Contacts of the helix formed by residues 241 - 256 (chain D) 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 HIS 241 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54D MSE 3.0 35.9 + - + +
55D TRP* 5.7 0.9 - + - -
236D GLU* 4.0 22.9 + - + +
237D SER 2.7 13.5 + - - -
240D LEU* 1.3 108.9 + - + +
242D MSE 1.3 51.8 + - - +
243D ASP* 2.8 15.6 + - - +
244D ILE* 3.1 39.0 + - + -
245D ILE* 2.7 38.4 + - - +
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Residues in contact with MSE 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 LEU* 3.3 41.4 + - + +
240D LEU 4.0 0.8 - - - -
241D HIS* 1.3 74.5 - - - +
243D ASP* 1.3 56.1 + - - +
245D ILE* 3.9 4.7 - - + -
246D GLU* 3.2 23.6 + - - +
324D PHE* 4.3 9.4 - - + +
325D ALA* 3.3 37.0 - - + +
328D VAL* 3.6 33.0 - - + +
329D ILE* 3.6 27.6 - - - -
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Residues in contact with ASP 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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240D LEU 4.6 1.2 - - - +
241D HIS* 3.4 20.1 - - - +
242D MSE 1.3 76.5 + - - +
244D ILE* 1.3 81.9 + - - +
245D ILE 3.1 1.3 - - - -
246D GLU* 2.8 26.4 + - - +
247D ASP* 3.0 19.7 + - - +
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Residues in contact with ILE 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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205D PRO* 4.8 10.5 - - + -
213D PHE* 5.5 2.7 - - + -
236D GLU* 3.7 29.8 - - + +
241D HIS* 3.1 33.8 + - + -
243D ASP* 1.3 97.9 + - - +
245D ILE* 1.3 62.9 + - - +
247D ASP* 3.1 14.4 + - + +
248D ILE* 3.0 31.2 + - + +
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Residues in contact with ILE 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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235D ALA* 3.5 15.9 - - + +
236D GLU* 3.6 8.7 - - + -
237D SER 3.4 12.3 - - - +
238D LEU* 3.3 30.3 - - + +
241D HIS 2.7 22.3 + - - +
242D MSE 4.0 5.4 - - - +
244D ILE* 1.3 76.3 - - - +
246D GLU* 1.3 58.0 + - - +
248D ILE* 3.4 7.8 + - - +
249D VAL* 2.9 35.4 + - + +
262D TYR* 3.2 44.6 - - + +
278D MSE 5.7 0.2 - - - -
329D ILE* 3.4 25.4 - - + -
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Residues in contact with GLU 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 MSE 3.2 15.3 + - - +
243D ASP* 2.8 14.5 + - - +
245D ILE* 1.3 77.7 - - - +
247D ASP* 1.3 67.6 + - - +
249D VAL* 3.9 6.0 - - + +
250D SER* 3.0 30.3 + - - -
328D VAL* 3.1 32.9 - - + +
329D ILE* 5.2 3.6 - - - +
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Residues in contact with ASP 247 (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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243D ASP* 3.0 21.0 + - - +
244D ILE* 3.1 15.1 + - + +
246D GLU* 1.3 87.0 - - - +
248D ILE* 1.3 58.4 - - + +
250D SER* 3.4 5.1 + - - -
251D ASN* 2.8 43.0 + - - +
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Residues in contact with ILE 248 (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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213D PHE* 3.5 43.5 - - + +
218D PHE* 4.3 11.2 - - + -
233D THR* 6.4 0.7 - - + -
234D GLN 5.1 0.2 - - - +
235D ALA* 4.2 17.5 - - + -
236D GLU* 4.3 6.5 - - + -
244D ILE* 3.0 30.4 + - + +
245D ILE* 3.7 8.3 - - - +
247D ASP* 1.3 74.6 - - + +
249D VAL* 1.3 67.6 + - - +
250D SER 3.1 0.2 + - - -
251D ASN* 3.2 7.5 + - - +
252D CYS* 2.9 34.3 + - - +
278D MSE 3.5 29.6 - - + -
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Residues in contact with VAL 249 (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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245D ILE* 2.9 29.5 + - + +
246D GLU* 3.9 5.6 - - + +
248D ILE* 1.3 75.5 - - - +
250D SER* 1.3 58.6 + - - +
252D CYS* 3.5 1.7 + - - +
253D ARG* 2.8 66.9 + - - +
260D VAL* 4.6 3.5 - - + +
262D TYR* 4.4 2.5 - - + -
278D MSE 3.6 31.6 - - + -
329D ILE* 3.6 31.0 - - + -
330D GLU* 5.0 1.1 - - - +
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Residues in contact with SER 250 (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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246D GLU* 3.0 22.0 + - - -
247D ASP* 3.5 7.0 - - - -
249D VAL* 1.3 76.4 - - - +
251D ASN* 1.3 70.6 + - - +
253D ARG* 3.1 17.3 + - - +
254D GLU* 3.2 28.5 + - - +
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Residues in contact with ASN 251 (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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213D PHE 3.3 21.0 + - - -
214D GLU* 4.2 7.5 - - - +
215D LYS* 3.5 39.9 - - + +
218D PHE* 4.4 12.3 - - + -
247D ASP* 2.8 34.4 + - - +
248D ILE* 3.7 3.3 - - - +
250D SER* 1.3 73.9 + - - +
252D CYS* 1.3 64.7 + - - +
254D GLU* 3.0 16.5 + - - +
255D ILE* 3.3 17.4 + - - +
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Residues in contact with CYS 252 (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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218D PHE* 3.7 41.5 - - - -
248D ILE* 2.9 24.9 + - - +
249D VAL 3.7 2.9 - - - +
251D ASN* 1.3 78.0 - - - +
253D ARG* 1.3 58.3 + - - +
255D ILE* 3.2 2.9 + - - +
256D PHE* 2.9 42.9 + - + +
260D VAL* 4.3 2.5 - - + -
278D MSE 4.0 11.9 - - + -
280D CYS* 3.7 27.6 - - - -
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Residues in contact with ARG 253 (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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249D VAL* 2.8 48.7 + - - +
250D SER* 3.1 10.3 + - - +
252D CYS* 1.3 72.8 - - - +
254D GLU* 1.3 61.1 + - + +
256D PHE 3.5 12.1 - - - +
257D LYS* 5.5 1.4 - - - +
260D VAL* 4.1 28.3 + - + +
329D ILE* 4.1 9.9 + - - +
330D GLU* 2.8 44.5 + - - -
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Residues in contact with GLU 254 (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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215D LYS* 2.8 38.0 + - - -
250D SER* 3.5 23.7 + - - +
251D ASN 3.0 7.4 + - - +
253D ARG* 1.3 80.4 - - + +
255D ILE* 1.3 64.6 - - + +
257D LYS* 3.0 27.6 + - - -
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Residues in contact with ILE 255 (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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215D LYS* 4.5 26.5 - - + +
218D PHE* 2.9 40.6 - - + +
219D GLN* 3.5 22.0 - - + +
222D ALA* 3.7 21.8 - - + +
251D ASN 3.6 12.8 - - - +
252D CYS 3.2 5.5 + - - +
254D GLU* 1.3 85.3 - - + +
256D PHE* 1.3 67.8 + - + +
257D LYS* 3.7 13.8 + - - +
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Residues in contact with PHE 256 (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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218D PHE* 3.7 41.5 - + + -
221D VAL* 4.3 5.4 - - + -
222D ALA* 4.3 18.8 - - + -
225D LEU* 4.6 0.7 - - + -
231D VAL* 3.2 34.8 - - + -
252D CYS* 2.9 29.2 + - - +
253D ARG* 3.5 15.1 - - - +
255D ILE* 1.3 80.4 - - + +
257D LYS* 1.3 63.2 + - - +
258D GLY 3.4 0.6 + - - -
260D VAL* 3.8 21.5 - - + +
280D CYS* 3.5 26.2 - - + -
281D SER 3.6 26.2 - - - +
282D THR* 4.2 12.6 - - + +
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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