU* 4.5 11.2 - - + -
387B LEU 6.0 0.2 - - - +
389B GLU 6.0 1.8 - - - +
392B LEU* 5.2 2.5 - - - +
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Residues in contact with GLN 246 (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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231B LEU* 3.5 50.3 + - + +
233B GLY 2.9 29.2 + - - +
234B PRO* 5.3 0.4 - - + -
237B LYS* 3.7 18.9 + - - +
242B THR* 2.9 31.6 + - - +
245B MSE 1.3 74.1 - - - +
247B LYS* 1.3 67.0 + - - +
249B LEU* 3.1 5.2 + - - +
250B PHE* 2.9 35.6 + - + -
319B ASP* 4.8 0.3 - - - +
341B VAL* 4.7 3.8 - - + -
424B ARG* 3.4 26.5 - - - -
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Residues in contact with LYS 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ASP 3.0 21.0 + - - +
244B MSE 3.3 6.3 + - - +
246B GLN* 1.3 77.4 - - - +
248B ALA* 1.3 62.0 + - - +
250B PHE* 3.9 0.7 - - - +
251B ASP* 2.9 53.7 + - - +
424B ARG* 3.5 38.0 - - - +
425B THR* 5.7 2.9 - - - +
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Residues in contact with ALA 248 (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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244B MSE 3.1 15.8 + - - +
245B MSE 3.8 8.3 - - - +
246B GLN 3.3 0.2 - - - -
247B LYS* 1.3 77.3 - - - +
249B LEU* 1.3 62.9 + - - +
251B ASP* 3.6 9.3 - - - +
252B PHE* 3.1 21.5 + - - +
392B LEU* 3.9 32.0 - - + +
396B CYS* 4.8 1.9 - - - -
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Residues in contact with LEU 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 4.0 15.7 - - + -
245B MSE 3.5 15.7 + - + +
246B GLN 3.1 6.3 + - - +
248B ALA* 1.3 75.0 - - - +
250B PHE* 1.3 66.5 + - - +
252B PHE* 3.2 6.0 + - + +
253B LEU* 3.0 27.9 + - + +
341B VAL* 3.6 37.5 - - + -
387B LEU* 4.2 22.2 - - + -
392B LEU* 4.3 11.2 - - + -
395B ALA* 4.6 4.9 - - + -
396B CYS* 4.0 30.1 - - - +
399B LEU* 4.7 11.9 - - + -
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Residues in contact with PHE 250 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B LEU* 3.8 29.6 - - + -
237B LYS* 6.3 0.7 - - - -
246B GLN* 2.9 36.3 + - + +
247B LYS 3.9 2.9 - - - +
249B LEU* 1.3 76.3 - - - +
251B ASP* 1.3 64.5 + - - +
253B LEU* 3.2 8.3 + - + +
254B LYS* 3.0 24.3 + - + +
263B ILE* 3.6 25.7 - - + +
317B VAL* 3.4 32.5 - - + -
318B LEU 4.1 9.0 - - - -
319B ASP* 4.0 23.8 - - + -
424B ARG* 3.6 41.3 - - + +
425B THR* 4.7 6.3 - - - +
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Residues in contact with ASP 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247B LYS* 2.9 56.3 + - - +
248B ALA* 3.6 8.9 - - - +
250B PHE* 1.3 77.7 - - - +
252B PHE* 1.3 64.6 + - - +
254B LYS* 3.4 23.8 + - - +
255B HIS* 3.5 14.4 + - - +
424B ARG 4.7 3.3 - - - +
425B THR* 6.0 0.3 - - - -
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Residues in contact with PHE 252 (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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248B ALA 3.1 12.2 + - - +
249B LEU* 3.2 8.5 + - + +
251B ASP* 1.3 80.3 - - - +
253B LEU* 1.3 73.5 + - + +
255B HIS* 2.9 25.6 - + - -
256B ARG* 2.9 59.7 + - + +
396B CYS* 3.1 61.9 - - + -
397B GLU* 4.5 12.3 - - - -
399B LEU* 5.3 2.5 - - + -
400B ALA* 3.9 14.4 - - + -
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Residues in contact with LEU 253 (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 VAL* 5.3 4.0 - - + -
231B LEU* 5.3 2.5 - - + -
249B LEU* 3.0 21.2 + - + +
250B PHE* 3.2 12.5 + - + +
252B PHE* 1.3 83.8 - - + +
254B LYS* 1.3 66.1 + - - +
257B PHE* 2.9 46.5 + - + +
261B ILE* 4.1 9.4 - - + +
263B ILE* 4.2 7.4 - - + -
317B VAL* 4.2 29.6 - - + -
399B LEU* 3.9 32.8 - - + -
403B LEU* 3.9 21.1 - - + -
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Residues in contact with LYS 254 (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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250B PHE* 3.0 12.3 + - + +
251B ASP* 3.6 18.8 + - - +
252B PHE 3.3 0.4 - - - -
253B LEU* 1.3 77.2 - - - +
255B HIS* 1.3 61.0 + - + +
257B PHE 4.0 0.3 - - - -
258B GLU* 3.4 23.9 + - - +
261B ILE* 4.2 12.2 - - + +
263B ILE* 3.7 31.6 - - + +
425B THR* 4.6 17.8 + - - +
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Residues in contact with HIS 255 (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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251B ASP 3.5 5.6 + - - +
252B PHE* 2.9 53.5 + + - -
253B LEU 3.1 0.4 - - - -
254B LYS* 1.3 79.3 - - + +
256B ARG* 1.3 67.6 + - - +
257B PHE 3.3 0.6 + - - -
258B GLU* 3.5 18.7 + - + +
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Residues in contact with ARG 256 (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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252B PHE* 2.9 43.2 + - + +
255B HIS* 1.3 79.0 - - + +
257B PHE* 1.3 77.1 + - + +
258B GLU 3.4 0.8 + - - -
260B ARG* 3.7 12.1 + - - -
397B GLU* 2.6 33.5 + - - -
400B ALA* 3.7 16.9 - - - +
401B ASP* 4.8 4.6 + - - -
404B GLU* 3.1 29.9 + - - +
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Residues in contact with PHE 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 2.9 42.0 + - + +
254B LYS 4.0 0.2 - - - -
256B ARG* 1.3 91.6 - - + +
258B GLU* 1.3 66.5 + - - +
260B ARG* 2.9 42.4 + - + +
261B ILE* 3.3 30.8 + - + +
315B LEU* 3.6 28.3 - - + -
400B ALA* 3.7 31.4 - - + -
403B LEU* 3.8 15.7 - - + -
404B GLU* 3.4 31.0 - - + -
407B TRP* 5.7 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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