Contacts of the helix formed by residues 243 - 256 (chain B) in PDB entry 2Q41
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 ASP 243 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241B HIS* 2.9 2.3 - - - -
242B MSE 1.3 82.9 + - - +
244B ILE* 1.3 65.0 + - + +
245B ILE 3.1 0.7 - - - -
246B GLU* 2.9 30.3 + - - +
247B ASP* 3.0 19.9 + - - +
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Residues in contact with ILE 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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54B MSE 4.2 17.3 - - + -
205B PRO* 3.4 31.4 - - + +
210B LYS* 5.8 2.2 - - - +
236B GLU* 5.1 4.5 - - + -
241B HIS* 3.3 37.4 + - + -
243B ASP* 1.3 79.0 - - + +
245B ILE* 1.3 62.2 + - + +
247B ASP* 3.5 10.7 + - + +
248B ILE* 3.3 33.9 + - + +
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Residues in contact with ILE 245 (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 ALA* 3.2 28.5 - - + +
236B GLU* 3.7 12.6 - - + -
237B SER 3.2 31.6 - - - +
238B LEU* 4.0 6.1 - - + +
241B HIS* 2.8 19.2 + - + +
242B MSE 4.5 3.1 - - - -
244B ILE* 1.3 78.3 - - + +
246B GLU* 1.3 56.2 + - - +
248B ILE* 4.0 9.7 - - + +
249B VAL* 3.0 26.2 + - + +
262B TYR* 3.3 38.6 - - + +
278B MSE 5.5 0.2 - - - -
329B ILE* 3.5 18.2 - - + -
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Residues in contact with GLU 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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242B MSE 3.3 11.9 + - - +
243B ASP* 2.9 23.6 + - - +
245B ILE* 1.3 78.8 - - - +
247B ASP* 1.3 67.3 + - - +
249B VAL* 3.5 5.3 + - + +
250B SER* 3.0 22.7 + - - -
328B VAL* 3.0 41.6 - - + +
329B ILE* 4.6 4.9 - - + -
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Residues in contact with ASP 247 (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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213B PHE 6.1 0.2 - - - +
243B ASP 3.0 17.8 + - - +
244B ILE* 3.9 11.0 - - + +
246B GLU* 1.3 79.1 - - - +
248B ILE* 1.3 63.9 + - + +
250B SER* 2.8 18.4 + - - -
251B ASN* 2.9 25.6 + - - +
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Residues in contact with ILE 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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213B PHE* 3.5 46.0 - - + +
218B PHE* 4.2 8.3 - - + -
233B THR* 4.9 2.9 - - + -
234B GLN 5.1 0.2 - - - +
235B ALA* 4.6 15.7 - - + -
236B GLU* 5.7 1.6 - - + +
244B ILE* 3.3 28.8 + - + +
245B ILE* 4.0 10.8 - - + +
247B ASP* 1.3 77.7 - - + +
249B VAL* 1.3 64.1 + - - +
250B SER 3.0 0.5 + - - -
251B ASN* 3.1 8.3 + - - +
252B CYS* 3.0 32.3 + - - -
278B MSE 3.3 32.3 - - + -
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Residues in contact with VAL 249 (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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245B ILE* 3.0 22.0 + - + +
246B GLU* 3.8 5.4 - - + +
247B ASP 3.3 0.2 - - - -
248B ILE* 1.3 77.3 - - - +
250B SER* 1.3 57.8 + - - +
252B CYS* 4.3 0.3 - - - +
253B ARG* 3.0 56.9 + - - +
260B VAL* 4.6 3.4 - - + +
261B ASN 5.7 0.4 - - - +
262B TYR* 4.5 5.6 - - + -
278B MSE 3.5 30.1 - - + -
329B ILE* 3.3 40.2 - - + -
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Residues in contact with SER 250 (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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246B GLU 3.0 14.2 + - - -
247B ASP* 2.8 16.4 + - - -
249B VAL* 1.3 77.0 - - - +
251B ASN* 1.3 65.5 + - - -
253B ARG* 3.4 7.7 + - - +
254B GLU* 3.1 26.4 + - - +
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Residues in contact with ASN 251 (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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213B PHE 3.2 23.6 + - - -
214B GLU* 4.1 2.2 - - - +
215B LYS* 3.3 46.3 + - + +
218B PHE* 3.8 13.4 - - + -
247B ASP* 2.9 30.5 + - - +
248B ILE* 3.8 3.5 - - - +
250B SER* 1.3 73.4 + - - +
252B CYS* 1.3 59.2 + - - +
254B GLU* 2.7 25.0 + - - +
255B ILE* 2.8 19.0 + - - +
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Residues in contact with CYS 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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218B PHE* 3.5 36.6 - - - -
248B ILE* 3.0 19.8 + - - +
251B ASN* 1.3 78.6 - - - +
253B ARG* 1.3 57.4 + - - +
255B ILE* 4.7 0.2 - - - -
256B PHE* 2.8 46.3 + - + +
260B VAL* 3.4 3.0 - - + +
278B MSE 3.5 35.0 - - + -
280B CYS* 3.6 21.1 - - - -
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Residues in contact with ARG 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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249B VAL* 3.0 47.4 + - - +
250B SER* 3.6 7.8 - - - +
251B ASN 3.1 0.6 - - - -
252B CYS* 1.3 77.5 - - - +
254B GLU* 1.3 60.7 + - - +
256B PHE 3.5 11.2 - - - +
260B VAL* 4.1 30.8 + - + +
329B ILE* 4.6 18.4 + - - +
330B GLU* 4.9 9.5 - - - +
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Residues in contact with GLU 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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215B LYS* 3.2 40.5 + - + +
250B SER* 3.1 17.3 + - - +
251B ASN* 2.7 11.2 + - - +
253B ARG* 1.3 80.8 - - - +
255B ILE* 1.3 62.5 + - + +
256B PHE 4.6 1.4 - - - +
257B LYS* 5.5 3.1 - - - +
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Residues in contact with ILE 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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215B LYS* 4.0 28.5 - - + +
218B PHE* 4.1 17.9 - - + +
219B GLN* 3.3 55.8 + - + +
222B ALA* 3.7 19.6 - - + +
251B ASN 2.8 17.6 + - - +
254B GLU* 1.3 82.3 - - + +
256B PHE* 1.3 72.9 + - + +
257B LYS* 4.0 10.3 + - - +
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Residues in contact with PHE 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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218B PHE* 4.2 28.3 - + + -
221B VAL* 4.5 6.1 - - + -
222B ALA* 4.2 9.4 - - + -
225B LEU* 4.2 5.4 - - + -
231B VAL* 3.6 26.0 - - + -
252B CYS* 2.8 45.9 + - + +
253B ARG 3.5 17.3 - - - +
254B GLU 4.6 0.9 - - - +
255B ILE* 1.3 83.6 - - + +
257B LYS* 1.3 62.5 + - - +
260B VAL* 3.5 17.3 - - + +
280B CYS* 3.6 26.0 - - + -
281B SER 4.0 10.5 - - - +
282B THR* 3.7 32.3 - - + +
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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